Gene detail

Detailed information of evm.model.Ap1.3276 in Astrangia poculata

Genomic Location: Ap1:33492288...33507511
NR annotation: XP_020612293.1, laminin subunit gamma-1-like isoform X1 [Orbicella faveolata]
Species Astrangia poculata · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

evm.model.Ap1.3276

atgaaagaatatgctgagctgctgagagcttgtgactgcttcccagagggtattacaaataatgggacatgtctgcaggaagccacacccactgagcagcttgggcaatgtcagtgtaagaacaacgtgtttggacggcagtgtgatcagtgtataccaggttactggggattcagaggaaatccacctggtgaatgcagagattgtgggtgtaataaccttggaacagttaacaacaccatacagtgtgaccagtatacaggggagtgtccatgtatggcaagtgtgcaaggcagatactgcacggaatgcaaagatggcttttacttttttccaattactgaggatacagattgcttgcggtgtccctgtgatttaggtggagctttccctcgttgtgataaagtgtcaggatcttgtttctgtcgtcctggttttgaaggaagccagtgtgaaaggacttggcaaggcggcttttatccagcactggactttgtcaagtttgaagtagaagacacaagtggtacttttacaaccttaactccctctgaaggtcaaggaatatacttcactggccatggctatgccatcctccatcctggagagtatgctcacatcagtgatgctgaagtcttggccagccatcagttctatgctgttattcgttatagcatgactagattttgcacatttgggtttgccacaaagcttgttttgagcatcacaagcaccagctcaaatgacagtgtggaatttgccgtcttagcaaaccagctaccacaaggctcaagacaagcatggaggtcacctcaaactgtagcactgctggctggtgaaatgtacaacttatcactgacttacaacagtactgacagtggtgataactgctcgatccttgttgactcagtggtcttgattcctgatgttagtctcactagagtttacactgagtctggaagtgaaatccgaaatcagttgcagaactgtgagcaggtatcattgtctcgcgtgcaacaagaaccagcttattgtaatggactggtgctgtctgctagtgcagaaatatacaatggtactttagcctgcgattgtgatcctgttggtagtgtgtcattacaatgtgaagcttatggaggcaagtgtagctgtcgccctggtgtggtgggacgtacctgcgactcctgtgacaatggattttatggattctctcttgcgggatgcaggcgttgtcagtgttcaattgctgggtcgttgcatgatgcctgccatttgataacaggggaatgctcctgtaaggacaatgttgaaggccataactgtgacagctgtaaagatggtacattcaatttggacactgccaatcaacagggatgtctgcactgttttggttatggtcgagcactcagttgtaaatcagccaatggatttgttgcatcagccataacaagtctttttgtcaatgaaacaggcaagtgtcttttatctgtgcagtccccggactgttttgaaggagctacgtcacagacaacacatcttgaaaaaatgtttgactggttcgtggtggacagagctggtgacggtgttccattttccaactcgtcatctgatggcctggtcgtcacctctactgtctcggtattgtacattacagcaccagcatcgttccttggcacacagttcagatcttacggtcagcagctacatgtcgaaatggatataagagatccgagtcctggacaagaactagctccagtagatggtgacgtcatcctagtgagtggagctagtgaagtggcattgaacctcataccctccccctcccctaacatcacctcttatcacgtgatactggacgaaacgcacgtggttggcgatgggtcagtttcaccgctggagttccagtccattctggctgagctgacatcgctcaggatccttgctacctattatgcacccggaagtgtgacatttaaggcgatctctttagagacagctgtgaacgaacaaggcgcacctggtgaagtaaatgttggatttgtagagaatgctacgtgtcacgtgaactacactgggctgtcttgtgaactgtgcgcgcaaggatacactcgcgagattagtggtagcgggccaagtggtcgttgtgttctgtgttcttgtaacaacagaagtacagagtgtgacggggagactggtgtatgcaccaactgccaagtgggtacctatggagatcgctgtgagctgtgtacaaacaatgtacaaggaccagagtgcactcggtgcaaacctggctactggggactgtcagagaacggctgtcaagcttgtgaatgtcaccggctcggtaccgctttcggtaacgtgtcgttgtgtgaccaagagacgggccagtgcgtgtgtaacacaacagcaaaaattgggggcaggcgctgtgacaggtgcatggaaaacagctggaattcttcagctagcttgttcagctgtaaagagtgctcatcctgctactcgtctattcaagaggatgttaatttacttcgtgcccagatcacgaacatacaggttcctctcacggcccttatgagccatcccaccatgattcacaatcagacttttgttgaacgcctgcgtcagcttgttacggagatcagcgcaatcgctccaaaagtcatcatggccatagaagtggataacaattcaacatctcagtggctgcgatttagtgcagctttccacgatctaagtgcaaggctgaacaacactgaaacaactgctgtgaatcacacacttcattacacatccatcgtggatgataacaggaaagagatcgaaaggattgagacgcagattcgtgatgtcattagggaggcattccgcctattggacacgcctatgagactggaactagagcaagacgaagtcttgtccagatccctgtcgcgtgtagcagaacagatagtaaatcttaccgatggtgtgatgcaacatgaaaatcgtactcttatagctaatgagaccatccatgcgcgtgtggagtacgcggtggagacagcggaaaaggccgctgaaagggtgcgaactgtgaacagtacgcaagctcaagttgctgctctgttgaaaccgctgtatgaaaacgcctctgcggtgaatgtacttggagatcaaacggtggcactggtgcttgacaaactagcgagtgctagcaaagcgtacaatgacagcttagcgatgttggcggaggccagtcaggcaaaccctgacaggagcagtgtattacaagacttgaacagtaaaacagccgatgcaaggaatgtggtagagcagtacctcaatcaaaccagtagcttataccaatccagtgcgcctgtgataggtcaggtcaacgcggccattgagagatcggaacttttgggtaaggaggtgcaagctgtggtctcaaatggtacacaacaactgcagggatcccaaaccgcacttacttctgcccagactgctgtgtcaagagcaaaccgagtgcacgaacatgcacaaagaatgctggatgttgctagcgattttcaggcagaaactcatcgtgcacaagcttctgcaaaccagtctctgttgaccgttgccagcgttcgaaatagcgcccataggattataaggaatgtctcagcggtgaacgaatcatctgcacacgcgctgtttacggctgaagaggctctatgtcttggaatgacggtgaaaaatctctctgtctccgagcagcaggtggtggagagggcccatcgccttgctcttgacttgaggaacgagactgctgtggatagcatggtgggaaacaataccatggaaaacttcatggccagagaaatagaaccagtgcagaaactctgccaaaatttgtccaccatggctactaatgcgtcaaccaacagcgaagttcttcttaagagggccgttaatgcaaacactactgtccagcggctgatttctttgaccaggcgcttgctgaatgaaagctctgatttgccgcgagtcaatgtagacaacctgcccactctcaggggagaggtgaattcagcaagacaactatttaacgggctgcagctggagccgcagctagtggagttaagaagagagcttcaactgcagcagaggaagatggctttctataaagagcggattcgccagcttcggtctgatatcacgagatataaggagttgttgaggtcgctaccttctgtttctccttgctaa

Transcript

evm.model.Ap1.3276

ATGAAAGAATATGCTGAGCTGCTGAGAGCTTGTGACTGCTTCCCAGAGGGTATTACAAATAATGGGACATGTCTGCAGGAAGCCACACCCACTGAGCAGCTTGGGCAATGTCAGTGTAAGAACAACGTGTTTGGACGGCAGTGTGATCAGTGTATACCAGGTTACTGGGGATTCAGAGGAAATCCACCTGGTGAATGCAGAGATTGTGGGTGTAATAACCTTGGAACAGTTAACAACACCATACAGTGTGACCAGTATACAGGGGAGTGTCCATGTATGGCAAGTGTGCAAGGCAGATACTGCACGGAATGCAAAGATGGCTTTTACTTTTTTCCAATTACTGAGGATACAGATTGCTTGCGGTGTCCCTGTGATTTAGGTGGAGCTTTCCCTCGTTGTGATAAAGTGTCAGGATCTTGTTTCTGTCGTCCTGGTTTTGAAGGAAGCCAGTGTGAAAGGACTTGGCAAGGCGGCTTTTATCCAGCACTGGACTTTGTCAAGTTTGAAGTAGAAGACACAAGTGGTACTTTTACAACCTTAACTCCCTCTGAAGGTCAAGGAATATACTTCACTGGCCATGGCTATGCCATCCTCCATCCTGGAGAGTATGCTCACATCAGTGATGCTGAAGTCTTGGCCAGCCATCAGTTCTATGCTGTTATTCGTTATAGCATGACTAGATTTTGCACATTTGGGTTTGCCACAAAGCTTGTTTTGAGCATCACAAGCACCAGCTCAAATGACAGTGTGGAATTTGCCGTCTTAGCAAACCAGCTACCACAAGGCTCAAGACAAGCATGGAGGTCACCTCAAACTGTAGCACTGCTGGCTGGTGAAATGTACAACTTATCACTGACTTACAACAGTACTGACAGTGGTGATAACTGCTCGATCCTTGTTGACTCAGTGGTCTTGATTCCTGATGTTAGTCTCACTAGAGTTTACACTGAGTCTGGAAGTGAAATCCGAAATCAGTTGCAGAACTGTGAGCAGGTATCATTGTCTCGCGTGCAACAAGAACCAGCTTATTGTAATGGACTGGTGCTGTCTGCTAGTGCAGAAATATACAATGGTACTTTAGCCTGCGATTGTGATCCTGTTGGTAGTGTGTCATTACAATGTGAAGCTTATGGAGGCAAGTGTAGCTGTCGCCCTGGTGTGGTGGGACGTACCTGCGACTCCTGTGACAATGGATTTTATGGATTCTCTCTTGCGGGATGCAGGCGTTGTCAGTGTTCAATTGCTGGGTCGTTGCATGATGCCTGCCATTTGATAACAGGGGAATGCTCCTGTAAGGACAATGTTGAAGGCCATAACTGTGACAGCTGTAAAGATGGTACATTCAATTTGGACACTGCCAATCAACAGGGATGTCTGCACTGTTTTGGTTATGGTCGAGCACTCAGTTGTAAATCAGCCAATGGATTTGTTGCATCAGCCATAACAAGTCTTTTTGTCAATGAAACAGGCAAGTGTCTTTTATCTGTGCAGTCCCCGGACTGTTTTGAAGGAGCTACGTCACAGACAACACATCTTGAAAAAATGTTTGACTGGTTCGTGGTGGACAGAGCTGGTGACGGTGTTCCATTTTCCAACTCGTCATCTGATGGCCTGGTCGTCACCTCTACTGTCTCGGTATTGTACATTACAGCACCAGCATCGTTCCTTGGCACACAGTTCAGATCTTACGGTCAGCAGCTACATGTCGAAATGGATATAAGAGATCCGAGTCCTGGACAAGAACTAGCTCCAGTAGATGGTGACGTCATCCTAGTGAGTGGAGCTAGTGAAGTGGCATTGAACCTCATACCCTCCCCCTCCCCTAACATCACCTCTTATCACGTGATACTGGACGAAACGCACGTGGTTGGCGATGGGTCAGTTTCACCGCTGGAGTTCCAGTCCATTCTGGCTGAGCTGACATCGCTCAGGATCCTTGCTACCTATTATGCACCCGGAAGTGTGACATTTAAGGCGATCTCTTTAGAGACAGCTGTGAACGAACAAGGCGCACCTGGTGAAGTAAATGTTGGATTTGTAGAGAATGCTACGTGTCACGTGAACTACACTGGGCTGTCTTGTGAACTGTGCGCGCAAGGATACACTCGCGAGATTAGTGGTAGCGGGCCAAGTGGTCGTTGTGTTCTGTGTTCTTGTAACAACAGAAGTACAGAGTGTGACGGGGAGACTGGTGTATGCACCAACTGCCAAGTGGGTACCTATGGAGATCGCTGTGAGCTGTGTACAAACAATGTACAAGGACCAGAGTGCACTCGGTGCAAACCTGGCTACTGGGGACTGTCAGAGAACGGCTGTCAAGCTTGTGAATGTCACCGGCTCGGTACCGCTTTCGGTAACGTGTCGTTGTGTGACCAAGAGACGGGCCAGTGCGTGTGTAACACAACAGCAAAAATTGGGGGCAGGCGCTGTGACAGGTGCATGGAAAACAGCTGGAATTCTTCAGCTAGCTTGTTCAGCTGTAAAGAGTGCTCATCCTGCTACTCGTCTATTCAAGAGGATGTTAATTTACTTCGTGCCCAGATCACGAACATACAGGTTCCTCTCACGGCCCTTATGAGCCATCCCACCATGATTCACAATCAGACTTTTGTTGAACGCCTGCGTCAGCTTGTTACGGAGATCAGCGCAATCGCTCCAAAAGTCATCATGGCCATAGAAGTGGATAACAATTCAACATCTCAGTGGCTGCGATTTAGTGCAGCTTTCCACGATCTAAGTGCAAGGCTGAACAACACTGAAACAACTGCTGTGAATCACACACTTCATTACACATCCATCGTGGATGATAACAGGAAAGAGATCGAAAGGATTGAGACGCAGATTCGTGATGTCATTAGGGAGGCATTCCGCCTATTGGACACGCCTATGAGACTGGAACTAGAGCAAGACGAAGTCTTGTCCAGATCCCTGTCGCGTGTAGCAGAACAGATAGTAAATCTTACCGATGGTGTGATGCAACATGAAAATCGTACTCTTATAGCTAATGAGACCATCCATGCGCGTGTGGAGTACGCGGTGGAGACAGCGGAAAAGGCCGCTGAAAGGGTGCGAACTGTGAACAGTACGCAAGCTCAAGTTGCTGCTCTGTTGAAACCGCTGTATGAAAACGCCTCTGCGGTGAATGTACTTGGAGATCAAACGGTGGCACTGGTGCTTGACAAACTAGCGAGTGCTAGCAAAGCGTACAATGACAGCTTAGCGATGTTGGCGGAGGCCAGTCAGGCAAACCCTGACAGGAGCAGTGTATTACAAGACTTGAACAGTAAAACAGCCGATGCAAGGAATGTGGTAGAGCAGTACCTCAATCAAACCAGTAGCTTATACCAATCCAGTGCGCCTGTGATAGGTCAGGTCAACGCGGCCATTGAGAGATCGGAACTTTTGGGTAAGGAGGTGCAAGCTGTGGTCTCAAATGGTACACAACAACTGCAGGGATCCCAAACCGCACTTACTTCTGCCCAGACTGCTGTGTCAAGAGCAAACCGAGTGCACGAACATGCACAAAGAATGCTGGATGTTGCTAGCGATTTTCAGGCAGAAACTCATCGTGCACAAGCTTCTGCAAACCAGTCTCTGTTGACCGTTGCCAGCGTTCGAAATAGCGCCCATAGGATTATAAGGAATGTCTCAGCGGTGAACGAATCATCTGCACACGCGCTGTTTACGGCTGAAGAGGCTCTATGTCTTGGAATGACGGTGAAAAATCTCTCTGTCTCCGAGCAGCAGGTGGTGGAGAGGGCCCATCGCCTTGCTCTTGACTTGAGGAACGAGACTGCTGTGGATAGCATGGTGGGAAACAATACCATGGAAAACTTCATGGCCAGAGAAATAGAACCAGTGCAGAAACTCTGCCAAAATTTGTCCACCATGGCTACTAATGCGTCAACCAACAGCGAAGTTCTTCTTAAGAGGGCCGTTAATGCAAACACTACTGTCCAGCGGCTGATTTCTTTGACCAGGCGCTTGCTGAATGAAAGCTCTGATTTGCCGCGAGTCAATGTAGACAACCTGCCCACTCTCAGGGGAGAGGTGAATTCAGCAAGACAACTATTTAACGGGCTGCAGCTGGAGCCGCAGCTAGTGGAGTTAAGAAGAGAGCTTCAACTGCAGCAGAGGAAGATGGCTTTCTATAAAGAGCGGATTCGCCAGCTTCGGTCTGATATCACGAGATATAAGGAGTTGTTGAGGTCGCTACCTTCTGTTTCTCCTTGCTAA

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
A0JP86	Laminin subunit gamma-1 OS=Xenopus tropicalis OX=8364 GN=lamc1 PE=2 SV=1
P15800	Laminin subunit beta-2 OS=Rattus norvegicus OX=10116 GN=Lamb2 PE=1 SV=1
A4D0S4	Laminin subunit beta-4 OS=Homo sapiens OX=9606 GN=LAMB4 PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0001807 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00053 all species →	Laminin_EGF	Laminin EGF domain	Domain	Interproscan
PF00052 all species →	Laminin_B	Laminin B (Domain IV)	Domain	Interproscan
PF21199 all species →	LAMININ_IV_B	Laminin IV type B domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR002049 all species →	Domain	Laminin-type EGF domain	Interproscan
IPR000034 all species →	Domain	Laminin IV	Interproscan
IPR013015 all species →	Domain	Laminin IV type B	Interproscan
IPR000742 all species →	Domain	EGF-like domain	Interproscan
IPR050440 all species →	Family	Laminin/Netrin Extracellular Matrix	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR10574 all species →	NETRIN/LAMININ-RELATED	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005604 all species →	Cellular Component	basement membrane	Interproscan
GO:0008045 all species →	Biological Process	motor neuron axon guidance	Interproscan
GO:0009887 all species →	Biological Process	animal organ morphogenesis	Interproscan
GO:0009888 all species →	Biological Process	tissue development	Interproscan
GO:0016358 all species →	Biological Process	dendrite development	Interproscan

Search by domain instead of by gene. Any accession above (InterPro, Pfam, PANTHER, GO, KEGG) can be used as a query on the Functional Domain Search page, which searches all 148 annotated genomes at once.

KEGG pathway

No KEGG orthology assignment for evm.model.Ap1.3276.

Searching by KO or pathway ID across all species is available on the KEGG Pathway page.

Expression pattern (RNA-seq)

Transcript abundance of evm.model.Ap1.3276 across 49 RNA-seq samples of Astrangia poculata. Values are TPM (transcripts per million) from the StringTie quantification; one bar is one sample, grouped and coloured by condition, sorted by expression within each group.

49Samples

29TPM > 0

4Conditions

1,118.8Max TPM

162.8Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
whole organism · cold control	14	8	86.00	333.51
whole organism · heat control	12	8	101.34	320.88
whole organism · cold challenge	12	9	361.98	1,118.82
whole organism · heat challenge	11	4	110.47	426.35

Per sample · hover a bar for the full sample record · show / hide the sample table

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR10674715	whole organism · cold control	whole organism	not recorded	cold control	SRP237293	333.51
SRR10674737	whole organism · cold control	whole organism	not recorded	cold control	SRP237293	301.58
SRR10674746	whole organism · cold control	whole organism	not recorded	cold control	SRP237293	204.33
SRR10674747	whole organism · cold control	whole organism	not recorded	cold control	SRP237293	102.96
SRR10674739	whole organism · cold control	whole organism	not recorded	cold control	SRP237293	87.28
SRR10674735	whole organism · cold control	whole organism	not recorded	cold control	SRP237293	77.67
SRR10674750	whole organism · cold control	whole organism	not recorded	cold control	SRP237293	57.60
SRR10674734	whole organism · cold control	whole organism	not recorded	cold control	SRP237293	39.10
SRR10674714	whole organism · cold control	whole organism	not recorded	cold control	SRP237293	0.00
SRR10674724	whole organism · cold control	whole organism	not recorded	cold control	SRP237293	0.00
SRR10674733	whole organism · cold control	whole organism	not recorded	cold control	SRP237293	0.00
SRR10674736	whole organism · cold control	whole organism	not recorded	cold control	SRP237293	0.00
SRR10674743	whole organism · cold control	whole organism	not recorded	cold control	SRP237293	0.00
SRR10674748	whole organism · cold control	whole organism	not recorded	cold control	SRP237293	0.00
SRR10674752	whole organism · heat control	whole organism	not recorded	heat control	SRP237293	320.88
SRR10674717	whole organism · heat control	whole organism	not recorded	heat control	SRP237293	217.01
SRR10674706	whole organism · heat control	whole organism	not recorded	heat control	SRP237293	188.38
SRR10674708	whole organism · heat control	whole organism	not recorded	heat control	SRP237293	177.57
SRR10674718	whole organism · heat control	whole organism	not recorded	heat control	SRP237293	88.02
SRR10674720	whole organism · heat control	whole organism	not recorded	heat control	SRP237293	83.87
SRR10674753	whole organism · heat control	whole organism	not recorded	heat control	SRP237293	82.84
SRR10674741	whole organism · heat control	whole organism	not recorded	heat control	SRP237293	57.46
SRR10674707	whole organism · heat control	whole organism	not recorded	heat control	SRP237293	0.00
SRR10674721	whole organism · heat control	whole organism	not recorded	heat control	SRP237293	0.00
SRR10674725	whole organism · heat control	whole organism	not recorded	heat control	SRP237293	0.00
SRR10674731	whole organism · heat control	whole organism	not recorded	heat control	SRP237293	0.00
SRR10674740	whole organism · cold challenge	whole organism	not recorded	cold challenge	SRP237293	1,118.82
SRR10674749	whole organism · cold challenge	whole organism	not recorded	cold challenge	SRP237293	662.46
SRR10674730	whole organism · cold challenge	whole organism	not recorded	cold challenge	SRP237293	552.32
SRR10674744	whole organism · cold challenge	whole organism	not recorded	cold challenge	SRP237293	547.19
SRR10674738	whole organism · cold challenge	whole organism	not recorded	cold challenge	SRP237293	525.64
SRR10674712	whole organism · cold challenge	whole organism	not recorded	cold challenge	SRP237293	419.27
SRR10674723	whole organism · cold challenge	whole organism	not recorded	cold challenge	SRP237293	221.18
SRR10674713	whole organism · cold challenge	whole organism	not recorded	cold challenge	SRP237293	170.07
SRR10674745	whole organism · cold challenge	whole organism	not recorded	cold challenge	SRP237293	126.87
SRR10674711	whole organism · cold challenge	whole organism	not recorded	cold challenge	SRP237293	0.00
SRR10674722	whole organism · cold challenge	whole organism	not recorded	cold challenge	SRP237293	0.00
SRR10674732	whole organism · cold challenge	whole organism	not recorded	cold challenge	SRP237293	0.00
SRR10674719	whole organism · heat challenge	whole organism	not recorded	heat challenge	SRP237293	426.35
SRR10674716	whole organism · heat challenge	whole organism	not recorded	heat challenge	SRP237293	409.66
SRR10674728	whole organism · heat challenge	whole organism	not recorded	heat challenge	SRP237293	274.25
SRR10674729	whole organism · heat challenge	whole organism	not recorded	heat challenge	SRP237293	104.91
SRR10674709	whole organism · heat challenge	whole organism	not recorded	heat challenge	SRP237293	0.00
SRR10674710	whole organism · heat challenge	whole organism	not recorded	heat challenge	SRP237293	0.00
SRR10674726	whole organism · heat challenge	whole organism	not recorded	heat challenge	SRP237293	0.00
SRR10674727	whole organism · heat challenge	whole organism	not recorded	heat challenge	SRP237293	0.00
SRR10674742	whole organism · heat challenge	whole organism	not recorded	heat challenge	SRP237293	0.00
SRR10674751	whole organism · heat challenge	whole organism	not recorded	heat challenge	SRP237293	0.00
SRR10674754	whole organism · heat challenge	whole organism	not recorded	heat challenge	SRP237293	0.00

Source: CnidoSite RNA-seq expression matrices (APOCU_TPM, StringTie quantification over 49 runs), joined to SRA sample metadata. Samples whose tissue/treatment is not recorded in the source metadata are grouped by the descriptor carried in the expression matrix itself.