Gene detail

Detailed information of scaffold2.g2.t1 in Aurelia aurita complex sp. Pacific

Genomic Location: scaffold2:25897...47284
NR annotation: no NCBI-NR hit recorded
Species Aurelia aurita complex sp. Pacific · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

scaffold2.g2.t1

atgttgttgttgttgttgttgctattgttgtttgacgtatgttgtttgatttcacgtaagatttatttcgttgttttctcaagttttgtggtgttgatgttgttgttgttgttgttgttgtttccattgtggtttgacgttggtcgtttggtttcacgtcagattgtagagttgctgcccgcgatcgcgggtttatgtctgtgttcttgtctttgaccgatttcgtcggttcttcgtttgttgttgttaatgtgttgctcttagtttacatatatgtttctacatgacttgaaaaccccaaaagaatgtccagaatttgaagaaagaatcagggccaatgaagccaataattccaaatttaactttttgaatccaaatgatccctaccatgcatactatcaacacaagaagaaggaattttatgaaggagatcaacaagctccagtcagtgtcacccagaaagctgctcctgttactcaaacaaatcaaattaaacaaatcaagcaagcagtctcgcaagtggttgaacaagttgttccaaaggagcctccaccagaatttgaattcacggctgacccaccttccatctcagccattgatctggatattgtcaagttaacagcacaatttgtggcaaagaatggcaggacatttctgactaatttgatcaacagggaacaacgaaattaccagtttgactttctgagaccacagcacagtttatttcaatatttcaccaaactcgtagaacaatataccaaggtccttctgccaccttccgatttaaacaaaaaattgaaagaaagcatagaagtgcctttcaaggttatggaaactgtgcagcatcgtgtccttctgcctccttcggatttaaacaaaaaattgaaagaaagcatagaagtgcctttcaaggttatggaaactgtgcagcatcgtgttgaatgggcaaaatatcaagaaagggaaaggaagaaggaagaagaagagagagaaagagaaagagttgctttcgctcaagttgactggcatgattttgtggttgttgaaacagttaactttcgagaagatgaaatagcgaatcttccacctcccgttactttggagcaactcggagcaagaatcctggcccaggaaaggttcgagcgcatgcaggaaactggtgaaatcaatgcggaagaaatggagatggaagtcgaggaagaagaggaagaagaggaagtaaacgaggaagaagaaatcaatttcgaaaaactcaagttatcaaaagaaagcgaacaaccacccttccctcccaaacccccttcttcaaacataaaacaacccccattacccccacctgcacctggaccaaatgtgaatatcaggagagattacgatccaaaagcccccaagcccccaccaccatcgagtgccccaccgccggataaatatctgatatcaccccttactggagaaagggtccctgcagaggcaatggctgagcatatgaaaattaacttgctggatccgcgatggaaggagttgaagcaaagggctgcagatgagaaaagacaacaagaacaaatgtttgctgaaggtgtatcagtgggtagcaccctcaaagatcttgcgcaatatcgtcctgatatcttcggagttggttcggaggagacgatgattggcaaaaaggcaggcgaagaggagaaaaaaggagacaaagttgtatgggatggtcatactgcaagtatggaaagagcgactaaattggcacaagcgaatatcacgttggatgaacagattgaagctattcataaagctaagggtttgatagcaactgacgaagatgacaaaatcggaccagcaattcctcgaccacctggccacgaccagtcccatttcagacctggacctcctgtaccaagaccccaaccgcctccaatgttaaagccaagagagccaccaaaacgacccgaaccacccaaaatgcccgagcccccaccacctgttcaaccgcctcccttaatgcccccaccatcctcgcagccaatgaacccaccaatggatcttcagcaaagaatgagtatgccacgaccgccaatcttaccgccacccgttccgccacctggcttggtgatgcaaccgccgattccaccgccgaatgtgaaacctgggttgttaggtcttgcacctggtcaagcaccccctggtatgccaatgcctcctgtcccccttccccagggtctcccacagcccatcccaccaccacaaatgccagagcctccctcacaggacagatcagatgagccgatggcaaagaaagccagggctgatccggaaagtgaattgatgcatgaacaagaattcctggctacacatccaagtccggtcgcatttaaagttcaagttccggatatgagggaaaagacggaatggagatgtcacgggcaaacgttgatgttcacattaccactgactgaccagatatctgttatcaaagctaaagttcatgacgcaactggaatgcctgctggaaaacagaaactgcacattgagaccctgtttctgaaagactcgaatacattggcctattacaacttccaagcaataacagtcgttggtctacagctgaaagaacgtggtggaagaaagaaataaagggataaataaattaaagtagacgaaacgagcgcacgaagttaacaatggcttagttgacattagaatccctccggggatcttcagtccacagccacctcttgttaaacatggctttaaaatgtttaaacagcctgaaaaaacttcagctttcttcgcaaatcaattttgataaagttttcatgactgcaactattcagtccacagctacccgttgtttatcaaagctttaaaatgttttaagcatcctgaaaaaatctcagctttcttcgaaaatcgattttgatgaagttttcacgactgcaactattcagtccacagctacccgttgtttatcagggctttaaaatgttttaaacatcctgaaaaaatctcagctttccacgcacatcgattttgatgaatttttcacgactgcaactattcagtccacagctgcctgttgttcagggctttaaaaagattttaaacatcctgaaaaatctcagctttccacgcagatcgactttgatgaagttttcacgactgcaactattcagtccacagctacccgttgtt

Transcript

scaffold2.g2.t1

ATGTTGTTGTTGTTGTTGTTGCTATTGTTGTTTGACGTATGTTGTTTGATTTCACGTAAGATTTATTTCGTTGTTTTCTCAAGTTTTGTGGtgttgatgttgttgttgttgttgttgttgttTCCATTGTGGTTTGACGTTGGTCGTTTGGTTTCACGTCAGATTGTAGAGTTGCTGCCCGCGATCGCGGGTTTATGTCTGTGTTCTTGTCTTTGACCGATTTCGTCGGTTCTTCGTTTGTTGTTGTTAATGTGTTGCTCTTAGTTTACATATATGTTTCTACATGACTTGAAAACCCCAAAAGAATGTCCAGAATTTGAAGAAAGAATCAGGGCCAATGAAGCCAATAATTCCAAATTTAACTTTTTGAATCCAAATGATCCCTACCATGCATACTATCAACACAAGAAGAAGGAATTTTATGAAGGAGATCAACAAGCTCCAGTCAGTGTCACCCAGAAAGCTGCTCCTGTTACTCAAACAAATCAAATTAAACAAATCAAGCAAGCAGTCTCGCAAGTGGTTGAACAAGTTGTTCCAAAGGAGCCTCCACCAGAATTTGAATTCACGGCTGACCCACCTTCCATCTCAGCCATTGATCTGGATATTGTCAAGTTAACAGCACAATTTGTGGCAAAGAATGGCAGGACATTTCTGACTAATTTGATCAACAGGGAACAACGAAATTACCAGTTTGACTTTCTGAGACCACAGCACAGTTTATTTCAATATTTCACCAAACTCGTAGAACAATATACCAAGGTCCTTCTGCCACCTTCCGATTTAAACAAAAAATTGAAAGAAAGCATAGAAGTGCCTTTCAAGGTTATGGAAACTGTGCAGCATCGTGTCCTTCTGCCTCCTTCGGATTTAAACAAAAAATTGAAAGAAAGCATAGAAGTGCCTTTCAAGGTTATGGAAACTGTGCAGCATCGTGTTGAATGGGCAAAATATCAagaaagggaaaggaagaaggaagaagaagagagagaaagagaaagagTTGCTTTCGCTCAAGTTGACTGGCATGATTTTGTGGTTGTTGAAACAGTTAACTTTCGAGAAGATGAAATAGCGAATCTTCCACCTCCCGTTACTTTGGAGCAACTCGGAGCAAGAATCCTGGCCCAGGAAAGGTTCGAGCGCATGCAGGAAACTGGTGAAATCAATGCGGAAGAAATGGAGATGGAAGTCGAGGAAGAAGAGGAAGAAGAGGAAGTAAACGAGGAAGAAGAAATCAATTTCGAAAAACTCAAGTTATCAAAAGAAAGCGAACAACCACCCTTCCCTCCCAAACCCCCTTCTTCAAACATAAAACAACCCCCATTACCCCCACCTGCACCTGGACCAAATGTGAATATCAGGAGAGATTACGATCCAAAAGCCCCCAAGCCCCCACCACCATCGAGTGCCCCACCGCCGGATAAATATCTGATATCACCCCTTACTGGAGAAAGGGTCCCTGCAGAGGCAATGGCTGAGCATATGAAAATTAACTTGCTGGATCCGCGATGGAAGGAGTTGAAGCAAAGGGCTGCAGATGAGAAAAGACAACAAGAACAAATGTTTGCTGAAGGTGTATCAGTGGGTAGCACCCTCAAAGATCTTGCGCAATATCGTCCTGATATCTTCGGAGTTGGTTCGGAGGAGACGATGATTGGCAAAAAGGCAGGCGAAGAGGAGAAAAAAGGAGACAAAGTTGTATGGGATGGTCATACTGCAAGTATGGAAAGAGCGACTAAATTGGCACAAGCGAATATCACGTTGGATGAACAGATTGAAGCTATTCATAAAGCTAAGGGTTTGATAGCAACTGACGAAGATGACAAAATCGGACCAGCAATTCCTCGACCACCTGGCCACGACCAGTCCCATTTCAGACCTGGACCTCCTGTACCAAGACCCCAACCGCCTCCAATGTTAAAGCCAAGAGAGCCACCAAAACGACCCGAACCACCCAAAATGCCCGAGCCCCCACCACCTGTTCAACCGCCTCCCTTAATGCCCCCACCATCCTCGCAGCCAATGAACCCACCAATGGATCTTCAGCAAAGAATGAGTATGCCACGACCGCCAATCTTACCGCCACCCGTTCCGCCACCTGGCTTGGTGATGCAACCGCCGATTCCACCGCCGAATGTGAAACCTGGGTTGTTAGGTCTTGCACCTGGTCAAGCACCCCCTGGTATGCCAATGCCTCCTGTCCCCCTTCCCCAGGGTCTCCCACAGCCCATCCCACCACCACAAATGCCAGAGCCTCCCTCACAGGACAGATCAGATGAGCCGATGGCAAAGAAAGCCAGGGCTGATCCGGAAAGTGAATTGATGCATGAACAAGAATTCCTGGCTACACATCCAAGTCCGGTCGCATTTAAAGTTCAAGTTCCGGATATGAGGGAAAAGACGGAATGGAGATGTCACGGGCAAACGTTGATGTTCACATTACCACTGACTGACCAGATATCTGTTATCAAAGCTAAAGTTCATGACGCAACTGGAATGCCTGCTGGAAAACAGAAACTGCACATTGAGACCCTGTTTCTGAAAGACTCGAATACATTGGCCTATTACAACTTCCAAGCAATAACAGTCGTTGGTCTACAGCTGAAAGAACGTGGTGGAAGAAAGAAATAAAGGGATAAATAAATTAAAGTAGACGAAACGAGCGCACGAAGTTAACAATGGCTTAGTTGACATTAGAATCCCTCCGGGGATCTTCAGTCCACAGCCACCTCTTGTTAAACATGGCTTTAAAATGTTTAAACAGCCTGAAAAAACTTCAGCTTTCTTCGCAAATCAATTTTGATAAAGTTTTCATGACTGCAACTATTCAGTCCACAGCTACCCGTTGTTTATCAAAGCTTTAAAATGTTTTAAGCATCCTGAAAAAATCTCAGCTTTCTTCGAAAATCGATTTTGATGAAGTTTTCACGACTGCAACTATTCAGTCCACAGCTACCCGTTGTTTATCAGGGCTTTAAAATGTTTTAAACATCCTGAAAAAATCTCAGCTTTCCACGCACATCGATTTTGATGAATTTTTCACGACTGCAACTATTCAGTCCACAGCTGCCTGTTGTTCAGGGCTTTAAAAAGATTTTAAACATCCTGAAAAATCTCAGCTTTCCACGCAGATCGACTTTGATGAAGTTTTCACGACTGCAACTATTCAGTCCACAGCTACCCGTTGTT

Protein

Gene family

Family type	Membership / link
Ubiquitin family	ULD\|UBL\|NEDD8 · all ubiquitin genes in this species
Ubiquitin family	ULD\|UFD/UBQ\|UBQ_Other · all ubiquitin genes in this species

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00240 all species →	ubiquitin	Ubiquitin family	Domain	Interproscan
PF12230 all species →	PRP21_like_P	Pre-mRNA splicing factor PRP21 like protein	Family	Interproscan
PF01805 all species →	Surp	Surp module	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR000061 all species →	Domain	SWAP/Surp	Interproscan
IPR045146 all species →	Family	Splicing factor 3A subunit 1	Interproscan
IPR035563 all species →	Domain	Splicing factor 3A subunit 1, ubiquitin domain	Interproscan
IPR000626 all species →	Domain	Ubiquitin-like domain	Interproscan
IPR035967 all species →	Homologous_superfamily	SWAP/Surp superfamily	Interproscan
IPR029071 all species →	Homologous_superfamily	Ubiquitin-like domain superfamily	Interproscan
IPR022030 all species →	Domain	Splicing factor 3A subunit 1, conserved domain	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR15316 all species →	SPLICEOSOME ASSOCIATED PROTEIN 114/SWAP SPLICING FACTOR-RELATED	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003723 all species →	Molecular Function	RNA binding	Interproscan
GO:0006396 all species →	Biological Process	RNA processing	Interproscan
GO:0000381 all species →	Biological Process	regulation of alternative mRNA splicing, via spliceosome	Interproscan
GO:0005686 all species →	Cellular Component	U2 snRNP	Interproscan
GO:0045292 all species →	Biological Process	mRNA cis splicing, via spliceosome	Interproscan
GO:0071004 all species →	Cellular Component	U2-type prespliceosome	Interproscan
GO:0071013 all species →	Cellular Component	catalytic step 2 spliceosome	Interproscan
GO:0005515 all species →	Molecular Function	protein binding	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

KO	Enzyme	Enzyme ID	Pathway	Map ID	Source
K12825	SF3A1, SAP114; splicing factor 3A subunit 1	-	Spliceosome	ko03041	deepkoala

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

Expression pattern (RNA-seq)

Transcript abundance of scaffold2.g2.t1 across 29 RNA-seq samples of Aurelia aurita complex sp. Pacific. 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.

29Samples

23TPM > 0

28Conditions

197.1Max TPM

58.2Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
jellyfish mesoglea cells	2	2	17.82	28.81
complete polyp induced 20h	1	1	67.80	67.80
jellyfish canal system endoderm	1	1	28.05	28.05
mesoglea cells	1	0	0.00	0.00
bell edge (ectoderm and canal)	1	1	71.03	71.03
tentacles (distal part)	1	0	0.00	0.00
planula complete	1	1	125.01	125.01
male gonad	1	1	197.11	197.11
jellyfish ectoderm (upper bell surface)	1	1	85.45	85.45
jellyfish ectoderm (muscle layer)	1	1	41.34	41.34
complete juvenile jellyfish ~1cm in diameter	1	0	0.00	0.00
strobila foot	1	1	45.87	45.87
jellyfish ectoderm from the upper side of the bell	1	0	0.00	0.00
complete juvenile jellyfish ~2.5cm in diameter	1	1	147.85	147.85
jellyfish striated muscle layer	1	1	36.51	36.51
strobila head	1	1	105.23	105.23
jellyfish gastric filaments	1	1	1.02	1.02
jellyfish bell edge	1	1	73.18	73.18
jellyfish oral arm	1	1	95.30	95.30
jellyfish bell middle part	1	1	70.19	70.19
polyp ectoderm from body column	1	1	74.53	74.53
polyp head region	1	1	56.80	56.80
polyp endoderm from body column	1	1	58.66	58.66
strobila non-segmented part	1	1	96.21	96.21
strobila segments	1	1	113.23	113.23
complete polyp induced 12h	1	1	63.17	63.17
complete polyp not induced	1	0	0.00	0.00
endoderm (canal system)	1	0	0.00	0.00

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR8040405	jellyfish mesoglea cells	jellyfish mesoglea cells	not recorded	not recorded	SRP165275	28.81
SRR8040400	jellyfish mesoglea cells	jellyfish mesoglea cells	not recorded	not recorded	SRP165275	6.83
SRR8040387	complete polyp induced 20h	complete polyp induced 20h	not recorded	not recorded	SRP165275	67.80
SRR8040407	jellyfish canal system endoderm	jellyfish canal system endoderm	not recorded	not recorded	SRP165275	28.05
SRR8089704	mesoglea cells	mesoglea cells	not recorded	not recorded	SRP165275	0.00
SRR8089703	bell edge (ectoderm and canal)	bell edge (ectoderm and canal)	not recorded	not recorded	SRP165275	71.03
SRR8089702	tentacles (distal part)	tentacles (distal part)	not recorded	not recorded	SRP165275	0.00
SRR8089701	planula complete	planula complete	not recorded	not recorded	SRP165275	125.01
SRR8089700	male gonad	male gonad	not recorded	not recorded	SRP165275	197.11
SRR8089699	jellyfish ectoderm (upper bell surface)	jellyfish ectoderm (upper bell surface)	not recorded	not recorded	SRP165275	85.45
SRR8089698	jellyfish ectoderm (muscle layer)	jellyfish ectoderm (muscle layer)	not recorded	not recorded	SRP165275	41.34
SRR8040411	complete juvenile jellyfish ~1cm in diameter	complete juvenile jellyfish ~1cm in diameter	not recorded	not recorded	SRP165275	0.00
SRR8040410	strobila foot	strobila foot	not recorded	not recorded	SRP165275	45.87
SRR8040409	jellyfish ectoderm from the upper side of the bell	jellyfish ectoderm from the upper side of the bell	not recorded	not recorded	SRP165275	0.00
SRR8040408	complete juvenile jellyfish ~2.5cm in diameter	complete juvenile jellyfish ~2.5cm in diameter	not recorded	not recorded	SRP165275	147.85
SRR8040406	jellyfish striated muscle layer	jellyfish striated muscle layer	not recorded	not recorded	SRP165275	36.51
SRR8040388	strobila head	strobila head	not recorded	not recorded	SRP165275	105.23
SRR8040404	jellyfish gastric filaments	jellyfish gastric filaments	not recorded	not recorded	SRP165275	1.02
SRR8040403	jellyfish bell edge	jellyfish bell edge	not recorded	not recorded	SRP165275	73.18
SRR8040402	jellyfish oral arm	jellyfish oral arm	not recorded	not recorded	SRP165275	95.30
SRR8040401	jellyfish bell middle part	jellyfish bell middle part	not recorded	not recorded	SRP165275	70.19
SRR8040399	polyp ectoderm from body column	polyp ectoderm from body column	not recorded	not recorded	SRP165275	74.53
SRR8040398	polyp head region	polyp head region	not recorded	not recorded	SRP165275	56.80
SRR8040397	polyp endoderm from body column	polyp endoderm from body column	not recorded	not recorded	SRP165275	58.66
SRR8040396	strobila non-segmented part	strobila non-segmented part	not recorded	not recorded	SRP165275	96.21
SRR8040395	strobila segments	strobila segments	not recorded	not recorded	SRP165275	113.23
SRR8040390	complete polyp induced 12h	complete polyp induced 12h	not recorded	not recorded	SRP165275	63.17
SRR8040389	complete polyp not induced	complete polyp not induced	not recorded	not recorded	SRP165275	0.00
SRR8089705	endoderm (canal system)	endoderm (canal system)	not recorded	not recorded	SRP165275	0.00

Source: CnidoSite RNA-seq expression matrices (AAURI2_TPM, StringTie quantification over 29 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.