Gene detail

Detailed information of scaffold10.g167.t1 in Aurelia aurita

Genomic Location: scaffold10:2522755...2530337
NR annotation: no NCBI-NR hit recorded
Species Aurelia aurita · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

scaffold10.g167.t1

cgcgctttcagtccgttgttcagctagtgagctcagagtgaatagacgtgtcaaagttgaatagacgagcggcctagtgactttcaatagctcgccctcctactattcaaagcatttctgaagaaatctgaagaaaagttgaccttttggtatcgtatacaaacggagaaagcgaggtcaaagacaaacactataacagagatttgactattgaggtattgaaaaagcttgcaacgatgagtcagataactcaaattaaaattgaaaatcagacgactgcgtctccaccaaccatcaacaacaaccagacgaccgtaacagccaatcctaactcggatcctaacaaaaacaaacaagagcatgtcaaaagaccaatgaatgcctttatggtatggtcacgtgaaaggagaagaaagatggctcaacacaacccccgaatgcacaactcagaaatttcaaaaattcttggtgcggaatggaaaagacttcccgactcagagaaaaacccgtatatcgacgaagcaaagcgactacaagcagagcacagtacccaacatcctaattacaaatataaaccaaggaggagaaaagcgaaacaaataatgaagaaggataaaatgggctttccataccctggtgcagacccaaatatggcaacagcgatcaaattcccatacccgtcaccattcactcaagacccaatgtaccccttgtataatatgacacccactggggcttacccgctgtatgacacatgtgggactttgacagctttgccaagacagaccatgatcactccacccggacagcctcgacactccagctcatccaacacccatgatttctacacgtcgatggccatgcaatccagaggtgcgagttctgctgcctccgagatgatggctctgcagacacgctatgctaaccctatggatgtagctgttacccaggcccctttcacaacgactcaaagcatgcatgtgcccgcacaggattcaccaacggtcagcagttattcgcagatgtatgcgcaacgacatttgtaaggagattcggaagagaaatgacagactgttactttgatggtgactcgatcattggattcgataaacagaacagtgacgatgtgaccagaaagaacagaggagaaaggagagaggataatttacagatgcttggacaagcagcacgattttttaacaataagaaatgagatgtactcaattgatattagcaaaaacataaattgctagtcgctcggatgtatatgtttttacagacagggatagtcgttgaatttttagcattaatacgttttttggcagtaaagcattaactcgagttatcacgttttaatttgcattataaataattcgacagaggggaatgaatatgttttatttcgttctaaggctgagactttttgtggctaggatcttttaaagctatgggcctaaatctgatatgtcccttttggtacaaaatttgcagccccccccccctaaacatgccttgcaatgttattttccctgacccccatcccggccatgccgtgccttgcaatgttgtgttccctgatggttgaagatgaggatgcctccctaccccattaaactggctataaaaatgggcccaagcttgatactttatgatgctttctaacctctttgttacaaaattgtgtgctccctacccttttagaaatttatagatttttgtgccctttcatataattaaaaattataacaatgggcctaacctggattctttattgtgttgggatctcgtttggtaattttgcggtcctcctgccgttttagaaacgttacaggttcaggcctaagcatgacttaccgtttcttacagagactctttattatagaaagaggacataagtcttatgatttattatattaagattattattgttacaacatttgatgcctccctaccacttcaaaaaatgtacagctatggcgtaagcccgataatagacctttcagatattctacaatagagtctggatctagtaatatttttgtatgaaatgttgaatggcgttatagcttctatcactgttttgcacgctcgaaaatacctcagatttcttaaaattgcataaaaatatcgctcgatccagtctctttgtgtagagtagctaagaaccctttaagtcttagctttcggccttaactaaaacataaacactttcatttccatccttatttaatttcgcctcgttatttaagcttatacgcaccgatatgtatatatatatatttatatgtatgaattgtgctatgtataaatatattatacatctaatatccatctttcatcgcatacaagtgctccgcaaattaataacagtgctaaacgcacagctagtttgtgttcataattaacaaagacgttcatatataattcaaaagatccgataaacttcactttttacc

Transcript

scaffold10.g167.t1

CGCGCTTTCAGTCCGTTGTTCAGCTAGTGAGCTCAGAGTGAATAGACGTGTCAAAGTTGAATAGACGAGCGGCCTAGTGACTTTCAATAGCTCGCCCTCCTACTATTCAAAGCATTTCTGAAGAAATCTGAAGAAAAGTTGACCTTTTGGTATCGTATACAAACGGAGAAAGCGAGGTCAAAGACAAACACTATAACAGAGATTTGACTATTGAGGTATTGAAAAAGCTTGCAACGATGAGTCAGATAACTCAAATTAAAATTGAAAATCAGACGACTGCGTCTCCACCAACCATCAACAACAACCAGACGACCGTAACAGCCAATCCTAACTCGGATCCTAACAAAAACAAACAAGAGCATGTCAAAAGACCAATGAATGCCTTTATGGTATGGTCACGTGAAAGGAGAAGAAAGATGGCTCAACACAACCCCCGAATGCACAACTCAGAAATTTCAAAAATTCTTGGTGCGGAATGGAAAAGACTTCCCGACTCAGAGAAAAACCCGTATATCGACGAAGCAAAGCGACTACAAGCAGAGCACAGTACCCAACATCCTAATTACAAATATAAACCAAGGAGGAGAAAAGCGAAACAAATAATGAAGAAGGATAAAATGGGCTTTCCATACCCTGGTGCAGACCCAAATATGGCAACAGCGATCAAATTCCCATACCCGTCACCATTCACTCAAGACCCAATGTACCCCTTGTATAATATGACACCCACTGGGGCTTACCCGCTGTATGACACATGTGGGACTTTGACAGCTTTGCCAAGACAGACCATGATCACTCCACCCGGACAGCCTCGACACTCCAGCTCATCCAACACCCATGATTTCTACACGTCGATGGCCATGCAATCCAGAGGTGCGAGTTCTGCTGCCTCCGAGATGATGGCTCTGCAGACACGCTATGCTAACCCTATGGATGTAGCTGTTACCCAGGCCCCTTTCACAACGACTCAAAGCATGCATGTGCCCGCACAGGATTCACCAACGGTCAGCAGTTATTCGCAGATGTATGCGCAACGACATTTGTAAGGAGATTCGGAAGAGAAATGACAGACTGTTACTTTGATGGTGACTCGATCATTGGATTCGATAAACAGAACAGTGACGATGTGACCAGAAAGAACAGAGGAGAAAGGAGAGAGGATAATTTACAGATGCTTGGACAAGCAGCACGATTTTTTAACAATAAGAAATGAGATGTACTCAATTGATATTAGCAAAAACATAAATTGCTAGTCGCTCGGATGTATATGTTTTTACAGACAGGGATAGTCGTTGAATTTTTAGCATTAATACGTTTTTTGGCAGTAAAGCATTAACTCGAGTTATCACGTTTTAATTTGCATTATAAATAATTCGACAGAGGGGAATGAATATGTTTTATTTCGTTCTAAGGCTGAGACTTTTTGTGGCTAGGATCTTTTAAAGCTATGGGCCTAAATCTGATATGTCCCTTTTGGTACAAAATTTGCAGCCCCCCCCCCCTAAACATGCCTTGCAATGTTATTTTCCCTGACCCCCATCCCGGCCATGCCGTGCCTTGCAATGTTGTGTTCCCTGATGGTTGAAGATGAGGATGCCTCCCTACCCCATTAAACTGGCTATAAAAATGGGCCCAAGCTTGATACTTTATGATGCTTTCTAACCTCTTTGTTACAAAATTGTGTGCTCCCTACCCTTTTAGAAATTTATAGATTTTTGTGCCCTTTCATATAATTAAAAATTATAACAATGGGCCTAACCTGGATTCTTTATTGTGTTGGGATCTCGTTTGGTAATTTTGCGGTCCTCCTGCCGTTTTAGAAACGTTACAGGTTCAGGCCTAAGCATGACTTACCGTTTCTTACAGAGACTCTTTATTATAGAAAGAGGACATAAGTCttatgatttattatattaagattattattgttaCAACATTTGATGCCTCCCTACCACTTCAAAAAATGTACAGCTATGGCGTAAGCCCGATaatagacctttcagatattctacaatagagtctggatctagtaatatttttgtatgaaatgttgaatggcgttatagcttctatcactgttttgcacgctcgaaaatacctcagatttcttaaaattgcataaaaatatcgctcgatccagtctctttgtgtagagtagctaaGAACCCTTTAAGTCTTAGCTTTCGGCCTTAACTAAAACATAAACACTTTCATTTCCATCCTTATTTAATTTCGCCTCGTTATTTAAGCTTATACGCACCGatatgtatatatatatatttatatgtatgaattgtgctatgtataaatatattatacatctaatatccatctttCATCGCATACAAGTGCTCCGCAAATTAATAACAGTGCTAAACGCACAGCTAGTTTGTGTTCATAATTAACAAAGACGTTCATATATAATTCAAAAGATCCGATAAACTTCACTTTTTACC

Protein

Gene family

Family type	Membership / link
Transcription factor family	HMG · all TF in this species

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00505 all species →	HMG_box	HMG (high mobility group) box	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR009071 all species →	Domain	High mobility group box domain	Interproscan
IPR036910 all species →	Homologous_superfamily	High mobility group box domain superfamily	Interproscan
IPR050140 all species →	Family	SRY-related HMG-box transcription factors	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR10270 all species →	SOX TRANSCRIPTION FACTOR	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0000978 all species →	Molecular Function	RNA polymerase II cis-regulatory region sequence-specific DNA binding	Interproscan
GO:0000981 all species →	Molecular Function	DNA-binding transcription factor activity, RNA polymerase II-specific	Interproscan
GO:0006355 all species →	Biological Process	regulation of DNA-templated transcription	Interproscan
GO:0009653 all species →	Biological Process	anatomical structure morphogenesis	Interproscan
GO:0030154 all species →	Biological Process	cell differentiation	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
K09267	SOX1S; transcription factor SOX1/3/14/21 (SOX group B)	-	Transcription factors	ko03000	deepkoala

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

Expression pattern (RNA-seq)

Transcript abundance of scaffold10.g167.t1 across 22 RNA-seq samples of Aurelia aurita. 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.

22Samples

22TPM > 0

19Conditions

148.3Max TPM

79.5Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
complete polyp	3	3	72.29	76.01
polyp not induced	2	2	50.23	59.40
polyp endoderm from body column	1	1	1.43	1.43
jellyfish bell edge	1	1	114.44	114.44
strobila non-segmented part	1	1	80.95	80.95
polyp 12h induction with 5M2MI +20C	1	1	68.55	68.55
polyp 24h induction with 5M2MI	1	1	77.80	77.80
strobila segments	1	1	91.46	91.46
strobila heads	1	1	106.22	106.22
polyp 24h induction with 5M2MI +20C	1	1	88.94	88.94
jellyfish ropalia	1	1	148.32	148.32
polyp head region	1	1	76.71	76.71
polyp 20h induction with 5M2MI +20C	1	1	55.57	55.57
complete strobila	1	1	100.65	100.65
13 jellyfish ropalia	1	1	82.20	82.20
complete juvenile jellyfish	1	1	77.51	77.51
polyp ectoderm from body column	1	1	103.54	103.54
jellyfish bell edge without ropalia	1	1	108.29	108.29
3 juvenile jellyfish (~7mm in diameter)	1	1	48.45	48.45

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR7992484	complete polyp	complete polyp	polyp	not recorded	SRP164891	76.01
SRR7992487	complete polyp	complete polyp	polyp	not recorded	SRP164891	72.29
SRR7992486	complete polyp	complete polyp	polyp	not recorded	SRP164891	68.57
SRR8090261	polyp not induced	polyp not induced	polyp	not recorded	SRP164891	59.40
SRR8090262	polyp not induced	polyp not induced	polyp	not recorded	SRP164891	41.05
SRR7992468	polyp endoderm from body column	polyp endoderm from body column	polyp	not recorded	SRP164891	1.43
SRR8090258	jellyfish bell edge	jellyfish bell edge	jellyfish	not recorded	SRP164891	114.44
SRR8090265	strobila non-segmented part	strobila non-segmented part	strobila	not recorded	SRP164891	80.95
SRR8090264	polyp 12h induction with 5M2MI +20C	polyp 12h induction with 5M2MI +20C	polyp	not recorded	SRP164891	68.55
SRR8090263	polyp 24h induction with 5M2MI	polyp 24h induction with 5M2MI	polyp	not recorded	SRP164891	77.80
SRR8090260	strobila segments	strobila segments	strobila	not recorded	SRP164891	91.46
SRR8090259	strobila heads	strobila heads	strobila	not recorded	SRP164891	106.22
SRR8090256	polyp 24h induction with 5M2MI +20C	polyp 24h induction with 5M2MI +20C	polyp	not recorded	SRP164891	88.94
SRR8090257	jellyfish ropalia	jellyfish ropalia	jellyfish	not recorded	SRP164891	148.32
SRR7992469	polyp head region	polyp head region	polyp	not recorded	SRP164891	76.71
SRR8090255	polyp 20h induction with 5M2MI +20C	polyp 20h induction with 5M2MI +20C	polyp	not recorded	SRP164891	55.57
SRR7992485	complete strobila	complete strobila	strobila	not recorded	SRP164891	100.65
SRR7992483	13 jellyfish ropalia	13 jellyfish ropalia	juvenile jellyfish	not recorded	SRP164891	82.20
SRR7992482	complete juvenile jellyfish	complete juvenile jellyfish	juvenile jellyfish	not recorded	SRP164891	77.51
SRR7992481	polyp ectoderm from body column	polyp ectoderm from body column	polyp	not recorded	SRP164891	103.54
SRR7992480	jellyfish bell edge without ropalia	jellyfish bell edge without ropalia	juvenile jellyfish	not recorded	SRP164891	108.29
SRR8090266	3 juvenile jellyfish (~7mm in diameter)	3 juvenile jellyfish (~7mm in diameter)	jellyfish	not recorded	SRP164891	48.45

Source: CnidoSite RNA-seq expression matrices (AAURI1_TPM, StringTie quantification over 22 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.