Gene detail

Detailed information of gene29641.t1 in Actinoscyphia liui

Genomic Location: chr10:17423809...17430336
NR annotation: XP_020896672.1, protein lin-28 [Exaiptasia diaphana]
Species Actinoscyphia liui · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

Transcript

gene29641.t1

GGCGAATGAGCGTCATTTGGTCTACCAAGCTATCAGATTGAGCATTCACCTCAAATTTATTGACGAAGGAAACCGTCGTTTTCAATGAAGATCGATGGCTGAGGATAGCTCTACATTAGCTGGTTCTGTAAAATGGTTCAATATTGTCAAAGGCTTTGGGTTTATTTCGAGGGACGACGGAGGCGAAGACGTCTTTGTACATCAGAGTGCCATAAAATCGGATGGATACCGAAGTCTCGTGGAAGGCGAACAAGTTTCATTCCAAATCATCGACAGCGACAAAGGACAAATAGCGGTCAGCGTGACCTCAACGAATGGCGGGAACGTGAAAGGCGCGTCCCGCAAAATTCGCGCGAAACAAGGCGCGCGAAAATATACGTCACTATGCTTCAACTGTAACCAAGGTGGGCATCGCGCAAAAAAATGCCCGTATGAAAGGACAGCAAGCAGAATTTGCCATAAATGTGGCTCAGGAACTCATATTATCAGAAAATGCCCCCTGATATTATCAGATAAAGAGCAAACCGAGAAAGAAACTCTACACAAAAGCTCTGAAGAGGAAGTAAAAAAACAATGTGATTTGAAAGGAGAACCTTTGGACATCAATCACAACGGCAACATTCCTCAAATTCCTAAAGGTTGAAATAAAAGTGGAAATTTGAAGGAAATAAAAAAAAATAATAATAAAGGGGATAAAATAATGGGATATTGGGATCCCATTTCTCTTGCTATGAATTGCCAGAATAGAATGAATGCGGATTCGATATTGCTTCATATTAGAACGCCTTTTATAACTACGCGACCCAGCTAAAAACTCCAGATGTCTAGATCTGCGGATGTTTTCACTTCTGAAAACCAATCAACGGTCAGAATTAGTACTACCCTGCGAGCAAAGTCGTTTTACCTTCCCGAGCGAAGGAAATTTCGTTGAGAACACTCTGCTCGCAGGGTAAATTAGTTCTTACACCTTTTTGCCCTTCATCACCAGAATAAAAAATATCAATAGCACCAAATAATTTTTCATTTACGCGAAAAGCGTAATCCATTAAACGAAACGGAACACGACCACTGGATGTTATAGCATACAGATTATGGTCTAGAACCCCCCTTACCAGACAGTCTGGCTACGCCCCTGCTCTCTACTCTTCGCAAGAAAATCTATTGCGCGAGAAGTGGTAATGAACGATTACCATGCAGAAGAAAATTATTTATTTCCCCCTGGTATTACCTAACCTTAACGTCATTCTGACTTTCATTTTTTCTATTTCCAAGCAAGCAAACGAACGAACAACAAACATTGCATTTCCATTGTATTTCCTTCATTTATGAAGAAACAATGATTGCTTTTTACACTGGCCTGGCGTAATATACAAAATAAAGTGCCACTGAACCGAAGCATTTTATTGCATTTTCTGACAGACTTTTGTTAGTAATGATAAGTATCATAATTTTTTTTAATTGTTTGGTTTACAAGATATTCAAGAAAAAACAGTTGCAAAGTGCGACGTCACACGGTTTACAAACATGCTAATTTGAATCGATGGCCTGTTGAAGAACATGAATTTAGAAAGTTTGTCTGTTTATTTTATTTTTTTATCTGCCCAACAATCATTTCCCAGATATTTAATTATGGTTTTTGTAACACTATATAATTAATATTAGGTTGGAGATAAATAATAGACCACTTTCTTAATTCAGTTTTTCTAGGTAGAGAAAATGAGACCTTTTTTTACTATAGAAATTGATCAATTAATATGTTATCTGAGAAAGTTCTCTTCTAGATCTAAAACTCAATACATTATCTAAATCAACAAGTAATAATAACAAGTAAAAAATAATATTTTTCAATTTTTATGCCAATTAGCAGCATTATTATGAAAGTGGGGCCATGCAATAAAAATAAACAAATAACTAATTTATTACAAACAAATAAATAATATATAATACTGTATAAAGCTATAATATTGACATTAAAGTATCATTGACAGTGTTTTGTAATAATAAATACAGTATTAAGTAAAAATATTAAATACATATTTCAATAAATAAAAAATTAATATGTACAGAGGGCCAGAGCTAGCCTCCCGCTTATGGTCACTCTGCGCCCTTCTCCTCCCCTGAGCAAATTTTAGGAGCCAATAGAGATGGGAGGGGGTGGTGGTCATAGGACCCCATCACCTTCCTTTGGCTACCCCTGTTGGTAGCTGCATAGCTGTCTATTATTATAAATATGTGCTAAGAAACCTAATGTTAGACATGATAGTTTAATTACAAGTAGATGAATAGGCCCTTTGCAACAAACTGTCATGTGACTGTAAGTACTGGGATGCAAATTTTTAAGTTTTATATTAGATTGCCGATTCTTTTTAGTCACTAGTAAATTACCGAATGAAGCGATGTGTAATAGATGTGTTGCAATGTGGTGCAGTTGTAGCGCAATCTCTCAAAACCAGTTGTTAGAAAGTTTGTTTGCCGTCCAGTAAATTTCACCCCTGGGAATCGAGGTGTTCATTCATTCGTTCTCAGTGAATTAATCAGCACGTGATTGTTGTGTTGCTAAGGGCCTATATTGTAAATAGAGCAGATATCACATGACTATGAAAAACTCACAGCATGTACTTTAATAACCCTAACATTAGAAATGGGGGACAAATTACTCACGTTATAATTAATAACACATCTACAAAAAAAAACTCATTTCTGATTGCAGGCTGTGAATTTTCTTTTGATGTTCTGAAGGGTATATTTATAAATGCTTATACACTCTTTGAAAATGCCCCAAATCTTTTTATTGCCAAAAATGTAATATTGATTGGATGTATCATATTAAAGCTGATGAAATGAGAATTCAAAAATTTATGAAATTATGACGTTGTCATGGCAACAACAGAATATTGGCAATTAGACCCAAAATTCTTCTTTAAAAAAATCATATCTGGATTTCCACTCAATGAAATTTCTTTTTTCCTTGTACATTTTGAGTTCCCACACTTGATCTTTCATTTGAGCGAAAACAAAAAAAATTCTGTAATAGACTAACTTTGCTATTACATAACTTCTTTAGATGTTGTTAATCTTAAATACAATTCTCAGCCAAAGTGGAAAAACATTACCAAAATTTGAGAAATTTCACCAAATAGTTTTTGAGTTATT

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q94C69	Cold shock domain-containing protein 3 OS=Arabidopsis thaliana OX=3702 GN=CSP3 PE=1 SV=1
P27484	Glycine-rich protein 2 OS=Nicotiana sylvestris OX=4096 GN=GRP-2 PE=2 SV=1
O65639	Cold shock protein 1 OS=Arabidopsis thaliana OX=3702 GN=CSP1 PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0002110 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00313 all species →	CSD	'Cold-shock' DNA-binding domain	Domain	Interproscan
PF00098 all species →	zf-CCHC	Zinc knuckle	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR051373 all species →	Family	Lin-28 homolog RNA-binding protein	Interproscan
IPR001878 all species →	Domain	Zinc finger, CCHC-type	Interproscan
IPR002059 all species →	Domain	Cold-shock protein, DNA-binding	Interproscan
IPR019844 all species →	Domain	Cold-shock (CSD) domain	Interproscan
IPR036875 all species →	Homologous_superfamily	Zinc finger, CCHC-type superfamily	Interproscan
IPR011129 all species →	Domain	Cold shock domain	Interproscan
IPR012340 all species →	Homologous_superfamily	Nucleic acid-binding, OB-fold	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR46109 all species →	PROTEIN LIN-28	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003729 all species →	Molecular Function	mRNA binding	Interproscan
GO:0005634 all species →	Cellular Component	nucleus	Interproscan
GO:0005737 all species →	Cellular Component	cytoplasm	Interproscan
GO:0031054 all species →	Biological Process	pre-miRNA processing	Interproscan
GO:0003676 all species →	Molecular Function	nucleic acid binding	Interproscan
GO:0008270 all species →	Molecular Function	zinc ion 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
K18754	LIN28; protein lin-28	-	Messenger RNA biogenesis	ko03019	deepkoala

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