RetrogeneDB ID: retro_chof_1278

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_246669:1334..2038(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: RBPJ
• Ensembl ID: ENSCHOG00000001582
• Aliases: None
• Description: recombination signal binding protein for immunoglobulin kappa J region [Source:HGNC Symbol;Acc:5724]

Sequence

>retro_chof_1278
CGGCCTCCATCTAAACAACTCACTAGGAAAGCTATGCGAAATTATTAAAAAGAGTGAGGGGATCAAACAGTACTTATTCT
TCATGCAAAAGTTGCACAGAAGTCATATGGAAATGAAAAAAGGTTTTTTGTCCTCCTCCTTGTGTGTATCTTATGGGCAG
AGGATTGAAGAAAAAAAAGACTAAATGGAACGCGATTGTTGTTCTGAACAAGAATCTCAACCATGTGCATTTATTAGAAT
AGGAAATAGTGACCAAGAAATGTAGCAGCTGAACTTAGATGGAAAGAACTATTGCACAGCCAAAACATTGTACATATCTG
ATTCAGACAAGAGAAAGCACTTCATGTTGTCTGTAAAGATGTTCTATGGTAACAGCGATGACATTGGTGTGTTCCTCAGC
AAGCAGATAAAAGTCATCTTCAAACCTTCCAAAAAGAAGCAGTCATTGAAAAACACTGACTTGTGCATTGCATCAAGGAC
AAAGGTGGCTCTGTTTAATCAACTTAGATCCCAGAAGTTAGTACCAGATACTTGCACGTAGGAGGTAATTTCCATGCCAG
TTCACAGAAGTGGGGAGCATTTTACATCATCTCCTGGATGATGATGAATCAGAAGAAGAATTCACAGTAGGCAACAGCTA
CATCCATTATGGACAAACAGTCACACTTGTGTGTTCAGTTACTGGCATGGCACTCCCAAGATTG

Alignment

ORF - retro_chof_1278 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.95 %
• Parental protein coverage: 51.52 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  RPQPKRLTREAMRNYLKERGDQTVLILHAKVAQKSYGNEKRFF-CPPPCVYLMGSGWKKKKEQ-MERDGC
          RP..K.LTR.AMRNY.KE.GDQTVLILHAKVAQKSYGNEKRFF.CPPPCVYLMG.G.K......MERD.C
Retrocopy RPPSKQLTRKAMRNY*KE*GDQTVLILHAKVAQKSYGNEKRFF<CPPPCVYLMGRGLKXXXTK<MERDCC

Parental  SEQESQPCAFIGIGNSDQEMQQLNLEGKNYCTAKTLYISDSDKRKHFMLSVKMFYGNSDDIGVFLSKRIK
          SEQESQPCAFI.IGNSDQEM.QLNL.GKNYCTAKTLYISDSDKRKHFMLSVKMFYGNSDDIGVFLSK.IK
Retrocopy SEQESQPCAFIRIGNSDQEM*QLNLDGKNYCTAKTLYISDSDKRKHFMLSVKMFYGNSDDIGVFLSKQIK

Parental  VISKPSKKKQSLKNADLCIASGTKVALFNRLRSQ-TVSTRYLHVEGGNFHASSQQWGAFYI-HLLDDDES
          VI.KPSKKKQSLKN.DLCIAS.TKVALFN.LRSQ..VSTRYLHV.GGNFHASSQ.WGAFYI.HLLDDDES
Retrocopy VIFKPSKKKQSLKNTDLCIASRTKVALFNQLRSQ<EVSTRYLHV-GGNFHASSQKWGAFYI<HLLDDDES

Parental  EGEEFTVRDGYIHYGQTVKLVCSVTGMALPRL
          E.EEFTV...YIHYGQTV.LVCSVTGMALPRL
Retrocopy E-EEFTVGNSYIHYGQTVTLVCSVTGMALPRL

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Choloepus hoffmanni was not studied using RNA-Seq expression data.

ChIP-Seq

Choloepus hoffmanni was not studied using ChIP-Seq data.

EST

Choloepus hoffmanni was not studied using EST data.

TSS

Choloepus hoffmanni was not studied using FANTOM5 data.

Lab

retro_chof_1278 was not experimentally validated.

Homology

Retrocopy orthology:

Choloepus hoffmanni does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000003602	1 retrocopy	retro_btau_1507,
Choloepus hoffmanni	ENSCHOG00000001582	4 retrocopies	retro_chof_1172, retro_chof_1278 , retro_chof_2449, retro_chof_371,
Homo sapiens	ENSG00000168214	6 retrocopies	retro_hsap_4169, retro_hsap_4171, retro_hsap_4173, retro_hsap_4174, retro_hsap_4256, retro_hsap_4316,
Gorilla gorilla	ENSGGOG00000004582	1 retrocopy	retro_ggor_2853,
Mus musculus	ENSMUSG00000039191	2 retrocopies	retro_mmus_2348, retro_mmus_2819,
Nomascus leucogenys	ENSNLEG00000016895	1 retrocopy	retro_nleu_2305,
Oryctolagus cuniculus	ENSOCUG00000013449	1 retrocopy	retro_ocun_1445,
Pan troglodytes	ENSPTRG00000015968	1 retrocopy	retro_ptro_2829,
Tursiops truncatus	ENSTTRG00000009022	2 retrocopies	retro_ttru_1151, retro_ttru_1593,