RetrogeneDB ID: retro_ocun_1258

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 4:66482446..66483958(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: OTUD4
• Ensembl ID: ENSOCUG00000014569
• Aliases: None
• Description: OTU domain containing 4 [Source:HGNC Symbol;Acc:24949]

Sequence

>retro_ocun_1258
TTTATAATTTATCGGGAACCGAATGTTTCTCCGGCACAAGTAACTGAAAATAATTTTCCTGAAAAGGTATTACTGTGTTT
TTCAAATGGAAATCACCATGATATTGTTTACCCCATAAAGTATAAAGATAGTTCTGCTATGTGTCAGTCTCTTCTTTATG
AATTGCTCTATGAGAAGGTGTTGAAAGCTGATGTCAGTAAAATCGTGATGGGACTAGACACTTCTGAAGTAGCTGATGGA
AACAACAGTGAAATATCAGATTCAGAGGATGATAGTTGCAAGAGGAAAACTGCTAATGATGTGAATGGATTTAAACCTTT
GTCAGGCGATGAGCACTTGAAGAACAATGGGAATTCTACTAGCCTTCCCTTGTCTAGAAAGGTTCTTAAGTCACTCAATC
CAGCAGTCTACAGAACTGTGGAATATGAAATTTGGCTGAAGTCTAAACAAACTCAACAAAAGCGTGATTATTCCATTGCT
GCTGGTTTACAATATGAAGTTGGAGAGAAATGCCAAGTTAGGTTGGATCACAATGGAAAATTTCCTAATGCAGATATTCA
AGGAGTTCACTCTGAGAATGGACCAGTTTTGGTTGAAGAATTGGGAAAAAAACATGCCGTGAAGACCCTCAAACCACCTC
CCCCAGAAAGCTGGAGCACAGTGTCAGGAAAGAAGATGAAAAAACCTTCTACTTCGGGACAAAATTTTCATTCTGAAATG
GATTACAGAGGGCCAAAGAATCCAAGCAAGCCAATAAAAGCCCCATCAGTACTACCTCCTCAGCTCCAGCATCCTTTGGG
AATAAGACAACATGCATTCTCTAGTCACTCTTCAGGGGCACAGTCTCAGAAATCCTCCAGTGAACACAAAAATCTTGCCA
GGACACCTTCACAGATCATGAGAAAACCTGATCGTGAGAGAGCTGAGGATTTTGATCACACGAATAGAGAATCTCACTAT
TTTGGCCTCTCCCCTGAAGAACGCAGAGAGAAGCAAGCCATAGAAGAATCTCTTATACTTTAAGAGATTCAGAACAGAGA
TGAACAGGCTTTCCCAACCCTTTCCATGTCATCAGTCAGTACATCAGCTTCTCAAAGTAGCAACCATGTGTCCAGAGAAA
ATCATCCCACGGAAGTGATAGAAAAGGAAACAGGCGGAGAATGGACACAAGAACGGAAGGACAAAGACTCTGTCCATGGA
TCTACTCACTTGGATAAAAAACCTGAACCAAGTACATTAGAGAATATTAGTGATGATAGATGTGCAAGAGTTTCATCACC
ATTGAAGTCAAAGAAATTAGAGTGCCCATCTCCTGCAGAACAAAAGCCAGCAGAACATGGGTCTCTGTCAAATCGACCAA
CAGGTGTCCCTGCTTCAATTCCTCTTTTATCGGTGACACAGACTCTGACCACTGGACCTGATTCTGCTGTATCCCAACCT
ACAACTTTTGGACCAACAGTTCCTGTGTCAATACAGGCAGTTAACCAGCCCTTGATGCCTTTGCCTCAGACA

Alignment

ORF - retro_ocun_1258 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.91 %
• Parental protein coverage: 78.94 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  FIIYREPNVSPAQVTENNFPEKVLLCFSNGNHYDIVYPIKYKDTSAMCQSLLYELLYEKVFKADVSKIVM
          FIIYREPNVSPAQVTENNFPEKVLLCFSNGNH.DIVYPIKYKD.SAMCQSLLYELLYEKV.KADVSKIVM
Retrocopy FIIYREPNVSPAQVTENNFPEKVLLCFSNGNHHDIVYPIKYKDSSAMCQSLLYELLYEKVLKADVSKIVM

Parental  GLDTSEVADGNNSEISDSEDDSCKRKTANDVNGFKPLSGDEHLKNNGNSTSLPLSRKVLKSLNPAVYRNV
          GLDTSEVADGNNSEISDSEDDSCKRKTANDVNGFKPLSGDEHLKNNGNSTSLPLSRKVLKSLNPAVYR.V
Retrocopy GLDTSEVADGNNSEISDSEDDSCKRKTANDVNGFKPLSGDEHLKNNGNSTSLPLSRKVLKSLNPAVYRTV

Parental  EYEIWLKSKQAQQKRDYSIAAGLQYEVGEKCQVRLDHNGKFPNADIQGVHSENGPVLVEELGKKHAVKTL
          EYEIWLKSKQ.QQKRDYSIAAGLQYEVGEKCQVRLDHNGKFPNADIQGVHSENGPVLVEELGKKHAVKTL
Retrocopy EYEIWLKSKQTQQKRDYSIAAGLQYEVGEKCQVRLDHNGKFPNADIQGVHSENGPVLVEELGKKHAVKTL

Parental  KPPPPESWSTVSGKKMKKPSTSGQNFHSEMDYRGPKNPSKPIKAPSVLPPRLQHPLGIRQHAF---SSGA
          KPPPPESWSTVSGKKMKKPSTSGQNFHSEMDYRGPKNPSKPIKAPSVLPP.LQHPLGIRQHAF...SSGA
Retrocopy KPPPPESWSTVSGKKMKKPSTSGQNFHSEMDYRGPKNPSKPIKAPSVLPPQLQHPLGIRQHAFSSHSSGA

Parental  QSQKSSSEHKNLARTPSQIMRKPDRERAEDFDHTNRESHYFGLSPEERREKQAIEESRLLYEIQNRDEQA
          QSQKSSSEHKNLARTPSQIMRKPDRERAEDFDHTNRESHYFGLSPEERREKQAIEES..L.EIQNRDEQA
Retrocopy QSQKSSSEHKNLARTPSQIMRKPDRERAEDFDHTNRESHYFGLSPEERREKQAIEESLIL*EIQNRDEQA

Parental  FPALSMSSVSTSASQSSN-PCVQRKSSHGSDRKGNRRRMD-TEERKDKDSVHGSTHLDKKPEPSTLENIS
          FP.LSMSSVSTSASQSSN.PCV....S.........RR...T.ERKDKDSVHGSTHLDKKPEPSTLENIS
Retrocopy FPTLSMSSVSTSASQSSN<PCV-QRKSSHGSDRKGNRRRM>TQERKDKDSVHGSTHLDKKPEPSTLENIS

Parental  DDRCARVSSPLKSKKLECPSPAEQKPAEHVSLSNPAPLLVSPEVHLTPAVPSLPATVPAWPSEPTTFGPT
          DDRCARVSSPLKSKKLECPSPAEQKPAEH.SLSN..P..V.....L......L........S.PTTFGPT
Retrocopy DDRCARVSSPLKSKKLECPSPAEQKPAEHGSLSN-RPTGVPASIPLLSVTQTLTTGPDSAVSQPTTFGPT

Parental  GVPAPIPVLSVTQTLTTGPDS
          ....P.....V.Q.L...P..
Retrocopy ---VPVSIQAVNQPLMPLPQT

Legend:

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

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP017611_brain	0.00 RPM	6.84 RPM
SRP017611_kidney	0.00 RPM	7.70 RPM
SRP017611_liver	0.00 RPM	6.47 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1258 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1258 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1258 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000164164	1 retrocopy	retro_hsap_947,
Oryctolagus cuniculus	ENSOCUG00000014569	2 retrocopies	retro_ocun_1258 , retro_ocun_330,