RetrogeneDB ID: retro_ocun_1369

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 7:100855326..100856250(-)
• Located in intron of: ENSOCUG00000008246

Retrocopy information

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

Parental gene information

• Parental gene symbol: SHOC2
• Ensembl ID: ENSOCUG00000014348
• Aliases: None
• Description: soc-2 suppressor of clear homolog (C. elegans) [Source:HGNC Symbol;Acc:15454]

Sequence

>retro_ocun_1369
ACTCTTGATAACTTGAAGAAGCTGCGGATGCTTGATTTACGACATAATAATCTAAGAGAAATTCCTTCAGTGGTGAATAG
GCTGGATTCTCTCACCACTCTATATCTTCCCTTTGATCATATAACTACTGTGGCAAAGGACATCAAAAACCTGTCAAAAC
TCAGCATGCTTTATATTCAGGAGAACAAAATCAAACAACTCCCTGCTGAAATTGGTGAATTATGTAACCTCATTACCCTG
GATGTAGCCCATGATCAACTTGAACACCTTCCAAAGGAGTCTGGAAACTGAATGCAGATAACTAACCTGGATTTGCAGCA
CAATGAACTGGTAGACCTCCCAGATACTATAGGAAACCTGTCCAGTTTAAGTCATCTTGGTCTAAGATACAATAAACTAT
CAGCAATACCCAGATAATTAGCAAAATCAGTGCACTGTAAGAATTAAATTTAGAGAACAATAACATTTCTACTTTACCAG
AGAGTCTTTTATCTAGTCTTGTGAAACTGAATAGATTAACTTTAACTAGAAATTCCTTCCAGTTATATCCAGTAGGTGGT
CCATCTCAGTTTCTACCATCTATTCTCTTTACAAAGAACACAATTGAATCAATAAAATCCCATTTGGGATTTTCTCCAGA
GCAAAAGTATTAAGCTGAATATGAAGGACAATCAGTTAACATCTCTTCTCCAGGATTTTGGAACTTGGACTAGTATGGTA
GAGTTGAATTTAGCTACTAATCAGCTCACAAAGATCCCTAAGGATGTGTCTGGTCTTCTTTCTCTTTAGGGTCTAATATT
ATCAAACAGTTTTCTCAAGAAATTTCTCTATGGCCTTGGAAACCTTAAGAGGTTAAGAGAATTGGATTTAGAGAATAAAT
TGGAATCCCTGCCAAATGAAATTGCTTATCATAGGGATCTGCAG

Alignment

ORF - retro_ocun_1369 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.76 %
• Parental protein coverage: 53.26 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  SLDN-KKLRMLDLRHNKLREIPSVVYRLDSLTTLYLRFNRITTVEKDIKNLSKLSMLSIRENKIKQLPAE
          .LDN.KKLRMLDLRHN.LREIPSVV.RLDSLTTLYL.F..ITTV.KDIKNLSKLSML.I.ENKIKQLPAE
Retrocopy TLDNLKKLRMLDLRHNNLREIPSVVNRLDSLTTLYLPFDHITTVAKDIKNLSKLSMLYIQENKIKQLPAE

Parental  IGELCNLITLDVAHNQLEHLPKEIGNCTQITNLDLQHNELLDLPDTIGNLSSLSRLGLRYNRLSAIPRSL
          IGELCNLITLDVAH.QLEHLPKE.GN..QITNLDLQHNEL.DLPDTIGNLSSLS.LGLRYN.LSAIPR.L
Retrocopy IGELCNLITLDVAHDQLEHLPKESGN*MQITNLDLQHNELVDLPDTIGNLSSLSHLGLRYNKLSAIPR*L

Parental  AKC-SALEELNLENNNISTLPESLLSSLVKLNSLTLARNCFQLYPVGGPSQF-STIYSLNMEHNRINKIP
          AK..SAL.ELNLENNNISTLPESLLSSLVKLN.LTL.RN.FQLYPVGGPSQF.STIYSL..EHN.INKIP
Retrocopy AKS<SAL*ELNLENNNISTLPESLLSSLVKLNRLTLTRNSFQLYPVGGPSQF<STIYSLYKEHN*INKIP

Parental  FGI-FSRAKVLSKLNMKDNQLTSLPLDFGTWTSMVELNLATNQLTKIPEDVSGLVSLEVLILSNNLLKKL
          FGI.F...K...KLNMKDNQLTSL..DFGTWTSMVELNLATNQLTKIP.DVSGL.SL..LILSN..LKK.
Retrocopy FGI<FLQSKSI-KLNMKDNQLTSLLQDFGTWTSMVELNLATNQLTKIPKDVSGLLSL*GLILSNSFLKKF

Parental  PHGLGNLRKLRELDLEENKLESLPNEIAYLKDLQ
          ..GLGNL..LRELDL.ENKLESLPNEIAY..DLQ
Retrocopy LYGLGNLKRLRELDL-ENKLESLPNEIAYHRDLQ

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	35.60 RPM
SRP017611_kidney	0.00 RPM	32.43 RPM
SRP017611_liver	0.00 RPM	7.48 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1369 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1369 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1369 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Myotis lucifugus	ENSMLUG00000013811	1 retrocopy	retro_mluc_690,
Oryctolagus cuniculus	ENSOCUG00000014348	1 retrocopy	retro_ocun_1369 ,
Pongo abelii	ENSPPYG00000002651	1 retrocopy	retro_pabe_252,