RetrogeneDB ID: retro_ocun_1145

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 20:21113000..21114408(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000011291
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RBBP8
• Ensembl ID: ENSOCUG00000007333
• Aliases: None
• Description: retinoblastoma binding protein 8 [Source:HGNC Symbol;Acc:9891]

Sequence

>retro_ocun_1145
GATAAGTCATCTTTTAACTTAGCTACAGTTGTTGCTGAAACACTTGGACTTGGTGTTCAAGAAGAATCTGAATGTCAAGG
TCCAAGGAGCCCTTTTGGTGATGAGCTCTATCCCTGTGTGGAAGGAAATCACAAGAAGCAGCCTTTTGAGGAATCCACAA
AAATTAGTGAAGATTGTTTAAGGTTTTCAGATTCTACTTCAATGATTCCTTCTCAAGAAGAAGTGTCGACTCGGGTGTCA
TCTCCTGTATTTGGAGCTACCTCTAATGTGAAAACTAGTTTAGTTTTGAATACAAGTTTATCCCCTTCTCTTTTAGAGAC
TGGGAAAAAAAAAAAAACATCTGAAATTGGCCCCTTTTAACAATACTTCGGTTTCAAGATCAGAGAGAACTAGATCAAAA
TCTGAGGACAGTGTCCTTTTCACACATCGTAATCTAGGGTCTGAAGTGAACAAGGTCATTAGCCAATCATCTTCTAATAA
GCAGATGCTTTTAAGCAAAAATGTAAGTGAATCCACTGATGAACAGGAGAGGGCTGATCATACTGAAGATTCTATTACTG
ATAAAGCTTTGGTGCCCTTGAAATCACTGGGAGGCAGAGCATCCAAAAGGAAGAAAACTGAGGAGGAAAATGAACTTGAA
GTCAGCTTCCCTCAAGCCTCTTTTGATAAAGAAAATCCTTTTCCTTTTCCAAGAGTCAGTCACTTTCCCTTGAATGGGGA
TTATATGGTGGATAAACCTCTAGATCTGTCAGATCGGTTTTCAGCTTCTCATCGGCAAGAGAAGAGCCAAGGAAGTGAGA
CCTCTAAAAACAGACTGAGACAAGTGACTCTATATGAGGCCTGGAAACCCATTCCCAAGGGCTCTTCCTCAAGCCGCGAG
GCTCTGGGTGGGAGCTACATGTTACCCAAAGATTCCCCAAGAAGAGCCCCATTCACAGGGGTGCACCCTCCAGTCCTTGA
GTGAATGCTCTCCAGAAAATAAAATACCATTACAAATAAAAGAAGAAAATCCTGTCTTCAAAATTCCTCTACGTCCACGT
GAAACTTTGGAAACAGAAAACATTTTGATGACATGAAGGGTGCTGGTTCTCATGAGCCAATAAGAATAAAAAATAGGTCT
GTCCAGGGAGGATGTGAACTTGCATCAGTTCTTCAGTTAAATCCGTGCAGAATGGCTAAAGCAAAGCCTCTGCAGAACAA
CCAAAATGTATCCTTTGAAAATATCCAGTGGAGTGTAGATCCAGGAGCAGACCTTTCTCAGTATAAAATGGGTATCACTG
TAATAGATACAAAGGATGGCAGTCAGTCAAGAGTAGGAGGAGAAACAGTAGACATGGACTGCACATTGGTCAGTGAAACC
ACACTTTCAAAAATGAAGAAGCAAGAGCAGAAGGGAGAAAAAAGTCCA

Alignment

ORF - retro_ocun_1145 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.22 %
• Parental protein coverage: 51.77 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  DKSSFNLTTVVAETPGLGVQEESECQGPRSPLGDELYPCVEGNHKKQPFEESTKISEDCLRFSDSTSMIP
          DKSSFNL.TVVAET.GLGVQEESECQGPRSP.GDELYPCVEGNHKKQPFEESTKISEDCLRFSDSTSMIP
Retrocopy DKSSFNLATVVAETLGLGVQEESECQGPRSPFGDELYPCVEGNHKKQPFEESTKISEDCLRFSDSTSMIP

Parental  SQEEVSTRVSSPVFGATSNVKTSLVLNTSLSPSLLETGKKSHL-KLAP-FNNTSVSRSEKTRSKSEDSVL
          SQEEVSTRVSSPVFGATSNVKTSLVLNTSLSPSLLETGKK.......P.FNNTSVSRSE.TRSKSEDSVL
Retrocopy SQEEVSTRVSSPVFGATSNVKTSLVLNTSLSPSLLETGKKKKTSEIGP>FNNTSVSRSERTRSKSEDSVL

Parental  FTHRNLGSEVNKVISQSSSNKQILLSKNVSESTDEQESADHTKDSITDKALVPLKSLGGRASKRKKTEEE
          FTHRNLGSEVNKVISQSSSNKQ.LLSKNVSESTDEQE.ADHT.DSITDKALVPLKSLGGRASKRKKTEEE
Retrocopy FTHRNLGSEVNKVISQSSSNKQMLLSKNVSESTDEQERADHTEDSITDKALVPLKSLGGRASKRKKTEEE

Parental  NELEVSCPQASFDKENAFPFPRDSHFPLNGDYMMDKPLDLSDRFSASHRQEKSQGSETSKNRLRQVTLYE
          NELEVS.PQASFDKEN.FPFPR.SHFPLNGDYM.DKPLDLSDRFSASHRQEKSQGSETSKNRLRQVTLYE
Retrocopy NELEVSFPQASFDKENPFPFPRVSHFPLNGDYMVDKPLDLSDRFSASHRQEKSQGSETSKNRLRQVTLYE

Parental  ALKPIPKGSSSSRKALGGSCMLPKDSP-EEPHSQECTLQSLSKCSPENKIPLQIKEENPVFKIPLRPRET
          A.KPIPKGSSSSR.ALGGS.MLPKDSP.EEPHSQ.CTLQSLS.CSPENKIPLQIKEENPVFKIPLRPRET
Retrocopy AWKPIPKGSSSSREALGGSYMLPKDSP>EEPHSQGCTLQSLSECSPENKIPLQIKEENPVFKIPLRPRET

Parental  LETENL-FDDMKGAGSHEPIRIKNRSVQGGCELASVLQLNPCRMAKAKPLQNNQDVSFENIQWSVDPGAD
          LETEN..FDDMKGAGSHEPIRIKNRSVQGGCELASVLQLNPCRMAKAKPLQNNQ.VSFENIQWSVDPGAD
Retrocopy LETENI<FDDMKGAGSHEPIRIKNRSVQGGCELASVLQLNPCRMAKAKPLQNNQNVSFENIQWSVDPGAD

Parental  LSQYKMDITVIDTKDGSQSRLGGETVGMDCTLVSETILSKMKKQEQKGEKSP
          LSQYKM.ITVIDTKDGSQSR.GGETV.MDCTLVSET.LSKMKKQEQKGEKSP
Retrocopy LSQYKMGITVIDTKDGSQSRVGGETVDMDCTLVSETTLSKMKKQEQKGEKSP

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	0.06 RPM	2.76 RPM
SRP017611_kidney	0.30 RPM	19.26 RPM
SRP017611_liver	0.00 RPM	1.62 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1145 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1145 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1145 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
Monodelphis domestica	ENSMODG00000021493	2 retrocopies	retro_mdom_1791, retro_mdom_445,
Oryctolagus cuniculus	ENSOCUG00000007333	1 retrocopy	retro_ocun_1145 ,