RetrogeneDB ID: retro_ocun_1939

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: X:76663004..76663997(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000025426
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RBBP7
• Ensembl ID: ENSOCUG00000000683
• Aliases: None
• Description: retinoblastoma binding protein 7 [Source:HGNC Symbol;Acc:9890]

Sequence

>retro_ocun_1939
CAGTTTGATGCTTCCCACTGTGATAGTGACAAGAGTAAATTTGGTGGCTTTGGTTCTGTAACAGGAAAAATTGAATGTGA
AAGTAAAATTAATCATGAAGGAGAAGTAAACCGTGCCCATTACATGCCACAGAATCCTCATATCATTGCTACAAAAACAC
CATCTTCTGATGTCTTGGTTTTTGACTATACAAAACACCCTATTAAACCAGACCCAAGTGGAGAATGCAATCCTGATCTT
AGGTTAGGAGGTCACCAAAAGGAAGGCTATGGTCTTTCCTGGAATTTTAATTTAAGTGGACATCTCCTAAGTGAATCTGA
TGAGCATACTGTCTGTCTGTGGGAAATAAATGCAGGACCAACGGAAGGCAAAATTGTGGATGCTAAAGCAATCTTTACTG
GCCACTCAACTGTTGTGGAGGATGTGGCCTGGCACCTGCTCCATGAGTCGTTGTTTGGATCTGTTGCTGATGATCAGAAA
CTTATGATATGGGATACCAGTCCAATACCACCTCCATCCTGAGTCACTTGGTGGATGCACATACCACCGAGGTCAACTGC
CTCTCGTTCAATCCCTACAGCGAGTTCATTCTAGCAACTGGCTCTGCGGATAAGACTGTAGCTTTATGGGATCTGCATAA
CTTGAAATTAAAACTTCATACCTTCGAATCTCATAAGGATGAAATTTTCCAGGTCCACTGGTCTCCACATATTGAAACTA
TTCTGGCTTCAAGTGGTACTGATTGCCGCCTGAATGTATGGGATTTAAGTAAAATTGAAGAACAATCAGCAGAAGATGCA
GAAGATGGGCCTCCAGAACTCCTGTTTATTCATGGAGGACACACTGCCAAGATCTCAGATTTTAGTTGGAATCCCAATGA
GCCTTGGGTCATCTGCTCCGTGTCTGAGGATAACATCCTGCAGATATGGCAAATGGCTGAAGATAATTTACAATGATAAA
GAGTCAGAAGTCACAACATCGGAACTGGAGGGA

Alignment

ORF - retro_ocun_1939 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.51 %
• Parental protein coverage: 78.12 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  QFDASHCDSDKGEFGGFGSVTGKIECEIKINHEGEVNRARYMPQNPHIIATKTPSSDVLVFDYTKHPAKP
          QFDASHCDSDK..FGGFGSVTGKIECE.KINHEGEVNRA.YMPQNPHIIATKTPSSDVLVFDYTKHP.KP
Retrocopy QFDASHCDSDKSKFGGFGSVTGKIECESKINHEGEVNRAHYMPQNPHIIATKTPSSDVLVFDYTKHPIKP

Parental  DPSGECNPDLRLRGHQKEGYGLSWNSNLSGHLLSASDDHTVCLWDINAGPKEGKIVDAKAIFTGHSAVVE
          DPSGECNPDLRL.GHQKEGYGLSWN.NLSGHLLS.SD.HTVCLW.INAGP.EGKIVDAKAIFTGHS.VVE
Retrocopy DPSGECNPDLRLGGHQKEGYGLSWNFNLSGHLLSESDEHTVCLWEINAGPTEGKIVDAKAIFTGHSTVVE

Parental  DVAWHLLHESLFGSVADDQKLMIWDT-RSNTTSKPSHLVDAHTAEVNCLSFNPYSEFILATGSADKTVAL
          DVAWHLLHESLFGSVADDQKLMIWDT..SNTTS..SHLVDAHT.EVNCLSFNPYSEFILATGSADKTVAL
Retrocopy DVAWHLLHESLFGSVADDQKLMIWDT<QSNTTSILSHLVDAHTTEVNCLSFNPYSEFILATGSADKTVAL

Parental  WDLRNLKLKLHTFESHKDEIFQVHWSPHNETILASSGTDRRLNVWDLSKIGEEQSAEDAEDGPPELLFIH
          WDL.NLKLKLHTFESHKDEIFQVHWSPH.ETILASSGTD.RLNVWDLSKI.EEQSAEDAEDGPPELLFIH
Retrocopy WDLHNLKLKLHTFESHKDEIFQVHWSPHIETILASSGTDCRLNVWDLSKI-EEQSAEDAEDGPPELLFIH

Parental  GGHTAKISDFSWNPNEPWVICSVSEDNIMQIWQMAEN-IYNDEESEVTTSELEG
          GGHTAKISDFSWNPNEPWVICSVSEDNI.QIWQMAE..IYND.ESEVTTSELEG
Retrocopy GGHTAKISDFSWNPNEPWVICSVSEDNILQIWQMAED>IYNDKESEVTTSELEG

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	41.67 RPM
SRP017611_kidney	0.00 RPM	38.52 RPM
SRP017611_liver	0.00 RPM	19.42 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1939 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1939 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1939 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000002820	1 retrocopy	retro_btau_1579,
Mus musculus	ENSMUSG00000031353	1 retrocopy	retro_mmus_3529,
Oryctolagus cuniculus	ENSOCUG00000000683	1 retrocopy	retro_ocun_1939 ,
Otolemur garnettii	ENSOGAG00000014995	1 retrocopy	retro_ogar_2220,
Petromyzon marinus	ENSPMAG00000007189	1 retrocopy	retro_pmar_26,
Pan troglodytes	ENSPTRG00000021702	5 retrocopies	retro_ptro_1802, retro_ptro_1909, retro_ptro_2226, retro_ptro_2987, retro_ptro_896,
Rattus norvegicus	ENSRNOG00000005157	1 retrocopy	retro_rnor_1182,
Sorex araneus	ENSSARG00000008079	3 retrocopies	retro_sara_308, retro_sara_571, retro_sara_602,
Tupaia belangeri	ENSTBEG00000010151	2 retrocopies	retro_tbel_3031, retro_tbel_4341,
Tarsius syrichta	ENSTSYG00000002385	4 retrocopies	retro_tsyr_1608, retro_tsyr_1838, retro_tsyr_1957, retro_tsyr_427,