RetrogeneDB ID: retro_ocun_1520

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 9:84943287..84944534(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000022527
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RTCB
• Ensembl ID: ENSOCUG00000008270
• Aliases: None
• Description: RNA 2',3'-cyclic phosphate and 5'-OH ligase [Source:HGNC Symbol;Acc:26935]

Sequence

>retro_ocun_1520
GGGGGTGGTGTTGGTGGCTTCCTGCCAGCTATGAAGCAGATTGGCAATGTGGCAGCCCTGCCTAGGATTATTCATCGATC
CATTGGGCTGCCCGATGTCCATTCAGGCTATGGGTTTGCTATTGGGAATATGGCAGCCTTTGATATGAATGACCTGGAAG
CAGTGGTATCCCCAGGTGGTGTCGGATTTGACATCAACTGTGGTGTCTGCTTGCTGAGAACCAATTTAGATGAAAGTGAT
GTCCAGCCTGTGAAGGAGCAGCTTGCACAAGCCATGTTTGACCACATTCCCATTGGGGTGGGATCAAAAGGTGTCATTCC
AATGAATGCCAAAGACTTGGAGGAGGCCTTGGAGATGGGTGTGGACTGTTCTCTAAGAGAAGGCTATGCCTGGGCCGAAG
ACAAGGAGCACTGTGAGGAGTATGGAAGGATGCTGCAAGCCGACCCCAATAAGGTGTCTCCACGGGCCAAAAAAGAGGCC
TTCCTCAGTTGGGGACCCTAGGAGCAGGCAACCACTGTGCAGAAATCCAGGTTGTAGATGAGATTTTCAATGAATATGCA
GCTAAGAAAATGGGCATCGACCATAAGGGACAGGTGTGCGTGATGATCCACAGTGGGAGCAGAGGCTTGGGCCACCAAGT
AGCCACAGATGCACTGGTGGCTATGGAAAAAGCCATGAAGAGAGACAAGATCATCGTAAATGACCGTCAGCTGGCTTGTG
AACGAATCGCTTCCGTGGACAGTCAGGACTACCTGAAGGGAATGGCAGCGGCTGAGAACTACACCTGGGTCAACCGCTCT
TCCATGACTGTCTTAACCCGTCAGGCTTTTGCCAAGGTCTTCAACACAACCCCTGACGAATTGGACCTGCACGTGATCTA
TGATGTCTCTAACAATATCGCCAAGGTCGAGCAGCACGTGGTGGACGGGAAGGAGCGGACGCTGCTGGTGCACAAGAAGG
GATCCACCCGGGCTTTCCCTCCTCCTCACCATCCCCTCATCGCGGTTGATTACCAGCTCACTGGACAACCAGTGCTCATT
GGTGGTACCATGGGAACCTGCAGTTACGTCCTTAATGACATTGAACAGGGCACGACTGAGACCTTCGGAACAAACTGTCA
TGGAGCGGGCAGTGCATTGTCCCTAGCAAAATCTCGGCGTAATCTAGATTTCCAGGACGTCTTAGACAAACTGGCAGATA
TGGGGATCGCAATCCGTGTTGCCTCGCCCAAACTGGTTATGGAAGAG

Alignment

ORF - retro_ocun_1520 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.0 %
• Parental protein coverage: 84.69 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GGGVGGFLPAMKQIGNVAALPGIVHRSIGLPDVHSGYGFAIGNMAAFDMNDPEAVVSPGGVGFDINCGVR
          GGGVGGFLPAMKQIGNVAALP.I.HRSIGLPDVHSGYGFAIGNMAAFDMND.EAVVSPGGVGFDINCGV.
Retrocopy GGGVGGFLPAMKQIGNVAALPRIIHRSIGLPDVHSGYGFAIGNMAAFDMNDLEAVVSPGGVGFDINCGVC

Parental  LLRTNLDESDVQPVKEQLAQAMFDHIPVGVGSKGVIPMNAKDLEEALEMGVDWSLREGYAWAEDKEHCEE
          LLRTNLDESDVQPVKEQLAQAMFDHIP.GVGSKGVIPMNAKDLEEALEMGVD.SLREGYAWAEDKEHCEE
Retrocopy LLRTNLDESDVQPVKEQLAQAMFDHIPIGVGSKGVIPMNAKDLEEALEMGVDCSLREGYAWAEDKEHCEE

Parental  YGRMLQADPNKVSPRAKK-RGLPQLGTLGAGNHYAEIQVVDEIFNEYAAKKMGIDHKGQVCVMIHSGSRG
          YGRMLQADPNKVSPRAKK.RGLPQLGTLGAGNH.AEIQVVDEIFNEYAAKKMGIDHKGQVCVMIHSGSRG
Retrocopy YGRMLQADPNKVSPRAKK<RGLPQLGTLGAGNHCAEIQVVDEIFNEYAAKKMGIDHKGQVCVMIHSGSRG

Parental  LGHQVATDALVAMEKAMKRDKIIVNDRQLACARIASVEGQDYLKGMAAAGNYAWVNRSSMTFLTRQAFAK
          LGHQVATDALVAMEKAMKRDKIIVNDRQLAC.RIASV..QDYLKGMAAA.NY.WVNRSSMT.LTRQAFAK
Retrocopy LGHQVATDALVAMEKAMKRDKIIVNDRQLACERIASVDSQDYLKGMAAAENYTWVNRSSMTVLTRQAFAK

Parental  VFNTTPDDLDLHVIYDVSHNIAKVEQHVVDGKERTLLVHRKGSTRAF-PPHHPLIAVDYQLTGQPVLIGG
          VFNTTPD.LDLHVIYDVS.NIAKVEQHVVDGKERTLLVH.KGSTRAF.PPHHPLIAVDYQLTGQPVLIGG
Retrocopy VFNTTPDELDLHVIYDVSNNIAKVEQHVVDGKERTLLVHKKGSTRAFPPPHHPLIAVDYQLTGQPVLIGG

Parental  TMGTCSYVLTGTEQGMTETFGTTCHGAGRALSRAKSRRNLDFQDVLDKLADMGIAIRVASPKLVMEE
          TMGTCSYVL...EQG.TETFGT.CHGAG.ALS.AKSRRNLDFQDVLDKLADMGIAIRVASPKLVMEE
Retrocopy TMGTCSYVLNDIEQGTTETFGTNCHGAGSALSLAKSRRNLDFQDVLDKLADMGIAIRVASPKLVMEE

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	0.77 RPM	66.28 RPM
SRP017611_kidney	0.20 RPM	55.75 RPM
SRP017611_liver	0.39 RPM	24.28 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1520 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1520 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1520 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000011070	1 retrocopy	retro_btau_1682,
Canis familiaris	ENSCAFG00000001785	2 retrocopies	retro_cfam_13, retro_cfam_977,
Myotis lucifugus	ENSMLUG00000007803	1 retrocopy	retro_mluc_1461,
Oryctolagus cuniculus	ENSOCUG00000008270	1 retrocopy	retro_ocun_1520 ,