RetrogeneDB ID: retro_ocun_517

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 12:88907704..88908457(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TMEM219
• Ensembl ID: ENSOCUG00000006318
• Aliases: None
• Description: transmembrane protein 219 [Source:HGNC Symbol;Acc:25201]

Sequence

>retro_ocun_517
CTCTCCCTGGAGGCCCAGACGCCTTTGCTCCCTATGGGCAGCTGCCAAGCAGGGCACAACCTGCATCTCTGTCTCGTCCA
CCATCCGCCTCTGGTCTGTGCCACTCTGATCCTGCTGCTCTTGGGCCTCTCCGGCCTGGGCCTCGGTGGCTTCCTCCTCA
CCCACAGGAGTGGCCTGTGCAGCCCTAACACCCCGGAGGACTAGGTCTCATTCTTGAGGTCTTTTGGCCAGCTGACCCTA
TGCTCTGTGAATGGGACGGTCATGGGGACACGGCAGGGGGCTCACGTGGTAGGCTTAGTGACCACGCTGAACTTCCGGGA
TGGTGCAGACAAGAACAAGACCCAGACCTTCCAAGCCAGCATCCCAGGTCGGCAGCTGGGATTGAAAGGGTCTTCTGCAG
AGGAGCCCATCCTCATCACAGCCAGGGTGACCTCGGAAAGGAAGCCAGGAGCCTGCCTGTATTTTAATGCTGTTCCAGGG
ATCCTGCCCTCCAGCCAGCCACCCCTCTTCTGCCTCGAGGAGGGAGCAGGCAATGCCACCCTGAGCCCTAGGATGGGTGA
GGAGTGTGTCCGGATCTGGAGCCACGAAGGCCTGGTGCTCACCAAGCTGCTCACCTCGGAGGAGCTGGCTCTGTGTGGCT
CCAGGCTGCTGATCTTGGGCTCCTTCCTGCTTCTCTTCTGTGGCCTTCTCAGCTGCGTCACTGCTGTGTGCTTCCATTCA
CACCGGGAGTCGCACTGGTCCAGAACCCGGCTG

Alignment

ORF - retro_ocun_517 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.03 %
• Parental protein coverage: 96.54 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LSLEAQTPLLPMGSCQAGHNLHLCLVHHPPLVCATLILLLLGLSGLGLGGFLLTHRSGLRSPDIPEDWVS
          LSLEAQTPLLPMGSCQAGHNLHLCLVHHPPLVCATLILLLLGLSGLGLGGFLLTHRSGL.SP..PED.VS
Retrocopy LSLEAQTPLLPMGSCQAGHNLHLCLVHHPPLVCATLILLLLGLSGLGLGGFLLTHRSGLCSPNTPED*VS

Parental  FLRSFGQLTLCPVDGTVTATRQGAHVVGLVTTLNFGDGADRNKTQTFQASIPGRQLGLKGSSAEEPILVT
          FLRSFGQLTLC.V.GTV..TRQGAHVVGLVTTLNF.DGAD.NKTQTFQASIPGRQLGLKGSSAEEPIL.T
Retrocopy FLRSFGQLTLCSVNGTVMGTRQGAHVVGLVTTLNFRDGADKNKTQTFQASIPGRQLGLKGSSAEEPILIT

Parental  ARVTPERTPGACLYFNAAPGILPSSQPPISCLEDGAGNATLSPRMGEECVRIWSHEGLVLTKLLTSEELA
          ARVT.ER.PGACLYFNA.PGILPSSQPP..CLE.GAGNATLSPRMGEECVRIWSHEGLVLTKLLTSEELA
Retrocopy ARVTSERKPGACLYFNAVPGILPSSQPPLFCLEEGAGNATLSPRMGEECVRIWSHEGLVLTKLLTSEELA

Parental  LCGSRLLILGSFLLLFCGLLCCVTAVCFHPRRESHWSRTRL
          LCGSRLLILGSFLLLFCGLL.CVTAVCFH..RESHWSRTRL
Retrocopy LCGSRLLILGSFLLLFCGLLSCVTAVCFHSHRESHWSRTRL

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	0.28 RPM	16.17 RPM
SRP017611_kidney	0.61 RPM	26.05 RPM
SRP017611_liver	0.31 RPM	14.80 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_517 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_517 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_517 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000021785	1 retrocopy	retro_btau_1792,
Microcebus murinus	ENSMICG00000009088	1 retrocopy	retro_mmur_610,
Macaca mulatta	ENSMMUG00000020273	1 retrocopy	retro_mmul_2266,
Oryctolagus cuniculus	ENSOCUG00000006318	1 retrocopy	retro_ocun_517 ,