RetrogeneDB ID: retro_ocun_842

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 15:79429455..79430104(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: VAMP7
• Ensembl ID: ENSOCUG00000001270
• Aliases: None
• Description: vesicle-associated membrane protein 7 [Source:HGNC Symbol;Acc:11486]

Sequence

>retro_ocun_842
CTCTTTTTTGCTCTTGTTGCCAGGGAACCACTATCCTTGCCAAACATGCTTGGTGTGGAAGAAACTTCCTCGATGTTACA
GAGCAGATTCTGACCAAGATATTGTATGAAAATAACAAACTATCTTACTCACATGACAATTACTTGTTTCATTACATCTA
ACAAGACGGGATAGTGTATCTTCGTATCACTAATAATATTTTGAATGTTCCCAAGCCTTTAATTTTCTGAATGAGGTAAG
GAAGAGATTTCAAACTTCTTATAGTTCAAGAGCAGAGACAGCATTTCCATACGCCATGAACAGCAAGTTTTCAAATGTCT
TGACTGCACAACTGAAGGATCACTCTGAGAACAAGGGCCTAGACAAAGAGGTGGAGACTCAAGCCCAGGTGGTCAAATTG
AAAGGAATCCTGGTCAAAAACACAGATCTGATAAAGCAGCGGAGAGAAAGACTGGAATTATTGATAGACAAAACAGAAAA
TTTTGTGGATTCATCTGTCACCTTCAAAGCTGCCAGCAGAAATCCTGCCCGAGCCATGTGTCTGAAGAATCTCAAGCTCA
CTGTCATCACTGTCGTATCAATTGTGTTCATCTACATCATTGTGTCAACTGCCTGTGGTGGATTTACATGGCCAAACTGT
ATGAAAAGA

Alignment

ORF - retro_ocun_842 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.82 %
• Parental protein coverage: 99.09 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  ILFAVVAR-GTTILAKHAWCGGNFLEVTEQILAKIPSENNKLTYSHGNYLFHYICQDRIVYLCITDDD-F
          ..FA.VAR.GTTILAKHAWCG.NFL.VTEQIL.KI..ENNKL.YSH.NYLFHYI.QD.IVYL.IT....F
Retrocopy LFFALVAR<GTTILAKHAWCGRNFLDVTEQILTKILYENNKLSYSHDNYLFHYI*QDGIVYLRITNNI<F

Parental  ERSRAFNFLNEVKKRFQTTYGSRAQTALPYAMNSEFSSVLAAQLKHHSENKGLDKVMETQAQVDELKGIM
          E.S.AFNFLNEV.KRFQT.Y.SRA.TA.PYAMNS.FS.VL.AQLK.HSENKGLDK..ETQAQV..LKGI.
Retrocopy ECSQAFNFLNEVRKRFQTSYSSRAETAFPYAMNSKFSNVLTAQLKDHSENKGLDKEVETQAQVVKLKGIL

Parental  VRNIDLVAQRGERLELLIDKTENLVDSSVTFKTTSRNLARAMCMKNLKLTIIIIIVSIVFIYIIVSTLCG
          V.N.DL..QR.ERLELLIDKTEN.VDSSVTFK..SRN.ARAMC.KNLKLT..I..VSIVFIYIIVST.CG
Retrocopy VKNTDLIKQRRERLELLIDKTENFVDSSVTFKAASRNPARAMCLKNLKLT-VITVVSIVFIYIIVSTACG

Parental  GFTWPNCVKK
          GFTWPNC.K.
Retrocopy GFTWPNCMKR

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	44.92 RPM
SRP017611_kidney	0.00 RPM	61.42 RPM
SRP017611_liver	0.00 RPM	15.18 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_842 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_842 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_842 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000016289	2 retrocopies	retro_cjac_1958, retro_cjac_2410,
Cavia porcellus	ENSCPOG00000024405	1 retrocopy	retro_cpor_714,
Mus musculus	ENSMUSG00000051412	1 retrocopy	retro_mmus_2131,
Oryctolagus cuniculus	ENSOCUG00000001270	1 retrocopy	retro_ocun_842 ,
Pteropus vampyrus	ENSPVAG00000000829	1 retrocopy	retro_pvam_513,
Ictidomys tridecemlineatus	ENSSTOG00000025036	1 retrocopy	retro_itri_720,
Tursiops truncatus	ENSTTRG00000010643	1 retrocopy	retro_ttru_66,