RetrogeneDB ID: retro_ocun_799

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 15:48484802..48485191(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TMEM216
• Ensembl ID: ENSOCUG00000001682
• Aliases: None
• Description: transmembrane protein 216 [Source:HGNC Symbol;Acc:25018]

Sequence

>retro_ocun_799
TTGTCATCAGCCTCACTAGAAATCCTGTTCTTTTTGAATGGGTGATATTATGCTACCTATTTGCTGCCAGAATTCTTCTT
ATTCCTATATGAAAGTCTCCTGCTACCATATCCAACAGTCAGTCTAGCACTGGATGTGGTGATGTGGTGATGCTTCTCCT
TTGTCTTGGAATTGAAGTGATTCAGCTGTTTTTGTTACAAGGGGAATCCTCTGCCAATGAAAGAGCACTTGGTGTTATTG
GGCCTTGGCCTTCCTATCTACTATGACGGCCTCTCATTGCCTCCTGCTACCCCACCTTCATGCTTCTCTTGAAAGCCATC
ATGAATGGCATCTTGCTCTTCCTGTGTGGCTCAGAGCTGCTGCCTGATCTGCTTGTCCTGGCTACTCTC

Alignment

ORF - retro_ocun_799 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.27 %
• Parental protein coverage: 98.46 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LSSTPLEILFFLNGWYYATYFLLELFIFLYKGLLLPYPTANLVLDVVMLLLYLGIEVIRLF--FGTKGNL
          LSS..LEILFFLNG.YYATY.L.E.F.FLY..LLLPYPT..L.L................F..F..KGN.
Retrocopy LSSASLEILFFLNG*YYATYLLPEFFLFLYESLLLPYPTVSLALXXXXXXXFSFVLELK*FSCFCYKGNP

Parental  CQRKMPLGISVALSFP-SAMMASYYLLL-QTYVLRLEAVMNGILLFFCGSELLLEVLTLAAL
          ...K..L.....L..P.S.M.AS..LLL..T..L.L.A.MNGILLF.CGSELL...L.LA.L
Retrocopy LPMKEHL-VLLGLGLP>STMTASHCLLL>PTFMLLLKAIMNGILLFLCGSELLPDLLVLATL

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	2.65 RPM
SRP017611_kidney	0.00 RPM	3.95 RPM
SRP017611_liver	0.00 RPM	0.92 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_799 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_799 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_799 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016592	1 retrocopy	retro_amel_1255,
Bos taurus	ENSBTAG00000021517	1 retrocopy	retro_btau_1184,
Canis familiaris	ENSCAFG00000016171	4 retrocopies	retro_cfam_1342, retro_cfam_331, retro_cfam_332, retro_cfam_333,
Monodelphis domestica	ENSMODG00000020362	1 retrocopy	retro_mdom_232,
Mustela putorius furo	ENSMPUG00000014169	4 retrocopies	retro_mputfur_1341, retro_mputfur_1536, retro_mputfur_1537, retro_mputfur_1538,
Oryctolagus cuniculus	ENSOCUG00000001682	1 retrocopy	retro_ocun_799 ,