RetrogeneDB ID: retro_ocun_638

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 13:24279206..24279715(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SAR1A
• Ensembl ID: ENSOCUG00000004547
• Aliases: None
• Description: SAR1 homolog A (S. cerevisiae) [Source:HGNC Symbol;Acc:10534]

Sequence

>retro_ocun_638
AGCAGTGTGTTCTGGTTCCTAGGACTCTATAAGAAATCTGGAAAGCCTGTATTCTTGGGTTTGGACAATGCGGACAAAAC
CATTCTTCTTCACATGATCAAAGATGACAGATTGAGCCAACATGTTCCAACACTACATACGCCATCAGAAGAGCTGACAA
TTGCTGGAATGACTTTTGCAACTTTTGATTTTGGTGGGGATGAGCAAGAACACCAGGTTTGGAAAAATTAACTCCCAGCA
ATTAATGGGATTGTCTTTCTGTTGGACTGTGCAGATCATTCTTGTCTCCTGGAATCCAAAGTTGAGCTTAATGTTTTAAT
GACTGATGAAACAATATCCAATGTGCCAATCCTTATCTTGGGCAACAAAATTGACAGAACAGATTCAGTTAGTGAAGAAA
AGCTCTGTGAAATATCTGGGCTTTCTGGAGAGACCACTGGGAAGAGGAATGTGACCCTGAAGGAACTGAATGCCCGCACC
TTGAAATGTTCACGTGCAGTATGCTCAAA

Alignment

ORF - retro_ocun_638 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.7 %
• Parental protein coverage: 85.86 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SSVLQFLGLYKKSGKLVFLGLDNAGKTTLLHMLKDDRLGQHVPTLHPTSEELTIAGMTFTTFDLGGHEQA
          SSV..FLGLYKKSGK.VFLGLDNA.KT.LLHM.KDDRL.QHVPTLH..SEELTIAGMTF.TFD.GG.EQ.
Retrocopy SSVFWFLGLYKKSGKPVFLGLDNADKTILLHMIKDDRLSQHVPTLHTPSEELTIAGMTFATFDFGGDEQE

Parental  RRVWKNYLPAINGIVFLVDCADHSRLMESKVELNALMTDETISNVPILILGNKIDRTDAISEEKLREIFG
          ..VWKN.LPAINGIVFL.DCADHS.L.ESKVELN.LMTDETISNVPILILGNKIDRTD..SEEKL.EI.G
Retrocopy HQVWKN*LPAINGIVFLLDCADHSCLLESKVELNVLMTDETISNVPILILGNKIDRTDSVSEEKLCEISG

Parental  LYGQTTGKGNVTLKELNARP-MEVFMCSVLK
          L.G.TTGK.NVTLKELNAR...E.F.CS.LK
Retrocopy LSGETTGKRNVTLKELNART<LEMFTCSMLK

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	23.34 RPM
SRP017611_kidney	0.00 RPM	34.16 RPM
SRP017611_liver	0.00 RPM	17.50 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_638 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_638 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_638 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017868	1 retrocopy	retro_amel_1698,
Gorilla gorilla	ENSGGOG00000024879	3 retrocopies	retro_ggor_144, retro_ggor_2408, retro_ggor_2929,
Mustela putorius furo	ENSMPUG00000004338	1 retrocopy	retro_mputfur_225,
Oryctolagus cuniculus	ENSOCUG00000004547	1 retrocopy	retro_ocun_638 ,
Oryctolagus cuniculus	ENSOCUG00000008250	1 retrocopy	retro_ocun_1004,