RetrogeneDB ID: retro_ocun_991

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 18:40335516..40336034(-)
• Located in intron of: ENSOCUG00000002827

Retrocopy information

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

Parental gene information

• Parental gene symbol: NABP1
• Ensembl ID: ENSOCUG00000017546
• Aliases: None
• Description: nucleic acid binding protein 1 [Source:HGNC Symbol;Acc:26232]

Sequence

>retro_ocun_991
TTTGTGAAAGATATTAAGCCTGGGCTGAAAAACTTGAATGTCATCTTTATTGTCTTCGAGATAGGACACATGACCAATAA
CAAAGACAGCCACAAAGTGAGATCCTGGGAAGTAGCTGCTTATAGGGGCAGCATCACTGTTTCTGTGTGGGATGAGATTG
GAGGTCTTAGATATCCAGGGACTGTTACTCAGTTGGTCAGAGGGACTGCATCCTTGTGGAAAGGATGTCTGACACTTTAT
ACTGGAAGAGGCGGTGAACTTCAGAAAATTGGGGAGTTTTGTGTGGTTTATTCAGAACTGCCAAGCTTCGTTGAACCCAA
ACCAGATTATCGAGGACAGCAGAGCAAAGGGACACACAGTGAACAGAAGAATAATTCCTTAAATAATAATATGGGAACAG
GTATACTTGGACCAGTGGGAAGCGGTGTTCAATTGGCTCTGAGTCACAGGGATACCAGTTTTCATATGCTGGTAGAAGCA
ATGGCCAGGCACTGCAGGCAGCAGTTTTACCCACTACG

Alignment

ORF - retro_ocun_991 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.84 %
• Parental protein coverage: 85.22 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  FIKDIKPGLKNLNVVFIVLEIGRVTKTKDGHEVRSCKVADKTGSITISVWDEIGGLIQPGDIIRLTRGYA
          F.KDIKPGLKNLNV.FIV.EIG..T..KD.H.VRS..VA...GSIT.SVWDEIGGL..PG....L.RG.A
Retrocopy FVKDIKPGLKNLNVIFIVFEIGHMTNNKDSHKVRSWEVAAYRGSITVSVWDEIGGLRYPGTVTQLVRGTA

Parental  SMWKGCLTLYTGRGGELQKIGEFCMVYSEVPNFSEPNPDYRGQQNKGAHSEQKNNSMNSNMGTGTFGPVG
          S.WKGCLTLYTGRGGELQKIGEFC.VYSE.P.F.EP.PDYRGQQ.KG.HSEQKNNS.N.NMGTG..GPVG
Retrocopy SLWKGCLTLYTGRGGELQKIGEFCVVYSELPSFVEPKPDYRGQQSKGTHSEQKNNSLNNNMGTGILGPVG

Parental  NGIQ-PGPESRGYQFSYAGRSNGRGPINPQLPGT
          .G.Q..G.ES.GYQFSYAGRSNG.......LP.T
Retrocopy SGVQ<IGSESQGYQFSYAGRSNGQALQAAVLPTT

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	3.81 RPM
SRP017611_kidney	0.00 RPM	10.14 RPM
SRP017611_liver	0.00 RPM	8.86 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_991 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_991 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_991 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
Monodelphis domestica	ENSMODG00000011862	1 retrocopy	retro_mdom_1393,
Oryctolagus cuniculus	ENSOCUG00000017546	2 retrocopies	retro_ocun_1146, retro_ocun_991 ,
Procavia capensis	ENSPCAG00000012746	1 retrocopy	retro_pcap_297,
Tupaia belangeri	ENSTBEG00000001158	1 retrocopy	retro_tbel_3393,