RetrogeneDB ID: retro_ocun_1146

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 20:22368588..22369059(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000026266
• Aliases: None
• Status: KNOWN_PSEUDOGENE

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_1146
ATAGGACACATGACCAAAACCAAAGATGGCCATGAAGTGAGATTGTGCAAAGTAGCAGATAAAATGGGCAGCATCACTAT
TTCTGTGTGGGATGAGATTGGAGGTCTCATACAGCCAGGGGATATAATTCAGTTGACCAGAGGGTATGTGTCCACGTGGA
AAGGATGTCTGACACTTTATACTGGAATGGGTGATGAACTTCAAAAAATTGGGGAGTTTTGTATGGTTTATTCAGAAGTG
CCAAATTTTAGTGAACCCAATGCAGATTATCCAGGACAGCAGAACAAAGGGGCACACAGTGAACAGAATAATTCCATGAA
TAGTACTATGGGTACAGGTACATTTGGACCAGTGGGAAATGGTATTCAACCTGGCCCTGAGTCATGGGGATACCAGTTTT
CATATGCTGGTAGAAGCAGTGGCCGGGGAACTATAAATCCACAGCTGCCAGGAACAGCCAAGAACCAGTCA

Alignment

ORF - retro_ocun_1146 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.61 %
• Parental protein coverage: 77.83 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  IGRVTKTKDGHEVRSCKVADKTGSITISVWDEIGGLIQPGDIIRLTRGYASMWKGCLTLYTGRGGELQKI
          IG..TKTKDGHEVR.CKVADK.GSITISVWDEIGGLIQPGDII.LTRGY.S.WKGCLTLYTG.G.ELQKI
Retrocopy IGHMTKTKDGHEVRLCKVADKMGSITISVWDEIGGLIQPGDIIQLTRGYVSTWKGCLTLYTGMGDELQKI

Parental  GEFCMVYSEVPNFSEPNPDYRGQQNKGAHSEQKNNSMNSNMGTGTFGPVGNGIQPGPESRGYQFSYAGRS
          GEFCMVYSEVPNFSEPN.DY.GQQNKGAHSEQ.NNSMNS.MGTGTFGPVGNGIQPGPES.GYQFSYAGRS
Retrocopy GEFCMVYSEVPNFSEPNADYPGQQNKGAHSEQ-NNSMNSTMGTGTFGPVGNGIQPGPESWGYQFSYAGRS

Parental  NGRGPINPQLPGTANNQT
          .GRG.INPQLPGTA.NQ.
Retrocopy SGRGTINPQLPGTAKNQS

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_1146 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1146 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1146 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,