RetrogeneDB ID: retro_pcap_297

Retrocopy location

• Organism: Hyrax (Procavia capensis)
• Coordinates: scaffold_28195:7331..7672(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPCAG00000010342
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: NABP1
• Ensembl ID: ENSPCAG00000012746
• Aliases: None
• Description: nucleic acid binding protein 1 [Source:HGNC Symbol;Acc:26232]

Sequence

>retro_pcap_297
TTCGTGAAGGATATCAAGCCAGGGCTCAAGAATCTGAACCTCATCTTCATTGTGCTGGAGACAGGCCAAGTGACCATGAC
AGAGGACAGGCACGAGGTTTGGATCTGCAAAGTGGCAGACAAAACTGGCAGCATCAACATCTCTGTCTGGATGACATGGG
CAATGTGATCCAGCCTGGGGACATTATCCGGCTCACCAAAGGGTATGCTTCAGTGTTCAAAGGCTGTCCGACACTATACA
CTGGCCATGGGGGTGATCTGCAGAAAACTAGAGAATTCTGTATGGTCTATTCTGAAGTTCCAAACTTTAGTGAGCCAAAC
CAAGAGTACAGTGCAAAGCAG

Alignment

ORF - retro_pcap_297 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.78 %
• Parental protein coverage: 55.61 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  FIKDIKPGLKNLNVVFIVLEIGRVTKTKDGHEVRSCKVADKTGSITISVW-DEIGALIQPGDIIRLTRGY
          F.KDIKPGLKNLN..FIVLE.G.VT.T.D.HEV..CKVADKTGSI.ISVW.D..G..IQPGDIIRLT.GY
Retrocopy FVKDIKPGLKNLNLIFIVLETGQVTMTEDRHEVWICKVADKTGSINISVW<DDMGNVIQPGDIIRLTKGY

Parental  ASMWKGCLTLYTGRGGELQKIGEFCMVYSEVPNFSEPNPDYGGQQ
          AS..KGC.TLYTG.GG.LQK..EFCMVYSEVPNFSEPN..Y...Q
Retrocopy ASVFKGCPTLYTGHGGDLQKTREFCMVYSEVPNFSEPNQEYSAKQ

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Procavia capensis was not studied using RNA-Seq expression data.

ChIP-Seq

Procavia capensis was not studied using ChIP-Seq data.

EST

Procavia capensis was not studied using EST data.

TSS

Procavia capensis was not studied using FANTOM5 data.

Lab

retro_pcap_297 was not experimentally validated.

Homology

Retrocopy orthology:

Procavia capensis does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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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,