RetrogeneDB ID: retro_pcap_424

Retrocopy location

• Organism: Hyrax (Procavia capensis)
• Coordinates: scaffold_80782:2783..3698(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HNRNPA1L2
• Ensembl ID: ENSPCAG00000001867
• Aliases: None
• Description: heterogeneous nuclear ribonucleoprotein A1-like 2 [Source:HGNC Symbol;Acc:27067]

Sequence

>retro_pcap_424
ATGTCTAAGTCAGAGTCTCCTAAAGAGCCTGAACAGCTGCGGAAACTCTTCAGTGGAGATTTGAGCTTTGAAACAACGGA
TGAGAGTCTGAGGAGCCGTTCTGAGCAATGGGGGACACTCACGGACTGTGTGGTAATGAGACATCCAAACACCAAGCGCT
CCAGAGGCTTTGGGTTCGTCACTTACTCCACTGTGGAAGAGGTGGATGCAGCCATGAATGCACGGCCACACAAGGTGGAT
GCCAGAGTTGTGGAACCAAAGAGAGCTTTTTCTCGAGAGGACTCTCAAAAGCCCAGGTGCTCACTTAACTGTGAAAAAGA
CTTTTGTTGGTGGTATTAAAGAAGACACTGAGGAACATCACCTAAGAGATTATTTTGAGCAGTATGGGAAAACTGAAGTG
ATTGAAATCATGACTGCCGAGGCAGTGGCAAGAAGAGGGGCTTTGCTTTTGTTACTTTTGATGACCACAACTCAGTAGAT
AAAATTGTCATTCAGAAATACCATACTGTGAATGGGCACAACTGTGAAGTAAGAAAAGCCCTGTCAAAGCAAGAGATGGC
CAGTGCCTCCTCCATCCAGAGAGGTTGGAGTGGTTCTGGAAACTTTGGTGGTGGCCATGGAGGTGGTTTTGTTGGGAATT
ACAACTTCGGTTGTGGAGGAAACTTCAGTGGACGAGGTGGCTTTGGTGGCAGCCGTGGTGGTGGTGGATATGGAGGCAGT
GGAGATGGTTATAATGGATTTGGTAATGACGGTGGTTATGGAGAAGGCAGTCCTGGTTACTCTGGAGGAAGCAGAGGCTA
TGGAAGTGGTGGACAGGGTTATGGAAACCAGGGCAGTGGCTATGGTGGAAGTGGCAGCTATAACAACGGAGGAGGCGGAG
GTGGCTTTGGCGGTGGTAGTGGAGGCAATTTTGGA

Alignment

ORF - retro_pcap_424 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.58 %
• Parental protein coverage: 82.5 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MSKSESPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYSTVEEVDA
          MSKSESPKEPEQLRKLF.G.LSFETTDESLRS..EQWGTLTDCVVMR.PNTKRSRGFGFVTYSTVEEVDA
Retrocopy MSKSESPKEPEQLRKLFSGDLSFETTDESLRSRSEQWGTLTDCVVMRHPNTKRSRGFGFVTYSTVEEVDA

Parental  AMNARPHKVDGRVVEPKRAVSREDSQRP-GAHLV--KKFVGG--EDTEHH--RDYFEQYGKIEV-EIMTD
          AMNARPHKVD.RVVEPKRA.SREDSQ.P.GAHL...K.FVGG..EDTE.H..RDYFEQYGK.EV.EIMT.
Retrocopy AMNARPHKVDARVVEPKRAFSREDSQKP>GAHLTVKKTFVGGIKEDTEEHHLRDYFEQYGKTEVIEIMTA

Parental  -RGSGKKR-FAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRKALSKQEMASASSSQRGRSGSGNFGGGRGG
          .RGSGKKR.FAFVTFDDH.SVDKIVIQKYHTVNGHNCEVRKALSKQEMASASS.QRG.SGSGNFGGG.GG
Retrocopy <RGSGKKRGFAFVTFDDHNSVDKIVIQKYHTVNGHNCEVRKALSKQEMASASSIQRGWSGSGNFGGGHGG

Parental  GFVGNDNFGRGGNFSGRGGFGGSRGGGGYGGSGDGYNGFGNDGGYGGGGPGYSGGSRGYGSGGQGYGNQG
          GFVGN.NFG.GGNFSGRGGFGGSRGGGGYGGSGDGYNGFGNDGGYG.G.PGYSGGSRGYGSGGQGYGNQG
Retrocopy GFVGNYNFGCGGNFSGRGGFGGSRGGGGYGGSGDGYNGFGNDGGYGEGSPGYSGGSRGYGSGGQGYGNQG

Parental  SGYGGSGSYNNGGGGGGFGGGSGSNFG
          SGYGGSGSYNNGGGGGGFGGGSG.NFG
Retrocopy SGYGGSGSYNNGGGGGGFGGGSGGNFG

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_424 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 9 parental genes, and 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000009228	7 retrocopies	retro_dnov_1059, retro_dnov_1670, retro_dnov_1944, retro_dnov_2081, retro_dnov_250, retro_dnov_320, retro_dnov_374,
Loxodonta africana	ENSLAFG00000029587	5 retrocopies	retro_lafr_1202, retro_lafr_1208, retro_lafr_192, retro_lafr_747, retro_lafr_961,
Mustela putorius furo	ENSMPUG00000004620	1 retrocopy	retro_mputfur_34,
Mustela putorius furo	ENSMPUG00000005735	2 retrocopies	retro_mputfur_1378, retro_mputfur_653,
Oryctolagus cuniculus	ENSOCUG00000013350	1 retrocopy	retro_ocun_1675,
Oreochromis niloticus	ENSONIG00000012248	1 retrocopy	retro_onil_38,
Procavia capensis	ENSPCAG00000001867	5 retrocopies	retro_pcap_111, retro_pcap_162, retro_pcap_377, retro_pcap_424 , retro_pcap_435,
Procavia capensis	ENSPCAG00000011543	1 retrocopy	retro_pcap_366,
Pongo abelii	ENSPPYG00000025850	4 retrocopies	retro_pabe_1765, retro_pabe_2285, retro_pabe_3492, retro_pabe_3835,