RetrogeneDB ID: retro_pcap_111

Retrocopy location

• Organism: Hyrax (Procavia capensis)
• Coordinates: GeneScaffold_6800:324398..325120(+)
• 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_111
ATGTCTAAGTCAGGGTCTCCTAACGACCCCGAACAGCTGCGGAAACTCTTCATCGGAGGTTTGAGCTTGGAAACAATGGA
TGAGAGTCTGAGGGGCCATTGTGAGCAACGGGGACACTCACGGACTGTGTGGTACCGAGATCCAAACACAAGCGCTCCTG
AGGCTTTGGGTTCGTCACTTACCCCACCGTGGAGGAGGTGGATGCAGCCATGAACACAAGGCCACACAAGGTGGATGGAA
GAGCTGTGGAACCAAAGAGGGCTGTTTCTCGAGGGGACTCTCAAAGACCAGGCACTCCCTTAACTGTGAAAAAGATTTTT
GTTGGTGGTATTAAAGAAGACACTGAGGAACATCACCTAAGAGATTATTTTGAGCAGTATGGGAAAATTGAAGTGATTGA
AATCATGACTGATCGAGGCAGTGGCAAGAAGAGGGGCTTTGCTTTCATTACTTTTGATGGCCACGACTCAGTAGATAAAA
TTGTCATTCAGAAATACCATACTGTGAATGGGCACAACTGTGAAGTAAGAAAAGCTCTGTCAAAGCAAGAGATGGCCAGT
GCCTCCTCCTCCAGCCAGAGAGGTCGGAGGGGTTCTGGAAAGTTTGGTGGTGGCCGTGGAGGTGGTTTTGTTGGGAAAGA
CAACTTCGGTAGTAGAGGAAACTTCAGTGGACGAGGTGGCTTTGGTGGCAGCCGTGGTGGCGGTGGATATGGAGGCCGTG
GA

Alignment

ORF - retro_pcap_111 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.3 %
• Parental protein coverage: 64.72 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSKSESPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNT-KRSRGFGFVTYSTVEEVD
          MSKS.SP..PEQLRKLFIGGLS.ET.DESLR.H.EQ.G.....V..RDPNT.KRS.GFGFVTY.TVEEVD
Retrocopy MSKSGSPNDPEQLRKLFIGGLSLETMDESLRGHCEQRGH-SRTVWYRDPNT<KRS*GFGFVTYPTVEEVD

Parental  AAMNARPHKVDGRVVEPKRAVSREDSQRPGAHLVKK--FVGG--EDTEHH--RDYFEQYGKIEV-EIMTD
          AAMN.RPHKVDGR.VEPKRAVSR.DSQRPG..L..K..FVGG..EDTE.H..RDYFEQYGKIEV.EIMTD
Retrocopy AAMNTRPHKVDGRAVEPKRAVSRGDSQRPGTPLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTD

Parental  RGSGKKR-FAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRKALSKQEMASASSS-QRGRSGSGNFGGGRGG
          RGSGKKR.FAF.TFD.HDSVDKIVIQKYHTVNGHNCEVRKALSKQEMASASSS.QRGR.GSG.FGGGRGG
Retrocopy RGSGKKRGFAFITFDGHDSVDKIVIQKYHTVNGHNCEVRKALSKQEMASASSSSQRGRRGSGKFGGGRGG

Parental  GFVGNDNFGRGGNFSGRGGFGGSRGGGGYGGSG
          GFVG.DNFG..GNFSGRGGFGGSRGGGGYGG.G
Retrocopy GFVGKDNFGSRGNFSGRGGFGGSRGGGGYGGRG

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_111 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,