RetrogeneDB ID: retro_pcap_12

Retrocopy location

• Organism: Hyrax (Procavia capensis)
• Coordinates: scaffold_26870:12530..13478(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPCAG00000011045
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: FOXR1
• Ensembl ID: ENSPCAG00000010132
• Aliases: None
• Description: forkhead box R1 [Source:HGNC Symbol;Acc:29980]

Sequence

>retro_pcap_12
ATGGACCTAAAATTAGAATATTCTGACTTCTGGTATAGTCTCCATGGCCAGGTTCCAGGGCTGCTGGACTGGGACATGGA
GAATGAGTTTTTCTTGCCTCGCACCACAGATCAGTGTTCCTTGGCTGAGAAGAACCTTCTCAAATACAAACTCCAAATAA
TTGAGTCCCCAAAGCTGCCTCTGAAGAGGAAAGCCAATCCTGACAATGATGGTCCTGACTATGAACCCAACCTGTGGATG
TGGGTGAACCCCAACAGTGTGTGTCCCCTAGGTGGCCAGCAGGCCTCAAATCCCGATATAAAGAAGGATCTTGCAAGCAT
GTGTGTCTCTCCTCAGCCACCCATGAAGAATGAAGAATCAGACTGCCCAGATGCCACAGTAGTGGAATCCCTACCATGTT
CCTTCAATGAGCAGTCTCCCCAGCAGATGCAATGTGTTTCTTCTCTCAGTGACTGGGAACTCACAAAAGTGGAAGCTGAG
AAAAAATGTAACCCCTCTGTGGCTCTACAGTCTCCTAAGAAAGAGGAGTGCTTCCAGAACCAAAAGCTGTGGCAAACCAA
CAGCCAAGAAAGGAGGTCCTGGCCACGGCCTCCACTCAATTATAGCCATCTAATTGCTTTGGCATTAAAGAACAGCCCCC
CTTGTGGCCTCAATGTTCAAGAAATCTATAATTTCACACGACAGCATTTCCCCTTTTTCTGGACAGCTCCAGATAGCTGG
AAGAACACGATCCGCCACAATCTCTGTTGCCTGGGCAACTTTGAGAAGGTGCCAGTCAGCCTTCAGAGTGGGCCTAATTC
AAGGCCTCGGTCATACCTCTGGAGGCTTACTGAGGAAGGACATCGCCGCTTTCAGGAAGACACCCGTGCCTTAGCTTCTG
CTAGGAGGGAGAGCATCCAACAGTGCATGAGCCAGCCAGATGTGATGACCTCCCTCTTTGACCTCTGA

Alignment

ORF - retro_pcap_12 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.87 %
• Parental protein coverage: 99.25 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RYSLQIVGPPTLPLAIKPNPDGDXXXXXXXXXXXXXXXXXXPPGELEVPEHSRKEDLIFPC--PPPPSEE
          .Y.LQI...P.LPL..K.NPD.D..................P.G.........K.DL...C..P.PP...
Retrocopy KYKLQIIESPKLPLKRKANPDNDGPDYEPNLWMWVNPNSVCPLGGQQASNPDIKKDLASMCVSPQPPMKN

Parental  EESKSSEATVLESLPLTSSEQSSSLKQLVCSPRNQKLQEEEAEDQDGSSSVTLPSTHKRAPLQSQSLQQT
          EES....ATV.ESLP....EQS....Q.V.S.....L...EAE......SV.L.S..K....Q.Q.L.QT
Retrocopy EESDCPDATVVESLPCSFNEQSPQQMQCVSSLSDWELTKVEAEKKC-NPSVALQSPKKEECFQNQKLWQT

Parental  DSQKGQLWPRPPLNYFHLIALALRNSPPSGLNVQQIYDFARQHFPFFRTAPEGWKNTVRHNLCFRDSFEK
          .SQ....WPRPPLNY.HLIALAL.NSPP.GLNVQ.IY.F.RQHFPFF.TAP..WKNT.RHNLC....FEK
Retrocopy NSQERRSWPRPPLNYSHLIALALKNSPPCGLNVQEIYNFTRQHFPFFWTAPDSWKNTIRHNLCCLGNFEK

Parental  VSASMQGEAGTRPRSCLWKLTEEGHRRFEAETQAFDTRRLEGIQQCMSQPDVMDFLFD
          V..S.Q.....RPRS.LW.LTEEGHRRF...T.A....R.E.IQQCMSQPDVM..LFD
Retrocopy VPVSLQSGPNSRPRSYLWRLTEEGHRRFQEDTRALASARRESIQQCMSQPDVMTSLFD

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_12 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 18 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000000053	1 retrocopy	retro_amel_39,
Bos taurus	ENSBTAG00000014606	1 retrocopy	retro_btau_189,
Canis familiaris	ENSCAFG00000012417	1 retrocopy	retro_cfam_209,
Callithrix jacchus	ENSCJAG00000013656	1 retrocopy	retro_cjac_4066,
Dasypus novemcinctus	ENSDNOG00000009414	1 retrocopy	retro_dnov_22,
Dipodomys ordii	ENSDORG00000001960	1 retrocopy	retro_dord_651,
Homo sapiens	ENSG00000176302	1 retrocopy	retro_hsap_72,
Microcebus murinus	ENSMICG00000002680	1 retrocopy	retro_mmur_38,
Macaca mulatta	ENSMMUG00000022722	1 retrocopy	retro_mmul_125,
Mustela putorius furo	ENSMPUG00000004890	1 retrocopy	retro_mputfur_161,
Nomascus leucogenys	ENSNLEG00000007376	1 retrocopy	retro_nleu_50,
Otolemur garnettii	ENSOGAG00000007258	1 retrocopy	retro_ogar_296,
Procavia capensis	ENSPCAG00000010132	1 retrocopy	retro_pcap_12 ,
Pongo abelii	ENSPPYG00000003947	1 retrocopy	retro_pabe_69,
Pan troglodytes	ENSPTRG00000004358	1 retrocopy	retro_ptro_94,
Sorex araneus	ENSSARG00000011319	1 retrocopy	retro_sara_38,
Sus scrofa	ENSSSCG00000015101	1 retrocopy	retro_sscr_36,
Ictidomys tridecemlineatus	ENSSTOG00000014321	1 retrocopy	retro_itri_158,