RetrogeneDB ID: retro_pcap_90

Retrocopy location

• Organism: Hyrax (Procavia capensis)
• Coordinates: GeneScaffold_5308:38112..39498(-)
• Located in intron of: ENSPCAG00000000350

Retrocopy information

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

Parental gene information

• Parental gene symbol: ABCE1
• Ensembl ID: ENSPCAG00000006183
• Aliases: None
• Description: ATP-binding cassette, sub-family E (OABP), member 1 [Source:HGNC Symbol;Acc:69]

Sequence

>retro_pcap_90
ACACATCGACATTGGGCCAGTGCCTCCCGGCTTCACAGGTTGCCTGTTCCTTGTCCAGGTGAAGTTTTGGGATTAGTTGG
AACTAATGGTATTGGAAAGTCAACTGCTTTAAAAATTTTAGCAGGAAAGCAAAAGCCAAACCTTGGAAAGTATGATGGTC
CACCTGATTGGCAAGAAATTTTGACTTACTTCTGAGGATCCGAATTGCAAAATTACTTTACCAAGATTCTAGAAGATGAC
TTAAAAGCCATTATTAAACCTCAGTATGTGGACCAGATTCCCAAGGCTGCAAAGGGGACAGTAGGATCTATTTTGGACCG
AAAGGATGAAACAAAGACACAAGCAGTTGTGTGTCAGCAGCTTGATTTAACCCACCTAAAAGAATGAAATGTTGAAGATC
TTTCGGGAGGAGAGTTGCAGAGATTTGCTTGTGCTGTTGTTTGCATACAGAAAGCTGATATTTTCATGTTTGATGAACCT
TCCAGTTACCTAGATGTCAAGCAGCATTTGAAGGCTGCTATTACTATACGATCTCTAATAAATCCACATAGGTATATCAT
TGTGGTGGAACATGATCTAAGTGTGTTAGACTATCTTTCTGACTTCATCTGCTGTCTGTATGGTGTGCCAAGTGCTTATG
GTGTTGTCACTGTGCCTTTCAGCATAAGAGAAGGCATCAACATCTTTTTAGATGGCTATGTTCCAACAGAAAACTTGAGA
TTCAGAGATGCATCACTTGTTTTTAAAGTGGCTGAGACAGCAAATGAGGAAGAAGTTAAAAAGATGTGTATGTATAAGTA
CCCAGGAATGAAGAAAAAGATGGGAGAGTTTGAGTTAGCAATTGTAGCTGGAGAGTTTACAGATTCTAAAATCATGGTGA
TGCTGGGGGAAAATGGTACTGGTAAAACGACATTTATAAGAATGCTTGCTGGAAGACTTAAACCTGATGAAGGAGAAGTA
CCAGTTCTAAATGTCAGTTATAAACCACAGAAGATCAGCCCCAGATCAACTGGAAGTGTTCGCCAGTTACTGCATGAAAA
AATAAGAGATGCCTGCACTCATCCACAATTTGTGACTGATGTAATGAAGCCTCTACAAATTGAAAACATCATTGATCAAG
AGGTGCAGATATTATCTGGTGGCGAACTGCAGCGAGTAGCTTTAGCTCTTTGTTTGGGCAAACCTGCTGACGTCTATTTA
TTTGATGAACCATCTGCATATTTGGATTCTGAGCAGCGATTGATGGCCGCGAGAGTTGTCAAATGCTTCATACTCCATGC
CAAAAAGACACCCTTTGTTGTGGAGCACGACTTCATCATGGCTACGTATCTAGCAGATCGTGTCATTGTTTTTGATGGTA
TTCCATCTAAGAACACAGTTGCAAAC

Alignment

ORF - retro_pcap_90 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.03 %
• Parental protein coverage: 77.26 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  THRYCANAFKLHRLPIPRPGEVLGLVGTNGIGKSTALKILAGKQKPNLGKYDDPPDWQEILTYFRGSELQ
          THR..A.A..LHRLP.P.PGEVLGLVGTNGIGKSTALKILAGKQKPNLGKYD.PPDWQEILTYF.GSELQ
Retrocopy THRHWASASRLHRLPVPCPGEVLGLVGTNGIGKSTALKILAGKQKPNLGKYDGPPDWQEILTYF*GSELQ

Parental  NYFTKILEDDLKAIIKPQYVDQIPKAAKGTVGSILDRKDETKTQAVVCQQL-LTHLKERNVEDLSGGELQ
          NYFTKILEDDLKAIIKPQYVDQIPKAAKGTVGSILDRKDETKTQAVVCQQL.LTHLKE.NVEDLSGGELQ
Retrocopy NYFTKILEDDLKAIIKPQYVDQIPKAAKGTVGSILDRKDETKTQAVVCQQLDLTHLKE*NVEDLSGGELQ

Parental  RFACAVVCIQKADIFMFDEPSSYLDVKQRLKAAITIRSLINPDRYIIVVEHDLSVLDYLSDFICCLYGVP
          RFACAVVCIQKADIFMFDEPSSYLDVKQ.LKAAITIRSLINP.RYIIVVEHDLSVLDYLSDFICCLYGVP
Retrocopy RFACAVVCIQKADIFMFDEPSSYLDVKQHLKAAITIRSLINPHRYIIVVEHDLSVLDYLSDFICCLYGVP

Parental  SAYGVVTMPFSVREGINIFLDGYVPTENLRFRDASLVFKVAETANEEEVKKMCMYKYPGMKKKMGEFELA
          SAYGVVT.PFS.REGINIFLDGYVPTENLRFRDASLVFKVAETANEEEVKKMCMYKYPGMKKKMGEFELA
Retrocopy SAYGVVTVPFSIREGINIFLDGYVPTENLRFRDASLVFKVAETANEEEVKKMCMYKYPGMKKKMGEFELA

Parental  IVAGEFTDSEIMVMLGENGTGKTTFIRMLAGRLKPDEGGEVPVLNVSYKPQKISPKSTGSVRQLLHEKIR
          IVAGEFTDS.IMVMLGENGTGKTTFIRMLAGRLKPDE.GEVPVLNVSYKPQKISP.STGSVRQLLHEKIR
Retrocopy IVAGEFTDSKIMVMLGENGTGKTTFIRMLAGRLKPDE-GEVPVLNVSYKPQKISPRSTGSVRQLLHEKIR

Parental  DAYTHPQFVTDVMKPLQIENIIDQEVQTLSGGELQRVALALCLGKPADVYLIDEPSAYLDSEQRLMAARV
          DA.THPQFVTDVMKPLQIENIIDQEVQ.LSGGELQRVALALCLGKPADVYL.DEPSAYLDSEQRLMAARV
Retrocopy DACTHPQFVTDVMKPLQIENIIDQEVQILSGGELQRVALALCLGKPADVYLFDEPSAYLDSEQRLMAARV

Parental  VKRFILHAKKTAFVVEHDFIMATYLADRVIVFDGIPSKNTVAN
          VK.FILHAKKT.FVVEHDFIMATYLADRVIVFDGIPSKNTVAN
Retrocopy VKCFILHAKKTPFVVEHDFIMATYLADRVIVFDGIPSKNTVAN

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_90 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 10 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000004534	1 retrocopy	retro_chof_1280,
Cavia porcellus	ENSCPOG00000007367	1 retrocopy	retro_cpor_289,
Homo sapiens	ENSG00000164163	1 retrocopy	retro_hsap_3826,
Macaca mulatta	ENSMMUG00000004433	1 retrocopy	retro_mmul_1628,
Mus musculus	ENSMUSG00000058355	1 retrocopy	retro_mmus_1503,
Nomascus leucogenys	ENSNLEG00000005460	1 retrocopy	retro_nleu_2125,
Oryctolagus cuniculus	ENSOCUG00000001821	2 retrocopies	retro_ocun_1925, retro_ocun_668,
Procavia capensis	ENSPCAG00000006183	1 retrocopy	retro_pcap_90 ,
Pongo abelii	ENSPPYG00000015097	1 retrocopy	retro_pabe_3067,
Pan troglodytes	ENSPTRG00000016481	1 retrocopy	retro_ptro_2603,