RetrogeneDB ID:

retro_pcap_162

Retrocopy
location
Organism:Hyrax (Procavia capensis)
Coordinates:scaffold_124150:844..1631(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:HNRNPA1L2
Ensembl ID:ENSPCAG00000001867
Aliases:None
Description:heterogeneous nuclear ribonucleoprotein A1-like 2 [Source:HGNC Symbol;Acc:27067]


Retrocopy-Parental alignment summary:






>retro_pcap_162
AAGATTTTTGTTGGTGGTATTAAAGAAGACACTGAGGAACATCATCTAAGAGATTATTTTGAGCAGTATGGGAAACTTGA
AGTGATTGAAATCATGATGGACCGAGGCAGTGGCAAGAAGAGGGGCTTTGCTTTCCTTACTTTTGATAACCACGACTCAG
TAGATAAAATTGTCATTCAGAAATACCAAACTGTGAATGGGCACAACTGTGAAGCAAGAAAAGCCCTGTCAAAGCAAGAG
ATGGCCAGTGCCTCCTCCAGCCAGAGAGGTCGGAGTGGTTCTGGAAACTTTGGTGGTAACCGTGGAGGTGGTTTTGTTGG
GAATGACAACTTCAGTCGTGGAGGAAACTTCAGTGGACGAGGTGGCTTTGGTGGCAGCCGTGGTGGCGGTGGATATGGAG
GCAGTGGAGATGGTTATAATGGATTTGGTAATGACGATAGTAATTGAGGAGGCGGTCCTGGTTACTCTGGAGGAAGCAGA
GGCTATGGAAGTGGTGGACTGGGTTATGGAAACCAGGGCCGTGGCTATGGCAGGAGTGGCAGCTATAACAACGGAGGAGT
GCGGAGGCAGCTTTGGCGGTGGTAGTGGAGGCAATTTTGGAGGTGGCAGAAGCTACAATGATTTTGGCAATTACAACAAT
CAGTCTTTAAATTTTGGACCTATGAAGGGAGGAAACTTTGGAGGCAGAAGTTCTGGCCCTTACGGTAGTGGAGGTCAATA
GTTTGCCAAACCATGAAACCAAGGTGGCTATGGTGGTTCAAGCAGCAGCAGTAGCTATGGCAGTGGC

ORF - retro_pcap_162 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 87.83 %
Parental protein coverage: 71.11 %
Number of stop codons detected: 3
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalKKFVGG--EDTEHH--RDYFEQYGKIEV-EIMTDRGSGKKR-FAFVTFDDHDSVDKIVIQKYHTVNGHNC
K.FVGG..EDTE.H..RDYFEQYGK.EV.EIM.DRGSGKKR.FAF.TFD.HDSVDKIVIQKY.TVNGHNC
RetrocopyKIFVGGIKEDTEEHHLRDYFEQYGKLEVIEIMMDRGSGKKRGFAFLTFDNHDSVDKIVIQKYQTVNGHNC
ParentalEVRKALSKQEMASASSSQRGRSGSGNFGGGRGGGFVGNDNFGRGGNFSGRGGFGGSRGGGGYGGSGDGYN
E.RKALSKQEMASASSSQRGRSGSGNFGG.RGGGFVGNDNF.RGGNFSGRGGFGGSRGGGGYGGSGDGYN
RetrocopyEARKALSKQEMASASSSQRGRSGSGNFGGNRGGGFVGNDNFSRGGNFSGRGGFGGSRGGGGYGGSGDGYN
ParentalGFGNDGGYGGGGPGYSGGSRGYGSGGQGYGNQGSGYGGSGSYNNGG-GGGGFGGGSGSNFGGGGSYNDFG
GFGND....GGGPGYSGGSRGYGSGG.GYGNQG.GYG.SGSYNNGG..GG.FGGGSG.NFGGG.SYNDFG
RetrocopyGFGNDDSN*GGGPGYSGGSRGYGSGGLGYGNQGRGYGRSGSYNNGG>CGGSFGGGSGGNFGGGRSYNDFG
ParentalNYNNQSSNFGPMKGGNFGGRSSGPYGGGGQYFAKPRNQGGYGGSSSSSSYGSG
NYNNQS.NFGPMKGGNFGGRSSGPYG.GGQ.FAKP.NQGGYGGSSSSSSYGSG
RetrocopyNYNNQSLNFGPMKGGNFGGRSSGPYGSGGQ*FAKP*NQGGYGGSSSSSSYGSG

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






Procavia capensis was not studied using RNA-Seq expression data.
Procavia capensis was not studied using ChIP-Seq data.
Procavia capensis was not studied using EST data.
Procavia capensis was not studied using FANTOM5 data.
retro_pcap_162 was not experimentally validated.

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.

Parental genes homology:
Parental genes homology involve 9 parental genes, and 27 retrocopies.

Species Parental gene accession Retrocopies number
Dasypus novemcinctus ENSDNOG000000092287 retrocopies
Loxodonta africana ENSLAFG000000295875 retrocopies
Mustela putorius furoENSMPUG000000046201 retrocopy
Mustela putorius furoENSMPUG000000057352 retrocopies
Oryctolagus cuniculus ENSOCUG000000133501 retrocopy
Oreochromis niloticus ENSONIG000000122481 retrocopy
Procavia capensis ENSPCAG00000001867 5 retrocopies
Procavia capensis ENSPCAG000000115431 retrocopy
Pongo abelii ENSPPYG000000258504 retrocopies



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