RetrogeneDB ID:

retro_pabe_2693

Retrocopy
location
Organism:Orangutan (Pongo abelii)
Coordinates:5:142071541..142072163(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:HAUS1
Ensembl ID:ENSPPYG00000009131
Aliases:None
Description:HAUS augmin-like complex, subunit 1 [Source:HGNC Symbol;Acc:25174]


Retrocopy-Parental alignment summary:






>retro_pabe_2693
TATCTTCAAGACCTTCTCATGGATAGTGTGAATTTTTCCCCTGCCAATTTCTCTAGCACTGGTTCCAGGTATCTGAATGC
ATTGGTTGACAGTGCGGTGGCCCTTGAAACAAAGGATACCTCACTAGCTAGTTTTATCCTTGCAGTGAATGATTTGACCT
CTGATCTCTTTCATACCAAATCCAAAGGTGAAGAAATCAAGATTGAACTGGAAAAACTTGAAAAAATCTAACTGCAACTT
AATATTAGAAAAATGTCTACAAGAGGATCTCAAGAAAGCAGAGTTGGATCTGTCTACAGAAAGGGCCAAAGTTGATAATC
ATCATCAGAACATGGACTTTCTAAAAGCAAAGTCAGAGGAATTCAGATTTGTAATCAAGGCTGCAGAGGAGCAACTTTCA
GCCAGAGGCATGGATGCTTCTCTGTCTCATCAGTCCCTAGTAGCACTGTCAGAGAAACTGGCAAAATTAAAACAACAGAC
TATACCTTTGAAGAAAAAATTTGAGTCCTATTTAGACTTAATACCGAATTCCCCTCTTGCTCAAATGAAAATTGAAGAAG
CAAAGTGAGAATTAGATAGCATTGAAGCTGAACTTACAAGGAGAGTAGACGTGATGGAACTG

ORF - retro_pabe_2693 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 90. %
Parental protein coverage: 74.82 %
Number of stop codons detected: 1
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalYLQDLLMESVNFSPANLSSTGSRYLNALVDSAVALETKDTSLASFIPAVNDLTSDLFRTKSKSEEIKIEL
YLQDLLM.SVNFSPAN.SSTGSRYLNALVDSAVALETKDTSLASFI.AVNDLTSDLF.TKSK.EEIKIEL
RetrocopyYLQDLLMDSVNFSPANFSSTGSRYLNALVDSAVALETKDTSLASFILAVNDLTSDLFHTKSKGEEIKIEL
ParentalEKLEK-NLTAT-LVLEKCLQEDVKKAELHLSTERAKVDNRRQNMDFLKAKSEEFRFGIKAAEEQLSARGM
EKLEK.NLTAT.L.LEKCLQED.KKAEL.LSTERAKVDN..QNMDFLKAKSEEFRF.IKAAEEQLSARGM
RetrocopyEKLEK<NLTAT<LILEKCLQEDLKKAELDLSTERAKVDNHHQNMDFLKAKSEEFRFVIKAAEEQLSARGM
ParentalDASLSHQSLVALSEKLARLKQQTIPLKKKLESYLDLMPNPSLAQVKIEEAKRELDSIEAELTRRVDMMEL
DASLSHQSLVALSEKLA.LKQQTIPLKKK.ESYLDL.PN..LAQ.KIEEAK.ELDSIEAELTRRVD.MEL
RetrocopyDASLSHQSLVALSEKLAKLKQQTIPLKKKFESYLDLIPNSPLAQMKIEEAK*ELDSIEAELTRRVDVMEL

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






(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)

Expression validation based on RNA-Seq data:
Library Retrocopy expression Parental gene expression
SRP007412_brain_prefrontal_cortex 0 .00 RPM 2 .21 RPM
SRP007412_cerebellum 0 .00 RPM 3 .04 RPM
SRP007412_heart 0 .00 RPM 1 .87 RPM
SRP007412_kidney 0 .00 RPM 1 .76 RPM
SRP007412_liver 0 .03 RPM 1 .10 RPM
Pongo abelii was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_pabe_2693 retrocopy.
Pongo abelii was not studied using FANTOM5 data.
retro_pabe_2693 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_pabe_2693 has 4 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_3247
Pan troglodytes retro_ptro_2195
Gorilla gorilla retro_ggor_2210
Macaca mulatta retro_mmul_2043

Parental genes homology:
Parental genes homology involve 10 parental genes, and 25 retrocopies.

Species Parental gene accession Retrocopies number
Choloepus hoffmanni ENSCHOG000000011393 retrocopies
Homo sapiens ENSG000001522403 retrocopies
Gorilla gorilla ENSGGOG000000100982 retrocopies
Loxodonta africana ENSLAFG000000108971 retrocopy
Macaca mulatta ENSMMUG000000031242 retrocopies
Monodelphis domestica ENSMODG000000032081 retrocopy
Nomascus leucogenys ENSNLEG000000112163 retrocopies
Pongo abelii ENSPPYG00000009131 3 retrocopies
retro_pabe_2693 , retro_pabe_3344, retro_pabe_3615,
Pan troglodytes ENSPTRG000000099923 retrocopies
Tupaia belangeri ENSTBEG000000109114 retrocopies



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