RetrogeneDB ID:

retro_amel_432

Retrocopy
location
Organism:Panda (Ailuropoda melanoleuca)
Coordinates:GL192440.1:2432843..2433340(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:GCSH
Ensembl ID:ENSAMEG00000013959
Aliases:None
Description:glycine cleavage system protein H (aminomethyl carrier) [Source:HGNC Symbol;Acc:4208]


Retrocopy-Parental alignment summary:






>retro_amel_432
GCGGTGCGGAGCATGCAGGCTGTGGGCTTGCAGCCTGGGCACCGCCTCTGCACCTCCCCCCCACCCAGGGCCTGCCTGCC
ACCATCTGGGGGGTTGAGGGCAGGTGCTGTTGGCCTGATGCTATGTGGGCTCCGCTGGGCTCTCTGTGCATTAACTCCCA
GAAAAACATGAATGGACAGCAACAGAAAATGGTATTGGAACAGTGCGAATCAGCAATTTTGTACGGGAAGTTGTTTACTG
TAGGCTGCCTGAAGTTGGGGCAAAATTGGAAAAACAAGATGAGTTTGGAGCCTTGGAAACTGTGAAAGCTGCTAGTGAAC
TCTCTCCTCTATGAGAAGTAACTGAAATCAATGAAGCTGTTGCAGAAAATCTGGGAATGTCAACAAATCTTGTTATGAAG
ATGGTTGGCTGATCAAGATACACTCAGTAATATTTCAGAACTGGATGAATTAATAAGTGAAGAAGCATATGAGAAATACA
TAAAATCTATTGAGGAG

ORF - retro_amel_432 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 64.57 %
Parental protein coverage: 99.42 %
Number of stop codons detected: 2
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalALRAVRSVRAAVRSLRVAAAPAATCLPRPWGLRAGPVRTLR-TGSALLSVRKFTDKHEWITTENGIGTVG
A.R....V............P...CLP...GLRAG.V......GSA.LSV.....KHEW..TENGIGTV.
RetrocopyAVRSMQAVGLQPGHRLCTSPPPRACLPPSGGLRAGAVGLML>VGSAGLSVH*LPEKHEWTATENGIGTVR
ParentalISNFAQEALGDVVYCSLPEVGTKLNKQDEFGALESVKAASELYAPLSGEVTEINEALAENPGL-VNKSCY
ISNF.......VVYC.LPEVG.KL.KQDEFGALE.VKAASEL..PL..EVTEINEA.AEN.G..VNKSCY
RetrocopyISNFVR----EVVYCRLPEVGAKLEKQDEFGALETVKAASEL-SPL-*EVTEINEAVAENLGM<VNKSCY
ParentalEDGWLIKI-ALSNPSELDELMSEEAYEKYIKSIEE
EDGWLIKI..LSN.SELDEL.SEEAYEKYIKSIEE
RetrocopyEDGWLIKI<TLSNISELDELISEEAYEKYIKSIEE

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






Ailuropoda melanoleuca was not studied using RNA-Seq expression data.
Ailuropoda melanoleuca was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_amel_432 retrocopy.
Ailuropoda melanoleuca was not studied using FANTOM5 data.
retro_amel_432 was not experimentally validated.

Retrocopy orthology:
Ailuropoda melanoleuca 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 29 parental genes, and 223 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000089051 retrocopy
Ailuropoda melanoleuca ENSAMEG00000013959 5 retrocopies
Bos taurus ENSBTAG000000067958 retrocopies
Canis familiaris ENSCAFG000000200145 retrocopies
Choloepus hoffmanni ENSCHOG0000000243437 retrocopies
Callithrix jacchus ENSCJAG000000166548 retrocopies
Cavia porcellus ENSCPOG000000099833 retrocopies
Dipodomys ordii ENSDORG000000078311 retrocopy
Erinaceus europaeus ENSEEUG000000096532 retrocopies
Felis catus ENSFCAG000000130388 retrocopies
Homo sapiens ENSG0000014090510 retrocopies
Gorilla gorilla ENSGGOG0000000023210 retrocopies
Loxodonta africana ENSLAFG000000155863 retrocopies
Myotis lucifugus ENSMLUG0000000578312 retrocopies
Macaca mulatta ENSMMUG000000130885 retrocopies
Mustela putorius furoENSMPUG000000096774 retrocopies
Mus musculus ENSMUSG000000344248 retrocopies
Nomascus leucogenys ENSNLEG000000268441 retrocopy
Ochotona princeps ENSOPRG000000032811 retrocopy
Procavia capensis ENSPCAG000000058201 retrocopy
Pongo abelii ENSPPYG0000000758515 retrocopies
Pan troglodytes ENSPTRG0000000838610 retrocopies
Pteropus vampyrus ENSPVAG000000099568 retrocopies
Rattus norvegicus ENSRNOG000000115356 retrocopies
Sarcophilus harrisii ENSSHAG000000055291 retrocopy
Ictidomys tridecemlineatus ENSSTOG000000164332 retrocopies
Tupaia belangeri ENSTBEG0000000005627 retrocopies
Tarsius syrichta ENSTSYG0000000024813 retrocopies
Tursiops truncatus ENSTTRG000000079928 retrocopies



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