RetrogeneDB ID:

retro_amel_980

Retrocopy
location
Organism:Panda (Ailuropoda melanoleuca)
Coordinates:GL192791.1:34862..35416(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSAMEG00000004601
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:RPL17
Ensembl ID:ENSAMEG00000009498
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_amel_980
CTGAAAATGGTTCTCTATTCACTTGACCCAGAAAACCCTACAAAATCATGCAAATCAAGAGGTTCAAATCTTCGTGTTCA
CTTTAAGAACACAGGTGAAACTGCCCAGGCCATCAAGGGTATGCCTATCCGAGAAGCCTGCAGGTATCTGAAAGATGTCC
CTTTGCAGAAGCCATGTGGGCCATTCCGTCCCTGCAGTGGTGGACCTGGCAGGTGTGCCCGGGCCAAACCAGGGGACTGC
ACACAGGCTTGGGGGCTCAAAAGGAGCGCTGAATTTTTAGTGCGCATGCTTAAAAATGCAGAGTGTAATGCTGAACTTCA
GGGTTTAGACGCAGATTCTCTGGTCATCGGGCACATCCAGGTGAGCAAAGCCCCCAAGATGCAGCATAGAGCTTACAGGG
CTCCTGGTCGGATTAATCCCTACATGCGCTCTCCCTGCCACACTGAGATGATGCTCCTTACTGAGAAAGAGCAGGTGGTT
CCTAGACCAGAAGAGGAGGTTGCACAGAGAAAAAGATATCCCAGAAGAAACTGAAGAAACAAAAACTTATGGCC

ORF - retro_amel_980 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 77.42 %
Parental protein coverage: 98.4 %
Number of stop codons detected: 0
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalLKMVRYSLDPENPTKSCKSRGSNLRVHFKNTRETAQAIKGMHIRKATKYLKDVTLQKQCVPFRRYNGGVG
LKMV.YSLDPENPTKSCKSRGSNLRVHFKNT.ETAQAIKGM.IR.A..YLKDV.LQK.C.PFR...GG.G
RetrocopyLKMVLYSLDPENPTKSCKSRGSNLRVHFKNTGETAQAIKGMPIREACRYLKDVPLQKPCGPFRPCSGGPG
ParentalRCAQAKQWGWTQGRWPKKSAEFLLHMLKNAESNAELKGLDVDSLVIEHIQVNKAPKMRRRTYRAHGRINP
RCA.AK....TQ....K.SAEFL..MLKNAE.NAEL.GLD.DSLVI.HIQV.KAPKM..R.YRA.GRINP
RetrocopyRCARAKPGDCTQAWGLKRSAEFLVRMLKNAECNAELQGLDADSLVIGHIQVSKAPKMQHRAYRAPGRINP
ParentalYMSSPCHIE-MILTEKEQIVPKPEEEVAQK-KKISQKKLKKQKLMA
YM.SPCH.E.M.LTEKEQ.VP.PEEEVAQ..KKISQKKLKKQKLMA
RetrocopyYMRSPCHTEMMLLTEKEQVVPRPEEEVAQR<KKISQKKLKKQKLMA

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_980 retrocopy.
Ailuropoda melanoleuca was not studied using FANTOM5 data.
retro_amel_980 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 24 parental genes, and 553 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG00000009498 40 retrocopies
Canis familiaris ENSCAFG000000190447 retrocopies
Choloepus hoffmanni ENSCHOG0000000787250 retrocopies
Callithrix jacchus ENSCJAG000000047794 retrocopies
Echinops telfairi ENSETEG0000001132210 retrocopies
Felis catus ENSFCAG0000001134243 retrocopies
Homo sapiens ENSG000002154721 retrocopy
Homo sapiens ENSG0000026568133 retrocopies
Gorilla gorilla ENSGGOG000000266971 retrocopy
Latimeria chalumnae ENSLACG000000088351 retrocopy
Loxodonta africana ENSLAFG0000000556916 retrocopies
Macropus eugenii ENSMEUG0000001670926 retrocopies
Microcebus murinus ENSMICG0000001710214 retrocopies
Macaca mulatta ENSMMUG0000001883726 retrocopies
Mustela putorius furoENSMPUG000000008017 retrocopies
Procavia capensis ENSPCAG000000031038 retrocopies
Pongo abelii ENSPPYG0000000915143 retrocopies
Pan troglodytes ENSPTRG0000001001251 retrocopies
Pteropus vampyrus ENSPVAG0000000196976 retrocopies
Sarcophilus harrisii ENSSHAG0000000306014 retrocopies
Sus scrofa ENSSSCG0000002964230 retrocopies
Tarsius syrichta ENSTSYG0000000740220 retrocopies
Tursiops truncatus ENSTTRG0000000579731 retrocopies
Vicugna pacos ENSVPAG000000095681 retrocopy



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