RetrogeneDB ID:

retro_amel_1514

Retrocopy
location
Organism:Panda (Ailuropoda melanoleuca)
Coordinates:GL193538.1:99149..99718(+)
Located in intron of:ENSAMEG00000013216
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RPS3A
Ensembl ID:ENSAMEG00000018425
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_amel_1514
ACCAAAATCGCCTCTGATGGCCTCAAGAGTTGTGCTTTTCAAGTGAGCCTTGCTGATTTGCAGAATGTTGAAGTCACATT
TTAAAAATTCAAAATAATTACTGAGGATGCCCTAGGCAAAAACTGTGTGATCAACATTCAGGACATGGATATCCACAACA
AAACATGCTCCCTCGTCACAACATGTTAGACTATGATTGAAAGCTCACGTTGTTGTCAAGACTATCAATGGTTGTTTCTG
TCTGTTCTGCATAGGCCTTATAAAAAATGCAATACCAGATCTAAATGACTTCTTATGCTCAGCACCAACAGGGTCCGCCA
AATCAGGAAGGCGACGGAAATCCTGATCCAAGAGGTAGAGACAAATGACTTCAAAGAAGTAGTCAATAATTTTATTCCAG
ACAGACTGGAAAGCCTTTTCTATATCTCTCCTAGTCTATTTATCCTCTCCATCATGTGTTTGTCAAAAAAGTAAAAATGT
TGAAGAAAATCAGGTTTGGATTGGGAAAACTCCTGAAGCTTCACATGGTGAAAGATAGTTCTAGAAATGCTACTGGGGAT
GACAAAGGC

ORF - retro_amel_1514 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 56.12 %
Parental protein coverage: 73.11 %
Number of stop codons detected: 4
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalTKIASDGLKGRVFEVSLADLQNDEVAFRKFKLITEDVQGKNCLTNFHGMDLTRDKMCSMVKKWQTMIE-A
TKIASDGLK...F.VSLADLQN.EV.F.KFK.ITED..GKNC..N...MD....K.CS.V....TMIE.A
RetrocopyTKIASDGLKSCAFQVSLADLQNVEVTF*KFKIITEDALGKNCVINIQDMDI-HNKTCSLVTTC*TMIE>A
ParentalHVDVKTTDGYLLRLFCVGFT-KKRNNQIRKTSYAQHQQVRQIRKKMMEIMTREVQTNDLKEVVNKLIPDS
HV.VKT..G....LFC.G...KK.N.............VRQIR.K..EI...EV.TND.KEVVN..IPD.
RetrocopyHVVVKTINGCFC-LFCIGLI<KKCNTRSK*LLMLSTNRVRQIR-KATEILIQEVETNDFKEVVNNFIPDR
ParentalI-GKDIEKACQSIYPLHDVFVRKVKMLKKPKFELGKLMELHGEGSSSGKATGDETG
..GK.......SIYPLH.VFV.KVKMLKK..F.LGKL..LH....SS..ATGD..G
RetrocopyL<GKPFLYLS*SIYPLHHVFVKKVKMLKKIRFGLGKLLKLHMVKDSSRNATGDDKG

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_1514 retrocopy.
Ailuropoda melanoleuca was not studied using FANTOM5 data.
retro_amel_1514 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 13 parental genes, and 60 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG00000018425 11 retrocopies
Bos taurus ENSBTAG000000099083 retrocopies
Canis familiaris ENSCAFG000000079907 retrocopies
Callithrix jacchus ENSCJAG000000022687 retrocopies
Gorilla gorilla ENSGGOG000000031822 retrocopies
Microcebus murinus ENSMICG000000049219 retrocopies
Macaca mulatta ENSMMUG000000218211 retrocopy
Monodelphis domestica ENSMODG000000009696 retrocopies
Mus musculus ENSMUSG000000280812 retrocopies
Oryctolagus cuniculus ENSOCUG000000070111 retrocopy
Rattus norvegicus ENSRNOG000000118931 retrocopy
Sarcophilus harrisii ENSSHAG000000150882 retrocopies
Vicugna pacos ENSVPAG000000042358 retrocopies



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