RetrogeneDB ID:

retro_amel_889

Retrocopy
location
Organism:Panda (Ailuropoda melanoleuca)
Coordinates:GL192713.1:974100..974673(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RPL19
Ensembl ID:ENSAMEG00000004121
Aliases:None
Description:ribosomal protein L19 [Source:HGNC Symbol;Acc:10312]


Retrocopy-Parental alignment summary:






>retro_amel_889
CTCAGGCTTTGGAAGAGGCTTGCCTCCGGTGTCCTCCATTATGGCAGAAAGAAGGTCTGGTTGGATCTCAATGAGACCAA
TGTAATTGCCAGTGCCAACTCCCATCAGCAGATCCAGAAGTTGACCAAAGACGGGCTGATCATCTGGGAGCCTGTGACTC
TCCATTCCTGGACTCCATGGCAGAAAAGCACTTTGGCCCCGCCAGAAGGACAGGCATGTGGGCATGGGGGAATGAAAGAC
TCCTGCCAGCACTCAGATGACCAAGAAGGTTGCCTGGATGAGGAGGATGAGAATTCTGTGATGGCTGCATAGAAGATACT
ATGAATCTAGGAAGGTTGACCACCACGCATATCACAGCCTGTACTTCAAAGTGAAGGTAAGATGTTGAAAAACAAGCAGA
TTCTCATGGACTACATCCATAAGCTGCAGTCAGACGAGGCTCACAAGATGCTTCTGGCTGACCAGGCTGAGGCCTGCGGT
ATAAGTAAGAAAGCACATGAGTGCCTTGAAGAGTGGCTCCAGGCCAGGAAAGAGGAAATTATCATGACTCTGTCCAAGGA
GGAAGAGGTCAAG

ORF - retro_amel_889 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 63.92 %
Parental protein coverage: 97.96 %
Number of stop codons detected: 2
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalLRLQKRLASSVLRCGKKKVWLDPNETNEIANANSRQQIRKLIKDGLIIRKPVTVHSRARCRKNTLA-RRK
LRL.KRLAS.VL..G.KKVWLD.NETN.IA.ANS.QQI.KL.KDGLII..PVT.HS.....K.TLA.R.K
RetrocopyLRLWKRLASGVLHYGRKKVWLDLNETNVIASANSHQQIQKLTKDGLIIWEPVTLHSWTPWQKSTLA>RQK
ParentalGRHMGIGKRKGTANARMPEKVTWMRRMRILRRLLRRYRESKKIDRHMYHSLYLKVK-GNVFKNKRILMEH
.RH.G.G..K..A...M..KV.WMRRMRIL..L.RRY.ES.K.D.H.YHSLY.KVK.G...KNK.ILM..
RetrocopyDRHVGMGE*KTPASTQMTKKVAWMRRMRIL*WLHRRYYESRKVDHHAYHSLYFKVK<GKMLKNKQILMDY
ParentalIHKLKADKARKKLLADQAEARRSKTKEARKRREERLQAKKEEIIKTLSKEEETK
IHKL..D.A.K.LLADQAEA.....K.A....EE.LQA.KEEII.TLSKEEE.K
RetrocopyIHKLQSDEAHKMLLADQAEA-CGISKKAHECLEEWLQARKEEIIMTLSKEEEVK

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_889 retrocopy.
Ailuropoda melanoleuca was not studied using FANTOM5 data.
retro_amel_889 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 14 parental genes, and 163 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG00000004121 5 retrocopies
Callithrix jacchus ENSCJAG000000085204 retrocopies
Dasypus novemcinctus ENSDNOG000000197427 retrocopies
Dipodomys ordii ENSDORG000000043301 retrocopy
Equus caballus ENSECAG000000250806 retrocopies
Homo sapiens ENSG0000010829821 retrocopies
Macaca mulatta ENSMMUG000000042352 retrocopies
Mus musculus ENSMUSG0000001740425 retrocopies
Nomascus leucogenys ENSNLEG0000000074819 retrocopies
Pongo abelii ENSPPYG0000000849220 retrocopies
Pteropus vampyrus ENSPVAG000000084989 retrocopies
Rattus norvegicus ENSRNOG0000000474137 retrocopies
Sarcophilus harrisii ENSSHAG000000164824 retrocopies
Sus scrofa ENSSSCG000000175093 retrocopies



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