RetrogeneDB ID:

retro_amel_687

Retrocopy
location
Organism:Panda (Ailuropoda melanoleuca)
Coordinates:GL192571.1:1653811..1654204(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:H3F3A
Ensembl ID:ENSAMEG00000014588
Aliases:None
Description:H3 histone, family 3A [Source:HGNC Symbol;Acc:4764]


Retrocopy-Parental alignment summary:






>retro_amel_687
AAAACTGTCTGCAAATCCACCTGTGGTAAAGCACCCAGGAAGCAACCAGCTACAAAACCCGCTCGCAAGACTGCGCCCTC
TACTGGAAGAGTGGAGAAACCGCATCGTTACAAGCTAGGTACTGTGACATCTCCGTGAAATTAGACCTTATCAAAAGTTG
ACCGGACTTCTGATTCGCTAACTTCTTTTCCAGAGTCTGATGCGAGAGTTTGCTCGGGACTTCAAACAGATCTGCGCTTC
CGGAGTGCAGTTGTTGGTGCTTTGCGGGAGGCAAGTGAGGCCTATCTGGAGGGCTTTATTTGAACACACCAACCTGTGTG
CTATCCGTGTCAAATTTGTAACAATTATGCCAAAGACATCTAGCTAGCATGCCACGTAGGTGGAGAATGTGCG

ORF - retro_amel_687 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 70.37 %
Parental protein coverage: 96.32 %
Number of stop codons detected: 2
Number of frameshifts detected 4


Retrocopy - Parental Gene Alignment:

ParentalQTARKSTGGKAPRKQLATKAARKSAPSTGGVKKPHRYRPGTVA-LREIRRYQKSTELLIRKLPFQRLVRE
.T..KST.GKAPRKQ.ATK.ARK.APSTG.V.KPHRY..GTV..LREIR.YQK.T.LLIR.L.FQ.L.RE
RetrocopyKTVCKSTCGKAPRKQPATKPARKTAPSTGRVEKPHRYKLGTVT>LREIRPYQKLTGLLIR*LLFQSLMRE
ParentalIAQDFK-TDLRFQSAAIGALQEASEAYLVG-LFEDTNLCAIHAKRVTIMP-KDIQLARRIRGERA
.A.DFK.TDLRF.SA..GAL.EASEAYL.G.LFE.TNLCAI..K.VTIMP.KDI.LA....GE.A
RetrocopyFARDFK<TDLRFRSAVVGALREASEAYLEG>LFEHTNLCAIRVKFVTIMP<KDI*LACHVGGECA

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_687 retrocopy.
Ailuropoda melanoleuca was not studied using FANTOM5 data.
retro_amel_687 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 19 parental genes, and 102 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000097653 retrocopies
Ailuropoda melanoleuca ENSAMEG00000014588 7 retrocopies
Bos taurus ENSBTAG000000245613 retrocopies
Canis familiaris ENSCAFG000000049162 retrocopies
Canis familiaris ENSCAFG000000161194 retrocopies
Erinaceus europaeus ENSEEUG000000137961 retrocopy
Felis catus ENSFCAG000000036174 retrocopies
Felis catus ENSFCAG000000304245 retrocopies
Gadus morhua ENSGMOG000000143061 retrocopy
Macaca mulatta ENSMMUG000000314839 retrocopies
Monodelphis domestica ENSMODG000000059833 retrocopies
Mustela putorius furoENSMPUG000000138113 retrocopies
Nomascus leucogenys ENSNLEG000000015772 retrocopies
Otolemur garnettii ENSOGAG0000002431211 retrocopies
Otolemur garnettii ENSOGAG0000002593314 retrocopies
Pongo abelii ENSPPYG000000086361 retrocopy
Pan troglodytes ENSPTRG0000000204520 retrocopies
Pteropus vampyrus ENSPVAG000000084592 retrocopies
Tursiops truncatus ENSTTRG000000158897 retrocopies



Copyright © RetrogeneDB 2014-2017