RetrogeneDB ID: retro_amel_579

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192510.1:2209596..2210277(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSAMEG00000008805
• Aliases: None
• Description: None

Sequence

>retro_amel_579
GCAAAGTTCTTCTGTGCAGTCCAGAGGGACCTGAATTGTTGCAACAGCATAGGTGCCCTGGAGATGCACCAGCACCTGGA
ACAGCTGAAGAGGAGCATCTACGGCATGCACTTCTACTCCCAGGATGTCAAGAGGAAGAGAAGAAAAAACTGTAGAAACC
AGAACCCATCCTCTTGCAAGACAGGTCAACCTCCCCATGCCTGCCACCCACGCTGCTGCCACCTCCACAGCACTGTCATC
AGCTGCTGTCACCATGGCCTTCATGATGGCCCCATCACCCCCTATCCACTGTGTGCCTAGGGTCTTTGGCCCTTTCCCCC
TGCCGCCTAGGAGGTCTGTGGTGAAGTTTGGAAGTTGTAAGGTCTGAAGTGAAATTAAACTGGGCTGGCCTGCCATTGAA
CCCAAAAAGCCAGATGGTAGATTTGACCCCCTTGGTCCTCAGCTCAGGAGGCTTCATTTCTCATACCTAGATGGAAACAG
TGAGCACAGGCTCCATTACCTTGGCTCCCCAGCTCCTGGGCCTGTAGTGGTTCCCCCAATACTGAGAAGATGCCACCTCC
TCATGTGAAGACCTCCATCTTCACCCAAACAGTCTTGCTCAACTTCTAGCCTGTGCTGAGACCCAAGGATGACTCTGAGA
AAGACCCTAGTAGCACAGAGTCCATGCCCCACAAAACAGGC

Alignment

ORF - retro_amel_579 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.8 %
• Parental protein coverage: 75.75 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  AKFFCAVQGELNCCNSMGALEMHQRLEQLKRSMHRVHLYSQDAKKKRR-KPKLKKPEPILLRDRSTSPCL
          AKFFCAVQ..LNCCNS.GALEMHQ.LEQLKRS....H.YSQD.K...R.K.KL.KPEPILL.DRSTSPCL
Retrocopy AKFFCAVQRDLNCCNSIGALEMHQHLEQLKRSIYGMHFYSQDVK-RKR<KKKL*KPEPILLQDRSTSPCL

Parental  PPTLL-PPP-PLPSPATTMVSVVAPSPPVYTMPRVFGPFPPLPSKSMEK-LEVAKSEVKLNWAGLSSNPK
          PPTLL.PP...L.S.A.TM....APSPP....PRVFGPFP..P..S..K.LEV..SEVKLNWAGL..NPK
Retrocopy PPTLLPPPQ<ALSSAAVTMAFMMAPSPPIHCVPRVFGPFPLPPRRSVVK>LEVVRSEVKLNWAGLPLNPK

Parental  RYMVDLTPLVLNPGGF-HFSYLAGNSAHKLH-CPGFPWTSACSGSPNTEETPLPPVKASSFTPPVLLKFQ
          ..MVDLTPLVL..GGF.HFSYL.GNS.H.LH..P..P...ACSGSPNTE..P.P.VK.S.FT..VLL.F.
Retrocopy SQMVDLTPLVLSSGGF<HFSYLDGNSEHRLH<LPWLPSSWACSGSPNTEKMPPPHVKTSIFTQTVLLNF*

Parental  PVPRPKDESEIDPSSTESVPHKRG
          PV.RPKD.SE.DPSSTES.PHK.G
Retrocopy PVLRPKDDSEKDPSSTESMPHKTG

Legend:

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

Expression

RNA-Seq

Ailuropoda melanoleuca was not studied using RNA-Seq expression data.

ChIP-Seq

Ailuropoda melanoleuca was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_amel_579 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_579 was not experimentally validated.

Homology

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.

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000008805	1 retrocopy	retro_amel_579 ,
Mustela putorius furo	ENSMPUG00000003165	1 retrocopy	retro_mputfur_1029,
Mus musculus	ENSMUSG00000049916	1 retrocopy	retro_mmus_1731,