RetrogeneDB ID: retro_amel_1927

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL207117.1:152..578(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSAMEG00000001005
• Aliases: None
• Description: None

Sequence

>retro_amel_1927
TATGTGGCCTTCCTGGAGCTGGTCCTGCAGACAGCGAAGAAGCACTTCATGGTGGGACACAGGGTCACCTCGTATGTCTT
CACCAACCACCAGCTGCTGGGCCTGTGTGCCTCCCCGGGAAGGCCATAAGGTGGTGGTCCTCGAGGTCCGCGGCGTCCTG
CGCTGGCAGGATGTGTGATGCAGCCCATGGCGATGATCAGACGCTTCTGTGAGCAGCGCTTCCTCCGTGAGGTGGACGAC
CTGGTGTGCGCAGGTGTGGACATGAAGTTCCATGACCACGTGGGTGTGGAGATCCTGTCCCCCCTTTCTCACCCTGTGCC
CCAGTTTCTACTGGGTGGCCAATGAGAACTTCAGCTACTCACACTGGCTGCAGTCCAGGCCCACGTCCCCAGGGACCAGG
GCAACTTTTACTATATGGGGACTTTT

Alignment

ORF - retro_amel_1927 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.97 %
• Parental protein coverage: 64.84 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  YVDFLELFLQTVKKHFMVGQRVTYYVFRDQ-PAAVPVC-PSE-GWRVVVLEVRGTPCWQDV-SMQHMAMI
          YV.FLEL.LQT.KKHFMVG.RVT.YVF....PAA.PVC.P...G..VVVLEVRG...WQDV..MQ.MAMI
Retrocopy YVAFLELVLQTAKKHFMVGHRVTSYVFTNH<PAAGPVCLPGK<GHKVVVLEVRGVLRWQDV<VMQPMAMI

Parental  SCFCEQCFLHEVDDLVCVGVDMMFRDHMGVEILS-PFVTLYPSFYWVANENFSYACRPQS-QAHVARDQG
          ..FCEQ.FL.EVDDLVC.GVDM.F.DH.GVEILS.PF.TL.PSFYWVANENFSY....QS.QAHV.RDQG
Retrocopy RRFCEQRFLREVDDLVCAGVDMKFHDHVGVEILS>PFLTLCPSFYWVANENFSYSHWLQS<QAHVPRDQG

Parental  NFYYMGAF
          NFYYMG.F
Retrocopy NFYYMGTF

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_1927 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1927 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001005	1 retrocopy	retro_amel_1927 ,
Bos taurus	ENSBTAG00000012525	1 retrocopy	retro_btau_699,
Loxodonta africana	ENSLAFG00000010293	1 retrocopy	retro_lafr_1256,
Mustela putorius furo	ENSMPUG00000012419	1 retrocopy	retro_mputfur_1076,