RetrogeneDB ID: retro_amel_183

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192348.1:5025934..5026236(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSAMEG00000001122
• Aliases: None
• Description: None

Sequence

>retro_amel_183
GCCAAAGAGCCAGGCATTGGCATGGGCCATGGGAAGACTAGCCAATGCCTTAAAGTTCTTTGTAACGACTTGGCGTTCTC
CTTCTATAGACATGCAATATGGGTGTGATCGATCCTGTCATCTGGGCAGCCAATGTGAGTTCTTCGGCAGAGCAGCCTCC
CTCTCTGGGGGCCCAGGGCTTCCTGGGAAAGAGGATGAGCCTGGAGCAGTGCTCCCTCAGCCACTGCCTGTTGGCCTGCA
GGGGCTCCATGGACTTCCTCCATCTTCTTGGATCCACTGAGATCTCAGTGGTCCAGGCCAGC

Alignment

ORF - retro_amel_183 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.95 %
• Parental protein coverage: 98.06 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  AKEPGIGTGHAKTGECLKVLLLLCDDS-GFLL--TFRMGMTGPVSWVANLSSSALSP-FLGAEGFLGKRM
          AKEPGIG.GH.KT..CLKV...LC.D..G.LL..T..MG...PV.W.AN.SSSA..P..LGA.GFLGKRM
Retrocopy AKEPGIGMGHGKTSQCLKV---LCNDL<GVLLL*TCNMGVIDPVIWAANVSSSAEQPPSLGAQGFLGKRM

Parental  SLERYSFSRCTLACRDSVDLFRRLGSTEIPMVRAT
          SLE..S.S.C.LACR.S.D....LGSTEI..V.A.
Retrocopy SLEQCSLSHCLLACRGSMDFLHLLGSTEISVVQAS

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_183 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_183 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 1 parental gene, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001122	3 retrocopies	retro_amel_1320, retro_amel_1608, retro_amel_183 ,