RetrogeneDB ID: retro_amel_82

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192357.1:4514153..4514618(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSAMEG00000020210
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSAMEG00000017969
• Aliases: None
• Description: None

Sequence

>retro_amel_82
GCGGCACCGGAGCAAGCAGTCACCATGCGGCTGCTCCTGGCTCTTGCCCTCCTCCTGGGTTTGGATTCTTCAGTGCAAGG
TTGTCCTGTGCGGAGAGCCGGGTACCAGTGGCTAGGCCGCAGTCCTGACGGTAATTTTGCAAGCTGCATTGATGAGAAGG
GACTGACATTCAGCCTACTTCCCGGTGAATCCAACAGAATCCTTCCTCCAAGGACCGACCCTGCCTCAATGACAAGGTCC
CAGAACTTGAATGGTGTCTTCCCTCTTTCTGAGAGCTATTTTGGATCCGGATCTGGCTCTGGATCCGGATCTAGAAGTGG
CTTCTTCACTGAAATTGAACAGGAATACCAAGCAGTTGATGAAAACAATGCTTTTTATTACAACTTTAGGCCTCTCAAGA
GAAATCGGCCATCGGACAGCCGGGACTTGGGTCAAGATGGACGAGAAGAGGATTTTATTATATAA

Alignment

ORF - retro_amel_82 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.19 %
• Parental protein coverage: 94.23 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RLVLALALLLVLDSPVQGSPVRKAKFQWVRCSPDSNSANCIDEKGPMFNLLPGESNRILPPRTDPSSMTR
          RL.LALALLL.LDS.VQG.PVR.A..QW...SPD.N.A.CIDEKG..F.LLPGESNRILPPRTDP.SMTR
Retrocopy RLLLALALLLGLDSSVQGCPVRRAGYQWLGRSPDGNFASCIDEKGLTFSLLPGESNRILPPRTDPASMTR

Parental  SQNWNDVFPLSEDYSGSGFGSGSESGSGSGFLTEIEQEYQPVDENSAFYYNFRPLKRNLPSDNQDLVQDG
          SQN.N.VFPLSE.Y.GSG.GSG..SGS.SGF.TEIEQEYQ.VDEN.AFYYNFRPLKRN.PSD..DL.QDG
Retrocopy SQNLNGVFPLSESYFGSGSGSG--SGSRSGFFTEIEQEYQAVDENNAFYYNFRPLKRNRPSDSRDLGQDG

Parental  PEGDFIM
          .E.DFI.
Retrocopy REEDFII

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_82 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_82 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 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017969	1 retrocopy	retro_amel_82 ,
Choloepus hoffmanni	ENSCHOG00000000448	9 retrocopies	retro_chof_1085, retro_chof_1907, retro_chof_1936, retro_chof_1950, retro_chof_227, retro_chof_2572, retro_chof_403, retro_chof_876, retro_chof_935,
Dasypus novemcinctus	ENSDNOG00000006889	2 retrocopies	retro_dnov_1745, retro_dnov_544,