RetrogeneDB ID: retro_amel_1768

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL194257.1:159579..160189(+)
• Located in intron of: ENSAMEG00000000829

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSAMEG00000000824
• Aliases: None
• Description: None

Sequence

>retro_amel_1768
TCTACAGCTGAGCATACATGACAGACATTCCTTTGGGTACAGGAGAGGCAGGGCCAGTCACAGCAGCGAAAGGGGTCCCA
CTGTGAGTGGCTACTGACCAGGAGGCGCTGCTCAGAGAGGCCAAGATCACAGAGGAGCTCAACTTAGGTTTACTAGAAAC
ATATGAGCAGATTCAGGCTGACAAAAACAAGTAAGTGCACCAGAAGCGGAAGTGCCCCGGGCCCATAATCACCTATCATT
CAGTGGCAGTACAGCTTGTTGGGGAGCCAGAGCCTGAAGAAGAGTGTGTGGATGTGGAAGGACTGGATCCCGCTCCCACA
ACTTTTGCACTGACTCCCCATGCCAGCACTGGACCCGTCAACCCTCCTGCTCACTGCTCCTATACCTTCATCATTTTCAG
TAATAATACGACATTTGAGGAATGGTTTCCCCAAGGGCAGCCCCCAAAGTCTCTGTCTGGGAGGTCTGCCCTGTGACCCA
CTGCCCAGCCCTATACTGGGACCCTGTCACAGACATCCGCTACGCCACTGCTCAAGGCTTCAAGAACATCCATGAGGCCT
TCAAGTAGAAAGTCACTGCCCATGGACTGCCGCCCACTGCCTCAGCACTT

Alignment

ORF - retro_amel_1768 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.24 %
• Parental protein coverage: 56.04 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  STAEHTRQTFLRVQERQGQSRRRKGPHFERPLT-QEELLREAKITEELNLRSLETYERLEADKKKQVHKK
          STAEHT.QTFL.VQERQGQS..RKG.H.E..LT.QE.LLREAKITEELNL..LETYE...ADK.K.VH.K
Retrocopy STAEHT*QTFLWVQERQGQSQQRKGSHCEWLLT<QEALLREAKITEELNLGLLETYEQIQADKNK*VHQK

Parental  RKCPGPIITYHSVTVPLVGEPGPKEENVDVEGLDPAPAASALTPRPGTGPVVPPASCSRTFITFSDDATF
          RKCPGPIITYHSV.V.LVGEP.P.EE.VDVEGLDPAP...ALTP...TGPV.PPA.CS.TFI.FS...TF
Retrocopy RKCPGPIITYHSVAVQLVGEPEPEEECVDVEGLDPAPTTFALTPHASTGPVNPPAHCSYTFIIFSNNTTF

Parental  EEWFPQGRP-PKVPVREVCPVTHRPALYRDPVTDIPYATARAFKIIREAYKKYITAHGLPPTASAL
          EEWFPQG.P.PKV.V.EVCPVTH.PALY.DPVTDI.YATA..FK.I.EA.K...TAHGLPPTASAL
Retrocopy EEWFPQGQP<PKVSVWEVCPVTHCPALYWDPVTDIRYATAQGFKNIHEAFK*KVTAHGLPPTASAL

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_1768 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1768 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 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000000824	1 retrocopy	retro_amel_1768 ,
Canis familiaris	ENSCAFG00000012540	1 retrocopy	retro_cfam_807,
Equus caballus	ENSECAG00000017754	1 retrocopy	retro_ecab_13,
Echinops telfairi	ENSETEG00000004257	1 retrocopy	retro_etel_101,
Mustela putorius furo	ENSMPUG00000004027	1 retrocopy	retro_mputfur_1542,
Mus musculus	ENSMUSG00000008958	1 retrocopy	retro_mmus_1570,