RetrogeneDB ID: retro_amel_1385

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL193297.1:511908..512316(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: UBE2L6
• Ensembl ID: ENSAMEG00000014519
• Aliases: None
• Description: ubiquitin-conjugating enzyme E2L 6 [Source:HGNC Symbol;Acc:12490]

Sequence

>retro_amel_1385
GATCTTCAGGCAAAGCTTCTCTCCTGTCTGTGGAACGTACTCAGCAATGGTGCCAACATCCTGGTGTGGCATGTACTCCT
CCTGCCTGAGAAAATGCTCTCCAACCCCAAGAACTTCAACATGCACATCAACTTCCCCAAGGACTATCTGTTCAAACCCC
TTCAGAGACATTCACAACCAGGATCTACCACCGTAATGTAGACACAACAGAGAGGTTTGCATGCCCATCAACAGAGTGAT
AACTGGAAGGCTTATAGCAAGACCTGCCATGTCTTGGAGGCCCTCGATGGGCTGGTGAATAAACCAGACCTGGGACAACC
CATTTGGGTGGAACTCGCTGATCTGCTAACATAGGAACCAGAGCTGTTCAACAGGGAGGTCAGAGAGTTCACCTTCAAGT
ATGGAGTA

Alignment

ORF - retro_amel_1385 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.86 %
• Parental protein coverage: 89.54 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  DLQAKLPPYLRDLFSDDADVLVWHVLLLPEKPPYNLKAFHLRINFPEDYPFKP-PTVTFTTRIYHPNVG-
          DLQAKL...L....S..A..LVWHVLLLPEK...N.K.F...INFP.DY.FKP.P..TFTTRIYH.NV..
Retrocopy DLQAKLLSCLWNVLSNGANILVWHVLLLPEKMLSNPKNFNMHINFPKDYLFKP<PSETFTTRIYHRNVD<

Parental  HNGRVCLPIT-SRENWKPHTKTCQVLEALSVLVNRPDLEQPVRVELADLLVQNPELFTREARDFTLKYGV
          HN..VC.PI.....NWK...KTC.VLEAL..LVN.PDL.QP..VELADLL...PELF.RE.R.FT.KYGV
Retrocopy HNREVCMPIN<QSDNWKAYSKTCHVLEALDGLVNKPDLGQPIWVELADLLT*EPELFNREVREFTFKYGV

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_1385 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1385 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 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000003515	2 retrocopies	retro_amel_1117, retro_amel_483,
Ailuropoda melanoleuca	ENSAMEG00000011216	6 retrocopies	retro_amel_1295, retro_amel_1427, retro_amel_1648, retro_amel_1750, retro_amel_620, retro_amel_995,
Ailuropoda melanoleuca	ENSAMEG00000014519	1 retrocopy	retro_amel_1385 ,
Choloepus hoffmanni	ENSCHOG00000001515	1 retrocopy	retro_chof_1084,
Microcebus murinus	ENSMICG00000004882	1 retrocopy	retro_mmur_1295,
Mustela putorius furo	ENSMPUG00000000263	1 retrocopy	retro_mputfur_1092,