RetrogeneDB ID: retro_amel_1305

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL193175.1:364549..365002(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CYB5R3
• Ensembl ID: ENSAMEG00000009549
• Aliases: None
• Description: cytochrome b5 reductase 3 [Source:HGNC Symbol;Acc:2873]

Sequence

>retro_amel_1305
GAGTTCCAGAGCTCAAATGGGCTGCTAGTCTATCTGGGCAAAGGGAAGTTTGCCATCTGTCCAGACAAGAAATCCCAACC
CTATCATCAAGATGGTGAAGTCTGTTGGTGTGACCATGGGAGGAATGGGCATCATTCAGATGCTGCAGGTGATCCATGAT
GAGCATCCCATGTACCAACTGCTCTTTGCTGATTGGACCAAGAAGGACATCCTGCTGCAGCCAAAGCTAGAGGAACTAAG
GAAAGAACATTCCGCTTGCTTCAAGCTCTGGTACATGGTGGAAAGAACCCCTGAAGCCTTGGACTACAGCTAGGGCTTCA
TGAATAAGAGATGATCTGGGACCACCTACCACCCCCAGGAGTGGAACCACTGCTGATCCTGCCCATGAGCCAGTATCCCT
GCCTGTCCAACATGGACCCCATGGGTCACTCAAAAGAGTGCTGCTTCACCTTC

Alignment

ORF - retro_amel_1305 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.96 %
• Parental protein coverage: 53.49 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  EFRGPNGLLVYEGKGKFAIRPDKKS-NPVIKTVKSVGMIAGGTGITPMLQVIRAIMKDPHDPTVCHLLFA
          EF...NGLLVY.GKGKFAI.PDKKS.NP.IK.VKSVG...GG.GI..MLQ.......D.H......LLFA
Retrocopy EFQSSNGLLVYLGKGKFAICPDKKS>NPIIKMVKSVGVTMGGMGIIQMLQ----VIHDEHP--MYQLLFA

Parental  NQTEKDILLRPELEELRNEHSARFKLWYTVDRAPEAWDYSQGFVNE-EMIRDHLPPPEEEPLILMCGPPP
          ..T.KDILL.P.LEELR.EHSA.FKLWY.V.R.PEA.DYS.GF.N..EMI.DHLPPP..EPL.......P
Retrocopy DWTKKDILLQPKLEELRKEHSACFKLWYMVERTPEALDYS*GFMNK<EMIWDHLPPPGVEPLLIL----P

Parental  MIQYACLPNLDRVGHPKERCFAF
          M.QY.CL.N.D..GH.KE.CF.F
Retrocopy MSQYPCLSNMDPMGHSKECCFTF

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_1305 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1305 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 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009549	1 retrocopy	retro_amel_1305 ,
Bos taurus	ENSBTAG00000016516	2 retrocopies	retro_btau_1244, retro_btau_1287,
Pteropus vampyrus	ENSPVAG00000014126	1 retrocopy	retro_pvam_310,
Tursiops truncatus	ENSTTRG00000015143	2 retrocopies	retro_ttru_408, retro_ttru_918,