RetrogeneDB ID: retro_amel_1051

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192868.1:751826..752426(+)
• Located in intron of: ENSAMEG00000010617

Retrocopy information

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

Parental gene information

• Parental gene symbol: TSPAN2
• Ensembl ID: ENSAMEG00000010910
• Aliases: None
• Description: tetraspanin 2 [Source:HGNC Symbol;Acc:20659]

Sequence

>retro_amel_1051
TTTTGGCTGACCAGGTCAGCTGTCATCGCTTTTGGACTATGGTTTTGGTTTGGAGGCACCATGAAGGACTTTTTATCAGA
GGTTGAGTCATCGCAGTATATCGACCTGGGGCTCTATGTGCTGGTTGGGGAAGGAGCCCTGATAATAGCGGTGGGCTTCT
TCAGGTGTTAGGAAGCCATGAGGCAGTTGCAGTGTGTGCTGGGGCTTTTCACCTGCCTACTGGTGATATTTGCCGCTGTG
GTAACCATTGGAGTATTTGTTTTTATGGGCAACGGTGTAGCTATACGACATATTCAGACCACGTATGAAGAGCCTTATTA
TAACTATTACCTTACAGATAGCGAAAAGGGAAATAGGACTCTCAGAACTTTCTGCTCAATGTTTCAGTGCCGTGAAACAA
AAGGTCTGAACGGGTCCAAACCACACGCCCAAAGGAAATTCTAGGACACAAGCATTGTATTGATGACACTGAGACCATAA
TCAGCGTTAAGCTTCAGGTCACCGGAATTTGTTGGTATTGGAATTGCAGGTCTCACAATCTTTAGCATGATGTTCAGCAT
GGTCCCTGGCTGTGCAAAGCTAAACTCATGAGATGTGATA

Alignment

ORF - retro_amel_1051 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.98 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  FQLAGSAVIGFGLWFRFGGTMKDFSSEDKSPEYFYMGLYVLVGAGALMMAVGFFGCCGAMRESQCVLGSF
          F.L..SAVI.FGLWF.FGGTMKDF.SE..S..Y...GLYVLVG.GAL..AVGFF.C..AMR..QCVLG..
Retrocopy FWLTRSAVIAFGLWFWFGGTMKDFLSEVESSQYIDLGLYVLVGEGALIIAVGFFRC*EAMRQLQCVLG-L

Parental  FTCLLVIFAAEVTTGVFAFIGKGVAIRHVQTMYEEA-YNDYLTDRERGNGTLITFHSTFQCCG-KESSEQ
          FTCLLVIFAA.VT.GVF.F.G.GVAIRH.QT.YEE..YN.YLTD.E.GN.TL.TF.S.FQC......SE.
Retrocopy FTCLLVIFAAVVTIGVFVFMGNGVAIRHIQTTYEEPYYNYYLTDSEKGNRTLRTFCSMFQCRE<NKRSER

Parental  VQPTCPKELLGPKNCIDEIEAIISVKLQLIGI-VGIGIAGLTIFGMIFSMVLCCAIRTSRDVI
          VQ.T.PKE.LG.K.CID..E.IISVKLQ..GI.VGIGIAGLTIF.M.FSMV..CA...S.DVI
Retrocopy VQTTRPKEILGHKHCIDDTETIISVKLQVTGI>VGIGIAGLTIFSMMFSMVPGCAKLNS*DVI

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_1051 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1051 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 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000010910	1 retrocopy	retro_amel_1051 ,
Canis familiaris	ENSCAFG00000009732	1 retrocopy	retro_cfam_1227,
Felis catus	ENSFCAG00000029385	1 retrocopy	retro_fcat_1028,
Mustela putorius furo	ENSMPUG00000001674	1 retrocopy	retro_mputfur_793,