RetrogeneDB ID: retro_amel_279

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192373.1:1896531..1897013(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TMEM138
• Ensembl ID: ENSAMEG00000016585
• Aliases: None
• Description: transmembrane protein 138 [Source:HGNC Symbol;Acc:26944]

Sequence

>retro_amel_279
ATGGTCCAGCGCAGTAACTATGACCTGATGCTCTGCCTACAGGTCCTGCTGCTGTCCTATGATCTGTTTGTTAATTCCTC
GGCAGAGCTACTCCGAATGGCTCCCATCTTCCTGCTGGTGTTTTTCATCACCCAGGATACTGCAATTCTCTTCAACATCA
TCATCATTTTCCTCCTGTTCTTTAACACCGTCGTCTTCCAGGCTGGCCTGGTCAACCCTGTTTTCTGTAAGTTCAAAGGG
ACCATCATCCTCACAGCTGTGATCTTCGCCCCAGCATCTCCCTTCATGTCAGGGTCATGAATTTACGCTGGAAAAACTCC
AACTGCTTTGTCTGGACAGAGGGACTTCAAACGCTGTTTGTATTCCAGAGAATAGCACGGCAGTTATACTGTTACTTCTA
CAAATGGACAGCTGTGAGACTGGGTGATTCTCGCTTCTACCAGGACTCTTTATGACTGCTCAAGTTCACACAAGTCCAAA
GG

Alignment

ORF - retro_amel_279 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.53 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MLQTSNYSLVLSLQFLLLSYDLFVNSFSELLRMAPVIQLVLFIIQDIAILFNIIIIFLMFFNTFVFQAGL
          M.Q.SNY.L.L.LQ.LLLSYDLFVNS..ELLRMAP...LV.FI.QD.AILFNIIIIFL.FFNT.VFQAGL
Retrocopy MVQRSNYDLMLCLQVLLLSYDLFVNSSAELLRMAPIFLLVFFITQDTAILFNIIIIFLLFFNTVVFQAGL

Parental  VNLLFHKFKGTIILTAVYFA-LSISLHVWVMNLRWKNSKRFVWTDGLQTLFVFQRLAAVLYCYFYKRTAV
          VN..F.KFKGTIILTAV.FA..SISLHV.VMNLRWKNS..FVWT.GLQTLFVFQR.A..LYCYFYK.TAV
Retrocopy VNPVFCKFKGTIILTAVIFA<PSISLHVRVMNLRWKNSNCFVWTEGLQTLFVFQRIARQLYCYFYKWTAV

Parental  RLGDPRFYQDSLWLRREFTQVQR
          RLGD.RFYQDSL.L...FTQVQR
Retrocopy RLGDSRFYQDSL*LLK-FTQVQR

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_279 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_279 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 2 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016585	1 retrocopy	retro_amel_279 ,
Mustela putorius furo	ENSMPUG00000014175	4 retrocopies	retro_mputfur_1250, retro_mputfur_291, retro_mputfur_883, retro_mputfur_959,