RetrogeneDB ID: retro_amel_416

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192432.1:2321856..2322222(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSAMEG00000010618
• Aliases: None
• Description: None

Sequence

>retro_amel_416
GAAGAGGCCAGAAAGACCCCCGCCTGACCAAATCCCGCACGCCTGCATCCTGGCGTCCAGCGCCTGCATCCCGCATCGTC
CCCATGCCCAAGAGAAAGGCTGAAGGGAATGCTCCAGGTAGTAAGGCCAAGGCGAAGTTCTGCAAGTTTATCTGCTAAAT
CTGCTCCTCCAGAGCCTGAGTCCAAGCCTAATAAGGCCTCCGCAAAGAGGGGAGATAAGGTACCCAAAGGGAAATGGGGA
GAGCTGATGCTGGCAAGGACGGGAATAACCCTGCAGTAAACAGAGATGCCAAAACACCCCAGGCACAGAAAGCCGAGGGT
GCTGGCGATGCCAAGTGAAGCGTGTGCATTCCTGACACCTGGGTAC

Alignment

ORF - retro_amel_416 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.29 %
• Parental protein coverage: 97.64 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  EEARTTPG-PAKARAPLHPRVQRLVPPPSPPCPRERLKGMLKEIKPR-EDLQGYLLNLLLQSQSPSLKRP
          EEAR.TP..P..AR..LHP.VQRL..P.S.PCPRERLKGML....PR.E.LQ.YLLNLLLQS.SPSL.RP
Retrocopy EEARKTPA*PNPAR--LHPGVQRL-HPASSPCPRERLKGMLQVVRPR>EVLQVYLLNLLLQSLSPSLIRP

Parental  LQRRERRY-PKGKRGKLMLARMGITLQKTETPKQTRHRKLKVLEMPSELCAFLITVY
          .QR.E.RY.PKGK.G.LMLAR.GITLQ.TE.PK..RHRK..VL.MPSE.CAFL...Y
Retrocopy PQRGEIRY<PKGKWGELMLARTGITLQ*TEMPKHPRHRKPRVLAMPSEACAFLTPGY

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_416 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_416 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 1 parental gene, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000010618	7 retrocopies	retro_amel_1286, retro_amel_1287, retro_amel_1351, retro_amel_1557, retro_amel_1780, retro_amel_416 , retro_amel_593,