RetrogeneDB ID: retro_amel_386

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192416.1:502385..502796(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PIGX
• Ensembl ID: ENSAMEG00000003759
• Aliases: None
• Description: phosphatidylinositol glycan anchor biosynthesis, class X [Source:HGNC Symbol;Acc:26046]

Sequence

>retro_amel_386
GCCAGGGCTATAGACATCCAGGTGGTGGCCCAGCTGCTCCTCTGGGACGTGGCTGGGCTTACCAACACACCGACCACAGT
CTTCACTGCCACCTCCACTGATCCTGGCACAAGGGCCATTTGATCTGAAATTATTCTGAGGCAAGAAGTTTTAAAAGATG
GTTCCCATAGCGACCTTTTAGTAAAAGTGAAATTTGGAGAAAATACTGAGGACTTCTAGACTTGCTGCCTCTTGACTAAA
CAGTACATCCTGACAGGACTTTCTGTGAATCCATATGAGTTGGCTTCATTTCGAGAGGCAAACATAACAGAGGCAGTGAT
GGTTTCGGAGAATTTTAATATAGAAGCTCCCAATTATTTCTCCAAGTAATCTAAAGTTCTAATTTATGCCAGACAAGATT
CACAGTGCATC

Alignment

ORF - retro_amel_386 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.61 %
• Parental protein coverage: 53.1 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ARAVGVRAVAWLLLWEAAGLTSTPAAIFQASKAYSSIRATCSEIILRQEVLKGGFHRDLLIKVKFGESIE
          ARA.....VA.LLLW..AGLT.TP...F.A.......RA..SEIILRQEVLK.G.H.DLL.KVKFGE..E
Retrocopy ARAIDIQVVAQLLLWDVAGLTNTPTTVFTATSTDPGTRAI*SEIILRQEVLKDGSHSDLLVKVKFGENTE

Parental  ALQTCRFLIKQYIPTGLFVDPYELASLRERNITEAVMVSEDFNIEAPNYLSKESEVLIYARQDSQCI
          ...TC..L.KQYI.TGL.V.PYELAS.RE.NITEAVMVSE.FNIEAPNY.SK.S.VLIYARQDSQCI
Retrocopy DF*TCCLLTKQYILTGLSVNPYELASFREANITEAVMVSENFNIEAPNYFSK*SKVLIYARQDSQCI

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_386 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_386 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 7 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000003759	1 retrocopy	retro_amel_386 ,
Callithrix jacchus	ENSCJAG00000013676	1 retrocopy	retro_cjac_2794,
Monodelphis domestica	ENSMODG00000018455	1 retrocopy	retro_mdom_1758,
Mustela putorius furo	ENSMPUG00000003841	1 retrocopy	retro_mputfur_1090,
Mus musculus	ENSMUSG00000023791	1 retrocopy	retro_mmus_943,
Oryctolagus cuniculus	ENSOCUG00000012329	1 retrocopy	retro_ocun_977,
Rattus norvegicus	ENSRNOG00000033623	2 retrocopies	retro_rnor_1998, retro_rnor_2555,