RetrogeneDB ID: retro_amel_604

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192522.1:779917..780280(+)
• Located in intron of: ENSAMEG00000001095

Retrocopy information

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

Parental gene information

• Parental gene symbol: GOLT1B
• Ensembl ID: ENSAMEG00000016231
• Aliases: None
• Description: golgi transport 1B [Source:HGNC Symbol;Acc:20175]

Sequence

>retro_amel_604
TTAATGGACACCCAGAAAATTGGAATGGGATTAACAGGATATTGAGTGTTTTTCCTCTCCCTTGGAATGATTCTCTTATT
TGACAAAGCACTATTGGCTGTTGGTAATGTTTTCTTTGTAGCTGGGTTGGCTTTTGTAATTGGTTTATGAAGAAGATGCA
GATTCTTCTTCCAAAAACCTAAAATTAAAGCTATAGGGTTTTTCCTGGGTGGTGTATTTGTAGTCCTTGTTGGTTGGCCT
TTGATAGGCATGATCTTTGAAATTTATGAATTCTTTCTCATGTTCAAGGGCTTCTTTCCTATGGTCATTGGCTTTATAGG
AAGAGTGCCAGTCTTTGGGTTCCTCTAGAATCTACCTGGAATT

Alignment

ORF - retro_amel_604 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.17 %
• Parental protein coverage: 87.68 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LTDTQKIGMGLTGFGVFFLFFGMILFFDKALLAIGNVLFVAGLAFVIGLERTFRFFFQKHKMKATGFFLG
          L.DTQKIGMGLTG..VFFL..GMIL.FDKALLA.GNV.FVAGLAFVIGL.R..RFFFQK.K.KA.GFFLG
Retrocopy LMDTQKIGMGLTGY*VFFLSLGMILLFDKALLAVGNVFFVAGLAFVIGL*RRCRFFFQKPKIKAIGFFLG

Parental  GVFVVLIGWPLIGMIFEIYGFFLLFRGFFPVVVGFIRRVPVLGSLLNLPGI
          GVFVVL.GWPLIGMIFEIY.FFL.F.GFFP.V.GFI.RVPV.G.L.NLPGI
Retrocopy GVFVVLVGWPLIGMIFEIYEFFLMFKGFFPMVIGFIGRVPVFGFL*NLPGI

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_604 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_604 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	ENSAMEG00000016231	1 retrocopy	retro_amel_604 ,
Canis familiaris	ENSCAFG00000012256	1 retrocopy	retro_cfam_1835,
Dasypus novemcinctus	ENSDNOG00000013576	2 retrocopies	retro_dnov_158, retro_dnov_1730,
Felis catus	ENSFCAG00000028655	1 retrocopy	retro_fcat_1782,
Oryctolagus cuniculus	ENSOCUG00000008797	1 retrocopy	retro_ocun_1706,
Otolemur garnettii	ENSOGAG00000004756	1 retrocopy	retro_ogar_3234,
Ictidomys tridecemlineatus	ENSSTOG00000006352	1 retrocopy	retro_itri_1786,