RetrogeneDB ID: retro_amel_680

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192564.1:1858101..1858425(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FHIT
• Ensembl ID: ENSAMEG00000017139
• Aliases: None
• Description: fragile histidine triad [Source:HGNC Symbol;Acc:3701]

Sequence

>retro_amel_680
GTCCTTGTGTGTCCCCTTCAGCCAGTGGAGCTCTTCTGAGATACGGGTACTGAAGAAGTGGCCAACTTGTTCCAAGCAAT
CCAGAGCATCTGACGGTGGTGGGGAAGCTTTTCCAGGGGACTTCTTTCACCTTTTCCACACGGGATGGCCCCAAAGCAAA
ATGGACTATAAAGCCCATTCGCATCCACATTCTTCTCAAGAAGGCTAGAGATTTTCACAGGACGATAGGATCCACAATGA
GCTCCAACACCACGATGAAGAGGAGGGAAACTAGGCAACTCTGCAGTGACCAGAGAAGAGATGGCGGCAGAAACTGAGGC
TCTG

Alignment

ORF - retro_amel_680 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.36 %
• Parental protein coverage: 95.61 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  VLVCPLRPVERFRDLRPEEVADLFQATQRVGM-VVEKHFQGTSLTFSMQDGPEAGQTVKHVHVHVLPRKA
          VLVCPL.PVE.F.D...EEVA.LFQA.Q.....VV.K.FQGTS.TFS..DGP.A..T.K....H.L..KA
Retrocopy VLVCPLQPVELF*DTGTEEVANLFQAIQSI*R<VVGKLFQGTSFTFSTRDGPKAKWTIKPIRIHILLKKA

Parental  GDFHR-NDSIYDELQRHDKAEEDTPALWRSE-EEMAAEAATL
          .DFHR..D.I..ELQ.HD..E.....L...E.EEMAAE...L
Retrocopy RDFHR<DDRIHNELQHHDEEEGN*ATLQ*PE<EEMAAETEAL

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_680 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_680 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 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017139	1 retrocopy	retro_amel_680 ,
Canis familiaris	ENSCAFG00000007194	1 retrocopy	retro_cfam_840,
Myotis lucifugus	ENSMLUG00000013987	1 retrocopy	retro_mluc_156,
Sorex araneus	ENSSARG00000008738	1 retrocopy	retro_sara_92,
Tarsius syrichta	ENSTSYG00000010547	1 retrocopy	retro_tsyr_1570,