RetrogeneDB ID: retro_amel_742

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192602.1:1553352..1553802(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TSPAN5
• Ensembl ID: ENSAMEG00000013851
• Aliases: None
• Description: tetraspanin 5 [Source:HGNC Symbol;Acc:17753]

Sequence

>retro_amel_742
TGGCTCAAAGACCATCTGTATTTCTTTATAAGCAACATCAGAGCATACAGAGATGACACTGATTTGCAGAACCTCATAGA
CTTCATCCAGGAATATCAGCAGTTCCATGAGGCTTCTGGAGCTGATGACTGGAACCTGAATATTTACTTCAATTGCACAG
ATCCCAACACAAGTCAAGAGTGATGCGGGATGCCATTCTCCTACCGTATTGAAGATCCTGCCGAAAATGTCATTGACACT
CAGTGTGGCTATGATGTCAGGCAAAAACCAGAAGTTGACCAGCAGATGGTAATCTGCACAAAAGGCTGTGTGCCCCAGTT
TGAGAAGCAGTTGCAGGACAATTTAACCCTCGTGGTTGGTATTTTCATAGGCATTGCATTGCTACAGATTTGGGGGATAT
GTCTGGCACAGAATTTGGTTCATGATATTGAAGCTGTCAGGGCTAGCTGG

Alignment

ORF - retro_amel_742 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.13 %
• Parental protein coverage: 56.34 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  WIKDQLYFFINNNIRAYRDDIDLQNLIDFTQEYWQCCGAFGADDWNLNIYFNCTDSNASRERCGVPFSCC
          W.KD.LYFFI.N.IRAYRDD.DLQNLIDF.QEY.Q...A.GADDWNLNIYFNCTD.N.S.E.CG.PFS..
Retrocopy WLKDHLYFFISN-IRAYRDDTDLQNLIDFIQEYQQFHEASGADDWNLNIYFNCTDPNTSQE*CGMPFSYR

Parental  TKDPAEDVINTQCGYDARQKPEVDQQIVIYTKGCVPQFEKWLQDNLTIVAGIFIGIALLQIFGICLAQNL
          ..DPAE.VI.TQCGYD.RQKPEVDQQ.VI.TKGCVPQFEK.LQDNLT.V.GIFIGIALLQI.GICLAQNL
Retrocopy IEDPAENVIDTQCGYDVRQKPEVDQQMVICTKGCVPQFEKQLQDNLTLVVGIFIGIALLQIWGICLAQNL

Parental  VSDIEAVRASW
          V.DIEAVRASW
Retrocopy VHDIEAVRASW

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_742 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_742 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	ENSAMEG00000007218	2 retrocopies	retro_amel_1365, retro_amel_979,
Ailuropoda melanoleuca	ENSAMEG00000013851	1 retrocopy	retro_amel_742 ,
Canis familiaris	ENSCAFG00000010287	1 retrocopy	retro_cfam_314,
Choloepus hoffmanni	ENSCHOG00000013549	1 retrocopy	retro_chof_2337,
Dasypus novemcinctus	ENSDNOG00000012685	1 retrocopy	retro_dnov_91,
Echinops telfairi	ENSETEG00000007405	1 retrocopy	retro_etel_1985,
Pteropus vampyrus	ENSPVAG00000003024	1 retrocopy	retro_pvam_79,