RetrogeneDB ID: retro_amel_1782

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL194302.1:251232..251944(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TRNAU1AP
• Ensembl ID: ENSAMEG00000011367
• Aliases: None
• Description: tRNA selenocysteine 1 associated protein 1 [Source:HGNC Symbol;Acc:30813]

Sequence

>retro_amel_1782
CTCGCTGGCATCCCAGCTGACTACTGCTCTGTGGAAGGCACAGATTTGGCCACAGCTGAAAAGAGTTTGCATAAAATTAA
TGGGAAACGTCTTCCAGGAGCCACACCTGCAAAACATTTTAAACTAAACTATGCCACTTATGGGAAATAACCAGATAATA
GCCCTGTGTACTCCCTTTCTTTTTTTGGCGGGGGCGGGGGGCTGACTCCAGATGTGGATGGTGGTGTGTTGTATGGTTGA
TTGTCCGCGTCCACCTCTCCTGTTGGGGAGACAAGGTGGTTTGGGATCAGACAGTATGTCTCAGGGTTTTGGTTTTATGG
AATTCATGGACGAACTGCAACAGAAGCAAAGTCTGACAGAATGCCAGGGCACAGCAGGACTGGGGGCCACACCAGCGCTT
CTGAGCATGGCGATCACTAAAGTGAACTATATGTAGCCGTTGGAATACAATCGGATGTGCATTTATAGCTACAACTAGTG
TTAGCAGCAGCACCAGAACTACCGTGTCTGGTGGAGGTGTGACTAGAACACAGGCAACAACAGCTGTAGTTACCCCCAAA
ATGGCTCTCCCCGGAGCACCACACAGACACGTGAGGAAGTTGGAGACAATACACCTAATGACCCCAGGCCATAGCCGGGT
GTGGCTGAGGCCACCGAGGAGTTCCCGGAGCAGAGTAAGGAGCTGTACGATGCACCTATGGACTGTCACTGG

Alignment

ORF - retro_amel_1782 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.25 %
• Parental protein coverage: 81.53 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LTGIPAGYCFVEFADLATAEKCLHKINGKPLPGATPAKRFKLNYATYGKQPDNSPEYSL-FVG---DLTP
          L.GIPA.YC.VE..DLATAEK.LHKINGK.LPGATPAK.FKLNYATYGK.PDNSP.YSL.F.G....LTP
Retrocopy LAGIPADYCSVEGTDLATAEKSLHKINGKRLPGATPAKHFKLNYATYGK*PDNSPVYSLSFFGGGGGLTP

Parental  DVDDGMLYE-FFVKVYPSCRGGKVVLDQT-GVSKGYGFVKFTDELEQKRALSECQGAVGLGSKPVRLSVA
          DVD.G.LY....V.V..SC.G.KVV.DQT...S.G.GF..F.DEL.QK..L.ECQG..GLG..P..LS.A
Retrocopy DVDGGVLYG<LIVRVHLSCWGDKVVWDQT<SMSQGFGFMEFMDELQQKQSLTECQGTAGLGATPALLSMA

Parental  IPKASRVKPVEYSQMYSYSYNQYYQQYQSYYAQWGYDQNTGSYSYSYPQYGYTQSAMQTYEEVGDDALED
          I.K.....P.EY..M..YSYN...QQ.Q.Y...W..D.NTG..S.SYPQ.G...S..QT.EEVGD....D
Retrocopy ITKVNYM*PLEYNRMCIYSYN*C*QQHQNYRVWWRCD*NTGNNSCSYPQNGSPRSTTQTREEVGDNTPND

Parental  PMPQLDVTEANKEFMEQSEELYDALMDCHW
          P.P...V.EA..EF.EQS.ELYDA.MDCHW
Retrocopy PRP*PGVAEATEEFPEQSKELYDAPMDCHW

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_1782 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1782 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	ENSAMEG00000002583	1 retrocopy	retro_amel_1114,
Ailuropoda melanoleuca	ENSAMEG00000011367	1 retrocopy	retro_amel_1782 ,
Callithrix jacchus	ENSCJAG00000009717	1 retrocopy	retro_cjac_3928,
Equus caballus	ENSECAG00000012980	1 retrocopy	retro_ecab_452,
Mustela putorius furo	ENSMPUG00000015511	2 retrocopies	retro_mputfur_1185, retro_mputfur_856,
Pelodiscus sinensis	ENSPSIG00000006864	1 retrocopy	retro_psin_41,
Tupaia belangeri	ENSTBEG00000008049	1 retrocopy	retro_tbel_923,