RetrogeneDB ID: retro_psin_41

Retrocopy location

• Organism: Chinese softshell turtle (Pelodiscus sinensis)
• Coordinates: JH207279.1:3318..3723(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TRNAU1AP
• Ensembl ID: ENSPSIG00000006864
• Aliases: None
• Description: tRNA selenocysteine 1 associated protein 1 [Source:HGNC Symbol;Acc:30813]

Sequence

>retro_psin_41
GTCTCAAGAGCCTTTGCCACCATGGAAGAACTTGTTCTGAGTGTAAAAATCATCCGAAATAGATTGACAGGAATTCCGGC
AGGCTGTTGCTTTGTAGAATTGGCAGATCTGGCTACTGCAGAGGAGCGTTCACACAAAATCAATGGAAACCCACTTCCTG
GTGCCACACCAGCAATGCGATTTAAACTGAACTACGCAACGTATGGAAAACAGCCTGATAACAGTCCAGAATACTCGCTC
TTTGTGGGAGATCTCACCCCAGATGTGGATGACGGCATGTTAGATGAGGTTTCTGTTAAATCATGTAGAGGTGGAAAAGT
TGTTTTGGACCAGATGGGAGTTTCCAAAGGTTATGGGTTTGTGAAATTCACGGATGAGCTGGAACAGAAAAGAGCCCTGA
CAGAG

Alignment

ORF - retro_psin_41 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.13 %
• Parental protein coverage: 50.36 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VSRAFATMGELVLSVKIIRNRLTGIPAGYCFVEFADLATAEKCLHKINGKPLPGATPAKRFKLNYATYGK
          VSRAFATM.ELVLSVKIIRNRLTGIPAG.CFVE.ADLATAE...HKING.PLPGATPA.RFKLNYATYGK
Retrocopy VSRAFATMEELVLSVKIIRNRLTGIPAGCCFVELADLATAEERSHKINGNPLPGATPAMRFKLNYATYGK

Parental  QPDNSPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKFTDELEQKRALTE
          QPDNSPEYSLFVGDLTPDVDDGML.E..VK...SCRGGKVVLDQ.GVSKGYGFVKFTDELEQKRALTE
Retrocopy QPDNSPEYSLFVGDLTPDVDDGMLDEVSVK---SCRGGKVVLDQMGVSKGYGFVKFTDELEQKRALTE

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Pelodiscus sinensis was not studied using RNA-Seq expression data.

ChIP-Seq

Pelodiscus sinensis was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_psin_41 retrocopy.

TSS

Pelodiscus sinensis was not studied using FANTOM5 data.

Lab

retro_psin_41 was not experimentally validated.

Homology

Retrocopy orthology:

Pelodiscus sinensis 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 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
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,