RetrogeneDB ID: retro_psin_57

Retrocopy location

• Organism: Chinese softshell turtle (Pelodiscus sinensis)
• Coordinates: JH210369.1:7732149..7732630(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: STX6
• Ensembl ID: ENSPSIG00000009402
• Aliases: None
• Description: syntaxin 6 [Source:HGNC Symbol;Acc:11441]

Sequence

>retro_psin_57
GTCACAAGCAAACGGCAAGTGGTTAAGGAAATGAAGGATTAGATGTCTATCTCATCTGTGCAGGGATTGGCTGAAAGAAA
AAATAAGCAGGCACTTCTGGGAGAAAGGGGAGGTCAGAGTTGGAACTCTGGCTCAGATAAATATGGCTGTTTGGATCAAA
AGCTGCAGTTAGCCAATTCACACTTCATTGAGAAACAGCAGGCTCAGCAATAGTTGATTGTGGAACAGCAGGATTAGCAA
TTGGAGCTGGTATCTGGCAGCATTGCCCTGCTGAGGAACATGTCTCAGCGCATTTCTTGGGGAGCTGGAGGAACAAACAG
TGATGTTGGATGACTTGTCCCAGGAGTTAGACAACACTCAGTCATGGCTTGATAATGTGATGAAAAAGCTTGCAAAAGTG
TCCCACATGACCAGTGATCGACGACAGTGGGGTGTAATCGTCATTCTCTTCGTTATCTTATTGGTGGAACATAACCTGTT
T

Alignment

ORF - retro_psin_57 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.12 %
• Parental protein coverage: 66.12 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ITSTRQVVREMKDQMSNSSVQALAERKNRQALLGESGGQNWNSGSDKYGRLDRELQLANSHFIEEQQAQQ
          .TS.RQVV.EMKD.MS.SSVQ.LAERKN.QALLGE.GGQ.WNSGSDKYG.LD..LQLANSHFIE.QQAQQ
Retrocopy VTSKRQVVKEMKD*MSISSVQGLAERKNKQALLGERGGQSWNSGSDKYGCLDQKLQLANSHFIEKQQAQQ

Parental  QLIVEQQDEQLELVSGSIGVLKNMSQRIG-GELEEQAVMLDDFSHEIDSTQSRLDNVMKKLAKVSHMTSD
          .LIVEQQD.QLELVSGSI..L.NMSQRI..GELEEQ.VMLDD.S.E.D.TQS.LDNVMKKLAKVSHMTSD
Retrocopy *LIVEQQD*QLELVSGSIALLRNMSQRIS>GELEEQTVMLDDLSQELDNTQSWLDNVMKKLAKVSHMTSD

Parental  RRQWCAIIILFVILLVVLILF
          RRQW..I.ILFVILLV...LF
Retrocopy RRQWGVIVILFVILLVEHNLF

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_57 retrocopy.

TSS

Pelodiscus sinensis was not studied using FANTOM5 data.

Lab

retro_psin_57 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Mustela putorius furo	ENSMPUG00000011478	1 retrocopy	retro_mputfur_905,
Oryctolagus cuniculus	ENSOCUG00000004714	1 retrocopy	retro_ocun_552,
Pelodiscus sinensis	ENSPSIG00000009402	1 retrocopy	retro_psin_57 ,