RetrogeneDB ID: retro_psin_46

Retrocopy location

• Organism: Chinese softshell turtle (Pelodiscus sinensis)
• Coordinates: JH208379.1:4312578..4313121(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPSIG00000003190
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SOCS7
• Ensembl ID: ENSPSIG00000005627
• Aliases: None
• Description: suppressor of cytokine signaling 7 [Source:HGNC Symbol;Acc:29846]

Sequence

>retro_psin_46
ACGAGCCTCACGGAGGAACTGAAAAAACTTGCAAGACAAGGATGGTACTGGGGCCCTATTACACGTTGGGAGGCAGAAGG
AAAACTGGCGAATGTGCCCGATGGTTCATTTCTTGTTCGAGATAGCTCTGACGACCGTTATCTTTTAAGTCTAAGTTTTC
GCTCCCATGGTAAAACTCTTCATACTAGAATTGAACATTCAAATGGTAGGTTTAGCTTTTATGAACAACCAGATGTGGAA
GGACATACTTCTATTGTTGATTTAATTGAACATTCAATCAGGGACTCTGAAAATGGAGCTTTTTGCTATTCTAGGTCTCG
ATTGCCTGGATCTGCAACTTATCCAGTGAGATTGACAAATCCAGTATCTCGGTTTATGCAGGTGCGTTCCTTACAGTACC
TGTGTCGTTTTGTTATACGTCAGTATACCAGAATAGACCTGATCCAGAAACTGCCTTTGCCAAACAAAATGAAGGATTAT
TTACAGGAAAAGCACTACTGAAAGCTTATGGGAATCTTGCATCTTGCACTTTGGGAACAACAA

Alignment

ORF - retro_psin_46 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 50.27 %
• Parental protein coverage: 57.37 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SSFAASLRELEKCGWYWGPMNWEDAEMKLKGKPDGSFLVRDSSDPRYILSLSFRSQGITHHTRMEHYRGT
          .S....L..L...GWYWGP.....AE.KL...PDGSFLVRDSSD.RY.LSLSFRS.G.T.HTR.EH..G.
Retrocopy TSLTEELKKLARQGWYWGPITRWEAEGKLANVPDGSFLVRDSSDDRYLLSLSFRSHGKTLHTRIEHSNGR

Parental  FSLWCHPKFEDRCQSVVEFIKRAIMHSKNGKFLYFLRSRVPGLPPTPVQLLYPVSRFSNVKSLQHLCRFR
          FS....P..E....S.V..I...I..S.NG.F.Y..RSR.PG....PV.L..PVSRF..V.SLQ.LCRF.
Retrocopy FSFYEQPDVEGH-TSIVDLIEHSIRDSENGAFCY-SRSRLPGSATYPVRLTNPVSRFMQVRSLQYLCRFV

Parental  IRQLVRVDHIPELPLPKPLISYIRKFYYYDPQEEVYLSLKEAQ
          IRQ..R.D.I..LPLP.....Y.....Y........L.L.E.Q
Retrocopy IRQYTRIDLIQKLPLPNKMKDYLQEKHY*KLMGILHLALWEQQ

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_46 retrocopy.

TSS

Pelodiscus sinensis was not studied using FANTOM5 data.

Lab

retro_psin_46 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Pelodiscus sinensis	ENSPSIG00000005627	1 retrocopy	retro_psin_46 ,