RetrogeneDB ID: retro_psin_26

Retrocopy location

• Organism: Chinese softshell turtle (Pelodiscus sinensis)
• Coordinates: JH204949.1:32732..33416(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSPSIG00000015992
• Aliases: None
• Description: None

Sequence

>retro_psin_26
CTGGCGAATTTCCTCTCAGAAGACAAGAGCATTTCCTACCTGGGCTTTGTTGCCCAGATGTTCTTCCTGCTCTTCCTTGG
GATCTCCGAGTGCTTCCTTCTGGCTGCCATGGTGTACGACCGCTACGTGGCCATATGCCGCCCACTGAGGTACAGCCTCA
TCATGAACAGGAGGGTCTGCCTGGCCTTGACCGTTCTCTCTGTGTTCTGTGGTAATGTGGTGTCCCTAGTACAGACAGCC
TGGGTTTTCACCTTACCCTTCTCTGGGTCGAACCAGATCAATTATTTCTTCTATGACATTCCCCCGTTGATTAAGCTTTC
TTACATCGACCTCCCTCTGTATGAAATGCAGTTGCTTATGGCTGCAGTGCTGGTGATTTTCATTCCATTTACTCTCATCC
TTGCATCATACACCTGTATTATCTCCACCATCTTAAAGATGGCCTCTGCTGAAGGCCAACAGAAGGCCTTCTCCACCTGC
TCCTCCCACCTCATTGTGGTGATGTTGTACTATGGGAGCTGTAGCCTTATCTATTTAAGACCCAAGTCCATCCACTTAAT
GTCAACAAAGTCCTCTCTCTGATATACACGACCATTACCCCCATCCTGAACCCCCTTCATCTACAGCCTGAGGAACAAGG
AGGCCATAGGGGCTCTGAGGAGGTTGTTGAAAGGCAGGATGAAG

Alignment

ORF - retro_psin_26 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.85 %
• Parental protein coverage: 72.14 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LVNFLSKDRTISYTGCARHGSQLFFKYFFSENKCNVFATLVFFVQSIAKCGPDQGNHIMNRRVCLALTVL
          L.NFLS.D..ISY.G......Q.FF..F.....C...A..V......A.C.P.....IMNRRVCLALTVL
Retrocopy LANFLSEDKSISYLGFV---AQMFFLLFLGISECFLLAAMVYD-RYVAICRPLRYSLIMNRRVCLALTVL

Parental  SWIYGTIVSLVQTIWVFTFPFCGSNQINYFFCDVTPLITLACTDTSLFELQLFTITMLCNFIPFCLILLS
          S...G..VSLVQT.WVFT.PF.GSNQINYFF.D..PLI.L...D..L.E.QL.....L..FIPF.LIL.S
Retrocopy SVFCGNVVSLVQTAWVFTLPFSGSNQINYFFYDIPPLIKLSYIDLPLYEMQLLMAAVLVIFIPFTLILAS

Parental  YIVIISTIFKMASAEGRQKAFSTCSSHLIVVMLYYGASGLIYLRPKSTTSLESNK-VIALLYTTVTPILN
          Y..IISTI.KMASAEG.QKAFSTCSSHLIVVMLYYG...LIYLRPKS...L.S.K.V..L.YTT.TPILN
Retrocopy YTCIISTILKMASAEGQQKAFSTCSSHLIVVMLYYGSCSLIYLRPKS-IHLMSTK<VLSLIYTTITPILN

Parental  PV-IYSLRNKEVKGALWRFFGGGLK
          P..IYSLRNKE..GAL.R...G..K
Retrocopy PL>IYSLRNKEAIGALRRLLKGRMK

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_26 retrocopy.

TSS

Pelodiscus sinensis was not studied using FANTOM5 data.

Lab

retro_psin_26 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	ENSPSIG00000015992	1 retrocopy	retro_psin_26 ,