RetrogeneDB ID: retro_psin_28

Retrocopy location

• Organism: Chinese softshell turtle (Pelodiscus sinensis)
• Coordinates: JH205657.1:1850387..1851161(-)
• Located in intron of: ENSPSIG00000013619

Retrocopy information

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

Parental gene information

• Parental gene symbol: SKP2
• Ensembl ID: ENSPSIG00000008375
• Aliases: None
• Description: S-phase kinase-associated protein 2, E3 ubiquitin protein ligase [Source:HGNC Symbol;Acc:10901]

Sequence

>retro_psin_28
CCTAAACAATGGTATTGGAAACCATTGTTTAAAAGCAACCAACCTCTTAGAGTGCAACATATGGATCTGTCCAACTGCAC
AGTAAATGTTGTAGATCTCCATAATATTCTTTGTCGTTGTGATCGACTACAGAATCTCAGCTTGGAAGGGCTGGTGCTTT
CTGATGATATCATTAGGTGTATTGCTCAGAACTCCAGGTTGGTACGATTAAATATCTCTGGATGTTCTAGATTTTCTGCA
GAAGCACTAGAGATGATGTTGATCAGCTGTTCTGGATTGGAAGAATTGAACTTATCCTGGTGTGACTTCACAGCTGATCA
TATTAAAGCAGCAGTCAGTCACATTTCTACAAATATAATCCAACTATGTTTTAGTGGATATCGACAAAATCTGCAGATAT
CAGATATTAAATCATTGGTTACAAGATGCCCATATCTCATCCACTTAGATTTAAGAGACAATGCAATGTTGAAGCCTGAA
TGTTTTCAATTTTTTCGTCAGCTTATCTGCCTACAGCATCTGTCTCTTAGCAGATGTTATCAGATATCTCCTGCTGATTT
ACTTGAACTTGGTGAAATTCCCACACTAAGGACTCTTCAAGCTTTTTGAATAGTGACTGACAGTTCCCTACAGCTCCTAA
AGGAAACACTTCCCCACATAAAAATCAATTGTTCGCATTTTTCAACCACTGCACGGCCAACTGTTGGCAGCAAAAAGAAC
CAAGAGATCTGGGGTATCAAATGCAGACTGATACTGAGAAATCCTAGAGATTTG

Alignment

ORF - retro_psin_28 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.47 %
• Parental protein coverage: 61.58 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PRSCIGKPLFKNNRPLRVQHMDLSNCTVNVADLHNILCHCDRLQNLSLEGLVLSDDIIRSIAQNSSLVRL
          P.....KPLFK.N.PLRVQHMDLSNCTVNV.DLHNILC.CDRLQNLSLEGLVLSDDIIR.IAQNS.LVRL
Retrocopy PKQWYWKPLFKSNQPLRVQHMDLSNCTVNVVDLHNILCRCDRLQNLSLEGLVLSDDIIRCIAQNSRLVRL

Parental  NISGCSRFSAEALEMMLISCSGLEEFNLSWCDFTADHIKAAVSHISTNITQLNFSGYRQNLQISDIKSLV
          NISGCSRFSAEALEMMLISCSGLEE.NLSWCDFTADHIKAAVSHISTNI.QL.FSGYRQNLQISDIKSLV
Retrocopy NISGCSRFSAEALEMMLISCSGLEELNLSWCDFTADHIKAAVSHISTNIIQLCFSGYRQNLQISDIKSLV

Parental  TRCPYLIHLDLSDSAMLKPECFQYFRQLICLQHLSLSRCYQISPADLLELGEIPTLRTLQAFGIVTDSSL
          TRCPYLIHLDL.D.AMLKPECFQ.FRQLICLQHLSLSRCYQISPADLLELGEIPTLRTLQAF.IVTDSSL
Retrocopy TRCPYLIHLDLRDNAMLKPECFQFFRQLICLQHLSLSRCYQISPADLLELGEIPTLRTLQAF*IVTDSSL

Parental  QLLKETLPHIKINCSHFTTIARPTVGSKKNQEIWGIKCRLTLRNPSDL
          QLLKETLPHIKINCSHF.T.ARPTVGSKKNQEIWGIKCRL.LRNP.DL
Retrocopy QLLKETLPHIKINCSHFSTTARPTVGSKKNQEIWGIKCRLILRNPRDL

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_28 retrocopy.

TSS

Pelodiscus sinensis was not studied using FANTOM5 data.

Lab

retro_psin_28 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 9 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000013562	4 retrocopies	retro_btau_1108, retro_btau_1612, retro_btau_525, retro_btau_555,
Choloepus hoffmanni	ENSCHOG00000006980	1 retrocopy	retro_chof_1604,
Callithrix jacchus	ENSCJAG00000018275	1 retrocopy	retro_cjac_2367,
Cavia porcellus	ENSCPOG00000013303	1 retrocopy	retro_cpor_1166,
Nomascus leucogenys	ENSNLEG00000016025	1 retrocopy	retro_nleu_2553,
Oryctolagus cuniculus	ENSOCUG00000009154	1 retrocopy	retro_ocun_158,
Pelodiscus sinensis	ENSPSIG00000008375	1 retrocopy	retro_psin_28 ,
Rattus norvegicus	ENSRNOG00000016823	1 retrocopy	retro_rnor_621,
Tupaia belangeri	ENSTBEG00000016814	1 retrocopy	retro_tbel_4354,