RetrogeneDB ID: retro_psin_20

Retrocopy location

• Organism: Chinese softshell turtle (Pelodiscus sinensis)
• Coordinates: JH208001.1:1922..4085(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPSIG00000001610
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSPSIG00000004688
• Aliases: None
• Description: None

Sequence

>retro_psin_20
AAATGTACCGATTGTGGGAAGAGCTTCAGCGTCAGCTCCAACCTCTTCCGGCACCAGCGCATCCACACTGGGGAGAAACC
CTACACATGCTCTGACTGCGGGAAGAGCTTCACAGACAAGTCCACCTTGACCCAGCACCAGCGCATCCACACGGGCGAGC
GGCCCAACACCTGCTCCGAGTGCGGCAAGAGCTTCACGCAGAGCTCCCACCTGATCCAGCACCAGCGCACCCACACCGGC
GAGAAGCCCTACCAGTGCGGGGAGTGCGGCAAGGCCTTCAGCCAGAGCACCAACCTCATCAAGCACCAGCGCTCCCACAC
CGGCGAGAAGCCCTACCAGTGCGGGGAGTGCGGCAAGGCCTTCAGCCAGAGCACCAACCTCATCAAGCACCAGCGCTCCC
ACACCGGCGAGAAGCCCTACCAGTGCGGGGAGTGCGGCAAGGCCTTCAGCCAGAGCACCAACCTCATCAAGCACCAGCGC
TCCCACACCGGCGAGAAGCCCTACCAGTGCGGGGAGTGCGGCAAGGCCTTCAGCCAGAGCACCAACCTCATCAAGCACCA
GCGCTCCCACACCGGCGAGAAGCCCTACCAGTGCGGGGAGTGCGGCAAGGCCTTCAGCCAGAGCACCAACCTCATCAAGC
ACCAGCGCTCCCACACCGGCGAGAAGCCCTACCAGTGCGGGGAGTGCGGCAAGGCCTTCAGCCAGAGCACCAACCTCATC
AAGCACCAGCGCTCCCACACCGGCGAGAAGCCCTACCAGTGCGGGGAGTGCGGCAAGGCCTTCAGCCAGAGCACCAACCT
CATCAAGCACCAGCGCTCCCACACCGGCGAGAAGCCCTACCAGTGCGGGGAGTGCGGCAAGGCCTTCAGCCAGAGCACCA
ACCTCATCAAGCACCAGCGCTCCCACACCGGCGAGAAGCCCTACCAGTGCGGGGAGTGCGGCAAGGCCTTCAGCCAGAGC
ACCAACCTCATCAAGCACCAGCGCTCCCACACCGGCGAGAAGCCCTACCAGTGCGGGGACTGCAAGAAGAGCTTCTACCG
CAGCTCCGACCTCATCCAGCACCAGATCACTCACACGGGCGAGCGCCCCTTCAAGTGCGCCCAGTGCGGCAAAGGCTTCA
CCCAGAGCGCCAACCTGGTGAAGCACCAGAAGATCCACGCCGGGGAGAAGCCCTTCCGCTGCACCGAGTGCGGGAAGACC
TTCATCCAGAGCACCAACCTCATCAAGCACCAGCGCTCCCACACCGGCGAGAAGCCCTACCAGTGCGGGGACTGCAAGAA
GAGCTTCTACCGCAGCTCCGACCTCATCCAGCACCAGATCACTCACACGGGCGAGCGCCCCTTCAAGTGCGCCCAGTGCG
GCAAAGGCTTCACCCAGAGCGCCAACCTGGTGAAGCACCAGAAGATCCACGCCGGGGAGAAGCCCTTCCGCTGCACCGAG
TGCGGGAAGACCTTCATCCAGAGCTCGGAGCTCATCCAGCACCAGCGCACCCACACCGGCGAGAAGCCCTACGAATGCCT
GCAGTGCGGGAAGAGCTTCGGGCACAGCGCCACGCTGGCCAAGCACGGCAGGATCCACACGGGGGAGCGGCCCTACCCGT
GCGAGGAGTGCGGGAAGAGCTTCTCGGAGAGCGCCAAGCTCCTGGAGCACCAGAGGATCCACACGGGCTTGAAACCCTAC
AAGTGCCCGAGCTGCGGGAAAGCCTTCTGCCACAGCTCCTCGCTGGCCAACCACCAGCGGGGGCACACGGGCGAGCGGCC
CTACACGTGCGCCCACTGCGGAAAGGGCTTCAGCCAGAGCTCCACCCACACCCAGCGCCTGAGAACCCACACCGGCGAGC
GGCCCTACACGTGCGCCCACTGCGGAAAGGGCTTCAGCCAGAGCTCCACCCACACCCAGCGCCTGAGAACCCACACCGGC
GAGCGGCCCTACACGTGCGCCCACTGCGGAAAGGGCTTCAGCCAGAGCTCCACCCACACCCAGCACCTGAGAACCCACAC
CGGCGAGCGGCCCTACCAGTGCGGGGAGTGCGGGAAGAGCTTCAGCGTGAGCTCCAGCCTGGTGGTCCACCAGAGGAGCC
ACACGGGAGAGAGACCCTACCAGTGTCCCGACTGCGGGAAGAGCTTTAGTGGCTGGCCAAATTTTAGCCGGCATCTGCGG
ACC

Alignment

ORF - retro_psin_20 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 53.8 %
• Parental protein coverage: 61.53 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RCIDCGKSYVQKSSLRVHQRTHTGERPHHCTDCGKSFTDKRSLKVHQRLHTGEWPHHCPHCDKGFSQISQ
          .C.DCGKS....S.L..HQR.HTGE.P..C.DCGKSFTDK..L..HQR.HTGE.P..C..C.K.F.Q.S.
Retrocopy KCTDCGKSFSVSSNLFRHQRIHTGEKPYTCSDCGKSFTDKSTLTQHQRIHTGERPNTCSECGKSFTQSSH

Parental  LREHQCMHTGERPHHCTDCGKSFAHSSSLRLHQHAHTGERPHHCTDCGKSFAHNRSLRLHQRVHTGEWLH
          L..HQ..HTGE.P..C..CGK.F..S..L..HQ..HTGE.P..C..CGK.F.....L..HQR.HTGE...
Retrocopy LIQHQRTHTGEKPYQCGECGKAFSQSTNLIKHQRSHTGEKPYQCGECGKAFSQSTNLIKHQRSHTGEKPY

Parental  NCTDCGKSFRDASSLRVHQRVHTGERPHHCTDCSKSFRDASSLRVHQRVHTGERPHQCSDCGKSFRDASS
          .C..CGK.F.....L..HQR.HTGE.P..C..C.K.F.....L..HQR.HTGE.P.QC..CGK.F.....
Retrocopy QCGECGKAFSQSTNLIKHQRSHTGEKPYQCGECGKAFSQSTNLIKHQRSHTGEKPYQCGECGKAFSQSTN

Parental  LRVHQRVHTGERPHHCTDCGKSFVCRSSLRVHQRTHTGERPHHCAHCNKSFTQSSSLRTHQRMHTGERPY
          L..HQR.HTGE.P..C..CGK.F.....L..HQR.HTGE.P..C..C.K.F.QS..L..HQR.HTGE.PY
Retrocopy LIKHQRSHTGEKPYQCGECGKAFSQSTNLIKHQRSHTGEKPYQCGECGKAFSQSTNLIKHQRSHTGEKPY

Parental  QCTDCGKSFADSSKLRIHQRTHTGERPYHCADCGKTFVQTAHLRSHQRTHTGERPYHCADCGKTFVQTAH
          QC..CGK.F..S..L..HQR.HTGE.PY.C..CGK.F.Q...L..HQR.HTGE.PY.C.DC.K.F.....
Retrocopy QCGECGKAFSQSTNLIKHQRSHTGEKPYQCGECGKAFSQSTNLIKHQRSHTGEKPYQCGDCKKSFYRSSD

Parental  LRSHQRTHTGERPYRCAVCGKDFADSSSLRVHQRTHTGERPYLCTDCGKSFVHLSHLRMHQLGHTGERPY
          L..HQ.THTGERP..CA.CGK.F..S..L..HQ..H.GE.P..CT.CGK.F.....L..HQ..HTGE.PY
Retrocopy LIQHQITHTGERPFKCAQCGKGFTQSANLVKHQKIHAGEKPFRCTECGKTFIQSTNLIKHQRSHTGEKPY

Parental  HCGDCGKSFIHASMLSNHQHTHTGERPHHCADCGKGFAHKSSLRAHQRVHTGEWPHHCADCGKGFAQISQ
          .CGDC.KSF...S.L..HQ.THTGERP..CA.CGKGF.....L..HQ..H.GE.P..C..CGK.F.Q.S.
Retrocopy QCGDCKKSFYRSSDLIQHQITHTGERPFKCAQCGKGFTQSANLVKHQKIHAGEKPFRCTECGKTFIQSSE

Parental  LRMHQRTHTGERPYCCTKCSKSFAHRASLRVHQCARIGERPHRCDDCGKSFSQAHMLTHHQRTHTGEQLY
          L..HQRTHTGE.PY.C..C.KSF.H.A.L..H.....GERP..C..CGKSFS....L..HQR.HTG...Y
Retrocopy LIQHQRTHTGEKPYECLQCGKSFGHSATLAKHGRIHTGERPYPCEECGKSFSESAKLLEHQRIHTGLKPY

Parental  RCADCGKTFRNANKLTQHQCTLSEEQAHHCADCGKGFSLISYLRAHQCMHTGEWPHHCAHCGKGFAQISQ
          .C..CGK.F.....L..HQ.....E....CA.CGKGFS..S........HTGE.P..CAHCGKGF.Q.S.
Retrocopy KCPSCGKAFCHSSSLANHQRGHTGERPYTCAHCGKGFSQSSTHTQRLRTHTGERPYTCAHCGKGFSQSST

Parental  LRVHQRTHTGERPHQCTVCSKSFAHRSSLRVHQRTHTGERPHHCTDCGKNFTDTSSLRVHQRVHTGERPH
          .....RTHTGERP..C..C.K.F...S....H.RTHTGERP..C..CGK.F...SSL.VHQR.HTGERP.
Retrocopy HTQRLRTHTGERPYTCAHCGKGFSQSSTHTQHLRTHTGERPYQCGECGKSFSVSSSLVVHQRSHTGERPY

Parental  QCTDCSKNFA
          QC.DC.K.F.
Retrocopy QCPDCGKSFS

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_20 retrocopy.

TSS

Pelodiscus sinensis was not studied using FANTOM5 data.

Lab

retro_psin_20 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
Equus caballus	ENSECAG00000023794	1 retrocopy	retro_ecab_61,
Macaca mulatta	ENSMMUG00000003688	1 retrocopy	retro_mmul_44,
Otolemur garnettii	ENSOGAG00000005643	1 retrocopy	retro_ogar_19,
Otolemur garnettii	ENSOGAG00000029638	2 retrocopies	retro_ogar_105, retro_ogar_193,
Pelodiscus sinensis	ENSPSIG00000004688	1 retrocopy	retro_psin_20 ,
Pelodiscus sinensis	ENSPSIG00000008115	1 retrocopy	retro_psin_11,