RetrogeneDB ID: retro_psin_11

Retrocopy location

• Organism: Chinese softshell turtle (Pelodiscus sinensis)
• Coordinates: JH208860.1:126093..128655(-)
• Located in intron of: ENSPSIG00000016083

Retrocopy information

• Ensembl ID: ENSPSIG00000001366
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSPSIG00000008115
• Aliases: None
• Description: None

Sequence

>retro_psin_11
ATGGAACCGCCGGAGACGTTCTCGGGAAGAGCCGGAGGGAGTTTTCCCCCGGGCGTGGCAGCGGGAAATTCCCAAGGAGA
GCGACACGGGGCAGAGAGGGAGAAGACACCGGATGGGTCCGTTCCACGTGGAGGAAGATCGGAGGATGCCGCGGGGCCGG
CTCGCCCCAAGGAGGAGAAACCGTACCAGTGCCCCGAGTGTGGGAAAAGCTTCCGTTTCTTTGCCCACCTTCACGCTCAC
TGGAGAGTCCACACGGGCGAGAAGCCCTATCGGTGTTTGCGGTGCGCGAAAGTTTTCAGCCAGCGCTCCGCCCTCGTGCG
GCACGAGAGGACCCACACGGGAGAGAAACCCCACGCGTGCGGGGAGTGCGGGAAATGCTTCACCAGGAAGCTGAGTCTGG
TGGCGCACCGGCGCGTGCACACTGGCGAGAAACCCTACGCCTGCTGGCAGTGCGCAAAGCTGTTCAGCGAGCATTCGGCC
CTCGTGAGGCACGAGAGAACGCACTCAGGAGAGAAACCCCACACCTGCCCGGAGTGCGGGAAAACGTTCGCTCAGAACGC
GTACCTCCTGAAACACAGGAGAATTCACTCCGGCGACAACCCTTACCAATGCCTGCAGTGCGGGAAAAGTTTTGTGGACA
GAACAAATCTCACTCGACATCAGCGAGTTCACACAGGCGAGAGACCCCATAAATGCTCGGCGTGCGGGAAAAGTTTCATC
CAGATATCCCACCTTATTATACACCGGAGACTTCACACCGGCGAGCGGCCTTATAAATGCCAGGAGTGTGGGAAAAGTTT
CATTCACCGCTCCCACCTTATTAAGCATCAGACGGTCCACAGGGGCGGCAGCCCCTATCCATGCCCCGAGTGTGGGAAAA
ATTTCACGGACCGATCCAATCTTACTCGACACCAGAGGATCCACACTGGGACCCGACTCCATAAATGCGTGGACTGTGGG
AAAAGTTTCTTTGAGAAGTCGCAACTTATTCTACACCAGCGGGTGCACACGGGAGAGAGGCCCTTTCAGTGCCAGGCGTG
CGGGAAACGCTTCATTCAGGAATCGCAGCTGGTTACGCACCAGCGAAACCACACCGGAGAGAGACCTTATGTCTGCCGGG
AGTGCGGGAAAAGTTTTATGGAAAGTTCGTCCCTCGCTCAGCATGGGCGAATCCACACGGGAGAAAGACCCTATAAATGC
CGGGAGTGCGGGAAAAGTTTCCTTCGTCACTCCCACGTGGAAAAGCACCAACGCATCCACACGGGCGACAAACCGTACAA
ATGCCTCCAGTGCGGGAAAAGTTTCATTGACGGGTCAAATTTAACGCGACATCAGAGGATCCACACGGGCGTGCGACCCC
ATCAATGCCCGGAGTGCGGGAAGAGCTTCATTCAGAAGTCAAAATTTATTCTACACCAGAGAGTGCACACGGGAGAGAGA
CCTTTTCAATGCCGGGAGTGCGAGAAAAGTTTTATTCAGGAATCACAGCTCGTCGCGCATCGGCGAACCCACACGGGAGA
GAGACCGTTTACGTGCCTGGAGTGTGGGAAAAGTTTTATGAAAAGTTCAGTCCTTATTCAGCACAGGAGAATTCACACCG
GACTAAAACCCTATACGTGCCCGGAGTGTGGGAAAAGTTTTCTAGAAAACTCATCCCTTACTAAACACAGGAGAATTCAC
ACGGGAGAAAGACCCTATACATGCGCTGAGTGTGGGAAAAGTTTTATGCAAAGTTCGTCCCTTACTAAACACAGGAGAAG
CCATGCTGCCGGCAACCCCTATAAATGCCTTGTGTGCGGGAAAGATTTCTTTGACAGAGCAAATCTGACGAGTCATCAGA
TAATCCACACAGGAGTGAGGCCCTATGAATGCGTGGAGTGTGGGAAAAGCTTCATTCAGAAGTCACAATTTATTATCCAC
CAGCGGGTGCACACGGGAGAGAGACCCTTTCAGTGCCGGGAGTGTGGGCAAAGTTTTATTCAGGAATCGCAATTTGTGAC
GCATCAGCGAACTCACACGGGGGAGAGACCCCATACGTGCCTCCAGTGTGGGAAAAGTTTTAGGAAGAGTTCGGCCCTTG
CTAAACACGGGCGAATCCACACCGGAGAGCGTCCTTACCAATGCCTGGAGTGCGGGAAAAGTTTTAGGCACAGTTCGTAC
CTCACTAAACACGGGCGAATCCACACCGGAGAGAAACCTTACCCATGCCTGGAGTGTGGGAAAAGTTTCAGTTTGAAATC
AAACCTGAATACACACCAGAAAACCCACACGGGAGAGAAACCCCACGCCTGCCCGGACTGCGGGAAATCTTTCATTCAGC
ACTCCCAGCTGATTAAGCACCGGCGAATCCACACGGGAGAGACCCCGTTTGAGTGCCCGGCCTGTGGGAAAACTTTCCGC
CAGTGTTCGCACCTTACTAAACACAGGAAAATCCACACGGGAGACTGTGGGAAGCGCTTCGAGCTGGGAGCTCACCAAAC
ATTGGACAATCCACAGAGGGGAGGGACCCCAGGAACAGCTGGGCCGCAGGAAAAGGATCGATTCGACTTCACACATCCGT
AA

Alignment

ORF - retro_psin_11 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 53.7 %
• Parental protein coverage: 65.97 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EKACNCLVCGKSFTRRSTLIAHQRIHTGERPFPCAECGKSFRVSSSLSEHQKVHRGERPYKCHHCGKSFY
          EK...C..CGKSF.....L.AH.R.HTGE.P..C..C.K.F...S.L..H...H.GE.P..C..CGK.F.
Retrocopy EKPYQCPECGKSFRFFAHLHAHWRVHTGEKPYRCLRCAKVFSQRSALVRHERTHTGEKPHACGECGKCFT

Parental  NNSALLVHQRAHTGERPYTCSVCGKSFYNNSALSIHQRTHTDERPYTCNDCGKSFRSSSHLLSHKRLHSA
          ....L..H.R.HTGE.PY.C..C.K.F...SAL..H.RTH..E.P.TC..CGK.F.....LL.H.R.HS.
Retrocopy RKLSLVAHRRVHTGEKPYACWQCAKLFSEHSALVRHERTHSGEKPHTCPECGKTFAQNAYLLKHRRIHSG

Parental  EKPYKCTDCGKDFRRSSNLSTHKKTHRKEKPFKCSDCGKGFKRNSDLVTHKKIHTGEKPFICSDCGKSFI
          ..PY.C..CGK.F....NL..H...H..E.P.KCS.CGK.F...S.L..H...HTGE.P..C..CGKSFI
Retrocopy DNPYQCLQCGKSFVDRTNLTRHQRVHTGERPHKCSACGKSFIQISHLIIHRRLHTGERPYKCQECGKSFI

Parental  QRSYLLRHRRTHTGEKPFSCSDCGKSFIQRSYLLRHRRTHTGEKPFSCSDCRKTFSQRSYLLRHRKTHTG
          .RS.L..H...H.G..P..C..CGK.F..RS.L.RH.R.HTG.....C.DC.K.F...S.L..H...HTG
Retrocopy HRSHLIKHQTVHRGGSPYPCPECGKNFTDRSNLTRHQRIHTGTRLHKCVDCGKSFFEKSQLILHQRVHTG

Parental  EKPFSCFECGKTFSRSSHLVTHRRTHTGEKPFRCSDCGKSFNQSSDLVTHRRTHTGEKPFRCSDCGKSFR
          E.PF.C..CGK.F...S.LVTH.R.HTGE.P..C..CGKSF..SS.L..H.R.HTGE.P..C..CGKSF.
Retrocopy ERPFQCQACGKRFIQESQLVTHQRNHTGERPYVCRECGKSFMESSSLAQHGRIHTGERPYKCRECGKSFL

Parental  QSSELVRHRRIHTGEKPFSCSECGKNFKQSSELVTHRRIHTGERPFSCSDCGKSFKQSSELVTHRRTHTG
          ..S....H.RIHTG.KP..C..CGK.F...S.L..H.RIHTG.RP..C..CGKSF.Q.S....H.R.HTG
Retrocopy RHSHVEKHQRIHTGDKPYKCLQCGKSFIDGSNLTRHQRIHTGVRPHQCPECGKSFIQKSKFILHQRVHTG

Parental  EKPFNCSECGKTFRQSSELVAHRRTHTGERPFSCSDCGKSFSRRSVLVIHKRSHTGEKPFSCCDCGKSFS
          E.PF.C.EC.K.F.Q.S.LVAHRRTHTGERPF.C..CGKSF...SVL..H.R.HTG.KP..C..CGKSF.
Retrocopy ERPFQCRECEKSFIQESQLVAHRRTHTGERPFTCLECGKSFMKSSVLIQHRRIHTGLKPYTCPECGKSFL

Parental  RRSVLVIHKRTHTGEKPFSCSDCGKSYSERSSLIVHQRTHTGEKLYNCSECGKSFNKRSVLVLHGRIHTG
          ..S.L..H.R.HTGE.P..C..CGKS....SSL..H.R.H.....Y.C..CGK.F..R..L..H..IHTG
Retrocopy ENSSLTKHRRIHTGERPYTCAECGKSFMQSSSLTKHRRSHAAGNPYKCLVCGKDFFDRANLTSHQIIHTG

Parental  ERPFNCSDCGKSFSKLSHFVRHQRTHTGEKPFTCSDCGKCFKQRSSEFIPHSRMHTGEKPFSCSECGKRF
          .RP..C..CGKSF...S.F..HQR.HTGE.PF.C..CG..F.Q..S.F..H.R.HTGE.P..C..CGK.F
Retrocopy VRPYECVECGKSFIQKSQFIIHQRVHTGERPFQCRECGQSFIQ-ESQFVTHQRTHTGERPHTCLQCGKSF

Parental  STSSNLVSHKRIHTGEKPFCCSDCGKSFSTSSNLVSHKRIHTGEKPFCCSDCGKSFSTSSHLVIHRRTHT
          ..SS.L..H.RIHTGE.P..C..CGKSF..SS.L..H.RIHTGEKP..C..CGKSFS..S.L..H..THT
Retrocopy RKSSALAKHGRIHTGERPYQCLECGKSFRHSSYLTKHGRIHTGEKPYPCLECGKSFSLKSNLNTHQKTHT

Parental  GEKPFKCCDCGKNFRQSSEFVRHRRIHTGARPFSCSDCGKSFRQSSDLTRHRWTHT
          GEKP..C.DCGK.F.Q.S....HRRIHTG..PF.C..CGK.FRQ.S.LT.HR..HT
Retrocopy GEKPHACPDCGKSFIQHSQLIKHRRIHTGETPFECPACGKTFRQCSHLTKHRKIHT

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_11 retrocopy.

TSS

Pelodiscus sinensis was not studied using FANTOM5 data.

Lab

retro_psin_11 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 ,