RetrogeneDB ID: retro_psin_40

Retrocopy location

• Organism: Chinese softshell turtle (Pelodiscus sinensis)
• Coordinates: JH207148.1:301852..302779(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSPSIG00000006205
• Aliases: None
• Description: None

Sequence

>retro_psin_40
ACCATAGAAATGACCTGGTCAAACTGCACCGAAGCCACAGAGTTCATTTTCTCGGGATTCACAGATCGCCCGGAGCTCCA
GATCGCCCTCTTTGTGCTGTTCCTTGTGGTCTATGCTGTGACACTGCTGGGGAATCTTGGGATGATCCTGCTAATCAGGC
TGGCTGCCCAGCTGCAGACTCCTATGTACTTTTTCCTGAGTACTTTGGCTTTTGTGGATTTCTGGTACTCCACATTTATC
ACTCCCAAGTTTTTAGCTGACCTGCTAGCAGAAAGGAAAGTCATCTCTTATGCCGCCTGTGTGTGCCAATACTGCTTTGT
CAGCTTCTTTGGGGTGACAGAGTCTTTCCTTCTGACTGTGATGGCGTACGACCGTTACGTGGCCATCTGTAACCCCCTGC
TTTATACTGCTGTCATGTCCCCCAGATTCTGTGTCCAGCTGGTCGCTGGGTCCTTCCTCGCTGGGTTTATAAATGGAATG
ATCCAAACCATCACCACATTAAAATTATCCTTCTGTGGTCCCAATGTCATTGACCTGTTCTTCTGTGACATCTCCCCACT
GTTGTCCCTCTCCTGTTCCAACACCAGCGTCTACCACGTGATCCTCTTGGCTGTGGCTTGTGTGGCTGGGATCTTCACCA
GCCTGACCATCCTCATCTCCTACGTGTTGATCTTCTCCAACATCCTAAAGATCCGCTCCGCCGAGGGAAAGCGCAAAGGG
TTCAACACCTGCACCTCCCATGTGACCGTCGTCACCATCTTCTATGGCCCAGCTCTGTTTATCTATATGCAGCCCAGCAC
CCAGCATTCGCGGGACCAGGACAAAGTGGTCTCCGTGTTCTACACCATGGTCACCCCCATGTTGAACCCCTTAATCTACA
GCCTGAGGAACAAAGAGGTGAAGAACGCTGTGAAAAGGGTCATAGAA

Alignment

ORF - retro_psin_40 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.19 %
• Parental protein coverage: 97.17 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TLEMAGGNCTQVSEFMLTGFSDSPEIQAPLFVVFLLIYVTALVGNLGMILIVRLDSQLRTPMYFFLSNLS
          T.EM...NCT...EF...GF.D.PE.Q..LFV.FL..Y...L.GNLGMIL..RL..QL.TPMYFFLS.L.
Retrocopy TIEMTWSNCTEATEFIFSGFTDRPELQIALFVLFLVVYAVTLLGNLGMILLIRLAAQLQTPMYFFLSTLA

Parental  FIDLCYSTVVAPKMLADLLAERKAISYTACAIQICVFSQFDVMECFLLAAMAYDRYVAICHPLLYRVVMC
          F.D..YST...PK.LADLLAERK.ISY.AC..Q.C..S.F.V.E.FLL..MAYDRYVAIC.PLLY..VM.
Retrocopy FVDFWYSTFITPKFLADLLAERKVISYAACVCQYCFVSFFGVTESFLLTVMAYDRYVAICNPLLYTAVMS

Parental  PRLCVQLVAGSFLVGCVNVIAQTTGMLTLTFCGSNVIDLFFCDISPLLSLASSDSRVNHILLLVLASLTG
          PR.CVQLVAGSFL.G..N...QT...L.L.FCG.NVIDLFFCDISPLLSL..S...V.H..LL..A...G
Retrocopy PRFCVQLVAGSFLAGFINGMIQTITTLKLSFCGPNVIDLFFCDISPLLSLSCSNTSVYHVILLAVACVAG

Parental  VFTGLVISVVLHRNMCIFVYILEQPGRKPGFTSCVSWLIVTECFLLTGLFIYLQPSTKYSRDQDKVVSVF
          .FT.L.I.............I....G...GF..C.S...V...F....LFIY.QPST..SRDQDKVVSVF
Retrocopy IFTSLTILISYVLIFSNILKIRSAEGKRKGFNTCTSHVTVVTIFYGPALFIYMQPSTQHSRDQDKVVSVF

Parental  YTVVTPMLNPLIYSLRNKEVKAALRRAIE
          YT.VTPMLNPLIYSLRNKEVK.A..R.IE
Retrocopy YTMVTPMLNPLIYSLRNKEVKNAVKRVIE

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_40 retrocopy.

TSS

Pelodiscus sinensis was not studied using FANTOM5 data.

Lab

retro_psin_40 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Nomascus leucogenys	ENSNLEG00000012541	1 retrocopy	retro_nleu_2581,
Pelodiscus sinensis	ENSPSIG00000006205	1 retrocopy	retro_psin_40 ,