RetrogeneDB ID: retro_psin_10

Retrocopy location

• Organism: Chinese softshell turtle (Pelodiscus sinensis)
• Coordinates: JH210322.1:435719..436511(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPSIG00000001288
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSPSIG00000013998
• Aliases: None
• Description: None

Sequence

>retro_psin_10
GGCAAAAGGCAGCCCTCCTTGGGCAAGGCCGCCTGCATCCTCACCGGAGCATCTCGGGGCTTCGGCCGCAGCTTAGCCCT
GTTGCTGGCTCCGCGGTTGAAGGCTGGCTCCGTCCTGATCCTGGTGGCCCGATCGCAGGGGGGGTTGGCAGAGCTGAAGG
ATGAGATGCGGTGCAGTTTCCCCGACTTGAAAGTGAGTTCAGTGCAGGCCGACCTGAGCACGGAGGACGGACTACAGCCG
GTGCTCCGAGCAGTCCAGGACAAGCTGCCGGCAGCGGCTGATCTGGAGCGGCTCATCATCATCAACAACGCAGGATCACT
CGGAGATATTTCCAAAGCTTTTGTGGACTTCACCAGCCCAGCTGAAGTCAACAGCTACTTTGCCTTCAATGTCACCTCGG
CGCTGTGCCTCACATCCTCCATCCTGAAGGCCTTCTCAGGGCGCCCTGGCTTGTGCAAGACTGTTGTAAACATCTCTTCA
CTGTGTGCCCTCAAGCCCTTCAAGAGCTGGACGTTGTACTGCACCGGGAAGGCCTCACGGGACATGATGTTCCAGGTCCT
GGCACTTGAACAGCCTGAGGTGAGAGTCCTCAGTTATGCCCCCGGTCCTCTGGACACAGACATGCAGCAGCTGGCTCGCA
CGTCATCAGGAGACCCAGAACTGCGCCAGCACTTCCGCAACATGAAGGAGCGTGGCCAGCTGCTGGACTGCAGCGTGTCA
GCCCAAAAGCTAGTGCGTCTTCTGCTGGAGGACACCTTCGCCTCTGGGGCACATATAGACTTCTATGAAATC

Alignment

ORF - retro_psin_10 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.61 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QRQPSLGKAACIITGASRGFGRSLALLLAPQLEAGSILFLVARSRGALAELEAKLQCSFPGLTVNSVPAD
          .RQPSLGKAACI.TGASRGFGRSLALLLAP.L.AGS.L.LVARS.G.LAEL.....CSFP.L.V.SV.AD
Retrocopy KRQPSLGKAACILTGASRGFGRSLALLLAPRLKAGSVLILVARSQGGLAELKDEMRCSFPDLKVSSVQAD

Parental  LGTEDGVQLVLQVVLHKLLGAADLQRLLIINNAGSLGDISKSFVDFTSAAEVNSYFAFNVTSALCLTSSI
          L.TEDG.Q.VL..V..KL..AADL.RL.IINNAGSLGDISK.FVDFTS.AEVNSYFAFNVTSALCLTSSI
Retrocopy LSTEDGLQPVLRAVQDKLPAAADLERLIIINNAGSLGDISKAFVDFTSPAEVNSYFAFNVTSALCLTSSI

Parental  LKAFPGQPGLCKTVVNVSSLCALKPFKSWTLYCTGKASRDMMFQVLALEEPGVRVINYAPGPLDTEMQQL
          LKAF.G.PGLCKTVVN.SSLCALKPFKSWTLYCTGKASRDMMFQVLALE.P.VRV..YAPGPLDT.MQQL
Retrocopy LKAFSGRPGLCKTVVNISSLCALKPFKSWTLYCTGKASRDMMFQVLALEQPEVRVLSYAPGPLDTDMQQL

Parental  ARTKSGDPEIRQQFLNMKNSGQLVDCSLSAQKLVSLLLEDMFDSGAHVDFYAI
          ART.SGDPE.RQ.F.NMK..GQL.DCS.SAQKLV.LLLED.F.SGAH.DFY.I
Retrocopy ARTSSGDPELRQHFRNMKERGQLLDCSVSAQKLVRLLLEDTFASGAHIDFYEI

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_10 retrocopy.

TSS

Pelodiscus sinensis was not studied using FANTOM5 data.

Lab

retro_psin_10 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Otolemur garnettii	ENSOGAG00000012959	1 retrocopy	retro_ogar_2301,
Pelodiscus sinensis	ENSPSIG00000013998	1 retrocopy	retro_psin_10 ,
Pteropus vampyrus	ENSPVAG00000016383	1 retrocopy	retro_pvam_802,
Sus scrofa	ENSSSCG00000008309	1 retrocopy	retro_sscr_410,