RetrogeneDB ID: retro_psin_51

Retrocopy location

• Organism: Chinese softshell turtle (Pelodiscus sinensis)
• Coordinates: JH209032.1:4455479..4456133(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DDX49
• Ensembl ID: ENSPSIG00000008625
• Aliases: None
• Description: DEAD (Asp-Glu-Ala-Asp) box polypeptide 49 [Source:HGNC Symbol;Acc:18684]

Sequence

>retro_psin_51
CATCTTATTGTTGCCACACCCAGCAGGTTGGGTGATCATCTCTGAAGTTCCAGCACTTTCAGCCTCAGAAAGTTCAAGTT
TTTGGTTTTGGACAAAGCTGACCGGCTGCTGAAGCTGGACTGTATTGACTTCACCAAGGTTCTGGAGGTGATTCTGGGGG
CTGTTCCAGCGACCAAGCAGATGCTGCTCTTTAGTGTCAGGCTGAATGAGCTGAAAAGGCTCACCATGAACAAACCCTTC
TTCTGGGAGTCTCAGGCTGAGGTATGGATGGTGGATGAGATGGTTCAGCACTACCTGCTTGTGCTGGAGAAAGTCAAGGA
TGTCTGCCTCATCTGTCTAATTCAGACCTTTCAGGATGAAGAAGAGGACTGATCCATCATCATGTTCACCAGCACCTGCA
AGAACTGACAGATCTTGAACATGATGCTGAAGAAGTTCAACTTCCCGTCAGTGGCTTTTCATTCCATAATGAAGCAGAAG
CAGTGCTTTGAAACATTAGTAAAATTCAAGTACAGTGTCTTTAAGATCCTCGTCACCACCGACGTGGCTGTCAGGGGTCT
AGGCAGTCCAATGGTCCAAGTCATCATCAGCCACAACACCCCTGGTCTGCTGAAAATCTGCATCCATCGGGTAGATCGGA
AGGCCCATGCAGGC

Alignment

ORF - retro_psin_51 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.97 %
• Parental protein coverage: 50.57 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  HVVIATPGRLADHLRSSNTFSLRKIKFLVLDEADRLLEQGCTDFTKDLEVILGAVPATRQTLLFSATLTD
          H...ATP.RL.DHL.SS.TFSLRK.KFLVLD.ADRLL...C.DFTK.LEVILGAVPAT.Q.LLFS.....
Retrocopy HLIVATPSRLGDHL*SSSTFSLRKFKFLVLDKADRLLKLDCIDFTKVLEVILGAVPATKQMLLFSVR---

Parental  TLNELKSLAMNKPFFWESQAEVRTVDELVQRYLLVPEKVKDAYLVHLIQTFQDEHEDWSIIIFTSTCKSC
          .LNELK.L.MNKPFFWESQAEV..VDE.VQ.YLLV.EKVKD..L..LIQTFQDE.ED.SII.FTSTCK..
Retrocopy -LNELKRLTMNKPFFWESQAEVWMVDEMVQHYLLVLEKVKDVCLICLIQTFQDEEED*SIIMFTSTCKN*

Parental  QILNMMLKKFNFPSVALHSMMRQKQRFAALAKFKSSVFRILIATDVAARGLDIPTVQVVINHNTPGLPKI
          QILNMMLKKFNFPSVA.HS.M.QKQ.F..L.KFK.SVF.IL..TDVA.RGL..P.VQV.I.HNTPGL.KI
Retrocopy QILNMMLKKFNFPSVAFHSIMKQKQCFETLVKFKYSVFKILVTTDVAVRGLGSPMVQVIISHNTPGLLKI

Parental  YIHRVGRTARAG
          .IHRV.R.A.AG
Retrocopy CIHRVDRKAHAG

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_51 retrocopy.

TSS

Pelodiscus sinensis was not studied using FANTOM5 data.

Lab

retro_psin_51 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.

---

Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Ornithorhynchus anatinus	ENSOANG00000004572	1 retrocopy	retro_oana_39,
Pelodiscus sinensis	ENSPSIG00000008625	1 retrocopy	retro_psin_51 ,