RetrogeneDB ID: retro_psin_63

Retrocopy location

• Organism: Chinese softshell turtle (Pelodiscus sinensis)
• Coordinates: JH212588.1:426827..428132(-)
• Located in intron of: ENSPSIG00000007195

Retrocopy information

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

Parental gene information

• Parental gene symbol: SPPL2C
• Ensembl ID: ENSPSIG00000017155
• Aliases: None
• Description: signal peptide peptidase like 2C [Source:HGNC Symbol;Acc:28902]

Sequence

>retro_psin_63
CTCTTGGGATACAACATGGGGATCATGTTTGTCCTTGCAGTAGGCACTGTCATCACTGGAGGCTACTGGGCAGGAAATAC
AGAAAAGAAAAGGCAGCAATACATGAAGTGGAGATGCAAAAATGAAGAAGATTTTGATGATGTAACAATTGACCCTGATG
TCCTCTTTATCTGTGCAAGTGTAGTAATATCTTCCTTCATGCTGCTTGCTCTCTACTTCTTCTATGATCACTTAGCGAAC
ATCATGATTGGATGTTTCAGCCTCTACGCATCCCTTGGGCTTTACAGTTGTTTGTCTCCCTGGGTGAACAAACTACCATT
TGGAGAATACAAACTCCATTTCCCATATTTTCACAATGGACCACAAGTCAGAACATTTTTCCTGGCAGGATTTTCTGGCT
CCATCAGTGTCACATGGATGATCTTCAGAAATGAGGATCAGTGGGCCTGGGTCCTACAAGACTTTCTAGGAATCTCGATC
TGCCTCTATGTTCTAAAAACAGTCCGCATGCCTACACTGAAGAACTGCAGTTTGTTTCTAGCTGTTCTTTTGGTCTATGA
TGTGTTTTTTGTATTTATCACTCCTTTTTTAACCAAGTCTGGGGAGAGCATAATGAAAGTGGCAGCTCTTGGACCATCTG
ACATTGCCAATCATGAAAAGATCCCCTTTCTGTTGAAAGTTCCGATATTATCCTCTGCATCAACCTTTGATGAAAGCCCC
TTTACTATCCTTGGTCTTGGTGACATTGTAATTCCTGGTTTCCTGATAGCCTACTGTCACAGATTTGATGTTCAGAAGCA
TTCCTCCAGAATCTACTTTGCATCTTCTACTATAGCCTATAGCTATGGTCTCCTGGTGACCTTTGTAGTGTCAGCATTAA
TGCAAAAGGGTCAGCCAGCTCTCCTCTACTTGGTGCCCTTTACGCTTACCACTAGCCTTGTTATTGCTCTTTTGCGCAAG
GAACTCACAATTTTTTGGACAGGCACTGGTTTTACAAACGAATTATCTCGTTCTTCCTCAAGGATAGCTATCAGCTATCC
AGATACCCCAAGAGATTCAAATATACAAGTATGTCAACAAGAAAGGGAAGAAAAACTGATCAATTTCACATTCAGTGAAG
AACAGCTAGATAACTCCATTCTAGTGACAGAAAAATTGACTAATCTCAACATCTACATTGAACAGAATTCAGACTCCATA
CTATGTAAAGAAGAACAAATCAATCAACATGATGGCAAGCACAAGAGAGACATTCATAAAGCAGAAAAGAATCAGTTAGA
CTCTATGACAGAGAAAAAGGATCCA

Alignment

ORF - retro_psin_63 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.36 %
• Parental protein coverage: 72.56 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VLDYNMVIIFVMAVGTVAIGGYWAGSRDVKKRYMKHKRDDGAEKHDDETVDVTPIMICIFVVMCCSMLVL
          .L.YNM.I.FV.AVGTV..GGYWAG....K.......R....E..DD.T.D.....IC..VV....ML..
Retrocopy LLGYNMGIMFVLAVGTVITGGYWAGNTEKKRQQYMKWRCKNEEDFDDVTIDPDVLFICASVVISSFMLLA

Parental  LYFFYDDLVYVIIGIFCLAASIGLYSCLSPFVRRFPLGKCRIPDNNLPYFHKRPQVRMLLLAVFCISVSV
          LYFFYD.L....IG.F.L.AS.GLYSCLSP.V...P.G.........PYFH..PQVR...LA.F..S.SV
Retrocopy LYFFYDHLANIMIGCFSLYASLGLYSCLSPWVNKLPFGEYKL---HFPYFHNGPQVRTFFLAGFSGSISV

Parental  VWGVFRNEDQWAWVLQDALGIAFCLYMLKTIRLPTFKGCTLLLTVLFVYDVFFVFITPYITKSGQSIMVE
          .W..FRNEDQWAWVLQD.LGI..CLY.LKT.R.PT.K.C.L.L.VL.VYDVFFVFITP..TKSG.SIM..
Retrocopy TWMIFRNEDQWAWVLQDFLGISICLYVLKTVRMPTLKNCSLFLAVLLVYDVFFVFITPFLTKSGESIMKV

Parental  VATGPTDSATHEKLPMVLKVPRLNSSPLALCDRPFSLLGFGDILVPGLLVAYCHRFDIQVQSSRIYFVAC
          .A.GP.D.A.HEK.P..LKVP.L.SS.......PF..LG.GDI..PG.L.AYCHRFD.Q..SSRIYF...
Retrocopy AALGPSDIANHEKIPFLLKVPIL-SSASTFDESPFTILGLGDIVIPGFLIAYCHRFDVQKHSSRIYFASS

Parental  TIAYGIGLLVTFVALALMQKGQPALLYLVPCTLLTSFTVALWRKELTMFWTGSGFAKDLPHPPLVLAPVS
          TIAY..GLLVTFV..ALMQKGQPALLYLVP.TL.TS...AL.RKELT.FWTG.GF...L.......A..S
Retrocopy TIAYSYGLLVTFVVSALMQKGQPALLYLVPFTLTTSLVIALLRKELTIFWTGTGFTNELSRSSSRIA-IS

Parental  CPNPPKDMNAPASQQESKQQMTNPTLHADDQNNPSVCAEEQPHLGTK-ELTSPSLQTDQPQIPIPQIQQE
          .P..P.D.N....QQE......N.T.......N.....E....L....E..S.S......QI........
Retrocopy YPDTPRDSNIQVCQQEREEKLINFTFSEEQLDNSILVTEKLTNLNIYIEQNSDSILCKEEQINQHDGKHK

Parental  SSQNKDDPESKNLRVEKTQP
          ....K..........EK..P
Retrocopy RDIHKAEKNQLDSMTEKKDP

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_63 retrocopy.

TSS

Pelodiscus sinensis was not studied using FANTOM5 data.

Lab

retro_psin_63 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Nomascus leucogenys	ENSNLEG00000011710	1 retrocopy	retro_nleu_2146,
Procavia capensis	ENSPCAG00000011127	1 retrocopy	retro_pcap_285,
Pelodiscus sinensis	ENSPSIG00000017155	1 retrocopy	retro_psin_63 ,