RetrogeneDB ID: retro_psin_24

Retrocopy location

• Organism: Chinese softshell turtle (Pelodiscus sinensis)
• Coordinates: JH224643.1:1890304..1891012(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPSIG00000001840
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSPSIG00000010721
• Aliases: None
• Description: None

Sequence

>retro_psin_24
ATGAACCGTTTTTCTAATAAAGGTCAATTAATACAATTAATCTTAACAGGTTGTTGTCTTTATAAATCTGATTATTTTTG
CTATTTAAAGGAAGAGCCGAGGCTGGATGTGCTCATCAATAATGCGGGGATATTCCAGTGTCCATACATGAAGACAGAGG
ATGGTTTCGAGATGCAGTTTGGTGTCAACCACTTGGGTCACTTCTTGCTCACTAACCTCCTCCTTGGTCTTCTCAAAAGT
TCTGCCCCAAGCAGGATTGTGGTAGTTTCTTCCAAACTTTACAAATATGGAGAGATCAACTTTGAAGACTTGAACAGTGA
AATAAGTTACAATAAAAGTTTTGGCTACAGTCGGAGTAAACTGGCAAACATACTATTTACAAGGGAGCTAGCTCGCCGAT
TGGAAGGCACAGGTGTCACTGTGAATGTGCTTCATCCTGGTATTGTCCGAACCAATCTAGGCAGATATATAAATATTCCT
TTGCTGGCAAAACCCCTCTTTAATTTGGTGTCATGGGCTTTCTTCAAAACCCCATTGGAAGGAGCCCAGACTTCTATTTA
TTTGGCCTCTTCTGCAGAAGTAGAGGGTGTATCAGGCAAGTATTTTGGGGATTGCAAAGAGGAGGAATTGCTGCCTAAAG
CCATGGATGAGTCTGTTGCAAGAAAACTGTGGGATATCAGTGAAGTGATGGTTGGATTATTAAAATAA

Alignment

ORF - retro_psin_24 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.33 %
• Parental protein coverage: 69.15 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  FLEEEKALHILINNAGVMLCPYSKTADGFEMHLGVNHLGKGHFLLTFLLLERLKQSAPARIVNVSSLAHH
          .L.EE..L..LINNAG...CPY.KT.DGFEM..GVNHLG..HFLLT.LLL..LK.SAP.RIV.VSS....
Retrocopy YLKEEPRLDVLINNAGIFQCPYMKTEDGFEMQFGVNHLG--HFLLTNLLLGLLKSSAPSRIVVVSSKLYK

Parental  GGRIRFHDLQGEKCYNKGLAYCHSKLANVLFTRELARRLKGTGVTANSLHPGSVHSELIRHSILMTLLWK
          .G.I.F.DL..E..YNK...Y..SKLAN.LFTRELARRL.GTGVT.N.LHPG.V...L.R......L...
Retrocopy YGEINFEDLNSEISYNKSFGYSRSKLANILFTRELARRLEGTGVTVNVLHPGIVRTNLGRYINIPLLAKP

Parental  TFSF----FLKTPREGAQTSIYCAVAEELESVTGQYFSDCRPAYVSPQGRNDELAKKLWNVSCELLGI
          .F......F.KTP.EGAQTSIY.A...E.E.V.G.YF.DC......P.......A.KLW..S....G.
Retrocopy LFNLVSWAFFKTPLEGAQTSIYLASSAEVEGVSGKYFGDCKEEELLPKAMDESVARKLWDISEVMVGL

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_24 retrocopy.

TSS

Pelodiscus sinensis was not studied using FANTOM5 data.

Lab

retro_psin_24 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 13 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000008036	1 retrocopy	retro_amel_673,
Canis familiaris	ENSCAFG00000016446	1 retrocopy	retro_cfam_2068,
Equus caballus	ENSECAG00000015001	1 retrocopy	retro_ecab_1059,
Felis catus	ENSFCAG00000014092	1 retrocopy	retro_fcat_1910,
Loxodonta africana	ENSLAFG00000022637	1 retrocopy	retro_lafr_847,
Macropus eugenii	ENSMEUG00000001473	1 retrocopy	retro_meug_41,
Meleagris gallopavo	ENSMGAG00000011960	1 retrocopy	retro_mgal_16,
Microcebus murinus	ENSMICG00000010855	1 retrocopy	retro_mmur_432,
Ornithorhynchus anatinus	ENSOANG00000015759	1 retrocopy	retro_oana_89,
Procavia capensis	ENSPCAG00000009359	1 retrocopy	retro_pcap_1,
Pelodiscus sinensis	ENSPSIG00000010721	1 retrocopy	retro_psin_24 ,
Sarcophilus harrisii	ENSSHAG00000012445	1 retrocopy	retro_shar_41,
Drosophila melanogaster	FBgn0033203	1 retrocopy	retro_dmel_79,