RetrogeneDB ID: retro_psin_66

Retrocopy location

• Organism: Chinese softshell turtle (Pelodiscus sinensis)
• Coordinates: JH224675.1:3396346..3396810(+)
• Located in intron of: ENSPSIG00000014789

Retrocopy information

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

Parental gene information

• Parental gene symbol: RAB14
• Ensembl ID: ENSPSIG00000003919
• Aliases: None
• Description: RAB14, member RAS oncogene family [Source:HGNC Symbol;Acc:16524]

Sequence

>retro_psin_66
ATGGCAACTGCACATTATAACTACTCTTACATCGTTATGTAAATCATTACTGGGACATGGGTGTTGGGAAGTTCCGCTTG
CTTCAGCAATTCAAAACAATTTATGGCTGACTGTCCCTACACAACTGGGGTAGCATTTGGTACAAGAATAATTGAAGTTA
GTGGACAAAAAATTAAACTGCAGATCTGGGATACAGGACATGAGTGATTTATGGCTGTAACATGAAGCTACCACAGAGAG
CAGCAGGAGCTCTCATGGTCTATGATATTACTAGAAGAACATATAACCATATAAGCAGCAGGTTGAGAGACACAAAGAAC
CTCACCAATCCAAATACTGTGATAATCCTCATAGGAAATAAAGGAGATCTGGAAGCACAGAGAGATGTGACATATGAAGA
AGCCAAACAATTTGCAGAAGAAAATCGGTTGCTGTTCCTTGAAGCAAGTGCAACACCAAGAGAA

Alignment

ORF - retro_psin_66 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.38 %
• Parental protein coverage: 73.95 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MATAPYNYSYIFKYIIIGDMGVGKSCLLHQFTEKKFMADCPHTIGVEFGTRIIEVSGQKIKLQIWDTAGQ
          MATA.YNYSYI...II.G....G.S........K.FMADCP.T.GV.FGTRIIEVSGQKIKLQIWDT.G.
Retrocopy MATAHYNYSYIVM*IITGTWVLGSSACFSN--SKQFMADCPYTTGVAFGTRIIEVSGQKIKLQIWDT-GH

Parental  ERFRAVTRSYYRG-AAGALMVYDITRRSTYNHLSSWLTDARNLTNPNTVIILIGNKADLEAQRDVTYEEA
          E.F.AVT.SY.R..AAGALMVYDITRR.TYNH.SS.L.D..NLTNPNTVIILIGNK.DLEAQRDVTYEEA
Retrocopy E*FMAVT*SYHRE<AAGALMVYDITRR-TYNHISSRLRDTKNLTNPNTVIILIGNKGDLEAQRDVTYEEA

Parental  KQFAEENGLLFLEASAKTGE
          KQFAEEN.LLFLEASA...E
Retrocopy KQFAEENRLLFLEASATPRE

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_66 retrocopy.

TSS

Pelodiscus sinensis was not studied using FANTOM5 data.

Lab

retro_psin_66 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 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000003669	1 retrocopy	retro_chof_2175,
Cavia porcellus	ENSCPOG00000006688	1 retrocopy	retro_cpor_1081,
Myotis lucifugus	ENSMLUG00000009818	1 retrocopy	retro_mluc_1875,
Oryctolagus cuniculus	ENSOCUG00000013654	1 retrocopy	retro_ocun_1667,
Otolemur garnettii	ENSOGAG00000012973	1 retrocopy	retro_ogar_710,
Pelodiscus sinensis	ENSPSIG00000003919	1 retrocopy	retro_psin_66 ,
Sarcophilus harrisii	ENSSHAG00000017800	1 retrocopy	retro_shar_80,