RetrogeneDB ID: retro_tbel_2557

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_112890:173816..174288(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PPIA
• Ensembl ID: ENSTBEG00000017484
• Aliases: None
• Description: peptidylprolyl isomerase A (cyclophilin A) [Source:HGNC Symbol;Acc:9253]

Sequence

>retro_tbel_2557
TTCAACATCACTGTTGATGGTGAGCTTTTGGTACATGTCTTCTTCAAGCTGTTTGCAGACAAAGTTCCAAGGACAACAGA
AAACATTCATGCTTTGAACGCTGGAGAGAGAGGATTTGGTTATAAGCGTTCCTGCTTTCACAGAATTATTCCAGGGTTTA
TGTGCCAGGGTGGCAATTTCACAAGCCATAATGGCGCTTGGCAGCAAGTCCATCAATGGTAAAAAATTCAATGATGAGAA
CTTCATCCTGAAACATACGGGTCCTGGCATTTTGTTCATGGCTAATACTGGATCCAACACAAATGGTTCTCAGTTTTTAA
TCTGCACTGCCAAGACTGAGTGGTTGGATGGTAAGCATGTGGCCTTTGGCAAGGTGAAAGAAAGCATGAATATTGTGGAA
GCCGTGGAATGCTTTTGGTCCAAGAATGGCAAGACAAGCAAGAAGATCACCATGGCTGACGGTAGGCAACTC

Alignment

ORF - retro_tbel_2557 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.58 %
• Parental protein coverage: 95.73 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  FDIAVDGEPLGRVSFELYADKVPKTAKNFRALSTGEKGFGYKGSCFHRIIPGFMCQGGDFTRHNGT-GGK
          F.I.VDGE.L..V.F.L.ADKVP.T..N..AL..GE.GFGYK.SCFHRIIPGFMCQGG.FT.HNG..G.K
Retrocopy FNITVDGELLVHVFFKLFADKVPRTTENIHALNAGERGFGYKRSCFHRIIPGFMCQGGNFTSHNGA>GSK

Parental  SIYGEKFEDENFILKHTGPGILSMANAGPNTNGSQFFICTAKTEWLDGKHVVFGKVKEGMNIVEAMERFG
          SI.G.KF.DENFILKHTGPGIL.MAN.G.NTNGSQF.ICTAKTEWLDGKHV.FGKVKE.MNIVEA.E.F.
Retrocopy SINGKKFNDENFILKHTGPGILFMANTGSNTNGSQFLICTAKTEWLDGKHVAFGKVKESMNIVEAVECFW

Parental  SKNGKTSKKITIADCGQL
          SKNGKTSKKIT.AD..QL
Retrocopy SKNGKTSKKITMADGRQL

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Tupaia belangeri was not studied using RNA-Seq expression data.

ChIP-Seq

Tupaia belangeri was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_tbel_2557 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_2557 was not experimentally validated.

Homology

Retrocopy orthology:

Tupaia belangeri 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 20 parental genes, and 453 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000012003	12 retrocopies	retro_btau_1005, retro_btau_1448, retro_btau_155, retro_btau_1696, retro_btau_1806, retro_btau_272, retro_btau_334, retro_btau_335, retro_btau_345, retro_btau_414, retro_btau_751, retro_btau_934,
Callithrix jacchus	ENSCJAG00000011969	54 retrocopies	retro_cjac_1065, retro_cjac_1080, retro_cjac_1083, retro_cjac_1092, retro_cjac_1097, retro_cjac_11, retro_cjac_1193, retro_cjac_1213, retro_cjac_1310, retro_cjac_1326, retro_cjac_1347, retro_cjac_1451, retro_cjac_147, retro_cjac_1678, retro_cjac_1710, retro_cjac_1760, retro_cjac_1782, retro_cjac_1982, retro_cjac_1989, retro_cjac_2043,