RetrogeneDB ID: retro_tbel_1906

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: GeneScaffold_5975:226889..227290(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PPIF
• Ensembl ID: ENSTBEG00000015457
• Aliases: None
• Description: peptidylprolyl isomerase F [Source:HGNC Symbol;Acc:9259]

Sequence

>retro_tbel_1906
GTTCCAAAGACAACAGAAAACATTCATGCTCTGAGAATTGGAGAGAAAGGATTTGGTTATAAGGGTTCCTGCTTTCACAA
ACTTATTCCAGAGTTTATATAACAGGGTGGTGACTTATATACCATAATGGTACTGGCAACAAATCCATTTATGGGAGAAA
TTGGAAGACGAGAACTTCATTTTGAGACATACAGGTCTTAGCATCTTGTCCATGGCAAACGCTTGACCCAATACAAACAG
TTCTCAGCTTTCCATCTGCACTGCCAAGACTGGTGATTGGAGGCCAAGCATGTGATCTTTGGCAAGGTGAAAAAGGGCAT
GAATTCCATGGAAACCATGGAGTGCTTTGGGTCCAAGAATGGCAAGACCAGTAAGAGATCACCATTGCTGACTGTGGACA
G

Alignment

ORF - retro_tbel_1906 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.15 %
• Parental protein coverage: 95.07 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  VPKTAENFRALCTGEKGFGYKGSTFHRVIPSFMCQAGDFTN-HNGTGGKSIYG-SRFPDENFTLKHVGPG
          VPKT.EN..AL..GEKGFGYKGS.FH..IP.F..Q.GD....HNGTG.KSIYG.....DENF.L.H.G..
Retrocopy VPKTTENIHALRIGEKGFGYKGSCFHKLIPEFI*QGGDLYT<HNGTGNKSIYG<EKLEDENFILRHTGLS

Parental  VLSMANAGPNTNGSQFFICTIKTD-WLDGKHVVFGHVKEGMDVVKKIESFGSKSGKPSKK-IVITDCGQ
          .LSMANA.PNTN.SQ..ICT.KT...L..KHV.FG.VK.GM......E.FGSK.GK.SK..I.I.DCGQ
Retrocopy ILSMANA*PNTNSSQLSICTAKTG<*LEAKHVIFGKVKKGMNSMETMECFGSKNGKTSKR<ITIADCGQ

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_1906 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_1906 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.

---

Parental genes homology:

Parental genes homology involve 10 parental genes, and 96 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000008796	3 retrocopies	retro_ecab_507, retro_ecab_649, retro_ecab_732,
Homo sapiens	ENSG00000108179	1 retrocopy	retro_hsap_1436,
Microcebus murinus	ENSMICG00000007086	8 retrocopies	retro_mmur_1266, retro_mmur_218, retro_mmur_515, retro_mmur_568, retro_mmur_605, retro_mmur_694, retro_mmur_769, retro_mmur_87,
Nomascus leucogenys	ENSNLEG00000010567	1 retrocopy	retro_nleu_70,
Procavia capensis	ENSPCAG00000009406	1 retrocopy	retro_pcap_275,
Pan troglodytes	ENSPTRG00000002669	1 retrocopy	retro_ptro_979,
Pteropus vampyrus	ENSPVAG00000001713	2 retrocopies	retro_pvam_380, retro_pvam_623,
Tupaia belangeri	ENSTBEG00000015457	1 retrocopy	retro_tbel_1906 ,
Tupaia belangeri	ENSTBEG00000017484	77 retrocopies	retro_tbel_1014, retro_tbel_1098, retro_tbel_1104, retro_tbel_1106, retro_tbel_1180, retro_tbel_1661, retro_tbel_1689, retro_tbel_1808, retro_tbel_1813, retro_tbel_1831, retro_tbel_1895, retro_tbel_1904, retro_tbel_1913, retro_tbel_1918, retro_tbel_1936, retro_tbel_1938, retro_tbel_2013, retro_tbel_2014, retro_tbel_204, retro_tbel_2054, retro_tbel_2098, retro_tbel_2144, retro_tbel_2175, retro_tbel_221, retro_tbel_2557, retro_tbel_267, retro_tbel_2681, retro_tbel_2691, retro_tbel_2714, retro_tbel_2824, retro_tbel_2834, retro_tbel_2851, retro_tbel_2897, retro_tbel_2938, retro_tbel_3004, retro_tbel_3054, retro_tbel_3104, retro_tbel_3142, retro_tbel_3153, retro_tbel_3311, retro_tbel_3337, retro_tbel_3421, retro_tbel_3423, retro_tbel_3477, retro_tbel_3639, retro_tbel_3691, retro_tbel_3767, retro_tbel_3847, retro_tbel_3880, retro_tbel_3890, retro_tbel_3979, retro_tbel_4019, retro_tbel_415, retro_tbel_4155, retro_tbel_4325, retro_tbel_4332, retro_tbel_4364, retro_tbel_4391, retro_tbel_4534, retro_tbel_4537, retro_tbel_4568, retro_tbel_4581, retro_tbel_4683, retro_tbel_4699, retro_tbel_521, retro_tbel_541, retro_tbel_618, retro_tbel_64, retro_tbel_764, retro_tbel_80, retro_tbel_831, retro_tbel_832, retro_tbel_887, retro_tbel_900, retro_tbel_910, retro_tbel_922, retro_tbel_946,
Xenopus tropicalis	ENSXETG00000018981	1 retrocopy	retro_xtro_20,