RetrogeneDB ID: retro_tbel_1000

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: GeneScaffold_3551:1966501..1967636(+)
• Located in intron of: ENSTBEG00000014413

Retrocopy information

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

Parental gene information

• Parental gene symbol: PES1
• Ensembl ID: ENSTBEG00000009825
• Aliases: None
• Description: pescadillo ribosomal biogenesis factor 1 [Source:HGNC Symbol;Acc:8848]

Sequence

>retro_tbel_1000
AAGAAGAAGTATGAACGGGGCTCTGCCACCAACTACATCACCCGAAATAAAGCCCGGAAGAAGCTGCAGCTGAGCCTGGC
TGACTTCAGGCAGCTGTGCATCCTCAAAGGCATTTATCCCCATGAGCCCAAACACAAGAAGAAGGTTAACAAGGGTTCCA
CAGCTGCCCGCACTTTCTACCTTCTCTAAGATACCAAGTTTCTCCTTCATGAACCCATCGTCAACAAGTTCCGGGAATAC
AAGGTCTTTGTCGGGAAGCTCCGGAAGGAGTATGGGAAGAGCGAGTGGAACACCGTGGAGCGTCTGAAGGACAATAAGCC
TAACTACAAACTTGACCACATTGCCAAGGAGCGGTACCCCACTTTCATCGACACCCTGCGGGACCTGGACGACACCCTGT
CTATATGCTTCTTCTTCTCCACCTTCCCGCGGACCGGCAAGTGCCACGTGCACACCATCCAGCTGTGCCGCCGGCTCTCT
GTGGAGTTCATGCACTACATCATCGCTGCCTGGGCCCTGCGCAAGGTCTTCCTGTCCATCAAAGGCATTTACTACCAGGT
GGAGGTGCTGAGGCAGCCCATCGTGTGGATCACCCCCTACGCCTTTTCCCACGACCACCCGACAAAGGTGGACTACAGGA
TCATGGCCACCTTCACCGAGTTCTACACCACCCTGCTGGGCTTCCTCAACTTCCTCCTTTACCAGTCACTGAACCTCCAC
TACGCCCCCAAGCTCGAGGGTCAGACCCAAGGAGAGGCAGAGGCCAGTGAGGGGACCTATGCTCTGGACACTGAGAGCTC
TATGGAGAAACTGGCAGCCTTCAGTGCCAGCCTGACCTGTGCGGTGGTGCCTGCCACAGAGGAGGAGGCCGAGGTAGATG
AGTTTCCCGCCGATGAGGAGATGGTGGCACAGGAGGACTGCAGGAAGGAGCTGGAGGTGCAGGAAAAACACAAGAAGCTG
TTTGAGGGCCTGAAGTTCTTCCTGAACCATGAGGTGCCGCGCGAGGCCCTGGCCTTCATCATCAGGAGTTTTGGTGGGGC
TGTGTCTTGGGACAAGTTGCTGTGCATCGGGGCCACCTATGATGTCACCGCCACCGTGCATCACCCACCAGATCATCGAC
TGGCCTGGGCAGATG

Alignment

ORF - retro_tbel_1000 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.26 %
• Parental protein coverage: 65.12 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ERVYERGSATNYITRNKARKKLQLSLADFRRLCILKGIYPHEPKHKKKVNKGSTAARTFYLLKDIKFLLH
          ...YERGSATNYITRNKARKKLQLSLADFR.LCILKGIYPHEPKHKKKVNKGSTAARTFYLL.D.KFLLH
Retrocopy KKKYERGSATNYITRNKARKKLQLSLADFRQLCILKGIYPHEPKHKKKVNKGSTAARTFYLL*DTKFLLH

Parental  EPIVNKFREYKVFVRKLRKAYGKSEWNTVERLKDNKPNYKLDHIVKERYPTFIDALRDLDDALSMCFLFS
          EPIVNKFREYKVFV.KLRK.YGKSEWNTVERLKDNKPNYKLDHI.KERYPTFID.LRDLDD.LS.CF.FS
Retrocopy EPIVNKFREYKVFVGKLRKEYGKSEWNTVERLKDNKPNYKLDHIAKERYPTFIDTLRDLDDTLSICFFFS

Parental  TFPRTGKCHVHTIQLCRRLSVEFMHYVIAARALRKVFLSIKGIYYQVEVLGQPIVWITPYTFSHDHPTDV
          TFPRTGKCHVHTIQLCRRLSVEFMHY.IAA.ALRKVFLSIKGIYYQVEVL.QPIVWITPY.FSHDHPT.V
Retrocopy TFPRTGKCHVHTIQLCRRLSVEFMHYIIAAWALRKVFLSIKGIYYQVEVLRQPIVWITPYAFSHDHPTKV

Parental  DYRVMATFTEFYTTLLGFVNFRLYQSLNLHYPPKLEGQTQGEAEASEGTYALDTESSMEKLAALSASLAR
          DYR.MATFTEFYTTLLGF.NF.LYQSLNLHY.PKLEGQTQGEAEASEGTYALDTESSMEKLAA.SASL..
Retrocopy DYRIMATFTEFYTTLLGFLNFLLYQSLNLHYAPKLEGQTQGEAEASEGTYALDTESSMEKLAAFSASLTC

Parental  AVVPATEEEAEVDEFPTDEEMAAQEEDRRKELEAQEKHKKLFEGLKFFLNREVPREALAFIIRSFGGAVS
          AVVPATEEEAEVDEFP.DEEM.AQ.ED.RKELE.QEKHKKLFEGLKFFLN.EVPREALAFIIRSFGGAVS
Retrocopy AVVPATEEEAEVDEFPADEEMVAQ-EDCRKELEVQEKHKKLFEGLKFFLNHEVPREALAFIIRSFGGAVS

Parental  WDKSLCIGATYDVTDS-CITHQIVDRPGQM
          WDK.LCIGATYDVT...CITHQI.D.PGQM
Retrocopy WDKLLCIGATYDVTAT>CITHQIIDWPGQM

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_1000 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_1000 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 8 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000010617	1 retrocopy	retro_cjac_3182,
Cavia porcellus	ENSCPOG00000003565	1 retrocopy	retro_cpor_986,
Homo sapiens	ENSG00000100029	1 retrocopy	retro_hsap_4133,
Otolemur garnettii	ENSOGAG00000005804	1 retrocopy	retro_ogar_1719,
Pongo abelii	ENSPPYG00000011716	1 retrocopy	retro_pabe_3471,
Pan troglodytes	ENSPTRG00000014251	2 retrocopies	retro_ptro_2018, retro_ptro_2809,
Rattus norvegicus	ENSRNOG00000004515	2 retrocopies	retro_rnor_2953, retro_rnor_824,
Tupaia belangeri	ENSTBEG00000009825	1 retrocopy	retro_tbel_1000 ,