RetrogeneDB ID: retro_tbel_3285

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_135911:124380..125329(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: USP12
• Ensembl ID: ENSTBEG00000012960
• Aliases: None
• Description: ubiquitin specific peptidase 12 [Source:HGNC Symbol;Acc:20485]

Sequence

>retro_tbel_3285
GCATTAGAGAAAGAGATTGGTCCAGACCAGTTTCCAGTCAACGAGCACTATTTTGGATTAGTCAATTTTGGGAGTACTTG
TTACTGCAATTCAGTTCTTTGAGCGCTTTATTTTTGTTGTCCACTTCAGGAAAAAGTTTTAGCATATACGAATCAACCTA
GGAAGGAGAACCTTCTTGCGTGCTTAGCAGACCTCTTCCATGGCATCATCATTCAGAAGGAGAAGGTTGGAGATACCTCC
TAAGAAGTTCCTCACAGGGTTGCAGAAAGAGAATGAGCTTTTGAAAACTACTTGTGACAACATGCCCATGAATTCTTAAA
TGACCCATTAATACCATTGCCAATATTTTACAAAAAGAGAGGAAGCAGGAGAAACAGCATGGCTGTTTACATAATGGTAA
CATTGATAGCGAAAACAACAGCACACCAGACCCAACATGGGTTCATGAGATTTTTCAGGGAACATTAACTGATGAAACCA
GATGTCTTATTTGTGAAACTGTAAGCAGTGAAGATGAATATGTTTTAGATCTTTCTGTTGACGTGGAACAAAACACATCA
ATTACTCACTGTTTAAGGGGTGTTAGCAACACAGAAACATTCTGCAATGAATGCAAATGTTACTGTGAAGTGTCACAGTA
GACATACAAATGGATGAAACTTAAAGTACCCATGATTCTAGCTCTGAACCTGAAGGGATTTAAATATATAGATCAACCTC
ATTGACATGCAAAACATTTTACTGGATAGTTTTTCCTTTACAAATTAATCTGTTCAACACTTCAGGCAATGCAACCTATT
CTGACAGGATATACAACTTTGTCACTGTGGTGCACTGTGGACATGGTCCCAGTCGAGGACATTGTATTGTAATAATTAGG
AGTCATGACTTTTGGTTGTTGTTGTTCTACATTGTAGAAAAAGTAGATGCTCAAGGTATTGAAGAATTC

Alignment

ORF - retro_tbel_3285 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.91 %
• Parental protein coverage: 92.33 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  ALEKEIGSGQFPVNEHYF-LVNFGNTCYCNSVLQALYFCRPFREKVLAYKSQPRKKENLLTCLADLFHSI
          ALEKEIG..QFPVNEHYF.LVNFG.TCYCNSVL.ALYFC.P..EKVLAY..QPR.KENLL.CLADLFH.I
Retrocopy ALEKEIGPDQFPVNEHYFGLVNFGSTCYCNSVL*ALYFCCPLQEKVLAYTNQPR-KENLLACLADLFHGI

Parental  ATQKKKVG-VIPPKKFITRLRKENEL-FDNYMQQDAHEFLNYLL-NTIADILQEERKQEKQNGRLPNGNI
          ..QK.KVG...P.K.F.T.L.KENEL.F.NY..Q.AHEFLN..L.NTIA.ILQ.ERKQEKQ.G.L.NGNI
Retrocopy IIQKEKVG>IPPKK-FLTGLQKENEL<FENYL*QHAHEFLNDPL<NTIANILQKERKQEKQHGCLHNGNI

Parental  DSENNNSTPDPTWVHEIFQGTLTNETRCLTCETISSKDEDFLDLSVDVEQNTSITHCLRGFSNTETLCSE
          DSE.NNSTPDPTWVHEIFQGTLT.ETRCL.CET.SS.DE..LDLSVDVEQNTSITHCLRG.SNTET.C.E
Retrocopy DSE-NNSTPDPTWVHEIFQGTLTDETRCLICETVSSEDEYVLDLSVDVEQNTSITHCLRGVSNTETFCNE

Parental  YKYYCEECRSKQEAHKRMKVKKLPMILALHLKRFKYMDQLHRYT-KLSYRVVFPLELRLFNTSGDATNPD
          .K.YCE.....Q...K.MK..K.PMILAL.LK.FKY.DQ.H....K..Y..VFPL...LFNTSG.AT..D
Retrocopy CKCYCE---VSQ*TYKWMKL-KVPMILALNLKGFKYIDQPH*HA<KTFYWIVFPLQINLFNTSGNATYSD

Parental  RMYDLVAVVVHCGSGPNRGHYIAIVKSHDFWLLFDDDIVEKIDAQAIEEF
          R.Y..V..VVHCG.GP.RGH.I.I..SHDFWLL....IVEK.DAQ.IEEF
Retrocopy RIYNFV-TVVHCGHGPSRGHCIVIIRSHDFWLLL-FYIVEKVDAQGIEEF

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_3285 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_3285 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 9 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000019344	5 retrocopies	retro_cjac_2734, retro_cjac_3901, retro_cjac_3964, retro_cjac_3965, retro_cjac_4011,
Homo sapiens	ENSG00000152484	4 retrocopies	retro_hsap_2328, retro_hsap_3266, retro_hsap_4726, retro_hsap_4918,
Microcebus murinus	ENSMICG00000006269	2 retrocopies	retro_mmur_1167, retro_mmur_1187,
Macaca mulatta	ENSMMUG00000021425	1 retrocopy	retro_mmul_937,
Nomascus leucogenys	ENSNLEG00000000323	3 retrocopies	retro_nleu_1817, retro_nleu_1995, retro_nleu_2426,
Otolemur garnettii	ENSOGAG00000030639	1 retrocopy	retro_ogar_2897,
Pongo abelii	ENSPPYG00000005232	3 retrocopies	retro_pabe_2110, retro_pabe_2705, retro_pabe_3672,
Pan troglodytes	ENSPTRG00000005727	3 retrocopies	retro_ptro_1701, retro_ptro_2209, retro_ptro_3143,
Tupaia belangeri	ENSTBEG00000012960	2 retrocopies	retro_tbel_3285 , retro_tbel_4692,