RetrogeneDB ID: retro_tbel_4692

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_97894:9097..9729(+)
• 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_4692
TCAGCATTAGAGAAAGAGATTGGTCCAGACCAGTTTCCAGTCAATGAGCACTATTTTGGATTAGTCAATTTTGGGAGTAC
TTGCTACTGCAATTCAATTCTTTGAGCACTTAATTTTTGTCGTCCACTTCAGGAAAAAGTTTCAGCATATACGAGTCAAC
CTAGGAAGGAGAACCTTCTTGCATGCTTATCAGACCTCTTCCATAGCACATCACTCAGAAGGAGAAGGTTGGAGGTACCT
CCTAAGAAGTTCTTCATAAAGTTACAGAAATAGAATGAGCTTTTGAAAACTACTTGTGACAAGATGCCCATGAATTCTTA
AATAACCCACTAAATACCATTGCCAATATTTTACAAAAAGAGAGGAAGCAAGAAAAACAGCATGGCTATTTACCTAATGG
TAACATTGATAGCGAAAACAACAGCACACTATACCCAACGTGGGTTCATGAGATTTTTCAGGGAACATTAACTGATGAAA
CCAGATGTCTTATTTGTGAAACTGTAAGCAGTAAAGATGAATATGTTTTAGATCTTTCTGTTGATGTGGAACGAAACACA
TCAATTACTCACAGTTTAAAGTGTGTTAGAAACACAGAAACACTCTGCAATGAATGCAAATGTTACTGTGAA

Alignment

ORF - retro_tbel_4692 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.95 %
• Parental protein coverage: 60.51 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SALEKEIGSGQFPVNEHYF-LVNFGNTCYCNSVLQALYFCRPFREKVLAYKSQPRKKENLLTCLADLFHS
          SALEKEIG..QFPVNEHYF.LVNFG.TCYCNS.L.AL.FCRP..EKV.AY.SQPRK.ENLL.CL.DLFHS
Retrocopy SALEKEIGPDQFPVNEHYFGLVNFGSTCYCNSIL*ALNFCRPLQEKVSAYTSQPRK-ENLLACLSDLFHS

Parental  IATQKKKVGVIPPKKFITRLRKENEL-FDNYMQQDAHEFLNYLLNTIADILQEERKQEKQNGRLPNGNID
          .........V.PPKKF...L.K.NEL.F.NY..QDAHEFLN..LNTIA.ILQ.ERKQEKQ.G.LPNGNID
Retrocopy TSLRRRRLEV-PPKKFFIKLQK*NEL<FENYL*QDAHEFLNNPLNTIANILQKERKQEKQHGYLPNGNID

Parental  SENNNSTPDPTWVHEIFQGTLTNETRCLTCETISSKDEDFLDLSVDVEQNTSITHCLRGFSNTETLCSEY
          SENN.ST..PTWVHEIFQGTLT.ETRCL.CET.SSKDE..LDLSVDVE.NTSITH.L....NTETLC.E.
Retrocopy SENN-STLYPTWVHEIFQGTLTDETRCLICETVSSKDEYVLDLSVDVERNTSITHSLKCVRNTETLCNEC

Parental  KYYCE
          K.YCE
Retrocopy KCYCE

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_4692 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_4692 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 ,