RetrogeneDB ID: retro_tbel_188

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: GeneScaffold_1406:317195..318088(+)
• Located in intron of: ENSTBEG00000008494

Retrocopy information

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

Parental gene information

• Parental gene symbol: TUBG1
• Ensembl ID: ENSTBEG00000015835
• Aliases: None
• Description: tubulin, gamma 1 [Source:HGNC Symbol;Acc:12417]

Sequence

>retro_tbel_188
GACATCAAAGACCATGTGGCAGATGACCACGAGATGGCTAGAGGGCTTTGTGCTGTGTCACTCCATCGCTGGTGTAACAG
GAACTGGTCTGAGCTCCTATTTCATAGAATTGCTGAATGACAGGTAACCCAAGAAGCTGATGCAGACACACTCAGTGTTT
CCCAACCAGTACAAGATGAGCCATGTAATGGTGCAGCCCTACAACTCACTATTCATTCTGAAGAGGTTGACTAGGAATGC
GACTACATGGTGGTGCTGGTCAACACAGCCTTCAAACAGATTACCACTGACCACTTGCACATCCAGAACCCATCCTTCTC
CCAGATCAACCAGCTGGTGTCCACCATCATGTTGGCCAGAACACCCCTCTGTGCTACCCTGGCTACAGGAACAATGATCT
CATTGGCATGATTGCTTCACTTATCCCCACACAGTGGCTCCACTTCCTCATGTCTAGTTACCCCCTCCTCACCACGGACC
AGTCAGTGGCAAGAGGGAGGAAGACCATGGTCTTGGATGTCATGAGGCAGCTGCTATAGTCCAAGAATGTGATAGTGTCC
ACAGGCCACTACCATAAGACCAATCATTGCTACATTGCCATCTTCAACATCATCCAGGGGTAAGTAGACCCTACTCAGGT
CCATAAGACCCTGTAGTATATCTGGGAATGGAAGTTGGCCAACTTCATCCCCTGGGGCCCAGACAGCATCCAGCTGGTCC
TGTGAAGGAAGTCCCCCTACCTACCATCAGCCCACTGGGTAAGCAGATTTATGATGGCCAACCATGCCAGCATCTCCTTG
CCCTTTGAGCGAACCTGTTGCCAGTATGATAAGCTGCAGAAGCAGGAAACCTTCTTGGAACAGTTCCTCAAAGAGGACAT
GTTCAAGGACAAC

Alignment

ORF - retro_tbel_188 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.75 %
• Parental protein coverage: 68.66 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  DIIDREADGSDS-LEGFVLCHSIAGGTGSGLGSYLLERLNDRYPKKLVQTYSVFPNQDEMSDVVVQPYNS
          DI.D..AD.....LEGFVLCHSIAG.TG.GL.SY..E.LNDR.PKKL.QT.SVFPNQ..MS.V.VQPYNS
Retrocopy DIKDHVADDHEM>LEGFVLCHSIAGVTGTGLSSYFIELLNDR*PKKLMQTHSVFPNQYKMSHVMVQPYNS

Parental  LLTLKRLTQNA-DCVVVLDNTALNRIATDRLHIQNPSFSQINQLVSTIMSAST-TTLRYPGYMNNDLIGL
          L..LKRLT.NA.D..VVL.NTA...I.TD.LHIQNPSFSQINQLVSTIM.A.T.T.L.YPGY.NNDLIG.
Retrocopy LFILKRLTRNA<DYMVVLVNTAFKQITTDHLHIQNPSFSQINQLVSTIMLART<TPLCYPGYRNNDLIGM

Parental  IASLIPTPRLHFLMTGYTPLTTDQSVASVRKTTVLDVMRRLLQPKNVMVSTGRDRQTNHCYIAILNIIQG
          IASLIPT..LHFLM..Y..LTTDQSVA..RKT.VLDVMR.LL..KNV.VSTG....TNHCYIAI.NIIQG
Retrocopy IASLIPTQWLHFLMSSYPLLTTDQSVARGRKTMVLDVMRQLL*SKNVIVSTGHYHKTNHCYIAIFNIIQG

Parental  EVDPTQVHKSLQRIRERKLANFIPWGPASIQVALSRKSPYLPSAHRVSGLMMANHTSISSLFERTCRQYD
          .VDPTQVHK.L..I.E.KLANFIPWGP.SIQ..L.RKSPYLPSAH.VS..MMANH.SIS..FERTC.QYD
Retrocopy *VDPTQVHKTL*YIWEWKLANFIPWGPDSIQLVL*RKSPYLPSAHWVSRFMMANHASISLPFERTCCQYD

Parental  KLRKREAFLEQFRKEDMFKDN
          KL.K.E.FLEQF.KEDMFKDN
Retrocopy KLQKQETFLEQFLKEDMFKDN

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_188 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_188 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 10 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000004907	1 retrocopy	retro_cjac_4142,
Echinops telfairi	ENSETEG00000008542	1 retrocopy	retro_etel_496,
Homo sapiens	ENSG00000131462	1 retrocopy	retro_hsap_3725,
Gorilla gorilla	ENSGGOG00000010899	1 retrocopy	retro_ggor_2515,
Macaca mulatta	ENSMMUG00000016797	1 retrocopy	retro_mmul_1692,
Nomascus leucogenys	ENSNLEG00000011686	1 retrocopy	retro_nleu_71,
Pongo abelii	ENSPPYG00000008384	1 retrocopy	retro_pabe_3132,
Pan troglodytes	ENSPTRG00000009211	1 retrocopy	retro_ptro_2520,
Rattus norvegicus	ENSRNOG00000020213	2 retrocopies	retro_rnor_2070, retro_rnor_2072,
Tupaia belangeri	ENSTBEG00000015835	3 retrocopies	retro_tbel_188 , retro_tbel_3516, retro_tbel_955,