RetrogeneDB ID: retro_tbel_3516

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_143503:19576..20859(-)
• Located in intron of: None

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_3516
AAACTGTGCACTGAGCATGGTATCAGCCCCAAGGGCATCGTGAAGGAGTTCGCCACCGAGGGCACTGACTGCAAGGACGT
CTTTTTCTACCAGGCAGATGATGAGCACTACATCCCCCGGGCCGTGCAGCTGGACTTAGAGCCCCAGGTGATCCATTTCA
TCTTTAACTCCCCCTATACCAAGCTCTACAACCCAGAGAACATCTACCTGTCAGAGCACGGAGAAGGAACTGGCAACAAT
TGGGCCAGCGGATTCTCTCAGGGAGAGAAGATCCATGAGGACATTTTTGACATCATAGATTGGGAGGCAGACGGCAGCGA
CAGTCTAGAGGACTTTGTGCTGTGTCACTCCATCACTAGTGGAACAGGCTCTGGCCTGGGCTCCCACCTCTTAGAATGGC
TGAATGACAGGTACCCCCAAAAGCTGGTGCAGACATACTCACTGTTTCCCAACCAGGACGAGATGAGCGATGTGGTGGTG
CAGCCCTACAACTCACTGCTCACTCTCAAGAGGCTGACCCAGAACACAGACTGTGTGGAGGTGCTGGACAACATAGCCCT
CAACAGATCGCCACAGACAGCCTGCACATCTAGAACCCACCCTTTTCCCAGATCAACCAGCTGGTGTCCACCATCATGTC
AGCCAGCACCACCACCCTGCACTACTCTGGCTACATGAACAATGACCCCATTGGCCTGATCACCTCACTCATCCCCATAC
CACAGCTCCACTTTCTCCTGACCAGCTACACCCTCCTCACCACGGACCAAACAGTGGCCAATGTGAGGAAGACTACAGTC
TTGGATTTCATGAGGTGGCTGCTATAGCTCAAGAACGTGATGGTATCCACAGGCCAGGACAGCCCAACCAACCACTGCTA
CATTGCCATTCTCAACATCATCCAGTGGGAAGTAGACCCCACCCAGGTCCACAAGAGCCTGCAGTGGATCCGGGAATGGA
AGTTGGCCAACTTCATCCCCTGGGGCCCAGCCAGCATCCAGGTGGCCCTGTCAAGGAAGTCTCCCTACCTGCCCTCGGCC
CACCATATCAGCAGACTCATAATGGCCAACCACACCAGCATCTCCTCGCTCTTCGAGTGAACCTGTCACCAGTACAACAA
GCTGCAGAAGCAGGAGACCTTCCTGGAGCAGTTCTGCAAGGAGGACATGTTCAAGGACAACTTGGATGAGATGGACATAT
CCAGGGCGATTGTGCAGCAACTCATCGATGAGTACCATGCAGCCACATGGCCAGACTACATCTCCTAGGGCACCCAGGAG
CAG

Alignment

ORF - retro_tbel_3516 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.08 %
• Parental protein coverage: 98.62 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  QLCAEHGISPEGIVEEFATEGTDRKDVFFYQADDEHYIPRAVLLDLEPRVIHCILNSPYAKLYNPENIYL
          .LC.EHGISP.GIV.EFATEGTD.KDVFFYQADDEHYIPRAV.LDLEP.VIH.I.NSPY.KLYNPENIYL
Retrocopy KLCTEHGISPKGIVKEFATEGTDCKDVFFYQADDEHYIPRAVQLDLEPQVIHFIFNSPYTKLYNPENIYL

Parental  SEHGGGAGNNWASGFSQGEKIHEDIFDIIDREADGSDSLEGFVLCHSIAGGTGSGLGSYLLERLNDRYPK
          SEHG.G.GNNWASGFSQGEKIHEDIFDIID.EADGSDSLE.FVLCHSI..GTGSGLGS.LLE.LNDRYP.
Retrocopy SEHGEGTGNNWASGFSQGEKIHEDIFDIIDWEADGSDSLEDFVLCHSITSGTGSGLGSHLLEWLNDRYPQ

Parental  KLVQTYSVFPNQDEMSDVVVQPYNSLLTLKRLTQNADCVVVLDNTALNR-IATDRLHIQNPSFSQINQLV
          KLVQTYS.FPNQDEMSDVVVQPYNSLLTLKRLTQN.DCV.VLDN.ALNR.IATD.LHI.NP.FSQINQLV
Retrocopy KLVQTYSLFPNQDEMSDVVVQPYNSLLTLKRLTQNTDCVEVLDNIALNR<IATDSLHI*NPPFSQINQLV

Parental  STIMSASTTTLRYPGYMNNDLIGLIASLIPTPRLHFLMTGYTPLTTDQSVASVRKTTVLDVMRRLLQPKN
          STIMSASTTTL.Y.GYMNND.IGLI.SLIP.P.LHFL.T.YT.LTTDQ.VA.VRKTTVLD.MR.LL..KN
Retrocopy STIMSASTTTLHYSGYMNNDPIGLITSLIPIPQLHFLLTSYTLLTTDQTVANVRKTTVLDFMRWLL*LKN

Parental  VMVSTGRDRQTNHCYIAILNIIQGEVDPTQVHKSLQRIRERKLANFIPWGPASIQVALSRKSPYLPSAHR
          VMVSTG.D..TNHCYIAILNIIQ.EVDPTQVHKSLQ.IRE.KLANFIPWGPASIQVALSRKSPYLPSAH.
Retrocopy VMVSTGQDSPTNHCYIAILNIIQWEVDPTQVHKSLQWIREWKLANFIPWGPASIQVALSRKSPYLPSAHH

Parental  VSGLMMANHTSISSLFERTCRQYDKLRKREAFLEQFRKEDMFKDNFDEMDTSREIVQQLIDEYHAATRPD
          .S.L.MANHTSISSLFE.TC.QY.KL.K.E.FLEQF.KEDMFKDN.DEMD.SR.IVQQLIDEYHAAT.PD
Retrocopy ISRLIMANHTSISSLFE*TCHQYNKLQKQETFLEQFCKEDMFKDNLDEMDISRAIVQQLIDEYHAATWPD

Parental  YISWGTQEQ
          YIS.GTQEQ
Retrocopy YIS*GTQEQ

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_3516 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_3516 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,