RetrogeneDB ID: retro_nleu_71

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397320.1:8715712..8717119(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSNLEG00000026683
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: TUBG2
• Ensembl ID: ENSNLEG00000011686
• Aliases: None
• Description: None

Sequence

>retro_nleu_71
ATGCGGCAGCGTTGCGGGTGGGAGCAGCTGCAACGCCGGTGCCTGAGGAGCGATGCCGAGGGAAATCATCACCCACAATT
GGGCCAGTGCAGCAATCAGATTGAGTTCGAGTTCTGGAAACAGCTGTGCACTGAGCATGGTATCAGCCCCGAGGGCACCA
TGGAGGAGTTCACCACTGAGGGCACTGACCGCAAGGACATCTTTTTCTACCAGGCAGACGATGAGCACTACATCCCCTGG
GTTGTGCTGCTGGACCTGGAGCCCCAGGTGATCCACTCCATCCTCTACTCTCCCTATGCCAAGCTCTACAACCCAGAGAA
CATCTACCTGTCGGAGCATGGAGGAAGAGCTGGCAACAACTGGGCCAGCAGATTCTCCCAGAGAGAGAAGATCCACGAGA
ACATTTTTAACATCACAGACCAGGAGGCAGATGGTAGTGACAATCTAGATGGCTTTGTGCTGTGTCGCTCCATTGCTGGG
GGGACAGGCTCTGGCCTGGGCTCCTGCCTCTTAGAATGGCTGAATGACAGGTATCCTAAGAAGCTGGTGCAGACGTACTC
AGTGTTTCCCAACCAGGACGAGATGAGCAACGTGGTGGTCCAGCTTTATAATTCACTCCTCACACTCAAGAGGCTGATGC
AGAACGCAGACTGTGTGGTGGTGCTATACAACACAGCCCTGAACCGGATTGCCACAGACCGCCTGCACATCCAGAACCCA
TCCTTCTCTCAGACCAACCAGCTGGTGTCCACCATCATCTCGGCCAGCACCATCACCGTGCGCTACCCCGGCCACATGAA
CAATGACCTCATCAGCCTCATCGCCTCACTCATTCCCACCCCATGGCTCCACTTTCTCATGACTGGCTACACCCCGCTGA
TTATGGACCAGTCAGTGGCCAGCATGAGGAAGACCATGGTCCTGGATGTCATGAGGTGGCTGCTGCAGCCCAAGAACGTG
ACGGTGTCCACAGGCCGAGACCGCCAGACCAACCACTCCTACATCGCCATCCTCAACACCATCCAAGGAGAGGTGGACCC
CACCCAGGTCCACAAGAGCCTGCAGAGGATCCAGGAATGGAAGTTGGCCAACTTCATCCTGTGGGGCCCCACCAGCATCC
AGGTGGCCCTGTCGAGGAAGTCTCCTTACCTGCCCTTGGCCCACTGGGTCAGTGGGCTTATGATGGCCAACCACACCAGC
ATCTCCTCACTCTTCGAGAGAACCTGTCGCCAATATGACAAGCTGCGGAAGTGGGAGGTCTTCCTGGAGCCGTTCCGCAA
GGAGGACATGTTCAAGGACAACTTTGATGAGATGGACACATCTAGGGAGATTGTGCAGCAGCTCATGGATAAGTACCATG
TGGCCACACGGCCAGACTACATCTCCTGGGGCACCCAGGAGCAGTGA

Alignment

ORF - retro_nleu_71 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.81 %
• Parental protein coverage: 98.23 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QLGQCGNQIGFEFWKQLCAEHGISPEGIVEEFATEGTDRKDVFFYQADDEHYIPRAVLLDLEPRVIHSIL
          QLGQC.NQI.FEFWKQLC.EHGISPEG..EEF.TEGTDRKD.FFYQADDEHYIP..VLLDLEP.VIHSIL
Retrocopy QLGQCSNQIEFEFWKQLCTEHGISPEGTMEEFTTEGTDRKDIFFYQADDEHYIPWVVLLDLEPQVIHSIL

Parental  NSPYAKLYNPENIYLSEHGGGAGNNWASGFSQGEKIHEDIFDIIDREADGSDSLEGFVLCHSIAGGTGSG
          .SPYAKLYNPENIYLSEHGG.AGNNWAS.FSQ.EKIHE.IF.I.D.EADGSD.L.GFVLC.SIAGGTGSG
Retrocopy YSPYAKLYNPENIYLSEHGGRAGNNWASRFSQREKIHENIFNITDQEADGSDNLDGFVLCRSIAGGTGSG

Parental  LGSYLLERLNDRYPKKLVQTYSVFPNQDEMSDVVVQPYNSLLTLKRLTQNADCVVVLDNTALNRIATDRL
          LGS.LLE.LNDRYPKKLVQTYSVFPNQDEMS.VVVQ.YNSLLTLKRL.QNADCVVVL.NTALNRIATDRL
Retrocopy LGSCLLEWLNDRYPKKLVQTYSVFPNQDEMSNVVVQLYNSLLTLKRLMQNADCVVVLYNTALNRIATDRL

Parental  HIQNPSFSQINQLVSTIMSASTTTLRYPGYMNNDLIGLIASLIPTPRLHFLMTGYTPLTTDQSVASVRKT
          HIQNPSFSQ.NQLVSTI.SAST.T.RYPG.MNNDLI.LIASLIPTP.LHFLMTGYTPL..DQSVAS.RKT
Retrocopy HIQNPSFSQTNQLVSTIISASTITVRYPGHMNNDLISLIASLIPTPWLHFLMTGYTPLIMDQSVASMRKT

Parental  TVLDVMRRLLQPKNVMVSTGRDRQTNHCYIAILNIIQGEVDPTQVHKSLQRIRERKLANFIPWGPASIQV
          .VLDVMR.LLQPKNV.VSTGRDRQTNH.YIAILN.IQGEVDPTQVHKSLQRI.E.KLANFI.WGP.SIQV
Retrocopy MVLDVMRWLLQPKNVTVSTGRDRQTNHSYIAILNTIQGEVDPTQVHKSLQRIQEWKLANFILWGPTSIQV

Parental  ALSRKSPYLPSAHRVSGLMMANHTSISSLFERTCRQYDKLRKREAFLEQFRKEDMFKDNFDEMDTSREIV
          ALSRKSPYLP.AH.VSGLMMANHTSISSLFERTCRQYDKLRK.E.FLE.FRKEDMFKDNFDEMDTSREIV
Retrocopy ALSRKSPYLPLAHWVSGLMMANHTSISSLFERTCRQYDKLRKWEVFLEPFRKEDMFKDNFDEMDTSREIV

Parental  QQLIDEYHAATRPDYISWGTQEQ
          QQL.D.YH.ATRPDYISWGTQEQ
Retrocopy QQLMDKYHVATRPDYISWGTQEQ

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Nomascus leucogenys was not studied using RNA-Seq expression data.

ChIP-Seq

Nomascus leucogenys was not studied using ChIP-Seq data.

EST

Nomascus leucogenys was not studied using EST data.

TSS

Nomascus leucogenys was not studied using FANTOM5 data.

Lab

retro_nleu_71 was not experimentally validated.

Homology

Retrocopy orthology:

Nomascus leucogenys 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,