RetrogeneDB ID: retro_cjac_4142

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: X:20233986..20235335(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TUBG1
• Ensembl ID: ENSCJAG00000004907
• Aliases: None
• Description: None

Sequence

>retro_cjac_4142
ATGCTCAGGGAAATCATCACCCTACAGTTGGGCCAGTGTGGCAATCAGATTGGGTTCGAGTTCTGGAAACAGCTGTGCAC
CGAGCATGGTATCAGCTCCAAGGGCATCATGGGAGAGTTCACCACTGAGGGCACTGACCACAAGGATGTCTTTGTCTACC
AGGCAGACAATGAGCACTACATCACCTGGGCCATACTGCTGGACCTGGAGCCCTGGGTGATCCACTCCATCCTCAACTCC
CCCCTATGCCAAGTTCTGTAACCCAGAGAACATCTACCTGTCGAAGCAGGGAGGAGGAGCTGGCAATAACTAGGCCAGCA
GATTTTCCCAGGGAGAGAAGATCCATGAGGACATTTTTGACATCATTGACTAGGAGGCAGATGGTAGTTACAGTCTAGAA
GGCTTTGTGCTGTGTCACTCCATTGCTGGGGAGCAGGCTCTGGCCTGGGTGCCTACCTCTTAGAATGACTGAATGGCAGT
TATCCTAAGAAGCTGGTGCAGACATAGTCAATGTTTCCCAACCAGGATGAGATGAGCGATGTGGTGGTCCAGCCTTACAT
TTCACTCTTCACACTCAAGAGGCTGATGCAGAACACAGACTGTGTTGTGGTGCTGGATGACACAGCCCTGAACTGGATTG
CCACAGACCACCTGCACATCCAGAATCCATCCTTCTACCAGATCAACCAACTGGTGTCCACCATCATGTCAACCAGCAGC
ACCACCCTACACTACCCCGACCACATGAACAGTGACCTCATCGGCCTCATCTTCTTGCTCATTCCCACTCCATGGCTCCA
ATTCCTCATGACCAGCTACACCCCACTCACCAAGGACCAGTCAATGGCCAGCATGAGGAAGACCACAGTCCTGGATGTCA
TGAGATGGCTACTGCAGCCCAAGAACATGATGGTATCCACAGGCCAAGACTACCAGACCAACCACTGCTCCATCACCATC
CTCAGCATCATCCACGGACAGGTGGACCCCACGCAGGTCCACAAGAGCCTGCAGAGCATCCAGGAACCGAAGTTGGCCAA
CTTCATCTCATGGGGCCCTGCCAGCATCCAGCTGGCCCTGTTGAGGAAGTCTCCCTACCTGCCTTCAGCCACCGGGTCAG
CGAGCTCATGATGGCCAACCACACCAGCATCTCCTTGCTCTTCAAGAGAACATGTCACCAATATGACAAGCTGTGGAAGC
AGGAGGCCTTCCTGGAGCAGTTCCGCAAGGAGGACATGTTCCAGGACTTTGATGAGATGGACATGTCCAGGGAGATTGTG
CAGCAGTTCATTGATGAGTGCCATGTGGCCACACGACCAGACTACATCTGCTGGGGTGCCCAGGAGCAG

Alignment

ORF - retro_cjac_4142 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.5 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MPREIITLQLGQCGNQIGFEFWKQLCAEHGISPEGIVEEFATEGTDRKDVFFYQADDEHYIPRAVLLDLE
          M.REIITLQLGQCGNQIGFEFWKQLC.EHGIS..GI..EF.TEGTD.KDVF.YQAD.EHYI..A.LLDLE
Retrocopy MLREIITLQLGQCGNQIGFEFWKQLCTEHGISSKGIMGEFTTEGTDHKDVFVYQADNEHYITWAILLDLE

Parental  PRVIHSILNSP-YAKLYNPENIYLSEHGGGAGNNWASGFSQGEKIHEDIFDIIDREADGSDSLEGFVLCH
          P.VIHSILNSP.YAK..NPENIYLS..GGGAGNN.AS.FSQGEKIHEDIFDIID.EADGS.SLEGFVLCH
Retrocopy PWVIHSILNSP>YAKFCNPENIYLSKQGGGAGNN*ASRFSQGEKIHEDIFDIID*EADGSYSLEGFVLCH

Parental  SIAG-GTGSGLGSYLLERLNDRYPKKLVQTYSVFPNQDEMSDVVVQPYNSLLTLKRLTQNADCVVVLDNT
          SIAG.G.GSGLG.YLLE.LN..YPKKLVQT.S.FPNQDEMSDVVVQPY.SL.TLKRL.QN.DCVVVLD.T
Retrocopy SIAG<GAGSGLGAYLLE*LNGSYPKKLVQT*SMFPNQDEMSDVVVQPYISLFTLKRLMQNTDCVVVLDDT

Parental  ALNRIATDRLHIQNPSFSQINQLVSTIMSASTTTLRYPGYMNNDLIGLIASLIPTPRLHFLMTGYTPLTT
          ALN.IATD.LHIQNPSF.QINQLVSTIMS.S.TTL.YP..MN.DLIGLI..LIPTP.L.FLMT.YTPLT.
Retrocopy ALNWIATDHLHIQNPSFYQINQLVSTIMSTSSTTLHYPDHMNSDLIGLIFLLIPTPWLQFLMTSYTPLTK

Parental  DQSVASVRKTTVLDVMRRLLQPKNVMVSTGRDRQTNHCYIAILNIIQGEVDPTQVHKSLQRIRERKLANF
          DQS.AS.RKTTVLDVMR.LLQPKN.MVSTG.D.QTNHC.I.IL.II.G.VDPTQVHKSLQ.I.E.KLANF
Retrocopy DQSMASMRKTTVLDVMRWLLQPKNMMVSTGQDYQTNHCSITILSIIHGQVDPTQVHKSLQSIQEPKLANF

Parental  IPWGPASIQVALSRKSPYLPSA-HRVSGLMMANHTSISSLFERTCRQYDKLRKREAFLEQFRKEDMFKEN
          I.WGPASIQ.AL.RKSPYLPSA.HRVS.LMMANHTSIS.LF.RTC.QYDKL.K.EAFLEQFRKEDMF...
Retrocopy ISWGPASIQLALLRKSPYLPSA<HRVSELMMANHTSISLLFKRTCHQYDKLWKQEAFLEQFRKEDMF-QD

Parental  FDEMDTSREIVQQLIDEYHAATRPDYISWGTQEQ
          FDEMD.SREIVQQ.IDE.H.ATRPDYI.WG.QEQ
Retrocopy FDEMDMSREIVQQFIDECHVATRPDYICWGAQEQ

Legend:

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

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP051959_colon	0.04 RPM	3.17 RPM
SRP051959_heart	0.11 RPM	8.00 RPM
SRP051959_kidney	0.29 RPM	6.52 RPM
SRP051959_liver	0.41 RPM	3.14 RPM
SRP051959_lung	0.21 RPM	4.99 RPM
SRP051959_lymph_node	0.11 RPM	3.63 RPM
SRP051959_skeletal_muscle	0.26 RPM	10.50 RPM
SRP051959_spleen	0.34 RPM	4.33 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_4142 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_4142 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_4142 has 0 orthologous retrocopies within eutheria group .

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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,