RetrogeneDB ID: retro_cjac_2667

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 5:132503819..132504955(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TUBB6
• Ensembl ID: ENSCJAG00000004826
• Aliases: None
• Description: None

Sequence

>retro_cjac_2667
ATAAGGGAGATCGTGTACATCCAGGCGGGCCAGTGCGGGAACCAGATCGGCACCAAGTTTTGGGAAGTGATCAGCGATGA
GCACGGCATCTACCCGGCCGGTGGCTACGTGGGAGACTCAGCGCTGCAACTGGAGAGAATCAACGCCTACTACAATGAGT
CATCGTCTCAGAAATATGTGCCCAGGGACGCCCTGGTGGACTTAGAGCCAGGCCCCCTGGAGAGCGTGCGCTCTGGGCCT
TTCGGGCAGCTTTTCCGGCCTGACAACTTCATCTTTGGCCAGACGGGCGGGCGCAGGGAACAACTGGGGGAAGGGGCACT
ACACCGAGGGTGCGAAGCTGGTAGACGCAGTGCTGGATGTGGTGCGGAAAGAGTGCGAGCACTGCGACTGCCGGCAGGGC
TTCCAGCTCACACACTCGGTGGGCGGCGGCACGGGCTCGGGCATGGGAGCGCTGCTCATCAGCAAGATTCGCGAGGAGTT
GCCGGACCGCGTCATGAACACCTTCAGCGTCATGCCCTCGCCCAAGGTGTCGGACACGGTGGTGGAGCCCTACAGTGCCA
CGCTGTCGGTGCACCAGCTGGTGGAAAATACCGATGAGACCTACTGCATCGACAACGAGGCGCTCTACGACAATTGCTTC
CGCACCCTCAAGCTGACCACGCCCACCTACGGGGACCTCAACCACCCCGGGGTGGTGTCAGCCACCATGAGCGGGGTCAC
CACCTCGCTGCGCTTCCCAGGCCAGCTCAACGTCGACCTGTGCAAGCTGGCGGTGAACATGGTGCCCTTCCCATGCCTGC
ACTTCTTCATGCCCGGCTTTGCGTCACTTACCAGCCGCGGCAGCCAGCCGCGACCTGACCCTGACCGTGCCCGAGCTCAC
CCAGCAGATGTTCGACGCCAGGAACATGATGGCCGTCTACGACCCCCGCCGTGGCCGCTACCTGACCGTGGCCACCGTGT
TCCGCGGCCCCATGTCCATGAAGGAGGTGGACGAACAGATGCTGGCCATCCAGAGTAAGAACAGAAGCTACTTCGGGGAG
TGGATCCCCAACAACATGAAGGCTGCCATGTGTGACATCCCGCCTCGCGGCCTGAAGATGGCCTCAACGTTCATCGGCTA
TCCAGGAGCTGTTCAA

Alignment

ORF - retro_cjac_2667 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.05 %
• Parental protein coverage: 83.33 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MREIVHIQAGQCGNQIGTKFWEVISDEHGIDPAGGYVGDSALQLERINVYYNESSSQKYVPRAALVDLEP
          .REIV.IQAGQCGNQIGTKFWEVISDEHGI.PAGGYVGDSALQLERIN.YYNESSSQKYVPR.ALVDLEP
Retrocopy IREIVYIQAGQCGNQIGTKFWEVISDEHGIYPAGGYVGDSALQLERINAYYNESSSQKYVPRDALVDLEP

Parental  GTMDSVRSGPFGQLFRPDNFIFGQTGA-GNNWAKGHYTEGAE-LVDAVLDVVRKECEHCDCLQGFQLTHS
          G...SVRSGPFGQLFRPDNFIFGQTG........G....G.E.LVDAVLDVVRKECEHCDC.QGFQLTHS
Retrocopy GPLESVRSGPFGQLFRPDNFIFGQTGGRREQLGEGALHRGCE>LVDAVLDVVRKECEHCDCRQGFQLTHS

Parental  LGGGTGSGMGTLLISKIREEFPDRIMNTFSVMPSPKVSDTVVEPYNATLSVHQLVENTDETYCIDNEALY
          .GGGTGSGMG.LLISKIREE.PDR.MNTFSVMPSPKVSDTVVEPY.ATLSVHQLVENTDETYCIDNEALY
Retrocopy VGGGTGSGMGALLISKIREELPDRVMNTFSVMPSPKVSDTVVEPYSATLSVHQLVENTDETYCIDNEALY

Parental  DICFRTLKLTTPTYGDLNH--LVSATMSGVTTSLRFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTSR
          D.CFRTLKLTTPTYGDLNH...VSATMSGVTTSLRFPGQLN.DL.KLAVNMVPFP.LHFFMPGFA.LTSR
Retrocopy DNCFRTLKLTTPTYGDLNHPGVVSATMSGVTTSLRFPGQLNVDLCKLAVNMVPFPCLHFFMPGFASLTSR

Parental  GSQ-QYRALTVPELTQQMFDARNMMAACDPRHGRYLTVATVFRGPMSMKEVDEQMLAIQSKNSSYFVEWI
          GSQ.....LTVPELTQQMFDARNMMA..DPR.GRYLTVATVFRGPMSMKEVDEQMLAIQSKN.SYF.EWI
Retrocopy GSQ>RDLTLTVPELTQQMFDARNMMAVYDPRRGRYLTVATVFRGPMSMKEVDEQMLAIQSKNRSYFGEWI

Parental  PNNVKVAVCDIPPRGLKMASTFIGNSTAIQ
          PNN.K.A.CDIPPRGLKMASTFIG...A.Q
Retrocopy PNNMKAAMCDIPPRGLKMASTFIGYPGAVQ

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	0.00 RPM	9.52 RPM
SRP051959_heart	0.02 RPM	10.96 RPM
SRP051959_kidney	0.00 RPM	2.20 RPM
SRP051959_liver	0.00 RPM	19.13 RPM
SRP051959_lung	0.03 RPM	14.38 RPM
SRP051959_lymph_node	0.00 RPM	2.63 RPM
SRP051959_skeletal_muscle	0.04 RPM	3.82 RPM
SRP051959_spleen	0.00 RPM	2.04 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2667 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2667 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2667 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000004826	2 retrocopies	retro_cjac_1632, retro_cjac_2667 ,
Callithrix jacchus	ENSCJAG00000010101	1 retrocopy	retro_cjac_800,
Callithrix jacchus	ENSCJAG00000010530	1 retrocopy	retro_cjac_1144,
Callithrix jacchus	ENSCJAG00000011697	1 retrocopy	retro_cjac_3284,
Callithrix jacchus	ENSCJAG00000017637	1 retrocopy	retro_cjac_1649,