RetrogeneDB ID: retro_cjac_1144

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 13:42391351..42392637(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TUBB3
• Ensembl ID: ENSCJAG00000010530
• Aliases: None
• Description: tubulin, beta 3 class III [Source:HGNC Symbol;Acc:20772]

Sequence

>retro_cjac_1144
GGGGCCAAGTTCTGGGAAGTCATCAGTGATGAGCATGGCATAGACCCCAGTGGCAACTATGTGGGCGACTCTGACTTGCA
GCTGGAGTGGATCAGCGTCTACTACAATGAGGCATCTTCTCACAAATATGTGCCTCGGGCCATCCTGGTGGACCTGGAGC
CTGGAACCATGGACAGCGCCTGCCCTGGAGCCTTCGGACATCTTTTCAGGCCTGACAACTTCATCTTCGGTCAGAGTGGG
GCCGGCAACAACTGGGCCAAGGGCCACTACACGGAGGCGGAGCTGGTGGATTCGGCCCTAGACGTCGTGCGGAAGGAGTG
TGAAAACTGCGACTGCCTGCAGGGCTTCCAGCTGACCAACTCGCTGGGCGGGGGCATAGGCTCTGGCATGGGCACGCTGC
TCATCAGCAAGGTACACCAGGAGTACCCCGACCGCATCATGAACACCTTCAGCGTGGTGCCCTAGTCCAAAGTGTCCGAC
ACAGTGGTGGAGCCTTACAACGCCACGCTGCCCATCCACCAGCTGGTGGAGAACACGGATGAGACCTACTGCATCGACAA
CAAGACGCTCTACGACATCGGCTTCCGCACCCTCAAGCTGGCCACGCCCACCTACGGGGACTTCAATCACCTGGTGTCGG
CCACCATGAGCTGGGTGACCACCTCGCTGCGCTTCCCAGGGCAGCTCAACGCCGATCTGTGCAAGCTGGCGGTGAACATG
GTGCCCTTCCCCCGCCTGCACTTCTTCATGCCCAACTTTGCGCCCCTACGGCCCGGGGCAGCCAGTAGTACCGGGCCCTG
ACCGTGCCCGAGCTCACTCAGCAGATATTTGACGCCAAGAACATGATAGCCGCCTGCTACCCACGCCACGGCCTCTACCT
GACCGTGGCCACTGTGTTCCGGGGCCGCATGTCCATGAAGGAGGTGGACGAGCAGATGCTGGCCATCCAGAGCAAGAACA
GCAGCTACTTCGTGGAGTGGATCCCCAACAATGTGTGCGACATCCCACCCCACGGCCTCAAGATGTCCTCCACCTTCATT
GGCAACAGCACTGCCATCCAGGAGCTGTTCAAGCTCATCTTTGAGCAGTTCACAGCCATGTTCCAGCGCAAGGCCTTCCT
GCACTGGTACACGGGCGGGGGCATGGACGAGATGGAGTTCACTGAGGCCGAGAGCAACATGAACGACCTGGTGTCCGAGT
ACCAGCAGTACTAGGACTCCACGGCCGAGGAGGAGGGCGAGAGGTATGAAGACTAGGACGAGGAGTCAGAGGCCCAGGGC
CCGAAG

Alignment

ORF - retro_cjac_1144 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.57 %
• Parental protein coverage: 54.18 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GSEFWEVISDEHGIDPSGNYVGDSDLQLERISVYYNEASSHKYVPRAILVDLEPGTMDSVRSGAFGHLFR
          G..FWEVISDEHGIDPSGNYVGDSDLQLE.ISVYYNEASSHKYVPRAILVDLEPGTMDS...GAFGHLFR
Retrocopy GAKFWEVISDEHGIDPSGNYVGDSDLQLEWISVYYNEASSHKYVPRAILVDLEPGTMDSACPGAFGHLFR

Parental  PDNFIFGQSGAGNNWAKGHYTEGAELVDSVLDVVRKECENCDCLQGFQLTHSLGGGTGSGMGTLLISKVR
          PDNFIFGQSGAGNNWAKGHYTE.AELVDS.LDVVRKECENCDCLQGFQLT.SLGGG.GSGMGTLLISKV.
Retrocopy PDNFIFGQSGAGNNWAKGHYTE-AELVDSALDVVRKECENCDCLQGFQLTNSLGGGIGSGMGTLLISKVH

Parental  EEYPDRIMNTFSVVPSPKVSDTVVEPYNATLSIHQLVENTDETYCIDNEALYDICFRTLKLATPTYGDLN
          .EYPDRIMNTFSVVP..KVSDTVVEPYNATL.IHQLVENTDETYCIDN..LYDI.FRTLKLATPTYGD.N
Retrocopy QEYPDRIMNTFSVVP*SKVSDTVVEPYNATLPIHQLVENTDETYCIDNKTLYDIGFRTLKLATPTYGDFN

Parental  HLVSATMSGVTTSLRFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPL-TARGSQQYRALTVPELTQQMFD
          HLVSATMS.VTTSLRFPGQLNADL.KLAVNMVPFPRLHFFMP.FAPL.TARGSQ.YRALTVPELTQQ.FD
Retrocopy HLVSATMSWVTTSLRFPGQLNADLCKLAVNMVPFPRLHFFMPNFAPL<TARGSQ*YRALTVPELTQQIFD

Parental  AKNMMAACDPRHGRYLTVATVFRGRMSMKEVDEQMLAIQSKNSSYFVEWIPNNVKVAVCDIPPRGLKMSS
          AKNM.AAC.PRHG.YLTVATVFRGRMSMKEVDEQMLAIQSKNSSYFVEWIPNNV....CDIPP.GLKMSS
Retrocopy AKNMIAACYPRHGLYLTVATVFRGRMSMKEVDEQMLAIQSKNSSYFVEWIPNNV----CDIPPHGLKMSS

Parental  TFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVSEYQQYQDATAEEEGE
          TFIGNSTAIQELFK.I.EQFTAMF.RKAFLHWYTG.GMDEMEFTEAESNMNDLVSEYQQY.D.TAEEEGE
Retrocopy TFIGNSTAIQELFKLIFEQFTAMFQRKAFLHWYTGGGMDEMEFTEAESNMNDLVSEYQQY*DSTAEEEGE

Parental  MYEDDDEESEAQGPK
          .YED.DEESEAQGPK
Retrocopy RYED*DEESEAQGPK

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	0.67 RPM
SRP051959_heart	0.02 RPM	1.11 RPM
SRP051959_kidney	0.00 RPM	0.29 RPM
SRP051959_liver	0.06 RPM	0.26 RPM
SRP051959_lung	0.00 RPM	0.65 RPM
SRP051959_lymph_node	0.00 RPM	0.91 RPM
SRP051959_skeletal_muscle	0.00 RPM	0.22 RPM
SRP051959_spleen	0.00 RPM	0.44 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1144 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1144 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1144 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 9 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,
Homo sapiens	ENSG00000258947	1 retrocopy	retro_hsap_155,
Gorilla gorilla	ENSGGOG00000002192	1 retrocopy	retro_ggor_2364,
Nomascus leucogenys	ENSNLEG00000015940	1 retrocopy	retro_nleu_3106,