RetrogeneDB ID: retro_cjac_1632

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 18:14872699..14874044(+)
• Located in intron of: ENSCJAG00000004757

Retrocopy information

• Ensembl ID: ENSCJAG00000004766
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

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

Sequence

>retro_cjac_1632
ATGAGGGAGATCGTGCACATCCAGGCCGGCCAGTGCGGCAACCAGATCGGGGCCAAGTTCTGGGAAGTCATCAGTGACGA
GCATGGCATAGACGCCAGTGGCAACTACGTGGGCGACTCTGACTTGCAGCTGGAGCGGATCAGCGTCTACTACAATGAGG
CATCTTCTCACAAGTATGTGCCTCGGGCCATCCTGGTGGACCTGGAGCCCGATACCATGGACAGCGTCCGCTCTGGGGCC
TTCGGACATCTTTTCAGGCCCGACAACTTCATCTTCGGTCAGAGTGGGGCCGGCAACAACTGGGCCAAGGGCCACTACAC
GGAGGGTGCGGAGCTGGTGGATTCGGTCCTGGACGTCGTGCGGAAGGAGTGTGAAAACTGCGACTGCCTCCAGGGCTTCC
AGCTGACCCACTTGCTGGGCGGGGGCACGGGCTCTGGCATGGGCACGCTGCTCATCAGCAAGGTGCGCGAGGAGTACCCC
GACCGCATCATGAACACCTTCAGCGTGGTGCCCTCGCCCAAAGTGTCCGACACGGTGGTGGAGCCTTACAACGCCACGCT
GTCCATCCACCAGCTGGTGGAGAACACAGATGAGACCTACTGCATCGACAACGAGGCGCTCTACGACATCTGCTTCCGCA
CCCTCAAGCTGGCCACGCCCACCTACGGGGACCTCAACCACCTGGTGTCGGCCACCATGAGCGGGGTGACCACCTCGCTG
CGCTTCCCAGGGCAGCTCAACGCCGACCTGCGCAAGCTGGCGGTGAACATGGTGCCCTTCCCCCGCCTGCACTTCTTCAT
GCCCGGCTTCGCGCCCCTCACGGCCCGGGGCAGCCAGCAGTACCGGGCCCTGACCGTGCCCGAGCTCACCCAGCAGATGT
TTGACGCCAAGAACATGATGGCCACCTGCGACCCACGCCACGGCCGCTACCTGGATGGCCACTGTGTTCCGGGGCCGCAT
GTCCATGAAGGAGGTGGACGAGCAGATGCTGGCCATCCAGAGCAAGAACAGCAGCTACTTCGTGGAGTGGATCCCCAACA
ATGTGAAGGTGGCCGTGTGCGACATCCCGCCCCGCGGCCTCAAGATGTCCTCCACCTTCATCGGCAACAGCACGGCCATC
CAGGAGCTGTTCAAGCGCATCTCTGAGCAGTTCACGGCCATGTTCCGGCGCAAGGCCTTCCTGCACTGGTACACGGGCGA
GGGCATGGACGAGATGGAGTTCACCGAGGCTGAGAGCAACATGAACGACCTGGTGTCCGAGTACCAGCAGTACCAGGACG
CCACGGCTGAGGAGGAGGGCGAGATGTATGAAGATGACGACGAGGAGTCGGAGGCCCAGGGCCCG

Alignment

ORF - retro_cjac_1632 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.56 %
• Parental protein coverage: 99.78 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MREIVHIQAGQCGNQIGTKFWEVISDEHGIDPAGGYVGDSALQLERINVYYNESSSQKYVPRAALVDLEP
          MREIVHIQAGQCGNQIG.KFWEVISDEHGID..G.YVGDS.LQLERI.VYYNE.SS.KYVPRA.LVDLEP
Retrocopy MREIVHIQAGQCGNQIGAKFWEVISDEHGIDASGNYVGDSDLQLERISVYYNEASSHKYVPRAILVDLEP

Parental  GTMDSVRSGPFGQLFRPDNFIFGQTGAGNNWAKGHYTEGAELVDAVLDVVRKECEHCDCLQGFQLTHSLG
          .TMDSVRSG.FG.LFRPDNFIFGQ.GAGNNWAKGHYTEGAELVD.VLDVVRKECE.CDCLQGFQLTH.LG
Retrocopy DTMDSVRSGAFGHLFRPDNFIFGQSGAGNNWAKGHYTEGAELVDSVLDVVRKECENCDCLQGFQLTHLLG

Parental  GGTGSGMGTLLISKIREEFPDRIMNTFSVMPSPKVSDTVVEPYNATLSVHQLVENTDETYCIDNEALYDI
          GGTGSGMGTLLISK.REE.PDRIMNTFSV.PSPKVSDTVVEPYNATLS.HQLVENTDETYCIDNEALYDI
Retrocopy GGTGSGMGTLLISKVREEYPDRIMNTFSVVPSPKVSDTVVEPYNATLSIHQLVENTDETYCIDNEALYDI

Parental  CFRTLKLTTPTYGDLNHLVSATMSGVTTSLRFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTSRGSQQ
          CFRTLKL.TPTYGDLNHLVSATMSGVTTSLRFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLT.RGSQQ
Retrocopy CFRTLKLATPTYGDLNHLVSATMSGVTTSLRFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTARGSQQ

Parental  YRALTVPELTQQMFDARNMMAACDPRHGRYLTVATVFRGP-MSMKEVDEQMLAIQSKNSSYFVEWIPNNV
          YRALTVPELTQQMFDA.NMMA.CDPRHGRYL....V..GP.MSMKEVDEQMLAIQSKNSSYFVEWIPNNV
Retrocopy YRALTVPELTQQMFDAKNMMATCDPRHGRYLDGHCV-PGP>MSMKEVDEQMLAIQSKNSSYFVEWIPNNV

Parental  KVAVCDIPPRGLKMASTFIGNSTAIQELFKRISEQFSAMFRRKAFLHWFTGEGMDEMEFTEAESNMNDLV
          KVAVCDIPPRGLKM.STFIGNSTAIQELFKRISEQF.AMFRRKAFLHW.TGEGMDEMEFTEAESNMNDLV
Retrocopy KVAVCDIPPRGLKMSSTFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLV

Parental  SEYQQYQDATINDGEEAFEDEEEEMDGQAP
          SEYQQYQDAT.....E..ED..EE...Q.P
Retrocopy SEYQQYQDATAEEEGEMYEDDDEESEAQGP

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	0.64 RPM	9.52 RPM
SRP051959_heart	0.61 RPM	10.96 RPM
SRP051959_kidney	0.75 RPM	2.20 RPM
SRP051959_liver	0.43 RPM	19.13 RPM
SRP051959_lung	0.63 RPM	14.38 RPM
SRP051959_lymph_node	0.43 RPM	2.63 RPM
SRP051959_skeletal_muscle	0.98 RPM	3.82 RPM
SRP051959_spleen	0.55 RPM	2.04 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1632 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1632 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1632 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,