RetrogeneDB ID: retro_cjac_1861

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 2:160122824..160124056(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TUBA1B
• Ensembl ID: ENSCJAG00000020874
• Aliases: None
• Description: tubulin, alpha 1b [Source:HGNC Symbol;Acc:18809]

Sequence

>retro_cjac_1861
ATGTGTGAGTGCATCTCCATCACATCGGTCAGGCTGGTGTTCAGGTTGGCAATGCCCGCTGGGATCCCTACTGCCTGGAA
CATGGCATACAGCCTAACGGCTAGATGCCAAGTGACAAGACTACTCGGGAGGAGATGACTCTTTCAACACCTTCTTCAGT
AAGAATGGTTCTAGCAAGCTTGTGCCCAGGGCAGTGTTTGTAGACCTGGAACCCACTGTAATTGATGAAGTTTGCACTGG
CACCTACCACCAGCTCTTCCACCCTGAGCATCTCACCACAGACAAGGAAGATGCTGCCAATAACTATGCCTGAAGGCACT
ACACCATTGGCCAGGAGATCACTGACCTCGTGTTGGACCAAATCTGTAAACTGGCTGACCAGTGCACAGTTCTCTCGGGC
TTCTTGGTTTTCCACAGCTTTGGTGCAGGAACTGGTTCTGGGTTCACCTCCCTGCTCATGAAACAACTTTCAGTTGATTA
TGGCAAAAAGTCCAAGCTGGAATTCTAAATTTACTCAGTGCCCCAGGTTTCCACAGCTGTAGTTGAGCCCTACAACTCCA
TCCTCACCACCCACACCCTGGAGCACTCTGATTGTGTCTTCAGGGTAGACAATAAGGCCGTCTACGACATCTGTCATAGA
ACCTTGATATCGAACACCCAATCTGTACTGAAGAGGTTGATACGTCAAATTCTGTCCTCCACTACTGCTTCCCTGAGATT
TGATGGAGCCCTAAATGTTGATCTGACAGAATTCCAAACCAACTTGGTGCCCTATCCCTGCATCCATCTCCCTCTGGACA
CATATGCCCCATCATTTCTGCTGAGAAAGCCTACAATGAAACAGCTTTCTGTAGCAGAGACTGCCAGTGCTTGCTTTGAG
CCTGCCATGCAGATGATGAAAGGTGAGCCTTGCCATGGTAAAGACATGGCTTGCTGCCTTTTGTACCATGGTGACGTGGT
TCCCAAAGATGTCAATGCTGCCATTGCCACCATCAAGAGCAACTGTACTGCCCAGTTTGTCGTTTGGTGCCCCCCTGCCT
TCAAGGTTGGCATTAACTACCACCCCTCCCACTGTGGTGACTGGTGGAGACCTGACCAAGATACAGAGAGCTCTGTGCAT
GCTGACCGATACCACAGCCATTGCTTAGGCCTGCGCTCGCCTGGACCACATGTTTGACTTGATGTATGCCAAGCGTGCAC
AGGTGTTCACTGGTACGTAGGTGAGGGAAGGG

Alignment

ORF - retro_cjac_1861 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.25 %
• Parental protein coverage: 92.24 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  MRECISI-HVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTI-GGGDDSFNTFFSETGAGKHVPRAVFV
          M.ECISI.H.GQAGVQ.GNA.W..YCLEHGIQP.G.MPSDKT...GGDDSFNTFFS..G..K.VPRAVFV
Retrocopy MCECISI<HIGQAGVQVGNARWDPYCLEHGIQPNG*MPSDKTT<SGGDDSFNTFFSKNGSSKLVPRAVFV

Parental  DLEPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLDRIRKLADQCTGLQGFLVF
          DLEPTVIDEV.TGTY.QLFHPE.L.T.KEDAANNYA..HYTIG.EI.DLVLD.I.KLADQCT.L.GFLVF
Retrocopy DLEPTVIDEVCTGTYHQLFHPEHLTTDKEDAANNYA*RHYTIGQEITDLVLDQICKLADQCTVLSGFLVF

Parental  HSFGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTAVVEPYNSILTTHTTLEHSDCAFMVDNEA
          HSFG.GTGSGFTSLLM..LSVDYGKKSKLEF.IY..PQVSTAVVEPYNSILTTHT.LEHSDC.F.VDN.A
Retrocopy HSFGAGTGSGFTSLLMKQLSVDYGKKSKLEF*IYSVPQVSTAVVEPYNSILTTHT-LEHSDCVFRVDNKA

Parental  IYDICRRNLDIERPTYTNLNRLISQIVSSITASLRFDGALNVDLTEFQTNLVPYPRIHFPLATYA-PVIS
          .YDIC.R.L.....T...L.RLI.QI.SS.TASLRFDGALNVDLTEFQTNLVPYP.IH.PL.TYA.P.IS
Retrocopy VYDICHRTLISN--TQSVLKRLIRQILSSTTASLRFDGALNVDLTEFQTNLVPYPCIHLPLDTYA<PIIS

Parental  AEKAYHE-QLSVAEITNACFEPANQMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRSIQFVDW
          AEKAY.E.QLSVAE...ACFEPA.QM.K..P.HGK.MACCLLY.GDVVPKDVNAAIATIK.....QFV.W
Retrocopy AEKAYNE>QLSVAETASACFEPAMQMMKGEPCHGKDMACCLLYHGDVVPKDVNAAIATIKSNCTAQFVVW

Parental  CPTGFKVGINYQ-PPTVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEE
          CP..FKVGINY..PPTVV.GGDL.K.QRA.CML..TTAIA.A.ARLDH.FDLMYAKRA.V....G....E
Retrocopy CPPAFKVGINYH>PPTVVTGGDLTKIQRALCMLTDTTAIA*ACARLDHMFDLMYAKRAQV--FTGT*VRE

Parental  G
          G
Retrocopy G

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	0.35 RPM	127.13 RPM
SRP051959_heart	0.26 RPM	89.60 RPM
SRP051959_kidney	0.13 RPM	55.67 RPM
SRP051959_liver	0.61 RPM	43.93 RPM
SRP051959_lung	0.41 RPM	84.92 RPM
SRP051959_lymph_node	0.27 RPM	68.26 RPM
SRP051959_skeletal_muscle	0.20 RPM	29.35 RPM
SRP051959_spleen	0.23 RPM	80.69 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1861 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1861 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1861 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 29 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000012244	1 retrocopy	retro_btau_402,
Choloepus hoffmanni	ENSCHOG00000008444	2 retrocopies	retro_chof_179, retro_chof_360,
Callithrix jacchus	ENSCJAG00000020874	2 retrocopies	retro_cjac_1603, retro_cjac_1861 ,
Callithrix jacchus	ENSCJAG00000020894	2 retrocopies	retro_cjac_1209, retro_cjac_3157,
Felis catus	ENSFCAG00000028689	3 retrocopies	retro_fcat_1802, retro_fcat_254, retro_fcat_798,
Homo sapiens	ENSG00000123416	1 retrocopy	retro_hsap_808,
Macropus eugenii	ENSMEUG00000010779	2 retrocopies	retro_meug_1648, retro_meug_2174,
Macropus eugenii	ENSMEUG00000011167	4 retrocopies	retro_meug_1121, retro_meug_157, retro_meug_1616, retro_meug_1964,
Monodelphis domestica	ENSMODG00000015206	2 retrocopies	retro_mdom_1632, retro_mdom_348,
Mus musculus	ENSMUSG00000023004	6 retrocopies	retro_mmus_1562, retro_mmus_1607, retro_mmus_1742, retro_mmus_1987, retro_mmus_3297, retro_mmus_3327,
Otolemur garnettii	ENSOGAG00000009435	1 retrocopy	retro_ogar_240,
Pan troglodytes	ENSPTRG00000012950	1 retrocopy	retro_ptro_2158,
Sus scrofa	ENSSSCG00000000190	2 retrocopies	retro_sscr_380, retro_sscr_702,