RetrogeneDB ID: retro_cjac_1349

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 15:69562724..69563268(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TOR1B
• Ensembl ID: ENSCJAG00000020343
• Aliases: None
• Description: torsin family 1, member B (torsin B) [Source:HGNC Symbol;Acc:11995]

Sequence

>retro_cjac_1349
GTCCAGGCCCAGTTACAGGAGTGGATTTGCAGTAGCGTGAGTGCATGTGTGAACTCTGTTTCCGTATTTGATGAGATGGG
TAGATTGCACCCTGGGATCACTGATGCAGTCAAGCCATTTCCAGACTACGAGCAGGTTGACGAAGTGTCTTAAGGCAAAA
CCATCTTCATCTTTCTCAGCAATGTAGGCAGGGACCTTATATCTAAGATGGCTCTGGACTTTTGGTGGGCTGGAAGAAAG
CAGGAAGACATTCAGCTGAAGGACCTGGAACATGTGCTGTCTGTCAGAGTCTTCAGTAATAAACACAGTGGCCTGTGGCG
CAGTGGACTGATCAACAAAAACCTGATTAATTACTTTATCCCCTTTCTGCCCTTGGAGTAGAGATGTGAAAATGTGTATG
AGGGCCGAGATGAGGGCCTGTGGTTCTGCCGTAGATGAAGACATTGTCACGAGTGTGGCAGACAAAATGACGCTTTTCCC
CAAAGACAAGAAGATCTACTCAGACAAGGGCTGCAAGACTGTGCAGTCATGGCTTGACTTCCAC

Alignment

ORF - retro_cjac_1349 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.09 %
• Parental protein coverage: 67.53 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VRDQLQKWIRGNVSACANSVFIFDEMDKLHPGIIDAIKPFLDYYEQVDGVSYRKAIFIFLSNAGGDLITK
          V..QLQ.WI...VSAC.NSV..FDEM..LHPGI.DA.KPF.DY.EQVD.VS..K.IFIFLSN.G.DLI.K
Retrocopy VQAQLQEWICSSVSACVNSVSVFDEMGRLHPGITDAVKPFPDY-EQVDEVS*GKTIFIFLSNVGRDLISK

Parental  TALDFWRAGRKREDIHLKDLEPVLSVGVFNNKHSGLWHSGLIDKNLIDYFIP-FLPLEYRHVKMCVRAEM
          .ALDFW.AGRK.EDI.LKDLE.VLSV.VF.NKHSGLW.SGLI.KNLI.YFIP.F.P...R.VKMC.RAEM
Retrocopy MALDFWWAGRKQEDIQLKDLEHVLSVRVFSNKHSGLWRSGLINKNLINYFIP>FCPWS-RDVKMCMRAEM

Parental  RARGSAVDEDIVSSVADEMTLFPKDEKIYSDKGCKTVQSRLDFH
          RA.GSAVDEDIV.SVAD.MTLFPKD.KIYSDKGCKTVQS.LDFH
Retrocopy RACGSAVDEDIVTSVADKMTLFPKDKKIYSDKGCKTVQSWLDFH

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	5.97 RPM
SRP051959_heart	0.00 RPM	5.21 RPM
SRP051959_kidney	0.00 RPM	7.06 RPM
SRP051959_liver	0.00 RPM	9.88 RPM
SRP051959_lung	0.00 RPM	6.34 RPM
SRP051959_lymph_node	0.02 RPM	6.16 RPM
SRP051959_skeletal_muscle	0.00 RPM	4.08 RPM
SRP051959_spleen	0.00 RPM	8.24 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1349 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1349 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1349 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000020343	1 retrocopy	retro_cjac_1349 ,
Callithrix jacchus	ENSCJAG00000020346	2 retrocopies	retro_cjac_2243, retro_cjac_2758,
Otolemur garnettii	ENSOGAG00000009763	1 retrocopy	retro_ogar_602,
Ictidomys tridecemlineatus	ENSSTOG00000004915	1 retrocopy	retro_itri_396,