RetrogeneDB ID: retro_cjac_1680

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 18:28088560..28089187(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TTC33
• Ensembl ID: ENSCJAG00000007398
• Aliases: None
• Description: tetratricopeptide repeat domain 33 [Source:HGNC Symbol;Acc:29959]

Sequence

>retro_cjac_1680
ATTCTTGAATGCCGTGCTGAGAAGAGTAAACAGCTGAAGGATGAAGGAGCCAGTTTGGCTGAAAATAAAAGATACCAGTA
GGCAGTTCAGAAGTGGGATGAAGTACTACAGTTAACTCCAAATCATGCTACCCTATATGAGATGAAATCACAGGTGCTAA
TGTCTCTGCATGAAATGTTCCCAGCAGTACCTGCAGCAGAAATCAGCGTGCAGCAAAATCCACATTCGTGGGAGTCTTGG
CAAACTTTGGGACATGCTCAACTTGGATTAGGAAAGATAATCCTGGCAATTCAAGTAGCCCTTCACATCTATCCAGTGAA
CCCTGAAATATGGAAAGAAGACCTCTCTTGGGCAAGAACACTCCAGGAGCAGCAGAAGGTAGCCCAGATGATTTTAAAAA
AAGTGAAGCACCAGCTGACGTAACACACTTTTCACCCAAGTCAATTCCAGACTATGACTCCAAAAGTGATGAGATTTATT
GCTGTTTGTGCGGCTATTGCTGAGAAACAGAAGACAGTTTCAGCAAATAAAACAATGGTTACTGTGTCCACTTCTGGGGC
CCTAGAGACTGTAACTGAAGAGGAAGATGGTGCTACACCACCAGATGGCTCTGTTTTTGTCAGAGCC

Alignment

ORF - retro_cjac_1680 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.42 %
• Parental protein coverage: 80.84 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ILEGCAEKSKQLKDEGASLAENKRYREAIQKWDEALQLTPNDATLYEMKSQVLMSLHEMFPAVHAAEMAV
          ILE..AEKSKQLKDEGASLAENKRY..A.QKWDE.LQLTPN.ATLYEMKSQVLMSLHEMFPAV.AAE..V
Retrocopy ILECRAEKSKQLKDEGASLAENKRYQ*AVQKWDEVLQLTPNHATLYEMKSQVLMSLHEMFPAVPAAEISV

Parental  QRNPHSWESWQTLGRAQLGLGEIILAIRSFQVALHIYPMNPEIWKEDLSWARTLQEQQKVAQRIKKSEAP
          Q.NPHSWESWQTLG.AQLGLG.IILAI...QVALHIYP.NPEIWKEDLSWARTLQEQQKVAQ.I.K....
Retrocopy QQNPHSWESWQTLGHAQLGLGKIILAI---QVALHIYPVNPEIWKEDLSWARTLQEQQKVAQMILKKVKH

Parental  AEVTH-FLPKSIPDYDFESDEIVAVCAAIAEKEKTVSANKTMVIVSASGAVETVTEKEDGATPPDGSVFI
          ....H.F.P..............AVCAAIAEK.KTVSANKTMV.VS.SGA.ETVTE.EDGATPPDGSVF.
Retrocopy QLT*HTFHPSQFQTMTPKVMRFIAVCAAIAEKQKTVSANKTMVTVSTSGALETVTEEEDGATPPDGSVFV

Parental  KA
          .A
Retrocopy RA

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	0.20 RPM	23.85 RPM
SRP051959_heart	0.14 RPM	27.87 RPM
SRP051959_kidney	0.00 RPM	30.84 RPM
SRP051959_liver	0.19 RPM	18.45 RPM
SRP051959_lung	0.10 RPM	24.97 RPM
SRP051959_lymph_node	0.21 RPM	27.05 RPM
SRP051959_skeletal_muscle	0.04 RPM	30.79 RPM
SRP051959_spleen	0.06 RPM	28.07 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1680 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1680 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1680 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000007398	1 retrocopy	retro_cjac_1680 ,
Otolemur garnettii	ENSOGAG00000011946	1 retrocopy	retro_ogar_1374,