RetrogeneDB ID: retro_cjac_433

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 1:81750641..81751275(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RTDR1
• Ensembl ID: ENSCJAG00000009770
• Aliases: None
• Description: rhabdoid tumor deletion region gene 1 [Source:HGNC Symbol;Acc:13437]

Sequence

>retro_cjac_433
CAAACCCTGAAGATTTACACTGGGGCTGAAGAAACCATCAGCAAAGGCTGATCTCCCCGCTGGTATGAAGCTGCAGGGCA
AGTGGAGGAGGAGTTCCAGGAGCTCATCCTAGACACTCTGGTGCTCTGCCTGTGGGAAGATGCCACCAAGGCCCTGAATA
GCAACGTGGTGCCCATCCTGAAGCAGAAGCTCATCAGCACCAACGAGAACATCCGAAGCAAGGCTGCTGGTGCGCTCCTT
AATGTCAGCATATCTCGTGTGGGCAAGAAACAGGTGTGTCAGTTTGACGTCATCCCCATCTGGTGCATCTACCGAAAGAC
CCAGTGGACCATGTGAGGTCTAACGCTGCTGGGGCCTTGATGTTCGCCACGGTGATCACCGAAGGGAATATGCGGCCCTG
GAGGCAGAAGCCATCAGCCCGCTTCTGGAGCTGCTGCATTCCCCCATGACTGTAGTGCACCTGAACGCCACCAAGGCCCT
CACCATGCTGGTGGAGGCTCCTGAGGACCGCAAGGTCCTACAGGCACATGTGCCCACCTTCCGTGCCATGGAAGTGGAGC
CTCACAAAAAGCTTCACATGGCCGAAGCCTTACAGCGGGCGGCCCGGATTGCTGTCAGTGTCATCAAGTTCAAA

Alignment

ORF - retro_cjac_433 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.7 %
• Parental protein coverage: 61.38 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  QLVQVPRGAEEIISKG-LISPLV-WKLQG-EVEEEFQELILDTLVLCLWEDATEALNSNVVPILKQKLIS
          Q......GAEE.ISKG.LISPLV..KLQG..VEEEFQELILDTLVLCLWEDAT.ALNSNVVPILKQKLIS
Retrocopy QTLKIYTGAEETISKG<LISPLV<MKLQG<QVEEEFQELILDTLVLCLWEDATKALNSNVVPILKQKLIS

Parental  TNENIRSKAARALLNVSISRVGKKQVCQFDVIPI-LVHLLKDPVEHVRSNAAGALMFALVITEG-KYAAL
          TNENIRSKAA.ALLNVSISRVGKKQVCQFDVIPI.LVHL.KDPV.HVRSNAAGALMFA.VITEG..YAAL
Retrocopy TNENIRSKAAGALLNVSISRVGKKQVCQFDVIPI<LVHLPKDPVDHVRSNAAGALMFATVITEG<EYAAL

Parental  EAEAIGPLLELLHSPMTVARLNATKALTMLAEAPEGRKVLQAHVPTFRAMEVEPHEKPHIAEALQRAARI
          EAEAI.PLLELLHSPMTV..LNATKALTML.EAPE.RKVLQAHVPTFRAMEVEPH.K.H.AEALQRAARI
Retrocopy EAEAISPLLELLHSPMTVVHLNATKALTMLVEAPEDRKVLQAHVPTFRAMEVEPHKKLHMAEALQRAARI

Parental  AVSVIEFK
          AVSVI.FK
Retrocopy AVSVIKFK

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	0.04 RPM	0.16 RPM
SRP051959_heart	0.02 RPM	0.14 RPM
SRP051959_kidney	0.02 RPM	0.64 RPM
SRP051959_liver	0.00 RPM	0.00 RPM
SRP051959_lung	0.16 RPM	0.73 RPM
SRP051959_lymph_node	0.18 RPM	0.34 RPM
SRP051959_skeletal_muscle	0.02 RPM	0.04 RPM
SRP051959_spleen	0.02 RPM	0.08 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_433 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_433 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_433 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000009770	2 retrocopies	retro_cjac_3818, retro_cjac_433 ,