RetrogeneDB ID: retro_cjac_3818

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: GL284783.1:1833..2474(-)
• 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_3818
ATGCAAACCCTAAAGATTTACACTGGGGCTGAAGAGACCATCAGCAAAGGTCTGATCTCCCCGCTGGTATGAAGCTGCAG
GGCAAGTGGAGGAGGAGTTCCAGGAGCTCATCCTAGACACTCTGGTGCTCTGCCTGTGGGAAGATGCCCACCGAGGCCCT
GAATAGCAACGTGGTGCCCATCCTGAAGCAGAAGCTCATTAGCACCAACGAGAACATCCGAAGCAAGGCTGCCGGTGGGC
TCCTTAATGTCAGCATATCTCGTGTGGGCAAGAAACAGGTGTGTCAGTTTGACGTCATCCCCATCCTGGTGCATCTACTG
AAAGACCCGGTGGAGCATGTGAGGTCTAACGCTGCTGGGGCCTTGATGTTTGCCACGGTGATCAGGGAAGGGAAGTATGT
GGCTCTGGAGGCAGAAGTCATCAGCCCGCTTCTGGAGCTGCTGCATTCCCCCATGACTGTAGTGCGCCTGAACGCCACCA
AGGCCCTCACCATGCTGTCGGAGGCTCCCGATGACCGCAAGGTCCTGCAGGCACAAGTGCCCACCTTCCATGCCATGGAA
GTGGAGCCTCACAAAAAGCTTCACATGGCCGAAGCCTTACAGCGGGTGGCCCGGATTGCTGTCAGTGTCATCAAGTTCAA
A

Alignment

ORF - retro_cjac_3818 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.18 %
• Parental protein coverage: 61.67 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MQLVQVPRGAEEIISKGLISPLV-WKLQG-EVEEEFQELILDTLVLCLWEDA-TEALNSNVVPILKQKLI
          MQ......GAEE.ISKGLISPLV..KLQG..VEEEFQELILDTLVLCLWEDA.TEALNSNVVPILKQKLI
Retrocopy MQTLKIYTGAEETISKGLISPLV<MKLQG<QVEEEFQELILDTLVLCLWEDA>TEALNSNVVPILKQKLI

Parental  STNENIRSKAARALLNVSISRVGKKQVCQFDVIPILVHLLKDPVEHVRSNAAGALMFALVITEGKYAALE
          STNENIRSKAA..LLNVSISRVGKKQVCQFDVIPILVHLLKDPVEHVRSNAAGALMFA.VI.EGKY.ALE
Retrocopy STNENIRSKAAGGLLNVSISRVGKKQVCQFDVIPILVHLLKDPVEHVRSNAAGALMFATVIREGKYVALE

Parental  AEAIGPLLELLHSPMTVARLNATKALTMLAEAPEGRKVLQAHVPTFRAMEVEPHEKPHIAEALQRAARIA
          AE.I.PLLELLHSPMTV.RLNATKALTML.EAP..RKVLQA.VPTF.AMEVEPH.K.H.AEALQR.ARIA
Retrocopy AEVISPLLELLHSPMTVVRLNATKALTMLSEAPDDRKVLQAQVPTFHAMEVEPHKKLHMAEALQRVARIA

Parental  VSVIEFK
          VSVI.FK
Retrocopy VSVIKFK

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	0.24 RPM	0.16 RPM
SRP051959_heart	0.14 RPM	0.14 RPM
SRP051959_kidney	0.33 RPM	0.64 RPM
SRP051959_liver	0.52 RPM	0.00 RPM
SRP051959_lung	1.79 RPM	0.73 RPM
SRP051959_lymph_node	4.25 RPM	0.34 RPM
SRP051959_skeletal_muscle	0.00 RPM	0.04 RPM
SRP051959_spleen	1.60 RPM	0.08 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3818 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3818 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3818 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,