RetrogeneDB ID: retro_cjac_410

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 1:71327597..71328035(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DR1
• Ensembl ID: ENSCJAG00000017815
• Aliases: None
• Description: down-regulator of transcription 1, TBP-binding (negative cofactor 2) [Source:HGNC Symbol;Acc:3017]

Sequence

>retro_cjac_410
ATGGCTTCCTCGTCTGGCAACGATGATGATCTCACTATCCTCAGAGCTGCTATCAATAAAATGATCAGAGAGACTCTTCC
TAATGTCCGAGTGGCCAACGATGCTGGAGAGCTGGTGGTGAACTGCTGCACTGAATTCATTCACCTTATATCTTCTGAAG
CCAATGAGAATTGTAACAAATCGGAAAAGACCATCTCACCAGAGCATGTCATACAAGCACTAGAAAGTTTGGGATTTGGC
TCTTATATCAGTGAAGTAAAAGAAGTCTTGCAAGAGTGTAAAACAGCAGCATTAAAAAGAAGAAAGGCCGGTTCTCGTTT
GGAAAACCTTGGCATTCCTGAAGAAGAGTTACTGAGACAGCAACAAGAATTATTTGCAAAAGCTAGACAGCAACAAGCAG
AATTGGCCCAACAGGAATGGCTTCAAATGCAGCAAGCC

Alignment

ORF - retro_cjac_410 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.24 %
• Parental protein coverage: 83.52 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MASSSGNDDDLTIPRAAINKMIKETLPNVRVANDARELVVNCCTEFIHLISSEANEICNKSEKKTISPEH
          MASSSGNDDDLTI.RAAINKMI.ETLPNVRVANDA.ELVVNCCTEFIHLISSEANE.CNKSEK.TISPEH
Retrocopy MASSSGNDDDLTILRAAINKMIRETLPNVRVANDAGELVVNCCTEFIHLISSEANENCNKSEK-TISPEH

Parental  VIQALESLGFGSYISEVKEVLQECKTVALKRRKASSRLENLGIPEEELLRQQQELFAKARQQQAELAQQE
          VIQALESLGFGSYISEVKEVLQECKT.ALKRRKA.SRLENLGIPEEELLRQQQELFAKARQQQAELAQQE
Retrocopy VIQALESLGFGSYISEVKEVLQECKTAALKRRKAGSRLENLGIPEEELLRQQQELFAKARQQQAELAQQE

Parental  WLQMQQA
          WLQMQQA
Retrocopy WLQMQQA

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	21.79 RPM
SRP051959_heart	0.04 RPM	20.19 RPM
SRP051959_kidney	0.04 RPM	21.25 RPM
SRP051959_liver	0.02 RPM	12.74 RPM
SRP051959_lung	0.03 RPM	29.00 RPM
SRP051959_lymph_node	0.00 RPM	41.28 RPM
SRP051959_skeletal_muscle	0.02 RPM	17.80 RPM
SRP051959_spleen	0.00 RPM	28.47 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_410 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_410 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_410 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000017815	1 retrocopy	retro_cjac_410 ,
Cavia porcellus	ENSCPOG00000003282	1 retrocopy	retro_cpor_518,
Loxodonta africana	ENSLAFG00000017540	1 retrocopy	retro_lafr_692,
Myotis lucifugus	ENSMLUG00000010684	1 retrocopy	retro_mluc_2349,