RetrogeneDB ID: retro_cjac_735

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 10:114052191..114052545(+)
• Located in intron of: ENSCJAG00000017345

Retrocopy information

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

Parental gene information

• Parental gene symbol: C19orf70
• Ensembl ID: ENSCJAG00000017076
• Aliases: None
• Description: chromosome 19 open reading frame 70 [Source:HGNC Symbol;Acc:33702]

Sequence

>retro_cjac_735
ATGGTGGCCCGGGTGTGGTCGCTGATGAGGTTCCTCATCAAGGGAAGTGTGGCTGGGGGCGCCGTCTACCTGGTGTATGA
CCAGGAGCTGCTGGGGTCCAGCGACAAGAGCCAGGCAGCCCTAAAGAAGGCTGGGAAAGTGGTTCCCCCGGCCATGTACC
AGTTCAGCCAGTACGTGTGTCAGCAGACAGGCCTGCAGATACCCCAGCTCCCAGCTCCTCCAAAGATTCACTTTCCCATC
TGTGACTCCTGGAATGCAGGAATCATCACAGTGATGTCAGCTCTGTCGGTAGCCCCCTCTAAGGCCTGCGAGTACTCCAA
GGAGGGCTGGGAGTACGTGAAGGCGCGCACCAAG

Alignment

ORF - retro_cjac_735 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.46 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MVARVWSLMRFLIKGSVAGGAVYLVYDQELLGSSDKSQAALKKAGEVVPPAMYQFSHYVCQQTGLQIPQL
          MVARVWSLMRFLIKGSVAGGAVYLVYDQELLGSSDKSQAALKKAG.VVPPAMYQFS.YVCQQTGLQIPQL
Retrocopy MVARVWSLMRFLIKGSVAGGAVYLVYDQELLGSSDKSQAALKKAGKVVPPAMYQFSQYVCQQTGLQIPQL

Parental  PAPPKIHFPIRDSWNAGIITVMSALSVAPSKACEYSKEGWEYVKARTK
          PAPPKIHFPI.DSWNAGIITVMSALSVAPSKACEYSKEGWEYVKARTK
Retrocopy PAPPKIHFPICDSWNAGIITVMSALSVAPSKACEYSKEGWEYVKARTK

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	0.73 RPM	8.08 RPM
SRP051959_heart	0.70 RPM	9.30 RPM
SRP051959_kidney	0.82 RPM	8.50 RPM
SRP051959_liver	0.50 RPM	9.51 RPM
SRP051959_lung	0.83 RPM	6.33 RPM
SRP051959_lymph_node	0.80 RPM	7.10 RPM
SRP051959_skeletal_muscle	0.90 RPM	14.41 RPM
SRP051959_spleen	0.65 RPM	7.27 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_735 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_735 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_735 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000018796	2 retrocopies	retro_cfam_1706, retro_cfam_756,
Callithrix jacchus	ENSCJAG00000017076	2 retrocopies	retro_cjac_2329, retro_cjac_735 ,
Felis catus	ENSFCAG00000011836	1 retrocopy	retro_fcat_287,
Loxodonta africana	ENSLAFG00000026050	1 retrocopy	retro_lafr_1241,
Macaca mulatta	ENSMMUG00000028920	1 retrocopy	retro_mmul_251,
Monodelphis domestica	ENSMODG00000001268	1 retrocopy	retro_mdom_1960,
Mustela putorius furo	ENSMPUG00000006136	2 retrocopies	retro_mputfur_1001, retro_mputfur_217,
Procavia capensis	ENSPCAG00000006583	1 retrocopy	retro_pcap_106,
Tupaia belangeri	ENSTBEG00000013386	1 retrocopy	retro_tbel_1443,