RetrogeneDB ID: retro_cjac_931

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 11:83540788..83541391(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RAB1B
• Ensembl ID: ENSCJAG00000001599
• Aliases: None
• Description: RAB1B, member RAS oncogene family [Source:HGNC Symbol;Acc:18370]

Sequence

>retro_cjac_931
ATGAACCCCGAATATGACTACCTGTTTAAGCTGCTTTTGATTGGCGACTGAGGCGTGGGCAAGTCATGCCTGCTTCTGCG
GTTTGCTGATGACACGTACACAGACAGCTACATCAGTACCATCGGGGTGGACTTCAAGATTCGAACCATTGAGCTGGATG
GAAAAACTATTAAACTTCAGATCTGGGACACAGCGGGCCAGGAGCGGTTCCGGACCATCACTTCCAGCTATTACCGGGGG
GCTCATGGCATCATCGTGGTGTATGACGTCACTGACCAGGAATCCTATGCCAACGTGAAGCAGTGGCTGCAGGAGATTGA
CCGCTACGCCAGCGAGAACGTCAATAAGCTCCTGGTGGGCAACAAGAGCGACCTCACCACCAAGAAGGTGGTGGACAACA
CCACAGCCAAGGACTTTGCAGACTCTCTGGGCATCCCTTTCCTGGAGATGAGTGCCAAGAACGCCACCAATGTCGAGCAG
GCGTTCATGACCATGGCTGCTGAGATCAAAAAGCGGATGGGCCCCGGAGCAGCCTCCGGGGGCGAGCGGCCCAATCTCAA
GATCGACAGCACCCCTGTAAAGCCGGCGGGTGGCGGCTGTTGC

Alignment

ORF - retro_cjac_931 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.01 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MNPEYDYLFKLLLIGDSGVGKSCLLLRFADDTYTESYISTIGVDFKIRTIELDGKTIKLQIWDTAGQERF
          MNPEYDYLFKLLLIGD.GVGKSCLLLRFADDTYT.SYISTIGVDFKIRTIELDGKTIKLQIWDTAGQERF
Retrocopy MNPEYDYLFKLLLIGD*GVGKSCLLLRFADDTYTDSYISTIGVDFKIRTIELDGKTIKLQIWDTAGQERF

Parental  RTITSSYYRGAHGIIVVYDVTDQESYANVKQWLQEIDRYASENVNKLLVGNKSDLTTKKVVDNTTAKEFA
          RTITSSYYRGAHGIIVVYDVTDQESYANVKQWLQEIDRYASENVNKLLVGNKSDLTTKKVVDNTTAK.FA
Retrocopy RTITSSYYRGAHGIIVVYDVTDQESYANVKQWLQEIDRYASENVNKLLVGNKSDLTTKKVVDNTTAKDFA

Parental  DSLGIPFLETSAKNATNVEQAFMTMAAEIKKRMGPGAASGGERPNLKIDSTPVKPAGGGCC
          DSLGIPFLE.SAKNATNVEQAFMTMAAEIKKRMGPGAASGGERPNLKIDSTPVKPAGGGCC
Retrocopy DSLGIPFLEMSAKNATNVEQAFMTMAAEIKKRMGPGAASGGERPNLKIDSTPVKPAGGGCC

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	2.62 RPM	11.16 RPM
SRP051959_heart	2.09 RPM	11.96 RPM
SRP051959_kidney	1.93 RPM	10.87 RPM
SRP051959_liver	1.49 RPM	9.23 RPM
SRP051959_lung	2.59 RPM	11.24 RPM
SRP051959_lymph_node	2.19 RPM	9.93 RPM
SRP051959_skeletal_muscle	2.66 RPM	13.21 RPM
SRP051959_spleen	1.97 RPM	8.91 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_931 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_931 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_931 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000001599	1 retrocopy	retro_cjac_931 ,
Callithrix jacchus	ENSCJAG00000014120	1 retrocopy	retro_cjac_1494,
Homo sapiens	ENSG00000174903	1 retrocopy	retro_hsap_4252,
Gorilla gorilla	ENSGGOG00000009755	2 retrocopies	retro_ggor_1792, retro_ggor_2850,
Macropus eugenii	ENSMEUG00000000023	1 retrocopy	retro_meug_1985,
Monodelphis domestica	ENSMODG00000008371	1 retrocopy	retro_mdom_196,
Pongo abelii	ENSPPYG00000003031	1 retrocopy	retro_pabe_3386,
Pan troglodytes	ENSPTRG00000003915	1 retrocopy	retro_ptro_2892,
Sarcophilus harrisii	ENSSHAG00000010376	1 retrocopy	retro_shar_68,
Ictidomys tridecemlineatus	ENSSTOG00000011052	1 retrocopy	retro_itri_1677,
Drosophila melanogaster	FBgn0016700	1 retrocopy	retro_dmel_36,