RetrogeneDB ID: retro_cjac_235

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 2:166016704..166017115(+)
• Located in intron of: ENSCJAG00000007784

Retrocopy information

• Ensembl ID: ENSCJAG00000034493
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000012702
• Aliases: None
• Description: None

Sequence

>retro_cjac_235
ATGGCTCGTACAAAGCAGACTGCCCACAAATCTACCGGTGGTAAAGCACCCAGGAAGCAACTGGCTACAAAAGCCGCTCG
CAAGAGTGCGCCCTCTACTGGAGGGGTGAAGAAACCTCATCGTTACAGGCCTGGTACTGTGGCACTCCGTGAAATTAGAC
GTTATCAGAAGTCCACTGAACTTCTGATTCGCAAACTTCCCTTCCAGCGTCTGGTACGAGAAATTGCTCAGGACTTTAAA
ACAGATCTGCGCTTCCAGAGCGCAGCTATTGGTGCTTTGCAGGAGGCAAGTGAGGCCTATCTGGTTGGCCTTTTTGAAGA
CACCAACCTTTGTGCTATCCATGCCAAACGTGTAACAATTATGCCAAAAGATATCCAGCTAGCACGCCGCATACATGGAG
AGCGTGCTTAA

Alignment

ORF - retro_cjac_235 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.53 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MARTKQTARKSTGGKAPRKQLATKAARKSAPSTGGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQR
          MARTKQTA.KSTGGKAPRKQLATKAARKSAPSTGGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQR
Retrocopy MARTKQTAHKSTGGKAPRKQLATKAARKSAPSTGGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQR

Parental  LVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA
          LVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRI.GERA
Retrocopy LVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIHGERA

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	0.11 RPM	17.53 RPM
SRP051959_heart	0.05 RPM	7.95 RPM
SRP051959_kidney	0.02 RPM	9.07 RPM
SRP051959_liver	0.09 RPM	7.99 RPM
SRP051959_lung	0.05 RPM	13.16 RPM
SRP051959_lymph_node	0.16 RPM	12.81 RPM
SRP051959_skeletal_muscle	0.02 RPM	6.16 RPM
SRP051959_spleen	0.04 RPM	11.11 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_235 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_235 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_235 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 60 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000012702	10 retrocopies	retro_cjac_145, retro_cjac_198, retro_cjac_201, retro_cjac_224, retro_cjac_235 , retro_cjac_238, retro_cjac_307, retro_cjac_334, retro_cjac_366, retro_cjac_68,
Dasypus novemcinctus	ENSDNOG00000024843	2 retrocopies	retro_dnov_1624, retro_dnov_775,
Equus caballus	ENSECAG00000006904	1 retrocopy	retro_ecab_916,
Equus caballus	ENSECAG00000016948	1 retrocopy	retro_ecab_266,
Homo sapiens	ENSG00000132475	11 retrocopies	retro_hsap_1212, retro_hsap_1552, retro_hsap_2180, retro_hsap_24, retro_hsap_2971, retro_hsap_3231, retro_hsap_3294, retro_hsap_3299, retro_hsap_389, retro_hsap_4236, retro_hsap_911,
Latimeria chalumnae	ENSLACG00000004118	1 retrocopy	retro_lcha_104,
Loxodonta africana	ENSLAFG00000008083	3 retrocopies	retro_lafr_837, retro_lafr_959, retro_lafr_99,
Microcebus murinus	ENSMICG00000002139	2 retrocopies	retro_mmur_36, retro_mmur_371,
Mustela putorius furo	ENSMPUG00000004555	4 retrocopies	retro_mputfur_389, retro_mputfur_82, retro_mputfur_99, retro_mputfur_990,
Oreochromis niloticus	ENSONIG00000019975	5 retrocopies	retro_onil_41, retro_onil_46, retro_onil_56, retro_onil_60, retro_onil_63,
Pongo abelii	ENSPPYG00000008636	1 retrocopy	retro_pabe_2662,
Pan troglodytes	ENSPTRG00000009655	12 retrocopies	retro_ptro_1742, retro_ptro_1915, retro_ptro_2009, retro_ptro_2227, retro_ptro_2231, retro_ptro_2234, retro_ptro_2238, retro_ptro_2640, retro_ptro_2879, retro_ptro_631, retro_ptro_695, retro_ptro_830,
Tupaia belangeri	ENSTBEG00000016171	7 retrocopies	retro_tbel_3459, retro_tbel_3605, retro_tbel_3824, retro_tbel_3856, retro_tbel_4243, retro_tbel_4350, retro_tbel_674,