RetrogeneDB ID: retro_cjac_4085

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: X:69004895..69005258(+)
• Located in intron of: ENSCJAG00000018916

Retrocopy information

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

Parental gene information

• Parental gene symbol: CLNS1A
• Ensembl ID: ENSCJAG00000014927
• Aliases: None
• Description: chloride channel, nucleotide-sensitive, 1A [Source:HGNC Symbol;Acc:2080]

Sequence

>retro_cjac_4085
ATGAGCTTCCTCAAAAGTTTCCCGCCGCCTGGGCCGGCGGAGGGGCTCCTGCGGCAGCAGCCAGACACCGAGGCTGTGCT
GAACGGGAAGGGCCTTGGCACCGGTACCCTTTACATCGCTGAGAGCCGCCTGTCTTGGTTAGATGGCTCCGGATTAGGAT
TCTCGCTGGAATACCCCACCATTAGCTTACATGCATTGTCCAGGGACAGAAGTGACTGTCTGGGAGAGCACTTGTATGTT
ATGGTGAATGCCAAATTTGAAGAAGAATCAAAAGAATCTGTTGCTGATGAAGAAGAAGAAGACAGTGATGATGATGTTGA
ACCTATTACTGAATTTAGATTTGTGCCTAGTGATAAATCAGCA

Alignment

ORF - retro_cjac_4085 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 100. %
• Parental protein coverage: 51.05 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSFLKSFPPPGPAEGLLRQQPDTEAVLNGKGLGTGTLYIAESRLSWLDGSGLGFSLEYPTISLHALSRDR
          MSFLKSFPPPGPAEGLLRQQPDTEAVLNGKGLGTGTLYIAESRLSWLDGSGLGFSLEYPTISLHALSRDR
Retrocopy MSFLKSFPPPGPAEGLLRQQPDTEAVLNGKGLGTGTLYIAESRLSWLDGSGLGFSLEYPTISLHALSRDR

Parental  SDCLGEHLYVMVNAKFEEESKESVADEEEEDSDDDVEPITEFRFVPSDKSA
          SDCLGEHLYVMVNAKFEEESKESVADEEEEDSDDDVEPITEFRFVPSDKSA
Retrocopy SDCLGEHLYVMVNAKFEEESKESVADEEEEDSDDDVEPITEFRFVPSDKSA

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	0.18 RPM	14.31 RPM
SRP051959_heart	0.14 RPM	17.86 RPM
SRP051959_kidney	0.11 RPM	20.50 RPM
SRP051959_liver	0.02 RPM	17.48 RPM
SRP051959_lung	0.11 RPM	18.68 RPM
SRP051959_lymph_node	0.21 RPM	20.57 RPM
SRP051959_skeletal_muscle	0.00 RPM	17.82 RPM
SRP051959_spleen	0.19 RPM	23.26 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_4085 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_4085 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_4085 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 33 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000019930	1 retrocopy	retro_btau_376,
Canis familiaris	ENSCAFG00000004900	6 retrocopies	retro_cfam_1112, retro_cfam_1448, retro_cfam_255, retro_cfam_327, retro_cfam_720, retro_cfam_727,
Choloepus hoffmanni	ENSCHOG00000007254	1 retrocopy	retro_chof_1685,
Callithrix jacchus	ENSCJAG00000014927	1 retrocopy	retro_cjac_4085 ,
Cavia porcellus	ENSCPOG00000005260	1 retrocopy	retro_cpor_67,
Dasypus novemcinctus	ENSDNOG00000008188	1 retrocopy	retro_dnov_477,
Felis catus	ENSFCAG00000026321	1 retrocopy	retro_fcat_736,
Homo sapiens	ENSG00000074201	2 retrocopies	retro_hsap_3010, retro_hsap_3595,
Gorilla gorilla	ENSGGOG00000003091	1 retrocopy	retro_ggor_2084,
Macropus eugenii	ENSMEUG00000005935	4 retrocopies	retro_meug_1825, retro_meug_2097, retro_meug_783, retro_meug_929,
Myotis lucifugus	ENSMLUG00000024623	2 retrocopies	retro_mluc_1501, retro_mluc_1507,
Mustela putorius furo	ENSMPUG00000015944	1 retrocopy	retro_mputfur_435,
Mus musculus	ENSMUSG00000025439	1 retrocopy	retro_mmus_1984,
Nomascus leucogenys	ENSNLEG00000016699	2 retrocopies	retro_nleu_300, retro_nleu_756,
Oryctolagus cuniculus	ENSOCUG00000024393	1 retrocopy	retro_ocun_1303,
Pongo abelii	ENSPPYG00000003712	1 retrocopy	retro_pabe_2494,
Sorex araneus	ENSSARG00000009460	2 retrocopies	retro_sara_247, retro_sara_682,
Ictidomys tridecemlineatus	ENSSTOG00000027980	3 retrocopies	retro_itri_239, retro_itri_319, retro_itri_490,
Tupaia belangeri	ENSTBEG00000001316	1 retrocopy	retro_tbel_2975,