RetrogeneDB ID: retro_cjac_1908

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 2:47956220..47956620(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SUB1
• Ensembl ID: ENSCJAG00000018718
• Aliases: None
• Description: SUB1 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:19985]

Sequence

>retro_cjac_1908
CTGCTGGAGCCGAGCGGAGTGATGCCTACATCACAGAAACTTGTTTCTTCAAGCTCTTCTGGCAGTGATTCTGACAGCGA
GGTTGACAAAAAGTTAAAGAGGAAAAAGCAAGTTGCTCCAGAAAAACCTGTAAGGAAGCAAAAGACAGGTGAAACTTCGA
GAGCTCTGTCATCTTCTAAACAGAGCGGCAGCAGCAGAGATGATAACATTTCAGACTGGGAAAATGAGGTATGTTAGCGT
TGGAGATTTAAAAAGGAAAGTGCTAATTGATATAAGAGAATATTGGATGGATCTAGAAGGTGAAATGAAACCAGGAAGAA
AAGGTATTTCTTTAAATCCAGAACAATGGAGCTAGCTGAAGGAACAGATTTCTGACATTGATGATGCAGTAAGAAAACTG

Alignment

ORF - retro_cjac_1908 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.7 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LLRHTEMMPKSKELVSSSSSGSDSDSEVDKKLKRKKQVAPEKPVKKQKTGETSRALSSSKQSSSSRDDN-
          LL.....MP.S..LVSSSSSGSDSDSEVDKKLKRKKQVAPEKPV.KQKTGETSRALSSSKQ.S.S..D..
Retrocopy LLEPSGVMPTSQKLVSSSSSGSDSDSEVDKKLKRKKQVAPEKPVRKQKTGETSRALSSSKQ-SGSSRDD>

Parental  MFQIGKMRYVSVRDFKGKVLIDIREYWMDPEGEMKPGRKGISLNPEQWSQLKEQISDIDDAVRKL
          .FQ.GKMRYVSV.D.K.KVLIDIREYWMD.EGEMKPGRKGISLNPEQWS.LKEQISDIDDAVRKL
Retrocopy TFQTGKMRYVSVGDLKRKVLIDIREYWMDLEGEMKPGRKGISLNPEQWS*LKEQISDIDDAVRKL

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	0.02 RPM	25.16 RPM
SRP051959_heart	0.00 RPM	29.40 RPM
SRP051959_kidney	0.07 RPM	36.21 RPM
SRP051959_liver	0.17 RPM	28.77 RPM
SRP051959_lung	0.15 RPM	31.85 RPM
SRP051959_lymph_node	0.07 RPM	34.11 RPM
SRP051959_skeletal_muscle	0.07 RPM	37.95 RPM
SRP051959_spleen	0.15 RPM	35.88 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1908 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1908 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1908 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 20 parental genes, and 73 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000018879	5 retrocopies	retro_cfam_1266, retro_cfam_1536, retro_cfam_1916, retro_cfam_2010, retro_cfam_215,
Callithrix jacchus	ENSCJAG00000018718	2 retrocopies	retro_cjac_1908 , retro_cjac_484,
Cavia porcellus	ENSCPOG00000005584	4 retrocopies	retro_cpor_1114, retro_cpor_1481, retro_cpor_834, retro_cpor_854,
Dasypus novemcinctus	ENSDNOG00000007611	5 retrocopies	retro_dnov_1230, retro_dnov_161, retro_dnov_1822, retro_dnov_2156, retro_dnov_400,
Homo sapiens	ENSG00000113387	2 retrocopies	retro_hsap_1662, retro_hsap_3934,
Gorilla gorilla	ENSGGOG00000027033	3 retrocopies	retro_ggor_1063, retro_ggor_1254, retro_ggor_2645,
Loxodonta africana	ENSLAFG00000011006	1 retrocopy	retro_lafr_19,
Macropus eugenii	ENSMEUG00000007770	4 retrocopies	retro_meug_1155, retro_meug_1820, retro_meug_2038, retro_meug_500,
Microcebus murinus	ENSMICG00000014535	2 retrocopies	retro_mmur_1115, retro_mmur_17,
Myotis lucifugus	ENSMLUG00000013685	6 retrocopies	retro_mluc_1649, retro_mluc_1696, retro_mluc_1785, retro_mluc_226, retro_mluc_2346, retro_mluc_621,
Macaca mulatta	ENSMMUG00000011470	2 retrocopies	retro_mmul_2318, retro_mmul_993,
Monodelphis domestica	ENSMODG00000020410	3 retrocopies	retro_mdom_840, retro_mdom_841, retro_mdom_895,
Mustela putorius furo	ENSMPUG00000015185	2 retrocopies	retro_mputfur_186, retro_mputfur_295,
Mus musculus	ENSMUSG00000022205	4 retrocopies	retro_mmus_1118, retro_mmus_2304, retro_mmus_2586, retro_mmus_3606,
Oryctolagus cuniculus	ENSOCUG00000006262	5 retrocopies	retro_ocun_1227, retro_ocun_1313, retro_ocun_1661, retro_ocun_1714, retro_ocun_902,
Otolemur garnettii	ENSOGAG00000009012	6 retrocopies	retro_ogar_1130, retro_ogar_1272, retro_ogar_218, retro_ogar_2481, retro_ogar_340, retro_ogar_525,
Pongo abelii	ENSPPYG00000015379	2 retrocopies	retro_pabe_124, retro_pabe_1371,
Rattus norvegicus	ENSRNOG00000050563	12 retrocopies	retro_rnor_1040, retro_rnor_1137, retro_rnor_1203, retro_rnor_1496, retro_rnor_1692, retro_rnor_1693, retro_rnor_1863, retro_rnor_2721, retro_rnor_2986, retro_rnor_420, retro_rnor_572, retro_rnor_735,
Sarcophilus harrisii	ENSSHAG00000014986	1 retrocopy	retro_shar_628,
Tarsius syrichta	ENSTSYG00000014069	2 retrocopies	retro_tsyr_528, retro_tsyr_895,