RetrogeneDB ID: retro_cjac_1686

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 18:37493370..37493673(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SUMO1
• Ensembl ID: ENSCJAG00000004961
• Aliases: None
• Description: small ubiquitin-like modifier 1 [Source:HGNC Symbol;Acc:12502]

Sequence

>retro_cjac_1686
ATGTCTGATCAGAAGGCAAAAGCTGCAACTGGTGGCTTGGGGGATAAGAAGGAATGAGAAAATGTTAAACTCAAAGTCAT
TGGACAGGATAGCAGTAAGATTCACTTCAAAGTGAAAATGACAAACATCTCAACAAACTCAGGGAATCATACTGTCAAAG
ACAGGGAGCTCCAATGAATTCACTCAGATTTGTCTTTGAAGATGAGAGAATTGCTGCTATTCATACTATAAAATAACTGG
GAATGGAGTTAAGAAGGTGTGATTGAAGTTCATCAGGAGCAAATGAGGTCATTCAGTAGTTTA

Alignment

ORF - retro_cjac_1686 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.9 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MSDQEAKPSTEDLGDKKEGEYIKLKVIGQDSSEIHFKVKMTT-HLKKLKESYCQRQGVPMNSLRFLFEGQ
          MSDQ.AK..T..LGDKKE.E..KLKVIGQDSS.IHFKVKMT..HL.KL.ESYCQRQG.PMNSLRF.FE..
Retrocopy MSDQKAKAATGGLGDKKE*ENVKLKVIGQDSSKIHFKVKMTN<HLNKLRESYCQRQGAPMNSLRFVFEDE

Parental  RIADNHTPKELGMEE-EDVIEVYQEQTGGHSTV
          RIA..HT.K.LGME..E.VIEV.QEQ....S..
Retrocopy RIAAIHTIK*LGMEL>EGVIEVHQEQMRSFSSL

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	0.00 RPM	23.21 RPM
SRP051959_heart	0.04 RPM	25.03 RPM
SRP051959_kidney	0.22 RPM	36.23 RPM
SRP051959_liver	0.15 RPM	31.04 RPM
SRP051959_lung	0.05 RPM	30.62 RPM
SRP051959_lymph_node	0.09 RPM	27.33 RPM
SRP051959_skeletal_muscle	0.13 RPM	30.90 RPM
SRP051959_spleen	0.65 RPM	28.07 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1686 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1686 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1686 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 83 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000009859	6 retrocopies	retro_btau_112, retro_btau_1512, retro_btau_1705, retro_btau_357, retro_btau_363, retro_btau_499,
Canis familiaris	ENSCAFG00000012431	8 retrocopies	retro_cfam_1226, retro_cfam_1253, retro_cfam_139, retro_cfam_1815, retro_cfam_1912, retro_cfam_2048, retro_cfam_386, retro_cfam_985,
Callithrix jacchus	ENSCJAG00000004961	3 retrocopies	retro_cjac_1686 , retro_cjac_1932, retro_cjac_2610,
Callithrix jacchus	ENSCJAG00000010529	20 retrocopies	retro_cjac_1110, retro_cjac_1128, retro_cjac_1525, retro_cjac_1752, retro_cjac_1938, retro_cjac_1957, retro_cjac_1993, retro_cjac_2460, retro_cjac_2481, retro_cjac_2616, retro_cjac_2651, retro_cjac_2886, retro_cjac_2899, retro_cjac_2985, retro_cjac_3088, retro_cjac_3137, retro_cjac_4123, retro_cjac_711, retro_cjac_771, retro_cjac_774,
Cavia porcellus	ENSCPOG00000012143	1 retrocopy	retro_cpor_1279,
Equus caballus	ENSECAG00000024693	4 retrocopies	retro_ecab_199, retro_ecab_365, retro_ecab_570, retro_ecab_935,
Felis catus	ENSFCAG00000031005	6 retrocopies	retro_fcat_1520, retro_fcat_218, retro_fcat_26, retro_fcat_472, retro_fcat_6, retro_fcat_862,
Homo sapiens	ENSG00000116030	5 retrocopies	retro_hsap_2007, retro_hsap_240, retro_hsap_2489, retro_hsap_262, retro_hsap_897,
Gorilla gorilla	ENSGGOG00000026439	5 retrocopies	retro_ggor_1451, retro_ggor_1550, retro_ggor_299, retro_ggor_311, retro_ggor_725,
Myotis lucifugus	ENSMLUG00000007504	2 retrocopies	retro_mluc_1346, retro_mluc_188,
Mustela putorius furo	ENSMPUG00000000335	2 retrocopies	retro_mputfur_257, retro_mputfur_33,
Mus musculus	ENSMUSG00000026021	5 retrocopies	retro_mmus_1594, retro_mmus_2129, retro_mmus_2135, retro_mmus_252, retro_mmus_2962,
Otolemur garnettii	ENSOGAG00000030345	1 retrocopy	retro_ogar_215,
Pongo abelii	ENSPPYG00000013083	3 retrocopies	retro_pabe_11, retro_pabe_1830, retro_pabe_775,
Pan troglodytes	ENSPTRG00000012817	1 retrocopy	retro_ptro_119,
Rattus norvegicus	ENSRNOG00000016133	2 retrocopies	retro_rnor_2015, retro_rnor_813,
Sarcophilus harrisii	ENSSHAG00000011968	1 retrocopy	retro_shar_375,
Ictidomys tridecemlineatus	ENSSTOG00000025405	4 retrocopies	retro_itri_1193, retro_itri_1232, retro_itri_216, retro_itri_668,
Tursiops truncatus	ENSTTRG00000000642	4 retrocopies	retro_ttru_1646, retro_ttru_1652, retro_ttru_309, retro_ttru_399,