RetrogeneDB ID: retro_cjac_442

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 1:86405286..86405785(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000003513
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SRSF9
• Ensembl ID: ENSCJAG00000001187
• Aliases: None
• Description: serine/arginine-rich splicing factor 9 [Source:HGNC Symbol;Acc:10791]

Sequence

>retro_cjac_442
GCCTTCATGCACTTCAAGGATCCCCGAGATGCAGAGGATGCAATTTATGGAAGGAATGGTTATGATTATGGCCAGTGTCG
GCTTCGTGTGGAGTTCCCCAGGACTTATGGAGGTCGGGGTGGGTGGCCCTATGGTGGGAGGAATGGGCCTCCTACAAGAA
GATCTGATTTCCGAGTTCTTGTTTCAGGACTTCCTCCATCAGGCAGCTGGCAGGACCTGAAGGATCACATGCAAGAAGCT
GGGGAATGTCTGTTATGCCGATGTGCAGAAGGATGGAGTGGGGATGGTTGAGTATCTCAGAAAAGAAGACATGGACTATG
CCCTGCATGAACTGGATGACACCAAATTCCGATCTCATGAGGGTGAAACTTCCTACATCCAAGTTTATCCTGAGAGAAGC
ACCAGCTATGGCTACTCACGGTCTCGGTCTGGGTCAAGGGGCTGTGACTCTCCATACCAAAGCAGGGGTTCCCCACACTA
CTTCTCTCCTTTCAGGCCC

Alignment

ORF - retro_cjac_442 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.72 %
• Parental protein coverage: 99.41 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  AFVRFEDPRDAEDAIYGRNGYDYGQCRLRVEFPRTYGGRGGWPRGGRNGPPTRRSDFRVLVSGLGLPPSG
          AF..F.DPRDAEDAIYGRNGYDYGQCRLRVEFPRTYGGRGGWP.GGRNGPPTRRSDFRVLVSGL..PPSG
Retrocopy AFMHFKDPRDAEDAIYGRNGYDYGQCRLRVEFPRTYGGRGGWPYGGRNGPPTRRSDFRVLVSGL--PPSG

Parental  SWQDLKDHMREAGD-VCYADVQKDGVGMVEYLRKEDMEYALRKLDDTKFRSHEGETSYIRVYPERSTSYG
          SWQDLKDHM.EAG..VCYADVQKDGVGMVEYLRKEDM.YAL..LDDTKFRSHEGETSYI.VYPERSTSYG
Retrocopy SWQDLKDHMQEAGE>VCYADVQKDGVGMVEYLRKEDMDYALHELDDTKFRSHEGETSYIQVYPERSTSYG

Parental  YSRSRSGSRGRDSPYQSRGSPHYFSPFRP
          YSRSRSGSRG.DSPYQSRGSPHYFSPFRP
Retrocopy YSRSRSGSRGCDSPYQSRGSPHYFSPFRP

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	0.95 RPM	9.74 RPM
SRP051959_heart	0.56 RPM	7.30 RPM
SRP051959_kidney	1.20 RPM	13.02 RPM
SRP051959_liver	0.65 RPM	9.96 RPM
SRP051959_lung	0.70 RPM	10.10 RPM
SRP051959_lymph_node	1.07 RPM	10.96 RPM
SRP051959_skeletal_muscle	0.37 RPM	5.35 RPM
SRP051959_spleen	0.92 RPM	12.65 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_442 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_442 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_442 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000012792	1 retrocopy	retro_btau_837,
Choloepus hoffmanni	ENSCHOG00000009241	1 retrocopy	retro_chof_1119,
Callithrix jacchus	ENSCJAG00000001187	1 retrocopy	retro_cjac_442 ,
Callithrix jacchus	ENSCJAG00000009971	3 retrocopies	retro_cjac_3688, retro_cjac_3883, retro_cjac_3899,
Callithrix jacchus	ENSCJAG00000016062	5 retrocopies	retro_cjac_1035, retro_cjac_1969, retro_cjac_2006, retro_cjac_620, retro_cjac_746,
Dasypus novemcinctus	ENSDNOG00000012598	2 retrocopies	retro_dnov_1555, retro_dnov_2648,
Homo sapiens	ENSG00000111786	1 retrocopy	retro_hsap_2530,
Macaca mulatta	ENSMMUG00000016494	1 retrocopy	retro_mmul_2154,
Nomascus leucogenys	ENSNLEG00000015661	1 retrocopy	retro_nleu_1931,
Otolemur garnettii	ENSOGAG00000003852	1 retrocopy	retro_ogar_2328,
Ochotona princeps	ENSOPRG00000004234	1 retrocopy	retro_opri_878,
Pongo abelii	ENSPPYG00000005031	1 retrocopy	retro_pabe_119,
Sarcophilus harrisii	ENSSHAG00000005685	1 retrocopy	retro_shar_598,
Sus scrofa	ENSSSCG00000009906	1 retrocopy	retro_sscr_745,
Tupaia belangeri	ENSTBEG00000008499	1 retrocopy	retro_tbel_2602,
Tarsius syrichta	ENSTSYG00000006848	4 retrocopies	retro_tsyr_1432, retro_tsyr_1648, retro_tsyr_585, retro_tsyr_891,