RetrogeneDB ID: retro_hsap_2530

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 21:37667631..37667959(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000214867
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SRSF9
• Ensembl ID: ENSG00000111786
• Aliases: SRSF9, SFRS9, SRp30c
• Description: serine/arginine-rich splicing factor 9 [Source:HGNC Symbol;Acc:10791]

Sequence

>retro_hsap_2530
GGGTGCATCTACGTGGGGAAACCTTCCGACCCACGTGCGCGAGAAGGAGCCGCAGGACCTGTTCTACAAGTACAGCCGCA
TCCGCGAGATCGAGCTCAAGAGCCGGTACGGCCTTGTGCCCTTCGCCTCCGTGCGCTTCGAGGACCCTCGAGATGCAGAG
GATGCTATTTATGGAAGAAATGGACTTCTTCCATCAGGCAGCTGGCAGGACCTGAAGGATCACACGCGAGAAGCTGGGGA
TGCCTGTTACACGGATGTGCAGAAGGATGGAGTGGGGATGGTTGGGTGTCTCAGAAAAGAAGACATGGAATATGCCCTGC
GTCAACTG

Alignment

ORF - retro_hsap_2530 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.55 %
• Parental protein coverage: 99.09 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GRIYVG-NLPTDVREKDLEDLFYKYGRIREIELKNRHGLVPFAFVRFEDPRDAEDAIYGRNGLPPSGSWQ
          G.IYVG.NLPT.VREK...DLFYKY.RIREIELK.R.GLVPFA.VRFEDPRDAEDAIYGRNGL.PSGSWQ
Retrocopy GCIYVG>NLPTHVREKEPQDLFYKYSRIREIELKSRYGLVPFASVRFEDPRDAEDAIYGRNGLLPSGSWQ

Parental  DLKDHMREAGDVCYADVQKDGVGMVEYLRKEDMEYALRKL
          DLKDH.REAGD.CY.DVQKDGVGMV..LRKEDMEYALR.L
Retrocopy DLKDHTREAGDACYTDVQKDGVGMVGCLRKEDMEYALRQL

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
bodymap2_adipose	0.00 RPM	79.99 RPM
bodymap2_adrenal	0.02 RPM	104.93 RPM
bodymap2_brain	0.00 RPM	70.27 RPM
bodymap2_breast	0.10 RPM	74.61 RPM
bodymap2_colon	0.08 RPM	92.95 RPM
bodymap2_heart	0.02 RPM	25.40 RPM
bodymap2_kidney	0.08 RPM	102.70 RPM
bodymap2_liver	0.09 RPM	61.45 RPM
bodymap2_lung	0.04 RPM	96.13 RPM
bodymap2_lymph_node	0.00 RPM	116.46 RPM
bodymap2_ovary	0.08 RPM	106.37 RPM
bodymap2_prostate	0.05 RPM	89.48 RPM
bodymap2_skeletal_muscle	0.00 RPM	23.66 RPM
bodymap2_testis	0.00 RPM	105.14 RPM
bodymap2_thyroid	0.08 RPM	105.96 RPM
bodymap2_white_blood_cells	0.00 RPM	102.16 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_2530 was not detected

EST

No EST(s) were mapped for retro_hsap_2530 retrocopy.

TSS

No TSS is located nearby retro_hsap_2530 retrocopy 5' end.

Lab

retro_hsap_2530 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_2530 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 23 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,
Dasypus novemcinctus	ENSDNOG00000012598	2 retrocopies	retro_dnov_1555, retro_dnov_2648,
Homo sapiens	ENSG00000111786	1 retrocopy	retro_hsap_2530 ,
Homo sapiens	ENSG00000112081	4 retrocopies	retro_hsap_2140, retro_hsap_2299, retro_hsap_2304, retro_hsap_757,
Homo sapiens	ENSG00000124193	1 retrocopy	retro_hsap_1809,
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,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.02 RPM
CEU_NA11843	0.00 RPM
CEU_NA11930	0.03 RPM
CEU_NA12004	0.00 RPM
CEU_NA12400	0.00 RPM
CEU_NA12751	0.05 RPM
CEU_NA12760	0.13 RPM
CEU_NA12827	0.05 RPM
CEU_NA12872	0.08 RPM
CEU_NA12873	0.10 RPM
FIN_HG00183	0.00 RPM
FIN_HG00277	0.00 RPM
FIN_HG00315	0.06 RPM
FIN_HG00321	0.00 RPM
FIN_HG00328	0.05 RPM
FIN_HG00338	0.04 RPM
FIN_HG00349	0.06 RPM
FIN_HG00375	0.02 RPM
FIN_HG00377	0.03 RPM
FIN_HG00378	0.00 RPM
GBR_HG00099	0.00 RPM
GBR_HG00111	0.11 RPM
GBR_HG00114	0.03 RPM
GBR_HG00119	0.00 RPM
GBR_HG00131	0.00 RPM
GBR_HG00133	0.02 RPM
GBR_HG00134	0.07 RPM
GBR_HG00137	0.14 RPM
GBR_HG00142	0.08 RPM
GBR_HG00143	0.03 RPM
TSI_NA20512	0.03 RPM
TSI_NA20513	0.02 RPM
TSI_NA20518	0.06 RPM
TSI_NA20532	0.07 RPM
TSI_NA20538	0.09 RPM
TSI_NA20756	0.00 RPM
TSI_NA20765	0.02 RPM
TSI_NA20771	0.03 RPM
TSI_NA20786	0.05 RPM
TSI_NA20798	0.09 RPM
YRI_NA18870	0.03 RPM
YRI_NA18907	0.07 RPM
YRI_NA18916	0.08 RPM
YRI_NA19093	0.03 RPM
YRI_NA19099	0.00 RPM
YRI_NA19114	0.00 RPM
YRI_NA19118	0.10 RPM
YRI_NA19213	0.00 RPM
YRI_NA19214	0.02 RPM
YRI_NA19223	0.10 RPM

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Indel association:

No indels were associated with its genomic coordinates. Based on Kabza et al. 2015 (PubMed).