RetrogeneDB ID: retro_hsap_4769

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: X:146882501..146882815(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000227505
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SLIRP
• Ensembl ID: ENSG00000119705
• Aliases: SLIRP, C14orf156, DC50, PD04872
• Description: SRA stem-loop interacting RNA binding protein [Source:HGNC Symbol;Acc:20495]

Sequence

>retro_hsap_4769
ATGGCTGCCTTAGCATGGAAAGGTGCCATGGTGCTTCATACAAGTATCAGTAGGCCGGTTGCTTTTGTTAGCAAAATTCC
TTGGACCGCAGCGTCAAATCAGCTGATGGTGTCTTTGCACAGTTTGGCCATATCCAAAAATGTGTTGTACCTTTTGACAA
GGAGACTGGCTTTCACAGAGGTTTGGGTTGGGTTCAGTTTTCTTCAGAAGAACTTCAGAATGCACTATAACAGGAAAATC
ATATTATAGATGGAGTAAAGCTCCAGATTGGAGCTCAAAGGCCAAAAGTTTTGTAAACATCTGATGAAGAGAAA

Alignment

ORF - retro_hsap_4769 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.16 %
• Parental protein coverage: 97.25 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAASAARGAAALRRSINQPVAFVRRIPWTAASSQLKEH-FAQFGHVRRCILPFDKETGFHRGLGWVQFSS
          MAA.A..GA..L..SI..PVAFV..IPWTAAS.QL....FAQFGH...C..PFDKETGFHRGLGWVQFSS
Retrocopy MAALAWKGAMVLHTSISRPVAFVSKIPWTAASNQLMVS<FAQFGHIQKCVVPFDKETGFHRGLGWVQFSS

Parental  EEGLRNALQQENHIIDGVKVQVHTRRPKLPQTSDDEK
          EE.L.NAL.QENHIIDGVK.Q....RPK...TSD.EK
Retrocopy EE-LQNAL*QENHIIDGVKLQIGAQRPKVL*TSDEEK

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	16.22 RPM
bodymap2_adrenal	0.00 RPM	21.04 RPM
bodymap2_brain	0.00 RPM	24.17 RPM
bodymap2_breast	0.00 RPM	14.57 RPM
bodymap2_colon	0.00 RPM	24.54 RPM
bodymap2_heart	0.00 RPM	32.60 RPM
bodymap2_kidney	0.00 RPM	30.26 RPM
bodymap2_liver	0.00 RPM	23.87 RPM
bodymap2_lung	0.00 RPM	13.36 RPM
bodymap2_lymph_node	0.00 RPM	15.11 RPM
bodymap2_ovary	0.00 RPM	12.57 RPM
bodymap2_prostate	0.00 RPM	22.34 RPM
bodymap2_skeletal_muscle	0.00 RPM	18.86 RPM
bodymap2_testis	0.00 RPM	25.41 RPM
bodymap2_thyroid	0.00 RPM	14.88 RPM
bodymap2_white_blood_cells	0.00 RPM	12.30 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_4769 was not detected

EST

No EST(s) were mapped for retro_hsap_4769 retrocopy.

TSS

No TSS is located nearby retro_hsap_4769 retrocopy 5' end.

Lab

retro_hsap_4769 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_4769 has 5 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_3176
Gorilla gorilla	retro_ggor_2972
Pongo abelii	retro_pabe_3712
Macaca mulatta	retro_mmul_2544
Callithrix jacchus	retro_cjac_4132

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 43 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000003975	3 retrocopies	retro_amel_307, retro_amel_326, retro_amel_340,
Bos taurus	ENSBTAG00000008135	3 retrocopies	retro_btau_1439, retro_btau_430, retro_btau_999,
Canis familiaris	ENSCAFG00000017230	1 retrocopy	retro_cfam_1303,
Callithrix jacchus	ENSCJAG00000016946	4 retrocopies	retro_cjac_1116, retro_cjac_1307, retro_cjac_3298, retro_cjac_4132,
Cavia porcellus	ENSCPOG00000001500	2 retrocopies	retro_cpor_1388, retro_cpor_579,
Dasypus novemcinctus	ENSDNOG00000007721	3 retrocopies	retro_dnov_1721, retro_dnov_2460, retro_dnov_612,
Echinops telfairi	ENSETEG00000010345	4 retrocopies	retro_etel_1095, retro_etel_1277, retro_etel_1471, retro_etel_1792,
Felis catus	ENSFCAG00000024050	2 retrocopies	retro_fcat_1696, retro_fcat_695,
Homo sapiens	ENSG00000119705	1 retrocopy	retro_hsap_4769 ,
Gorilla gorilla	ENSGGOG00000011059	1 retrocopy	retro_ggor_2972,
Microcebus murinus	ENSMICG00000012080	3 retrocopies	retro_mmur_1254, retro_mmur_1504, retro_mmur_238,
Macaca mulatta	ENSMMUG00000029256	1 retrocopy	retro_mmul_2544,
Mus musculus	ENSMUSG00000021040	1 retrocopy	retro_mmus_1954,
Pongo abelii	ENSPPYG00000006030	1 retrocopy	retro_pabe_3712,
Pan troglodytes	ENSPTRG00000030691	1 retrocopy	retro_ptro_3176,
Rattus norvegicus	ENSRNOG00000012314	3 retrocopies	retro_rnor_1670, retro_rnor_749, retro_rnor_923,
Sus scrofa	ENSSSCG00000028167	5 retrocopies	retro_sscr_344, retro_sscr_345, retro_sscr_383, retro_sscr_384, retro_sscr_820,
Tupaia belangeri	ENSTBEG00000013979	2 retrocopies	retro_tbel_1146, retro_tbel_3713,
Vicugna pacos	ENSVPAG00000001781	2 retrocopies	retro_vpac_398, retro_vpac_418,

Population studies

Expression level across human populations :

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

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Indel association:

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