RetrogeneDB ID: retro_hsap_372

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 1:44587827..44588184(-)
• Located in intron of: ENSG00000171872

Retrocopy information

• Ensembl ID: ENSG00000233514
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SNRPD1
• Ensembl ID: ENSG00000167088
• Aliases: SNRPD1, HsT2456, SMD1, SNRPD, Sm-D1
• Description: small nuclear ribonucleoprotein D1 polypeptide 16kDa [Source:HGNC Symbol;Acc:11158]

Sequence

>retro_hsap_372
ATGAAGCTCGTGAGATTTTTGATGAAATTGAGTCATGAAACTGTAACCATTGCATTGAAGAACAGAACACAGGTCCATGG
AACAGTCACAGGTGTGGATGTCAGCATGAATACACATCTTAAAGCTGTGAAAATGACCCCGAAGAACAGAGAACCTGTAC
AGCTGGAAACGCTGAGTATTCGAGGAAATAACATTCGGTATTTTATTCTACTAGACAGTTTACCTCTGGATACACTACTT
GTGGATGTTGAACCTAAGGTGAAATCTAAGAAAAGGGAAGCTGTTGCAGGAAGAGGCAGAGGCAGAGGAAGAGGAAGAGG
ACGTGGCCGTGGCAGAGGAAGAGGGGGTCCTAGGCGA

Alignment

ORF - retro_hsap_372 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.99 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MKLVRFLMKLSHETVTIELKNGTQVHGTITGVDVSMNTHLKAVKMTLKNREPVQLETLSIRGNNIRYFIL
          MKLVRFLMKLSHETVTI.LKN.TQVHGT.TGVDVSMNTHLKAVKMT.KNREPVQLETLSIRGNNIRYFIL
Retrocopy MKLVRFLMKLSHETVTIALKNRTQVHGTVTGVDVSMNTHLKAVKMTPKNREPVQLETLSIRGNNIRYFIL

Parental  PDSLPLDTLLVDVEPKVKSKKREAVAGRGRGRGRGRGRGRGRGRGGPRR
          .DSLPLDTLLVDVEPKVKSKKREAV....................GPRR
Retrocopy LDSLPLDTLLVDVEPKVKSKKREAVXXXXXXXXXXXXXXXXXXXXGPRR

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	24.07 RPM
bodymap2_adrenal	0.00 RPM	48.76 RPM
bodymap2_brain	0.02 RPM	34.76 RPM
bodymap2_breast	0.00 RPM	24.32 RPM
bodymap2_colon	0.00 RPM	31.05 RPM
bodymap2_heart	0.00 RPM	11.96 RPM
bodymap2_kidney	0.00 RPM	30.26 RPM
bodymap2_liver	0.00 RPM	19.94 RPM
bodymap2_lung	0.00 RPM	17.65 RPM
bodymap2_lymph_node	0.00 RPM	27.06 RPM
bodymap2_ovary	0.04 RPM	47.79 RPM
bodymap2_prostate	0.05 RPM	22.27 RPM
bodymap2_skeletal_muscle	0.00 RPM	14.35 RPM
bodymap2_testis	0.08 RPM	45.04 RPM
bodymap2_thyroid	0.00 RPM	32.62 RPM
bodymap2_white_blood_cells	0.00 RPM	26.68 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_372 was not detected

EST

No EST(s) were mapped for retro_hsap_372 retrocopy.

TSS

TSS No.	TSS Name	TSS expression level (Expr) in TPM range:
		no expression	0 < Expr ≤ 1	1 < Expr ≤ 5	5 < Expr ≤ 10	Expr > 10
TSS #1	TSS_94742	614 libraries	714 libraries	472 libraries	23 libraries	6 libraries

The graphical summary, for retro_hsap_372 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1829 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)

Lab

retro_hsap_372 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_372 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_291

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000006364	1 retrocopy	retro_acar_129,
Bos taurus	ENSBTAG00000008292	3 retrocopies	retro_btau_144, retro_btau_706, retro_btau_84,
Homo sapiens	ENSG00000167088	2 retrocopies	retro_hsap_1147, retro_hsap_372 ,
Mustela putorius furo	ENSMPUG00000005567	1 retrocopy	retro_mputfur_185,
Mus musculus	ENSMUSG00000002477	1 retrocopy	retro_mmus_1996,
Oryctolagus cuniculus	ENSOCUG00000023761	1 retrocopy	retro_ocun_224,
Sarcophilus harrisii	ENSSHAG00000011791	1 retrocopy	retro_shar_147,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.06 RPM
CEU_NA11843	0.23 RPM
CEU_NA11930	0.10 RPM
CEU_NA12004	0.19 RPM
CEU_NA12400	0.32 RPM
CEU_NA12751	0.05 RPM
CEU_NA12760	0.22 RPM
CEU_NA12827	0.14 RPM
CEU_NA12872	0.22 RPM
CEU_NA12873	0.19 RPM
FIN_HG00183	0.08 RPM
FIN_HG00277	0.22 RPM
FIN_HG00315	0.14 RPM
FIN_HG00321	0.18 RPM
FIN_HG00328	0.38 RPM
FIN_HG00338	0.26 RPM
FIN_HG00349	0.54 RPM
FIN_HG00375	0.24 RPM
FIN_HG00377	0.40 RPM
FIN_HG00378	0.11 RPM
GBR_HG00099	0.23 RPM
GBR_HG00111	0.28 RPM
GBR_HG00114	0.13 RPM
GBR_HG00119	0.22 RPM
GBR_HG00131	0.06 RPM
GBR_HG00133	0.14 RPM
GBR_HG00134	0.11 RPM
GBR_HG00137	0.16 RPM
GBR_HG00142	0.14 RPM
GBR_HG00143	0.32 RPM
TSI_NA20512	0.17 RPM
TSI_NA20513	0.22 RPM
TSI_NA20518	0.69 RPM
TSI_NA20532	0.14 RPM
TSI_NA20538	0.09 RPM
TSI_NA20756	0.15 RPM
TSI_NA20765	0.12 RPM
TSI_NA20771	0.14 RPM
TSI_NA20786	0.10 RPM
TSI_NA20798	0.06 RPM
YRI_NA18870	0.24 RPM
YRI_NA18907	0.14 RPM
YRI_NA18916	0.15 RPM
YRI_NA19093	0.13 RPM
YRI_NA19099	0.19 RPM
YRI_NA19114	0.08 RPM
YRI_NA19118	0.15 RPM
YRI_NA19213	0.10 RPM
YRI_NA19214	0.02 RPM
YRI_NA19223	0.18 RPM

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Indel association:

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