RetrogeneDB ID: retro_hsap_1175

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 13:23708416..23708703(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000233440
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: HMGA1
• Ensembl ID: ENSG00000137309
• Aliases: HMGA1, HMG-R, HMGA1A, HMGIY
• Description: high mobility group AT-hook 1 [Source:HGNC Symbol;Acc:5010]

Sequence

>retro_hsap_1175
ATGAGCGAGTTGAGCTTGAAGTCCAGCCAGCCCTTGGCCTCCAAGTGGGAAAAGGATGGCACTGAGAAGCGGGGCTGGGG
CAGGCCACGCAAGCAGCCTCCGAAAGAGCCCAGAGAAGTGCCAACACCTAAGAGACCTCTGGGCGACCAAAGGGAAGCAA
AAACAAAGGCGCTGCCAAGTCCCAGAAAACCATCACAACTCCAGGAAGGAAACCAAGGGGCAGACCCACAAAACTGGAAA
AGGAGGAAGAGGAGGGCATCTTGCAGGAGTCCTCGGGGGAGGAGCAG

Alignment

ORF - retro_hsap_1175 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.6 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSESSSKSSQPLASKQEKDGTEKRGRGRPRKQPPKEPSEVPTPKRP-RGRPKGSKNKGAAKTRKTTTTPG
          MSE.S.KSSQPLASK.EKDGTEKRG.GRPRKQPPKEP.EVPTPKRP..GRPKGSKNKGAAK..KT.TTPG
Retrocopy MSELSLKSSQPLASKWEKDGTEKRGWGRPRKQPPKEPREVPTPKRP<SGRPKGSKNKGAAKSQKTITTPG

Parental  RKPRGRPKKLEKEEEEGISQESSEEEQ
          RKPRGRP.KLEKEEEEGI.QESS.EEQ
Retrocopy RKPRGRPTKLEKEEEEGILQESSGEEQ

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	29.80 RPM
bodymap2_adrenal	0.00 RPM	22.37 RPM
bodymap2_brain	0.00 RPM	13.57 RPM
bodymap2_breast	0.00 RPM	16.17 RPM
bodymap2_colon	0.00 RPM	21.81 RPM
bodymap2_heart	0.00 RPM	15.71 RPM
bodymap2_kidney	0.00 RPM	8.36 RPM
bodymap2_liver	0.00 RPM	5.37 RPM
bodymap2_lung	0.00 RPM	68.62 RPM
bodymap2_lymph_node	0.00 RPM	49.23 RPM
bodymap2_ovary	0.00 RPM	5.96 RPM
bodymap2_prostate	0.00 RPM	19.02 RPM
bodymap2_skeletal_muscle	0.00 RPM	99.76 RPM
bodymap2_testis	0.00 RPM	98.55 RPM
bodymap2_thyroid	0.00 RPM	32.11 RPM
bodymap2_white_blood_cells	0.00 RPM	50.44 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_1175 was not detected

EST

No EST(s) were mapped for retro_hsap_1175 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_32008	1051 libraries	495 libraries	260 libraries	19 libraries	4 libraries
TSS #2	TSS_32009	915 libraries	616 libraries	277 libraries	19 libraries	2 libraries

The graphical summary, for retro_hsap_1175 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_1175 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_1175 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_807

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001061	1 retrocopy	retro_amel_1637,
Callithrix jacchus	ENSCJAG00000015226	2 retrocopies	retro_cjac_1197, retro_cjac_3158,
Homo sapiens	ENSG00000137309	4 retrocopies	retro_hsap_1175 , retro_hsap_2277, retro_hsap_4663, retro_hsap_695,
Myotis lucifugus	ENSMLUG00000010085	2 retrocopies	retro_mluc_1619, retro_mluc_2429,
Macaca mulatta	ENSMMUG00000019529	2 retrocopies	retro_mmul_1276, retro_mmul_2406,
Mus musculus	ENSMUSG00000046711	1 retrocopy	retro_mmus_188,
Nomascus leucogenys	ENSNLEG00000008303	1 retrocopy	retro_nleu_1097,
Pongo abelii	ENSPPYG00000029838	4 retrocopies	retro_pabe_1941, retro_pabe_2441, retro_pabe_3623, retro_pabe_960,
Pan troglodytes	ENSPTRG00000040884	6 retrocopies	retro_ptro_1611, retro_ptro_2053, retro_ptro_3098, retro_ptro_499, retro_ptro_789, retro_ptro_807,
Rattus norvegicus	ENSRNOG00000000488	1 retrocopy	retro_rnor_164,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.00 RPM
CEU_NA11843	0.00 RPM
CEU_NA11930	0.00 RPM
CEU_NA12004	0.00 RPM
CEU_NA12400	0.00 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	0.03 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	0.00 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	0.00 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).