RetrogeneDB ID: retro_hsap_2176

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 2:171608716..171609295(+)
• Located in intron of: ENSG00000234350

Retrocopy information

• Ensembl ID: ENSG00000128692
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: EIF2S2
• Ensembl ID: ENSG00000125977
• Aliases: EIF2S2, EIF2, EIF2B, EIF2beta, PPP1R67, eIF-2-beta
• Description: eukaryotic translation initiation factor 2, subunit 2 beta, 38kDa [Source:HGNC Symbol;Acc:3266]

Sequence

>retro_hsap_2176
GATGAGGATGAAGCTCTAGAAGATGAAGACAACAAAAAAGATGATGGTATCTCATTCAGTAATCAGACAGGCCCTGCTTG
GGCAGGCTCAGAAAGAGACTACACATACGAGGAGCTGCTGAATCGAGTGTTCAACATCATGAGGGAAAAGAATCCAGATA
TGGTTGCTGGGGAGAAAAGGAAATTTGTCATGAAACCTCCACAAGTCGTCCGAGTAGGAACCAAGAAAACTTCTTTTGTC
AACTTTACAGATATCTGTAAACTATTACATCGTCAACCCAAACATCTCCTTGCATTTTTATTGGCTGAATTGGGTACAAG
TGGTTCTATAGATGGTAATAACCAACTTGTAATCAAAGGAAGATTCCAACAGAAACAGATAGAAAATGTCTTGAGAAGAT
ATATCAAGGAGTATGTCACTTGTCACACATGCCGATCACCGGACACAATCCTGCAGAAGGACATGCGACTCTATTTCCTA
CAGTGCGAAACTTGTCATTCTAGATGTTCTGTTGCCATTATCAAAATTGGCTTCCAGGCTGTCATGGGCAAGCGAGCACA
GCTCCGTGCCAAAGCTAAC

Alignment

ORF - retro_hsap_2176 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.89 %
• Parental protein coverage: 57.96 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EKDEALEDEDNKKDDGISFSNQTGPAWAGSERDYTYEELLNRVFNIMREKNPDMVAGEKRKFVMKPPQVV
          ..DEALEDEDNKKDDGISFSNQTGPAWAGSERDYTYEELLNRVFNIMREKNPDMVAGEKRKFVMKPPQVV
Retrocopy DEDEALEDEDNKKDDGISFSNQTGPAWAGSERDYTYEELLNRVFNIMREKNPDMVAGEKRKFVMKPPQVV

Parental  RVGTKKTSFVNFTDICKLLHRQPKHLLAFLLAELGTSGSIDGNNQLVIKGRFQQKQIENVLRRYIKEYVT
          RVGTKKTSFVNFTDICKLLHRQPKHLLAFLLAELGTSGSIDGNNQLVIKGRFQQKQIENVLRRYIKEYVT
Retrocopy RVGTKKTSFVNFTDICKLLHRQPKHLLAFLLAELGTSGSIDGNNQLVIKGRFQQKQIENVLRRYIKEYVT

Parental  CHTCRSPDTILQKDTRLYFLQCETCHSRCSVASIKTGFQAVTGKRAQLRAKAN
          CHTCRSPDTILQKD.RLYFLQCETCHSRCSVA.IK.GFQAV.GKRAQLRAKAN
Retrocopy CHTCRSPDTILQKDMRLYFLQCETCHSRCSVAIIKIGFQAVMGKRAQLRAKAN

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	0.22 RPM	85.12 RPM
bodymap2_adrenal	0.33 RPM	97.50 RPM
bodymap2_brain	0.21 RPM	64.25 RPM
bodymap2_breast	0.23 RPM	65.00 RPM
bodymap2_colon	0.43 RPM	100.30 RPM
bodymap2_heart	0.04 RPM	46.08 RPM
bodymap2_kidney	0.10 RPM	69.80 RPM
bodymap2_liver	0.02 RPM	56.61 RPM
bodymap2_lung	0.23 RPM	109.70 RPM
bodymap2_lymph_node	0.15 RPM	73.37 RPM
bodymap2_ovary	0.35 RPM	114.99 RPM
bodymap2_prostate	0.16 RPM	77.73 RPM
bodymap2_skeletal_muscle	0.16 RPM	121.91 RPM
bodymap2_testis	0.25 RPM	91.55 RPM
bodymap2_thyroid	0.32 RPM	105.98 RPM
bodymap2_white_blood_cells	0.02 RPM	71.96 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_2176 was not detected

EST

No EST(s) were mapped for retro_hsap_2176 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_114658	910 libraries	294 libraries	493 libraries	108 libraries	24 libraries

The graphical summary, for retro_hsap_2176 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_2176 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_2176 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Gorilla gorilla	retro_ggor_1726

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000018334	2 retrocopies	retro_cjac_4196, retro_cjac_697,
Cavia porcellus	ENSCPOG00000015439	1 retrocopy	retro_cpor_1143,
Echinops telfairi	ENSETEG00000001922	1 retrocopy	retro_etel_1101,
Homo sapiens	ENSG00000125977	3 retrocopies	retro_hsap_2176 , retro_hsap_2260, retro_hsap_713,
Gorilla gorilla	ENSGGOG00000015546	5 retrocopies	retro_ggor_1683, retro_ggor_1726, retro_ggor_2007, retro_ggor_280, retro_ggor_604,
Microcebus murinus	ENSMICG00000006944	1 retrocopy	retro_mmur_1583,
Macaca mulatta	ENSMMUG00000018095	1 retrocopy	retro_mmul_1483,
Monodelphis domestica	ENSMODG00000002805	5 retrocopies	retro_mdom_1981, retro_mdom_365, retro_mdom_368, retro_mdom_370, retro_mdom_837,
Nomascus leucogenys	ENSNLEG00000010034	2 retrocopies	retro_nleu_2242, retro_nleu_466,
Otolemur garnettii	ENSOGAG00000001417	1 retrocopy	retro_ogar_196,
Pongo abelii	ENSPPYG00000010933	2 retrocopies	retro_pabe_1955, retro_pabe_2421,
Pan troglodytes	ENSPTRG00000013412	2 retrocopies	retro_ptro_1600, retro_ptro_508,
Rattus norvegicus	ENSRNOG00000017447	1 retrocopy	retro_rnor_2395,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.15 RPM
CEU_NA11843	0.17 RPM
CEU_NA11930	0.29 RPM
CEU_NA12004	0.08 RPM
CEU_NA12400	0.07 RPM
CEU_NA12751	0.19 RPM
CEU_NA12760	0.40 RPM
CEU_NA12827	0.33 RPM
CEU_NA12872	0.11 RPM
CEU_NA12873	0.13 RPM
FIN_HG00183	0.30 RPM
FIN_HG00277	0.18 RPM
FIN_HG00315	0.17 RPM
FIN_HG00321	0.09 RPM
FIN_HG00328	0.24 RPM
FIN_HG00338	0.21 RPM
FIN_HG00349	0.60 RPM
FIN_HG00375	0.32 RPM
FIN_HG00377	0.25 RPM
FIN_HG00378	0.30 RPM
GBR_HG00099	0.20 RPM
GBR_HG00111	0.17 RPM
GBR_HG00114	0.13 RPM
GBR_HG00119	0.07 RPM
GBR_HG00131	0.20 RPM
GBR_HG00133	0.14 RPM
GBR_HG00134	0.11 RPM
GBR_HG00137	0.19 RPM
GBR_HG00142	0.14 RPM
GBR_HG00143	0.16 RPM
TSI_NA20512	0.11 RPM
TSI_NA20513	0.24 RPM
TSI_NA20518	0.58 RPM
TSI_NA20532	0.17 RPM
TSI_NA20538	0.23 RPM
TSI_NA20756	0.29 RPM
TSI_NA20765	0.27 RPM
TSI_NA20771	0.34 RPM
TSI_NA20786	0.08 RPM
TSI_NA20798	0.22 RPM
YRI_NA18870	0.47 RPM
YRI_NA18907	0.00 RPM
YRI_NA18916	0.21 RPM
YRI_NA19093	0.21 RPM
YRI_NA19099	0.21 RPM
YRI_NA19114	0.08 RPM
YRI_NA19118	0.15 RPM
YRI_NA19213	0.31 RPM
YRI_NA19214	0.07 RPM
YRI_NA19223	0.08 RPM

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Indel association:

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