RetrogeneDB ID: retro_hsap_350

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 1:17012118..17012550(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000236698
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: EIF1AX
• Ensembl ID: ENSG00000173674
• Aliases: EIF1AX, EIF1A, EIF1AP1, EIF4C, eIF-1A, eIF-4C
• Description: eukaryotic translation initiation factor 1A, X-linked [Source:HGNC Symbol;Acc:3250]

Sequence

>retro_hsap_350
ATGCCCAAGAATAAAGGTAAAGGAGGTAAAAATAGACGCAGGGGTAAGAATGAGAATGAATCTGAAAAAAGAGAACTGGT
ATTCAAAGAGGATGGTCAGGAGTATGCTCAGGTAATCAAAATGTTGGGAAATGGACGGCTAGAAGCAATGTGTTTCGATG
GTGTAAAGAGGTTATGTCACATCAGAGGAAAATTGAGAAAAAAGGTTTGGATAAATACCTCGGACATTATTTTGGTTGGT
CTCCGAGACTACCAGGATAACAAAGCTGATGTAATTTTAAAATACAATGCAGACGAAGCTAGAAGTCTGCAGGCATACGG
CGAGCTTCCAGAGCATGCTAAAATCAATGAAACTGATACATTTGGTCCTGGAGATGATGATGAAATTCAGTTTGATGACA
TTGGAGATGATGATGAAGATATTGATGACATC

Alignment

ORF - retro_hsap_350 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.31 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MPKNKGKGGKNRRRGKNENESEKRELVFKEDGQEYAQVIKMLGNGRLEAMCFDGVKRLCHIRGKLRKKVW
          MPKNKGKGGKNRRRGKNENESEKRELVFKEDGQEYAQVIKMLGNGRLEAMCFDGVKRLCHIRGKLRKKVW
Retrocopy MPKNKGKGGKNRRRGKNENESEKRELVFKEDGQEYAQVIKMLGNGRLEAMCFDGVKRLCHIRGKLRKKVW

Parental  INTSDIILVGLRDYQDNKADVILKYNADEARSLKAYGELPEHAKINETDTFGPGDDDEIQFDDIGDDDED
          INTSDIILVGLRDYQDNKADVILKYNADEARSL.AYGELPEHAKINETDTFGPGDDDEIQFDDIGDDDED
Retrocopy INTSDIILVGLRDYQDNKADVILKYNADEARSLQAYGELPEHAKINETDTFGPGDDDEIQFDDIGDDDED

Parental  IDDI
          IDDI
Retrocopy IDDI

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	0.06 RPM	85.12 RPM
bodymap2_adrenal	0.27 RPM	54.65 RPM
bodymap2_brain	0.38 RPM	166.78 RPM
bodymap2_breast	0.08 RPM	106.32 RPM
bodymap2_colon	0.10 RPM	137.98 RPM
bodymap2_heart	0.04 RPM	40.71 RPM
bodymap2_kidney	0.31 RPM	116.18 RPM
bodymap2_liver	0.09 RPM	41.00 RPM
bodymap2_lung	0.21 RPM	90.37 RPM
bodymap2_lymph_node	0.09 RPM	74.08 RPM
bodymap2_ovary	0.37 RPM	126.24 RPM
bodymap2_prostate	0.09 RPM	101.34 RPM
bodymap2_skeletal_muscle	0.07 RPM	89.98 RPM
bodymap2_testis	0.21 RPM	78.32 RPM
bodymap2_thyroid	0.13 RPM	161.12 RPM
bodymap2_white_blood_cells	0.02 RPM	56.96 RPM

ChIP-Seq

RNA Polymerase II actvity may be related with retro_hsap_350 in 2 libraries

ENCODE library ID	Target	ChIP-Seq Peak coordinates
ENCFF002CFW	POLR2A	1:17012494..17012924
ENCFF002CZY	POLR2A	1:17012292..17012808
ENCFF002CZY	POLR2A	1:17012601..17012810

EST

No EST(s) were mapped for retro_hsap_350 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_85485	444 libraries	801 libraries	563 libraries	20 libraries	1 library

The graphical summary, for retro_hsap_350 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_350 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_350 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 28 parental genes, and 47 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000012660	1 retrocopy	retro_acar_151,
Ailuropoda melanoleuca	ENSAMEG00000016604	1 retrocopy	retro_amel_1421,
Bos taurus	ENSBTAG00000017633	3 retrocopies	retro_btau_1293, retro_btau_293, retro_btau_381,
Callithrix jacchus	ENSCJAG00000005371	1 retrocopy	retro_cjac_66,
Dipodomys ordii	ENSDORG00000011536	1 retrocopy	retro_dord_484,
Equus caballus	ENSECAG00000006469	2 retrocopies	retro_ecab_464, retro_ecab_634,
Erinaceus europaeus	ENSEEUG00000007518	3 retrocopies	retro_eeur_408, retro_eeur_567, retro_eeur_686,
Homo sapiens	ENSG00000173674	2 retrocopies	retro_hsap_1431, retro_hsap_350 ,
Gorilla gorilla	ENSGGOG00000012186	3 retrocopies	retro_ggor_1103, retro_ggor_363, retro_ggor_968,
Latimeria chalumnae	ENSLACG00000015565	1 retrocopy	retro_lcha_65,
Microcebus murinus	ENSMICG00000004110	2 retrocopies	retro_mmur_183, retro_mmur_197,
Myotis lucifugus	ENSMLUG00000012977	2 retrocopies	retro_mluc_250, retro_mluc_3,
Macaca mulatta	ENSMMUG00000000193	1 retrocopy	retro_mmul_1590,
Monodelphis domestica	ENSMODG00000027820	1 retrocopy	retro_mdom_274,
Mus musculus	ENSMUSG00000067194	1 retrocopy	retro_mmus_264,
Nomascus leucogenys	ENSNLEG00000009913	1 retrocopy	retro_nleu_1845,
Otolemur garnettii	ENSOGAG00000008182	1 retrocopy	retro_ogar_128,
Pongo abelii	ENSPPYG00000020176	1 retrocopy	retro_pabe_1185,
Pan troglodytes	ENSPTRG00000022504	1 retrocopy	retro_ptro_978,
Pteropus vampyrus	ENSPVAG00000003521	2 retrocopies	retro_pvam_780, retro_pvam_92,
Rattus norvegicus	ENSRNOG00000005736	1 retrocopy	retro_rnor_24,
Sorex araneus	ENSSARG00000013528	1 retrocopy	retro_sara_324,
Sarcophilus harrisii	ENSSHAG00000010995	1 retrocopy	retro_shar_707,
Sus scrofa	ENSSSCG00000029864	1 retrocopy	retro_sscr_948,
Ictidomys tridecemlineatus	ENSSTOG00000026117	1 retrocopy	retro_itri_1839,
Tupaia belangeri	ENSTBEG00000017492	6 retrocopies	retro_tbel_1604, retro_tbel_312, retro_tbel_3762, retro_tbel_4137, retro_tbel_4712, retro_tbel_798,
Tursiops truncatus	ENSTTRG00000002012	1 retrocopy	retro_ttru_1009,
Vicugna pacos	ENSVPAG00000009927	4 retrocopies	retro_vpac_47, retro_vpac_531, retro_vpac_550, retro_vpac_590,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.21 RPM
CEU_NA11843	0.20 RPM
CEU_NA11930	0.33 RPM
CEU_NA12004	0.23 RPM
CEU_NA12400	0.25 RPM
CEU_NA12751	0.05 RPM
CEU_NA12760	0.40 RPM
CEU_NA12827	0.38 RPM
CEU_NA12872	0.22 RPM
CEU_NA12873	0.26 RPM
FIN_HG00183	0.27 RPM
FIN_HG00277	0.44 RPM
FIN_HG00315	0.39 RPM
FIN_HG00321	0.30 RPM
FIN_HG00328	0.21 RPM
FIN_HG00338	0.17 RPM
FIN_HG00349	0.94 RPM
FIN_HG00375	0.39 RPM
FIN_HG00377	0.35 RPM
FIN_HG00378	0.40 RPM
GBR_HG00099	0.64 RPM
GBR_HG00111	0.24 RPM
GBR_HG00114	0.08 RPM
GBR_HG00119	0.14 RPM
GBR_HG00131	0.26 RPM
GBR_HG00133	0.39 RPM
GBR_HG00134	0.20 RPM
GBR_HG00137	0.25 RPM
GBR_HG00142	0.11 RPM
GBR_HG00143	0.19 RPM
TSI_NA20512	0.08 RPM
TSI_NA20513	0.29 RPM
TSI_NA20518	0.69 RPM
TSI_NA20532	0.17 RPM
TSI_NA20538	0.28 RPM
TSI_NA20756	0.47 RPM
TSI_NA20765	0.12 RPM
TSI_NA20771	0.51 RPM
TSI_NA20786	0.34 RPM
TSI_NA20798	0.31 RPM
YRI_NA18870	1.02 RPM
YRI_NA18907	0.45 RPM
YRI_NA18916	0.23 RPM
YRI_NA19093	0.05 RPM
YRI_NA19099	0.40 RPM
YRI_NA19114	0.34 RPM
YRI_NA19118	0.44 RPM
YRI_NA19213	0.19 RPM
YRI_NA19214	0.22 RPM
YRI_NA19223	0.14 RPM

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Indel association:

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