RetrogeneDB ID: retro_hsap_4144

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 9:30689105..30690274(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000215210
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RBMX
• Ensembl ID: ENSG00000147274
• Aliases: RBMX, HNRNPG, HNRPG, RBMXP1, RBMXRT, RNMX, hnRNP-G
• Description: RNA binding motif protein, X-linked [Source:HGNC Symbol;Acc:9910]

Sequence

>retro_hsap_4144
GTTGAAGCAGATTGCCCAGGAAAGCCGTTCACTGGTGGGCTTAACACGGAAACAAATGAGAAAGCTCTTGAAGCAGTATT
TGGCAAATATGGACGAATAGTGGAAGTACTCTTGGTGAAAGACCATGAAACCAACAAATCAGGAGGATTTGCTTTTGTCA
CCTTTGAAAGCCCAGCAGATGCTAAGGATGCAGCCAGAGACATGAATGGAAAGTCATTAGATGGAAAAGCCATCGAGGTG
GAACAAGCCAACAAACCATCATTTGAAAGTGGTAGACGTGGACCGCCTCCACCTCCAAGAAGTAGAGGCCCTCCAAGAGG
TCTTAGAGGTGGAAGAGGAGGAAGTGGAGGAACAAGGGGACCTCCCTCACGGGGAGGACACATGGATGACGGTGGATATT
CCATGAATTTTAACATGAGTTCTTCCAGGGGACCACATCCAGTAAAAAGAGGACCACCACCAAGAAGTGGGAGTCCTCCT
TCTAAGAGATCTGCACCTTCAGGACCAGTTCGCAGTAGCAGTGAAATGGGAGGAAGAGCTCCTGTATCACGTGGAAGAGA
TAGTTACGGAGGTCCACCTCGAAGGGAACTGCTGCCCTCTTGTAGAAATGATTATTTGTCCCCAAGAGATGATGGGTATT
CTACTAAAGACAGCTATTCAAGCAGAGATTACCCAAGTTCTCATGATACTAGAGCTTATGCACCACCACCACGAGATTAT
ACTTACCGTGATTATGGTCATTCCAGTTCACGTGTTGACTATCCATAAAGAGGCTATAGCGATAGAGATAGATATGGTCG
TGATCATGACTATTCAGATCATCCAGGTGGAGGTTCCTACAGAGATTCATATGAGAGTTATGGTAACTCACGTAGTGCTC
CACCTACACGAGGGCCCCCACCATCTTATGGTGGAAGCAGTCGCTATGATGATTACAGCAGCTCATGTGACGGATATGGT
GGAAGTCGAGACAGTTACTCAAGCAGCCGAAGTGATCTCTACTCAAGTGGTCGTGATCGGGTTGGCAGACAAGAAAGAGG
GCTTACCCCTTCTATGGAAAGAGGATACCCTCCTCCACGTGATTCCTACAGCAGTTCAAGTGCGGAGCACCAAGCGGTGG
TGGCTGTGGAGGAAGCCGATCTGATAGAGGGGGAGGTAGAAGCAGATAC

Alignment

ORF - retro_hsap_4144 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.03 %
• Parental protein coverage: 99.74 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VEADRPGKLFIGGLNTETNEKALEAVFGKYGRIVEVLLMKDRETNKSRGFAFVTFESPADAKDAARDMNG
          VEAD.PGK.F.GGLNTETNEKALEAVFGKYGRIVEVLL.KD.ETNKS.GFAFVTFESPADAKDAARDMNG
Retrocopy VEADCPGKPFTGGLNTETNEKALEAVFGKYGRIVEVLLVKDHETNKSGGFAFVTFESPADAKDAARDMNG

Parental  KSLDGKAIKVEQATKPSFESGRRGPPPPPRSRGPPRGLRGGRGGSGGTRGPPSRGGHMDDGGYSMNFNMS
          KSLDGKAI.VEQA.KPSFESGRRGPPPPPRSRGPPRGL..........RGPPSRGGHMDDGGYSMNFNMS
Retrocopy KSLDGKAIEVEQANKPSFESGRRGPPPPPRSRGPPRGLXXXXXXXXXXRGPPSRGGHMDDGGYSMNFNMS

Parental  SSRGPLPVKRGPPPRSGGPPPKRSAPSGPVRSSSGMGGRAPVSRGRDSYGGPPRREPLPSRRDVYLSPRD
          SSRGP.PVKRGPPPRSG.PP.KRSAPSGPVRSSS.MGGRAPVSRGRDSYGGPPRRE.LPS.R..YLSPRD
Retrocopy SSRGPHPVKRGPPPRSGSPPSKRSAPSGPVRSSSEMGGRAPVSRGRDSYGGPPRRELLPSCRNDYLSPRD

Parental  DGYSTKDSYSSRDYPSSRDTRDYAPPPRDYTYRDYGHSSSRDDYPSRGYSDRDGYGRDRDYSDHPSGGSY
          DGYSTKDSYSSRDYPSS.DTR.YAPPPRDYTYRDYGHSSSR.DYP.RGYSDRD.YGRD.DYSDHP.GGSY
Retrocopy DGYSTKDSYSSRDYPSSHDTRAYAPPPRDYTYRDYGHSSSRVDYP*RGYSDRDRYGRDHDYSDHPGGGSY

Parental  RDSYESYGNSRSAPPTRGPPPSYGGSSRYDDYSSSRDGYGGSRDSYSSSRSDLYSSGRDRVGRQERGLPP
          RDSYESYGNSRSAPPTRGPPPSYGGSSRYDDYSSS.DGYGGSRDSYSSSRSDLYSSGRDRVGRQERGL.P
Retrocopy RDSYESYGNSRSAPPTRGPPPSYGGSSRYDDYSSSCDGYGGSRDSYSSSRSDLYSSGRDRVGRQERGLTP

Parental  SMERGYPPPRDSYSSSSR-GAPRGGGRGGSRSDRGGGRSRY
          SMERGYPPPRDSYSSSS..GAP.GGG.GGSRSDRGGGRSRY
Retrocopy SMERGYPPPRDSYSSSSA<GAPSGGGCGGSRSDRGGGRSRY

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	0.14 RPM	111.30 RPM
bodymap2_adrenal	0.06 RPM	161.12 RPM
bodymap2_brain	0.00 RPM	90.38 RPM
bodymap2_breast	0.04 RPM	94.77 RPM
bodymap2_colon	0.02 RPM	124.83 RPM
bodymap2_heart	0.04 RPM	77.33 RPM
bodymap2_kidney	0.00 RPM	107.46 RPM
bodymap2_liver	0.51 RPM	52.49 RPM
bodymap2_lung	0.00 RPM	104.25 RPM
bodymap2_lymph_node	0.15 RPM	106.28 RPM
bodymap2_ovary	0.02 RPM	179.54 RPM
bodymap2_prostate	0.10 RPM	183.35 RPM
bodymap2_skeletal_muscle	0.15 RPM	175.20 RPM
bodymap2_testis	0.02 RPM	113.87 RPM
bodymap2_thyroid	0.06 RPM	159.88 RPM
bodymap2_white_blood_cells	0.02 RPM	136.42 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_hsap_4144 was not detected

EST

No EST(s) were mapped for retro_hsap_4144 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_192529	868 libraries	712 libraries	234 libraries	11 libraries	4 libraries

The graphical summary, for retro_hsap_4144 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_4144 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_4144 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 26 parental genes, and 53 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000013308	1 retrocopy	retro_btau_36,
Canis familiaris	ENSCAFG00000018962	4 retrocopies	retro_cfam_1106, retro_cfam_1244, retro_cfam_1649, retro_cfam_1914,
Choloepus hoffmanni	ENSCHOG00000012369	3 retrocopies	retro_chof_1240, retro_chof_2596, retro_chof_880,
Cavia porcellus	ENSCPOG00000012164	1 retrocopy	retro_cpor_778,
Dasypus novemcinctus	ENSDNOG00000017199	3 retrocopies	retro_dnov_1436, retro_dnov_2205, retro_dnov_696,
Dipodomys ordii	ENSDORG00000015481	1 retrocopy	retro_dord_793,
Echinops telfairi	ENSETEG00000013178	1 retrocopy	retro_etel_1952,
Felis catus	ENSFCAG00000004779	1 retrocopy	retro_fcat_1903,
Homo sapiens	ENSG00000102317	1 retrocopy	retro_hsap_265,
Homo sapiens	ENSG00000147274	7 retrocopies	retro_hsap_23, retro_hsap_3074, retro_hsap_3587, retro_hsap_4144 , retro_hsap_4846, retro_hsap_800, retro_hsap_91,
Homo sapiens	ENSG00000164548	1 retrocopy	retro_hsap_386,
Gorilla gorilla	ENSGGOG00000006944	1 retrocopy	retro_ggor_657,
Loxodonta africana	ENSLAFG00000005568	3 retrocopies	retro_lafr_1188, retro_lafr_276, retro_lafr_35,
Microcebus murinus	ENSMICG00000006856	2 retrocopies	retro_mmur_1252, retro_mmur_661,
Myotis lucifugus	ENSMLUG00000013209	5 retrocopies	retro_mluc_1630, retro_mluc_1746, retro_mluc_203, retro_mluc_2180, retro_mluc_80,
Monodelphis domestica	ENSMODG00000014054	1 retrocopy	retro_mdom_1231,
Mustela putorius furo	ENSMPUG00000001855	2 retrocopies	retro_mputfur_1539, retro_mputfur_956,
Mus musculus	ENSMUSG00000031134	2 retrocopies	retro_mmus_170, retro_mmus_187,
Oryctolagus cuniculus	ENSOCUG00000007220	1 retrocopy	retro_ocun_3,
Otolemur garnettii	ENSOGAG00000007839	5 retrocopies	retro_ogar_1057, retro_ogar_137, retro_ogar_1586, retro_ogar_2445, retro_ogar_2584,
Ochotona princeps	ENSOPRG00000016593	1 retrocopy	retro_opri_372,
Sorex araneus	ENSSARG00000000397	1 retrocopy	retro_sara_169,
Ictidomys tridecemlineatus	ENSSTOG00000006211	2 retrocopies	retro_itri_1205, retro_itri_1346,
Tupaia belangeri	ENSTBEG00000001154	1 retrocopy	retro_tbel_1919,
Tarsius syrichta	ENSTSYG00000009555	1 retrocopy	retro_tsyr_15,
Tursiops truncatus	ENSTTRG00000007322	1 retrocopy	retro_ttru_1450,