RetrogeneDB ID: retro_hsap_4

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 9:19049657..19050599(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000155876
• Aliases: RRAGA, FIP-1, FIP1, RAGA
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: RRAGB
• Ensembl ID: ENSG00000083750
• Aliases: RRAGB, RAGB, bA465E19.1
• Description: Ras-related GTP binding B [Source:HGNC Symbol;Acc:19901]

Sequence

>retro_hsap_4
ATGCCAAATACAGCCATGAAGAAAAAGGTGCTGCTGATGGGGAAGAGCGGGTCGGGGAAGACCAGCATGAGGTCGATAAT
CTTCGCCAATTACATTGCTCGCGACACCCGGCGCCTGGGGGCCACCATTGACGTGGAACACTCCCACGTCCGATTCCTAG
GGAACCTGGTGCTGAACCTGTGGGACTGTGGCGGTCAGGACACCTTCATGGAAAATTACTTCACCAGCCAGCGAGACAAT
ATCTTCCGTAACGTGGAAGTTTTGATTTACGTGTTTGACGTGGAGAGCCGCGAACTGGAAAAGGACATGCATTATTACCA
GTCGTGTCTGGAGGCCATCCTCCAGAACTCTCCTGACGCCAAAATCTTCTGCCTGGTGCACAAAATGGATCTGGTTCAGG
AGGATCAGCGTGACCTGATTTTTAAAGAGCGAGAGGAAGACCTGAGGCGTCTGTCTCGCCCGCTGGAGTGTGCTTGTTTT
CGAACGTCCATCTGGGATGAGACGCTCTACAAAGCCTGGTCCAGCATCGTCTACCAGCTGATTCCCAACGTTCAGCAGCT
GGAGATGAACCTCAGGAATTTTGCCCAAATCATTGAGGCCGATGAAGTTCTGCTGTTCGAAAGAGCTACATTCTTGGTTA
TTTCCCACTACCAGTGCAAAGAGCAGCGCGACGTCCACCGGTTTGAGAAGATCAGCAACATCATCAAACAGTTCAAGCTG
AGCTGCAGTAAATTGGCCGCTTCCTTCCAGAGCATGGAAGTTAGGAATTCCAACTTCGCTGCTTTCATCGACATCTTCAC
CTCAAATACGTACGTGATGGTGGTCATGTCAGATCCGTCGATCCCTTCTGCGGCCACTCTGATCAACATTCGCAATGCCC
GGAAACACTTTGAGAAGCTGGAGAGAGTGGATGGCCCCAAGCACAGTCTCCTTATGCGTTGA

Alignment

ORF - retro_hsap_4 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.08 %
• Parental protein coverage: 90.46 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LPNTAMKKKVLLMGKSGSGKTSMRSIIFANYIARDTRRLGATIDVEHSHVRFLGNLVLNLWDCGGQDTFM
          .PNTAMKKKVLLMGKSGSGKTSMRSIIFANYIARDTRRLGATIDVEHSHVRFLGNLVLNLWDCGGQDTFM
Retrocopy MPNTAMKKKVLLMGKSGSGKTSMRSIIFANYIARDTRRLGATIDVEHSHVRFLGNLVLNLWDCGGQDTFM

Parental  ENYFTSQRDNIFRNVEVLIYVFDVESRELEKDMHYYQSCLEAILQNSPDAKIFCLVHKMDLVQEDQRDLI
          ENYFTSQRDNIFRNVEVLIYVFDVESRELEKDMHYYQSCLEAILQNSPDAKIFCLVHKMDLVQEDQRDLI
Retrocopy ENYFTSQRDNIFRNVEVLIYVFDVESRELEKDMHYYQSCLEAILQNSPDAKIFCLVHKMDLVQEDQRDLI

Parental  FKEREEDLRRLSRPLECSCFRTSIWDETLYKAWSSIVYQLIPNVQQLEMNLRNFAEIIEADEVLLFERAT
          FKEREEDLRRLSRPLEC.CFRTSIWDETLYKAWSSIVYQLIPNVQQLEMNLRNFA.IIEADEVLLFERAT
Retrocopy FKEREEDLRRLSRPLECACFRTSIWDETLYKAWSSIVYQLIPNVQQLEMNLRNFAQIIEADEVLLFERAT

Parental  FLVISHYQCKEQRDAHRFEKISNIIKQFKLSCSKLAASFQSMEVRNSNFAAFIDIFTSNTYVMVVMSDPS
          FLVISHYQCKEQRD.HRFEKISNIIKQFKLSCSKLAASFQSMEVRNSNFAAFIDIFTSNTYVMVVMSDPS
Retrocopy FLVISHYQCKEQRDVHRFEKISNIIKQFKLSCSKLAASFQSMEVRNSNFAAFIDIFTSNTYVMVVMSDPS

Parental  IPSAATLINIRNARKHFEKLERVDGPKQCLLMR
          IPSAATLINIRNARKHFEKLERVDGPK..LLMR
Retrocopy IPSAATLINIRNARKHFEKLERVDGPKHSLLMR

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	59.14 RPM	7.93 RPM
bodymap2_adrenal	50.85 RPM	18.89 RPM
bodymap2_brain	64.04 RPM	30.66 RPM
bodymap2_breast	47.04 RPM	14.30 RPM
bodymap2_colon	46.48 RPM	16.05 RPM
bodymap2_heart	38.40 RPM	7.02 RPM
bodymap2_kidney	49.39 RPM	16.98 RPM
bodymap2_liver	31.20 RPM	3.30 RPM
bodymap2_lung	39.61 RPM	9.92 RPM
bodymap2_lymph_node	43.29 RPM	12.35 RPM
bodymap2_ovary	66.54 RPM	29.65 RPM
bodymap2_prostate	58.44 RPM	24.53 RPM
bodymap2_skeletal_muscle	47.91 RPM	6.67 RPM
bodymap2_testis	50.73 RPM	17.21 RPM
bodymap2_thyroid	56.85 RPM	36.21 RPM
bodymap2_white_blood_cells	45.14 RPM	5.87 RPM

ChIP-Seq

RNA Polymerase II activity may be related with retro_hsap_4 in 51 libraries

ENCODE library ID	Target	ChIP-Seq Peak coordinates
ENCFF002CFW	POLR2A	9:19049030..19049653
ENCFF002CFX	POLR2A	9:19048972..19049663
ENCFF002CGN	POLR2A	9:19049099..19049595
ENCFF002CHO	POLR2A	9:19048883..19049876
ENCFF002CIH	POLR2A	9:19049103..19049587
ENCFF002CIO	POLR2A	9:19049051..19049635
ENCFF002CJE	POLR2A	9:19048846..19049619
ENCFF002CJZ	POLR2A	9:19048975..19049654
ENCFF002CKX	POLR2A	9:19049090..19049631
ENCFF002CLM	POLR2A	9:19049129..19049403
ENCFF002CMI	POLR2A	9:19048967..19049671
ENCFF002COJ	POLR2A	9:19049071..19049507
ENCFF002COJ	POLR2A	9:19049271..19049707
ENCFF002CPG	POLR2A	9:19049106..19049549
ENCFF002CPH	POLR2A	9:19049066..19049456
ENCFF002CQA	POLR2A	9:19049077..19049508
ENCFF002CQC	POLR2A	9:19049075..19049647
ENCFF002CQE	POLR2A	9:19049112..19049626
ENCFF002CQG	POLR2A	9:19049099..19049618
ENCFF002CQI	POLR2A	9:19049086..19049626
ENCFF002CQK	POLR2A	9:19049017..19049668
ENCFF002CQM	POLR2A	9:19049091..19049624
ENCFF002CQO	POLR2A	9:19049051..19049660
ENCFF002CRK	POLR2A	9:19049009..19049533
ENCFF002CRO	POLR2A	9:19049144..19049355
ENCFF002CRO	POLR2A	9:19049272..19049692
ENCFF002CSY	POLR2A	9:19048909..19049727
ENCFF002CUP	POLR2A	9:19049382..19049522
ENCFF002CUQ	POLR2A	9:19049086..19049551
ENCFF002CVF	POLR2A	9:19049141..19049376
ENCFF002CVJ	POLR2A	9:19049042..19049672
ENCFF002CXM	POLR2A	9:19049179..19049380
ENCFF002CXM	POLR2A	9:19049236..19049726
ENCFF002CXN	POLR2A	9:19049214..19049372
ENCFF002CXO	POLR2A	9:19049161..19049364
ENCFF002CXO	POLR2A	9:19049270..19049694
ENCFF002CXP	POLR2A	9:19049119..19049532
ENCFF002CXR	POLR2A	9:19049137..19049574
ENCFF002CZC	POLR2A	9:19049018..19049667
ENCFF002CZD	POLR2A	9:19049018..19049646
ENCFF002CZQ	POLR2A	9:19049113..19049610
ENCFF002CZW	POLR2A	9:19048922..19049718
ENCFF002CZY	POLR2A	9:19049067..19049668
ENCFF002DAE	POLR2A	9:19049144..19049377
ENCFF002DAH	POLR2A	9:19049198..19049343
ENCFF002DAK	POLR2A	9:19049171..19049355
ENCFF002DAS	POLR2A	9:19049028..19049504
ENCFF002DAV	POLR2A	9:19049134..19049438
ENCFF002DAV	POLR2A	9:19049212..19049756
ENCFF002DAY	POLR2A	9:19048965..19049601
ENCFF002DBB	POLR2A	9:19049222..19049339
ENCFF002DBE	POLR2A	9:19049095..19049431
ENCFF002DBO	POLR2A	9:19049088..19049590
ENCFF002DBP	POLR2A	9:19049111..19049407
ENCFF002DBQ	POLR2A	9:19049140..19049393
ENCFF002DBT	POLR2A	9:19049151..19049380

EST

14 EST(s) were mapped to retro_hsap_4 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
AA186991	19049678	19050166	95.1	477	7	458
AA310124	19049718	19050118	99.3	397	0	396
AA338377	19049913	19050292	97.9	378	1	374
BE081500	19049775	19050115	99.8	339	1	338
BF845083	19049822	19050157	100	335	0	335
BF914635	19049776	19050153	99.5	375	2	373
BG955634	19049794	19050228	98.9	428	5	422
BG986382	19049774	19050137	99.2	360	3	357
BG986383	19049765	19050136	99.2	366	2	361
BM313253	19049659	19050047	99	384	4	380
BP213970	19049679	19050176	99.2	492	4	488
CD688621	19049674	19050165	99.4	488	3	485
DN989399	19049641	19050144	100	502	0	501
F06456	19049756	19050107	99.8	345	1	344

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_192057	5 libraries	0 libraries	0 libraries	4 libraries	1820 libraries

The graphical summary, for retro_hsap_4 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_4 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_4 has 8 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_48
Pongo abelii	retro_pabe_191
Macaca mulatta	retro_mmul_249
Callithrix jacchus	retro_cjac_117
Mus musculus	retro_mmus_159
Sus scrofa	retro_sscr_15
Canis familiaris	retro_cfam_421
Equus caballus	retro_ecab_608

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Parental genes homology:

Parental genes homology involve 21 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012920	1 retrocopy	retro_amel_1842,
Canis familiaris	ENSCAFG00000016503	1 retrocopy	retro_cfam_421,
Callithrix jacchus	ENSCJAG00000007317	1 retrocopy	retro_cjac_117,
Cavia porcellus	ENSCPOG00000011266	1 retrocopy	retro_cpor_86,
Equus caballus	ENSECAG00000006020	1 retrocopy	retro_ecab_608,
Felis catus	ENSFCAG00000013932	1 retrocopy	retro_fcat_21,
Homo sapiens	ENSG00000083750	1 retrocopy	retro_hsap_4 ,
Gorilla gorilla	ENSGGOG00000011501	1 retrocopy	retro_ggor_65,
Loxodonta africana	ENSLAFG00000016144	1 retrocopy	retro_lafr_102,
Myotis lucifugus	ENSMLUG00000015720	1 retrocopy	retro_mluc_40,
Macaca mulatta	ENSMMUG00000017635	1 retrocopy	retro_mmul_249,
Mustela putorius furo	ENSMPUG00000003730	1 retrocopy	retro_mputfur_87,
Mus musculus	ENSMUSG00000041658	1 retrocopy	retro_mmus_159,
Nomascus leucogenys	ENSNLEG00000016350	1 retrocopy	retro_nleu_13,
Oryctolagus cuniculus	ENSOCUG00000008666	1 retrocopy	retro_ocun_166,
Otolemur garnettii	ENSOGAG00000000345	1 retrocopy	retro_ogar_675,
Procavia capensis	ENSPCAG00000003417	1 retrocopy	retro_pcap_6,
Pongo abelii	ENSPPYG00000020398	1 retrocopy	retro_pabe_191,
Pan troglodytes	ENSPTRG00000021955	1 retrocopy	retro_ptro_48,
Rattus norvegicus	ENSRNOG00000003160	1 retrocopy	retro_rnor_2,
Sus scrofa	ENSSSCG00000029800	1 retrocopy	retro_sscr_15,