RetrogeneDB ID: retro_hsap_108

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 2:20647226..20647817(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000143878
• Aliases: RHOB, ARH6, ARHB, MST081, MSTP081, RHOH6
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: RHOA
• Ensembl ID: ENSG00000067560
• Aliases: RHOA, ARH12, ARHA, RHO12, RHOH12
• Description: ras homolog family member A [Source:HGNC Symbol;Acc:667]

Sequence

>retro_hsap_108
ATGGCGGCCATCCGCAAGAAGCTGGTGGTGGTGGGCGACGGCGCGTGTGGCAAGACGTGCCTGCTGATCGTGTTCAGTAA
GGACGAGTTCCCCGAGGTGTACGTGCCCACCGTCTTCGAGAACTATGTGGCCGACATTGAGGTGGACGGCAAGCAGGTGG
AGCTGGCGCTGTGGGACACGGCGGGCCAGGAGGACTACGACCGCCTGCGGCCGCTCTCCTACCCGGACACCGACGTCATT
CTCATGTGCTTCTCGGTGGACAGCCCGGACTCGCTGGAGAACATCCCCGAGAAGTGGGTCCCCGAGGTGAAGCACTTCTG
TCCCAATGTGCCCATCATCCTGGTGGCCAACAAAAAAGACCTGCGCAGCGACGAGCATGTCCGCACAGAGCTGGCCCGCA
TGAAGCAGGAACCCGTGCGCACGGATGACGGCCGCGCCATGGCCGTGCGCATCCAAGCCTACGACTACCTCGAGTGCTCT
GCCAAGACCAAGGAAGGCGTGCGCGAGGTCTTCGAGACGGCCACGCGCGCCGCGCTGCAGAAGCGCTACGGCTCCCAGAA
CGGCTGCATCAACTGCTGCAAGGTGCTATGA

Alignment

ORF - retro_hsap_108 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.34 %
• Parental protein coverage: 98.96 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAAIRKKLVIVGDGACGKTCLLIVFSKDQFPEVYVPTVFENYVADIEVDGKQVELALWDTAGQEDYDRLR
          MAAIRKKLV.VGDGACGKTCLLIVFSKD.FPEVYVPTVFENYVADIEVDGKQVELALWDTAGQEDYDRLR
Retrocopy MAAIRKKLVVVGDGACGKTCLLIVFSKDEFPEVYVPTVFENYVADIEVDGKQVELALWDTAGQEDYDRLR

Parental  PLSYPDTDVILMCFSIDSPDSLENIPEKWTPEVKHFCPNVPIILVGNKKDLRNDEHTRRELAKMKQEPVK
          PLSYPDTDVILMCFS.DSPDSLENIPEKW.PEVKHFCPNVPIILV.NKKDLR.DEH.R.ELA.MKQEPV.
Retrocopy PLSYPDTDVILMCFSVDSPDSLENIPEKWVPEVKHFCPNVPIILVANKKDLRSDEHVRTELARMKQEPVR

Parental  PEEGRDMANRIGAFGYMECSAKTKDGVREVFEMATRAALQARRGKKKSGCL
          ...GR.MA.RI.A..Y.ECSAKTK.GVREVFE.ATRAALQ.R.G....GC.
Retrocopy TDDGRAMAVRIQAYDYLECSAKTKEGVREVFETATRAALQKRYG-SQNGCI

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	128.79 RPM	757.45 RPM
bodymap2_adrenal	93.89 RPM	649.43 RPM
bodymap2_brain	44.44 RPM	361.28 RPM
bodymap2_breast	60.04 RPM	744.74 RPM
bodymap2_colon	71.89 RPM	587.60 RPM
bodymap2_heart	23.08 RPM	237.02 RPM
bodymap2_kidney	38.96 RPM	493.85 RPM
bodymap2_liver	44.68 RPM	198.94 RPM
bodymap2_lung	136.20 RPM	799.91 RPM
bodymap2_lymph_node	33.31 RPM	569.64 RPM
bodymap2_ovary	88.94 RPM	636.81 RPM
bodymap2_prostate	98.45 RPM	587.31 RPM
bodymap2_skeletal_muscle	31.68 RPM	593.82 RPM
bodymap2_testis	54.45 RPM	544.03 RPM
bodymap2_thyroid	49.83 RPM	519.31 RPM
bodymap2_white_blood_cells	22.78 RPM	1068.50 RPM

ChIP-Seq

RNA Polymerase II activity may be related with retro_hsap_108 in 50 libraries

ENCODE library ID	Target	ChIP-Seq Peak coordinates
ENCFF001VKU	POLR2A	2:20646455..20650954
ENCFF002CFW	POLR2A	2:20646426..20648260
ENCFF002CFX	POLR2A	2:20646438..20648135
ENCFF002CGN	POLR2A	2:20646686..20647057
ENCFF002CHO	POLR2A	2:20646430..20648143
ENCFF002CIH	POLR2A	2:20646687..20647060
ENCFF002CIO	POLR2A	2:20646659..20647094
ENCFF002CJE	POLR2A	2:20646544..20647139
ENCFF002CJE	POLR2A	2:20647379..20648015
ENCFF002CJZ	POLR2A	2:20646455..20648143
ENCFF002CKX	POLR2A	2:20646442..20648278
ENCFF002CLM	POLR2A	2:20646689..20647493
ENCFF002CMI	POLR2A	2:20646676..20647057
ENCFF002COJ	POLR2A	2:20646755..20646985
ENCFF002CPG	POLR2A	2:20646704..20647027
ENCFF002CPH	POLR2A	2:20646741..20646976
ENCFF002CQA	POLR2A	2:20646670..20647034
ENCFF002CQC	POLR2A	2:20646667..20647066
ENCFF002CQE	POLR2A	2:20646673..20647039
ENCFF002CQG	POLR2A	2:20646664..20647065
ENCFF002CQI	POLR2A	2:20646684..20647049
ENCFF002CQK	POLR2A	2:20646462..20647086
ENCFF002CQM	POLR2A	2:20646682..20647063
ENCFF002CQO	POLR2A	2:20646627..20647087
ENCFF002CRK	POLR2A	2:20646699..20647014
ENCFF002CRO	POLR2A	2:20646704..20647044
ENCFF002CSY	POLR2A	2:20646363..20648893
ENCFF002CUP	POLR2A	2:20646701..20647574
ENCFF002CUQ	POLR2A	2:20646446..20647162
ENCFF002CUQ	POLR2A	2:20647078..20648194
ENCFF002CVF	POLR2A	2:20646679..20647128
ENCFF002CVF	POLR2A	2:20647057..20647742
ENCFF002CVJ	POLR2A	2:20646438..20648018
ENCFF002CXM	POLR2A	2:20646604..20647094
ENCFF002CXN	POLR2A	2:20646641..20647137
ENCFF002CXO	POLR2A	2:20646639..20647063
ENCFF002CXP	POLR2A	2:20646608..20647088
ENCFF002CXR	POLR2A	2:20646697..20647006
ENCFF002CZC	POLR2A	2:20646520..20647117
ENCFF002CZD	POLR2A	2:20646558..20647106
ENCFF002CZW	POLR2A	2:20646458..20647168
ENCFF002DAE	POLR2A	2:20646732..20647004
ENCFF002DAH	POLR2A	2:20646758..20646985
ENCFF002DAK	POLR2A	2:20646607..20647107
ENCFF002DAS	POLR2A	2:20646776..20646923
ENCFF002DAV	POLR2A	2:20646649..20647096
ENCFF002DAY	POLR2A	2:20646633..20647184
ENCFF002DBB	POLR2A	2:20646766..20647019
ENCFF002DBB	POLR2A	2:20647345..20647545
ENCFF002DBE	POLR2A	2:20646760..20646970
ENCFF002DBO	POLR2A	2:20646709..20647069
ENCFF002DBO	POLR2A	2:20646933..20647317
ENCFF002DBP	POLR2A	2:20646724..20647023
ENCFF002DBQ	POLR2A	2:20646727..20647022
ENCFF002DBT	POLR2A	2:20646720..20647019

EST

No EST(s) were mapped for retro_hsap_108 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_117609	44 libraries	9 libraries	91 libraries	83 libraries	1602 libraries
TSS #2	TSS_117610	1097 libraries	547 libraries	177 libraries	7 libraries	1 library

The graphical summary, for retro_hsap_108 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_108 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_108 has 6 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_10
Gorilla gorilla	retro_ggor_18
Macaca mulatta	retro_mmul_977
Bos taurus	retro_btau_206
Canis familiaris	retro_cfam_186
Equus caballus	retro_ecab_112

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Parental genes homology:

Parental genes homology involve 24 parental genes, and 47 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000008297	1 retrocopy	retro_acar_41,
Anas platyrhynchos	ENSAPLG00000014687	1 retrocopy	retro_apla_10,
Canis familiaris	ENSCAFG00000023066	2 retrocopies	retro_cfam_1652, retro_cfam_186,
Callithrix jacchus	ENSCJAG00000003904	3 retrocopies	retro_cjac_1306, retro_cjac_2010, retro_cjac_411,
Cavia porcellus	ENSCPOG00000014073	1 retrocopy	retro_cpor_514,
Dipodomys ordii	ENSDORG00000003382	3 retrocopies	retro_dord_1, retro_dord_18, retro_dord_538,
Homo sapiens	ENSG00000067560	2 retrocopies	retro_hsap_108 , retro_hsap_3632,
Gasterosteus aculeatus	ENSGACG00000005670	1 retrocopy	retro_gacu_9,
Gallus gallus	ENSGALG00000003806	1 retrocopy	retro_ggal_5,
Gadus morhua	ENSGMOG00000008188	1 retrocopy	retro_gmor_18,
Latimeria chalumnae	ENSLACG00000016941	1 retrocopy	retro_lcha_15,
Meleagris gallopavo	ENSMGAG00000002280	1 retrocopy	retro_mgal_2,
Macaca mulatta	ENSMMUG00000012962	1 retrocopy	retro_mmul_977,
Monodelphis domestica	ENSMODG00000012981	2 retrocopies	retro_mdom_19, retro_mdom_294,
Mustela putorius furo	ENSMPUG00000013840	5 retrocopies	retro_mputfur_1015, retro_mputfur_140, retro_mputfur_1541, retro_mputfur_1588, retro_mputfur_650,
Mus musculus	ENSMUSG00000007815	9 retrocopies	retro_mmus_178, retro_mmus_191, retro_mmus_2041, retro_mmus_2507, retro_mmus_3728, retro_mmus_3729, retro_mmus_3964, retro_mmus_3965, retro_mmus_3966,
Ornithorhynchus anatinus	ENSOANG00000013807	1 retrocopy	retro_oana_7,
Oreochromis niloticus	ENSONIG00000018884	1 retrocopy	retro_onil_32,
Ochotona princeps	ENSOPRG00000009638	1 retrocopy	retro_opri_590,
Pelodiscus sinensis	ENSPSIG00000015328	1 retrocopy	retro_psin_7,
Rattus norvegicus	ENSRNOG00000050519	3 retrocopies	retro_rnor_127, retro_rnor_2899, retro_rnor_408,
Ictidomys tridecemlineatus	ENSSTOG00000004561	2 retrocopies	retro_itri_39, retro_itri_96,
Takifugu rubripes	ENSTRUG00000011944	1 retrocopy	retro_trub_19,
Tursiops truncatus	ENSTTRG00000017370	2 retrocopies	retro_ttru_27, retro_ttru_339,