RetrogeneDB ID: retro_hsap_36

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 14:50360454..50360982(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000165527
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: ARF3
• Ensembl ID: ENSG00000134287
• Aliases: None
• Description: ADP-ribosylation factor 3 [Source:HGNC Symbol;Acc:654]

Sequence

>retro_hsap_36
ATGGGGAAGGTGCTATCCAAAATCTTCGGGAACAAGGAAATGCGGATCCTCATGTTGGGCCTGGACGCGGCCGGCAAGAC
AACAATCCTGTACAAGTTGAAGCTGGGCCAGTCGGTGACCACCATTCCCACTGTGGGTTTCAACGTGGAGACGGTGACTT
ACAAAAATGTCAAGTTCAACGTATGGGATGTGGGCGGCCAGGACAAGATCCGGCCGCTCTGGCGGCATTACTACACTGGG
ACCCAAGGTCTCATCTTCGTAGTGGACTGCGCCGACCGCGACCGCATCGATGAGGCTCGCCAGGAGCTGCACCGCATTAT
CAATGACCGGGAGATGAGGGACGCCATAATCCTCATCTTCGCCAACAAGCAGGACCTGCCCGATGCCATGAAACCCCACG
AGATCCAGGAGAAACTGGGCCTGACCCGGATTCGGGACAGGAACTGGTATGTGCAGCCCTCCTGTGCCACCTCAGGGGAC
GGACTCTATGAGGGGCTCACATGGTTAACCTCTAACTACAAATCTTAA

Alignment

ORF - retro_hsap_36 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.54 %
• Parental protein coverage: 96.13 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GNLLKSLIGKKEMRILMVGLDAAGKTTILYKLKLGEIVTTIPTIGFNVETVEYKNISFTVWDVGGQDKIR
          G..L....G.KEMRILM.GLDAAGKTTILYKLKLG..VTTIPT.GFNVETV.YKN..F.VWDVGGQDKIR
Retrocopy GKVLSKIFGNKEMRILMLGLDAAGKTTILYKLKLGQSVTTIPTVGFNVETVTYKNVKFNVWDVGGQDKIR

Parental  PLWRHYFQNTQGLIFVVDSNDRERVNEAREELMRMLAEDELRDAVLLVFANKQDLPNAMNAAEITDKLGL
          PLWRHY...TQGLIFVVD..DR.R..EAR.EL.R.....E.RDA..L.FANKQDLP.AM...EI..KLGL
Retrocopy PLWRHYYTGTQGLIFVVDCADRDRIDEARQELHRIINDREMRDAIILIFANKQDLPDAMKPHEIQEKLGL

Parental  HSLRHRNWYIQATCATSGDGLYEGLDWLANQLKN
          ...R.RNWY.Q..CATSGDGLYEGL.WL....K.
Retrocopy TRIRDRNWYVQPSCATSGDGLYEGLTWLTSNYKS

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	29.74 RPM	222.28 RPM
bodymap2_adrenal	36.74 RPM	202.28 RPM
bodymap2_brain	9.21 RPM	477.85 RPM
bodymap2_breast	21.67 RPM	155.62 RPM
bodymap2_colon	16.53 RPM	182.88 RPM
bodymap2_heart	8.92 RPM	43.75 RPM
bodymap2_kidney	23.35 RPM	192.83 RPM
bodymap2_liver	13.03 RPM	55.17 RPM
bodymap2_lung	32.05 RPM	215.07 RPM
bodymap2_lymph_node	35.18 RPM	138.22 RPM
bodymap2_ovary	17.83 RPM	206.47 RPM
bodymap2_prostate	25.17 RPM	152.09 RPM
bodymap2_skeletal_muscle	21.01 RPM	17.62 RPM
bodymap2_testis	21.00 RPM	221.73 RPM
bodymap2_thyroid	16.95 RPM	265.03 RPM
bodymap2_white_blood_cells	64.67 RPM	309.73 RPM

ChIP-Seq

RNA Polymerase II activity may be related with retro_hsap_36 in 52 libraries

ENCODE library ID	Target	ChIP-Seq Peak coordinates
ENCFF001VKU	POLR2A	14:50359215..50360263
ENCFF002CFW	POLR2A	14:50359310..50360442
ENCFF002CFX	POLR2A	14:50359317..50360285
ENCFF002CGN	POLR2A	14:50359419..50360032
ENCFF002CHO	POLR2A	14:50358989..50361061
ENCFF002CIH	POLR2A	14:50359697..50360022
ENCFF002CIH	POLR2A	14:50359459..50359724
ENCFF002CIO	POLR2A	14:50359397..50360427
ENCFF002CJE	POLR2A	14:50359322..50360353
ENCFF002CJZ	POLR2A	14:50359258..50360341
ENCFF002CKX	POLR2A	14:50359403..50360032
ENCFF002CLM	POLR2A	14:50359797..50359932
ENCFF002CMI	POLR2A	14:50359368..50360492
ENCFF002COJ	POLR2A	14:50359604..50360040
ENCFF002CPG	POLR2A	14:50359455..50359748
ENCFF002CPG	POLR2A	14:50359686..50360004
ENCFF002CPH	POLR2A	14:50359425..50359815
ENCFF002CPH	POLR2A	14:50359645..50360035
ENCFF002CQA	POLR2A	14:50359446..50359774
ENCFF002CQA	POLR2A	14:50359765..50360008
ENCFF002CQC	POLR2A	14:50359419..50360032
ENCFF002CQE	POLR2A	14:50359394..50360036
ENCFF002CQG	POLR2A	14:50359467..50360013
ENCFF002CQI	POLR2A	14:50359415..50360025
ENCFF002CQK	POLR2A	14:50359384..50360051
ENCFF002CQM	POLR2A	14:50359424..50360038
ENCFF002CQO	POLR2A	14:50359360..50360388
ENCFF002CRK	POLR2A	14:50359352..50359876
ENCFF002CRK	POLR2A	14:50359560..50360084
ENCFF002CRO	POLR2A	14:50359390..50359810
ENCFF002CRO	POLR2A	14:50359742..50359948
ENCFF002CSY	POLR2A	14:50358981..50360515
ENCFF002CUP	POLR2A	14:50359667..50359947
ENCFF002CUQ	POLR2A	14:50359404..50360036
ENCFF002CVF	POLR2A	14:50359747..50359902
ENCFF002CVF	POLR2A	14:50359409..50359825
ENCFF002CVJ	POLR2A	14:50359400..50360354
ENCFF002CXM	POLR2A	14:50359584..50360074
ENCFF002CXN	POLR2A	14:50359334..50359830
ENCFF002CXN	POLR2A	14:50359610..50360106
ENCFF002CXO	POLR2A	14:50359733..50359910
ENCFF002CXO	POLR2A	14:50359522..50359672
ENCFF002CXP	POLR2A	14:50359696..50359982
ENCFF002CXR	POLR2A	14:50359439..50359771
ENCFF002CXR	POLR2A	14:50359670..50359995
ENCFF002CZC	POLR2A	14:50359373..50360064
ENCFF002CZD	POLR2A	14:50359393..50360060
ENCFF002CZQ	POLR2A	14:50359674..50360004
ENCFF002CZQ	POLR2A	14:50359442..50359763
ENCFF002CZW	POLR2A	14:50359261..50360273
ENCFF002CZY	POLR2A	14:50359378..50360049
ENCFF002DAE	POLR2A	14:50359555..50359633
ENCFF002DAE	POLR2A	14:50359782..50359881
ENCFF002DAH	POLR2A	14:50359691..50359975
ENCFF002DAK	POLR2A	14:50359342..50359842
ENCFF002DAK	POLR2A	14:50359543..50360043
ENCFF002DAS	POLR2A	14:50359364..50359840
ENCFF002DAS	POLR2A	14:50359593..50360069
ENCFF002DAV	POLR2A	14:50359339..50359883
ENCFF002DAV	POLR2A	14:50359772..50359919
ENCFF002DAY	POLR2A	14:50359278..50359914
ENCFF002DAY	POLR2A	14:50359520..50360156
ENCFF002DBB	POLR2A	14:50359503..50359703
ENCFF002DBB	POLR2A	14:50359774..50359974
ENCFF002DBE	POLR2A	14:50359693..50359967
ENCFF002DBO	POLR2A	14:50359432..50360035
ENCFF002DBP	POLR2A	14:50359464..50359746
ENCFF002DBP	POLR2A	14:50359696..50359983
ENCFF002DBQ	POLR2A	14:50359515..50359713
ENCFF002DBQ	POLR2A	14:50359758..50359897
ENCFF002DBT	POLR2A	14:50359585..50359677
ENCFF002DBT	POLR2A	14:50359804..50359897

EST

29 EST(s) were mapped to retro_hsap_36 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
AI940133	50360534	50360708	95.3	164	4	154
AI940136	50360551	50360660	98.1	105	0	100
AW751295	50360566	50360693	97.6	122	3	117
AW751296	50360551	50360666	98.2	107	1	102
BQ315629	50360533	50360696	95.1	159	3	153
BQ315631	50360525	50360735	99.6	203	1	196
BQ315632	50360556	50360725	98.3	164	3	159
BQ315633	50360542	50360724	99.5	175	0	169
BQ315634	50360562	50360720	99.4	157	1	156
BQ315635	50360576	50360724	99.4	147	1	146
BQ315636	50360539	50360735	99	188	2	181
BQ315637	50360536	50360724	99	181	1	175
BQ315638	50360573	50360726	99.4	150	0	147
BQ315639	50360543	50360724	98.3	171	2	164
BQ315640	50360547	50360714	100	163	0	159
BQ315641	50360547	50360724	99.4	164	0	157
BQ315642	50360527	50360724	99.5	190	1	184
BQ315643	50360517	50360715	97.9	183	3	174
BQ315644	50360565	50360724	99.4	158	1	157
BQ315645	50360532	50360724	99.5	186	1	182
BQ315646	50360542	50360724	98.9	173	1	167
BQ315647	50360575	50360724	100	148	0	147
BQ315648	50360551	50360728	99.5	175	1	173
BQ315707	50360529	50360724	100	195	0	195
BQ315714	50360529	50360724	100	195	0	195
BQ315722	50360519	50360693	98.3	169	3	164
BQ315746	50360584	50360735	97.2	138	2	132
BQ315747	50360581	50360717	97	130	1	124
EC481026	50360489	50360592	100	103	0	103

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_38365	743 libraries	835 libraries	246 libraries	4 libraries	1 library
TSS #2	TSS_38366	342 libraries	521 libraries	735 libraries	180 libraries	51 libraries
TSS #3	TSS_38369	1141 libraries	544 libraries	142 libraries	2 libraries	0 libraries
TSS #4	TSS_38370	919 libraries	643 libraries	229 libraries	30 libraries	8 libraries

The graphical summary, for retro_hsap_36 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_36 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_36 has 12 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_5
Gorilla gorilla	retro_ggor_161
Pongo abelii	retro_pabe_126
Macaca mulatta	retro_mmul_174
Callithrix jacchus	retro_cjac_300
Mus musculus	retro_mmus_147
Rattus norvegicus	retro_rnor_272
Oryctolagus cuniculus	retro_ocun_132
Bos taurus	retro_btau_26
Sus scrofa	retro_sscr_82
Canis familiaris	retro_cfam_119
Equus caballus	retro_ecab_106

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Parental genes homology:

Parental genes homology involve 20 parental genes, and 31 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000008240	1 retrocopy	retro_acar_12,
Cavia porcellus	ENSCPOG00000025074	1 retrocopy	retro_cpor_92,
Ciona savignyi	ENSCSAVG00000007011	1 retrocopy	retro_csav_2,
Homo sapiens	ENSG00000134108	1 retrocopy	retro_hsap_361,
Homo sapiens	ENSG00000134287	1 retrocopy	retro_hsap_36 ,
Homo sapiens	ENSG00000143761	3 retrocopies	retro_hsap_1008, retro_hsap_1160, retro_hsap_3763,
Homo sapiens	ENSG00000168374	2 retrocopies	retro_hsap_1296, retro_hsap_4221,
Latimeria chalumnae	ENSLACG00000019009	1 retrocopy	retro_lcha_10,
Loxodonta africana	ENSLAFG00000004207	1 retrocopy	retro_lafr_115,
Macropus eugenii	ENSMEUG00000005072	7 retrocopies	retro_meug_1036, retro_meug_1117, retro_meug_1857, retro_meug_29, retro_meug_395, retro_meug_616, retro_meug_946,
Microcebus murinus	ENSMICG00000017545	1 retrocopy	retro_mmur_37,
Monodelphis domestica	ENSMODG00000013804	1 retrocopy	retro_mdom_241,
Mus musculus	ENSMUSG00000051853	1 retrocopy	retro_mmus_147,
Nomascus leucogenys	ENSNLEG00000017859	2 retrocopies	retro_nleu_1348, retro_nleu_94,
Petromyzon marinus	ENSPMAG00000000531	1 retrocopy	retro_pmar_5,
Rattus norvegicus	ENSRNOG00000033155	1 retrocopy	retro_rnor_272,
Rattus norvegicus	ENSRNOG00000048089	1 retrocopy	retro_rnor_2521,
Sarcophilus harrisii	ENSSHAG00000003635	2 retrocopies	retro_shar_25, retro_shar_364,
Tetraodon nigroviridis	ENSTNIG00000011685	1 retrocopy	retro_tnig_19,
Tursiops truncatus	ENSTTRG00000004698	1 retrocopy	retro_ttru_1081,