RetrogeneDB ID: retro_hsap_15

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 6:28227149..28228358(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000189134
• Aliases: NKAPL, C6orf194, bA424I5.1
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: NKAP
• Ensembl ID: ENSG00000101882
• Aliases: None
• Description: NFKB activating protein [Source:HGNC Symbol;Acc:29873]

Sequence

>retro_hsap_15
ATGCCCCCAGTATCCCGGTCCAGCTATTCCGAGGACATCGTGGGCTCTCGGAGAAGGCGACGCAGCTCCTCGGGGAGCCC
ACCATCCCCGCAGAGCAGATGTTCCTCTTGGGATGGCTGTTCCCGCTCTCACTCCCGCGGCCGTGAGGGCCTCAGGCCTC
CTTGGAGTGAGTTGGACGTGGGCGCTCTTTACCCCTTTAGTCGCTCTGGGTCGCGAGGGCGGCTCCCAAGATTCCGCAAC
TACGCCTTCGCGTCCTCCTGGTCGACCTCGTATAGTGGATATCGCTACCATCGTCACTGCTATGCAGAAGAACGGCAGTC
AGCGGAAGACTACGAGAAGGAAGAGAGCCATCGGCAGAGGAGGCTGAAGGAGAGAGAGAGGATTGGGGAATTGGGAGCGC
CTGAAGTGTGGGGGCCGTCTCCAAAGTTCCCTCAGCTAGATTCTGACGAACATACCCCAGTTGAGGATGAAGAAGAGGTA
ACGCATCAGAAAAGCAGCAGTTCAGATTCCAACTCGGAAGAACATAGGAAAAAGAAGACCAGTCGTTCAAGAAACAAGAA
AAAAAGAAAGAATAAGTCGTCTAAAAGAAAGCATAGGAAATATTCTGATAGTGACAGTAACTCAGAGTCTGACACAAATT
CTGACTCTGATGATGATAAAAAGAGAGTTAAAGCCAAGAAGAAAAAGAAGAAAAAGAAACACAAAACAAAGAAAAAGAAG
AATAAGAAAACCAAAAAAGAATCCAGTGACTCAAGCTGTAAAGACTCAGAAGAGGACTTGTCAGAAGCTACCTGGATGGA
GCAGCCAAATGTGGCAGATACTATGGATTTAATAGGGCCAGAAGCACCTATAATACATACCTCTCAAGATGAAAAACCTT
TGAAGTATGGCCATGCTTTGCTTCCCGGTGAAGGTGCAGCTATGGCTGAGTATGTAAAAGCTGGAAAGCGAATCCCACGA
AGAGGTGAAATTGGGTTGACAAGTGAAGAGATCGGTTCTTTTGAATGCTCAGGTTATGTCATGAGTGGTAGCAGGCATCG
CAGAATGGAGGCTGTACGACTGCGTAAGGAGAACCAGATCTACAGTGCTGATGAGAAGAGAGCTCTTGCATCCTTTAACC
AAGAAGAGAGACGAAAGAGAGAAAGTAAGATTTTAGCCAGTTTCCGAGAGATGGTGCACAAAAAGACAAAAGAGAAAGAT
GACAAGTAA

Alignment

ORF - retro_hsap_15 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.1 %
• Parental protein coverage: 81.93 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SRSRSRERPSAPRGIPFASASSSVYYGSYSRPYGSDKPWPSLLDKEREESLRQKRLSERERIGELGAPEV
          SRS.SR.R....R...FAS..S..Y.G.............S..D.E.EES.RQ.RL.ERERIGELGAPEV
Retrocopy SRSGSRGRLPRFRNYAFASSWSTSYSGYRYHRHCYAEERQSAEDYEKEESHRQRRLKERERIGELGAPEV

Parental  WGLSPKNPEPDSDEHTPVEDEEP---KKSTTSASTSEEEKKKKSSRSKERSKKRRKKKSSKRKHKKYSED
          WG.SPK.P..DSDEHTPVEDEE.....KS..S.S.SEE..KKK.SRS..R.KK.RK.KSSKRKH.KYS.D
Retrocopy WGPSPKFPQLDSDEHTPVEDEEEVTHQKSSSSDSNSEEHRKKKTSRS--RNKKKRKNKSSKRKHRKYS-D

Parental  SDSDSDSETDSSDEDNKRRAKKAKKKEKKKKHRSKKYKKKRSKKSRKESSDSSSKESQEEFLENPWKDRT
          SDS.S.S.T.S...D.K.R.K.AKKK.KKKKH.....KKK..KK..KESSDSS.K.S.E...E..W....
Retrocopy SDSNSESDTNSDSDDDKKRVK-AKKKKKKKKHKT---KKKKNKKTKKESSDSSCKDSEEDLSEATWMEQP

Parental  KAEEPSDLIGPEAPKTLTSQDDKPLNYGHALLPGEGAAMAEYVKAGKRIPRRGEIGLTSEEIASFECSGY
          ......DLIGPEAP...TSQD.KPL.YGHALLPGEGAAMAEYVKAGKRIPRRGEIGLTSEEI.SFECSGY
Retrocopy NVADTMDLIGPEAPIIHTSQDEKPLKYGHALLPGEGAAMAEYVKAGKRIPRRGEIGLTSEEIGSFECSGY

Parental  VMSGSRHRRMEAVRLRKENQIYSADEKRALASFNQEERRKRENKILASFREMVYRKTKGKDDK
          VMSGSRHRRMEAVRLRKENQIYSADEKRALASFNQEERRKRE.KILASFREMV..KTK.KDDK
Retrocopy VMSGSRHRRMEAVRLRKENQIYSADEKRALASFNQEERRKRESKILASFREMVHKKTKEKDDK

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	2.33 RPM	12.90 RPM
bodymap2_adrenal	1.64 RPM	16.38 RPM
bodymap2_brain	2.11 RPM	17.72 RPM
bodymap2_breast	4.57 RPM	11.87 RPM
bodymap2_colon	2.55 RPM	16.32 RPM
bodymap2_heart	1.88 RPM	6.66 RPM
bodymap2_kidney	1.63 RPM	13.75 RPM
bodymap2_liver	0.13 RPM	10.22 RPM
bodymap2_lung	0.18 RPM	11.27 RPM
bodymap2_lymph_node	0.49 RPM	14.24 RPM
bodymap2_ovary	1.60 RPM	20.72 RPM
bodymap2_prostate	2.30 RPM	16.44 RPM
bodymap2_skeletal_muscle	5.37 RPM	9.40 RPM
bodymap2_testis	43.27 RPM	19.19 RPM
bodymap2_thyroid	4.69 RPM	14.20 RPM
bodymap2_white_blood_cells	0.28 RPM	17.36 RPM

ChIP-Seq

RNA Polymerase II actvity may be related with retro_hsap_15 in 4 libraries

ENCODE library ID	Target	ChIP-Seq Peak coordinates
ENCFF002CHO	POLR2A	6:28226873..28227222
ENCFF002CQI	POLR2A	6:28226824..28227260
ENCFF002CQM	POLR2A	6:28226747..28227227
ENCFF002CQO	POLR2A	6:28226821..28227351

EST

34 EST(s) were mapped to retro_hsap_15 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
AA193476	28227267	28227825	99.1	540	2	531
AA426031	28227497	28227826	100	329	0	329
AA719187	28227448	28227827	100	378	0	377
AA889640	28227347	28227703	99.8	354	1	352
AA993479	28227394	28227706	99.7	311	1	310
AI633740	28227369	28227827	99.8	457	1	456
AI825371	28227451	28227827	100	376	0	376
AI825424	28227566	28227856	99	290	0	289
AI970107	28227290	28227827	98.7	533	4	528
AI989981	28227300	28227827	99.7	525	2	523
AI129164	28227396	28227835	100	438	0	437
AI183972	28227359	28227833	100	474	0	474
AJ574107	28227325	28227696	99.8	370	1	369
AW003978	28227238	28227827	99.7	587	2	585
AW196436	28227357	28227827	98.8	469	1	466
AW207887	28227306	28227835	99.7	524	2	519
AW515746	28227326	28227827	99.9	500	1	499
BE042106	28227473	28227714	99.2	230	2	226
BF061938	28227363	28227827	99	459	5	454
BF222720	28227311	28227827	99.9	515	1	514
BF592882	28227224	28227827	97.2	588	13	571
BQ186305	28227168	28227714	99.5	542	0	541
BQ186490	28227177	28227805	99.6	626	0	625
BX115857	28227115	28227764	99.9	647	1	646
CK299257	28227168	28227714	99.9	542	1	541
DB454384	28227091	28227560	99.8	468	1	467
DB471905	28227074	28227570	99.8	495	1	494
DB473910	28227074	28227561	99.6	485	2	483
DB478241	28227074	28227566	99.6	490	2	488
EL737170	28227149	28227795	99.7	641	2	639
H86864	28227745	28228025	97.5	279	0	276
HY019101	28227157	28227608	100	451	0	451
HY202334	28227467	28227872	98.8	401	2	398
W78197	28227097	28227526	98.6	420	2	410

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_163202	897 libraries	253 libraries	539 libraries	111 libraries	29 libraries
TSS #2	TSS_163203	1620 libraries	196 libraries	11 libraries	2 libraries	0 libraries

The graphical summary, for retro_hsap_15 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_15 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_15 has 5 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_117
Pongo abelii	retro_pabe_198
Macaca mulatta	retro_mmul_121
Mus musculus	retro_mmus_279
Rattus norvegicus	retro_rnor_93

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000018433	1 retrocopy	retro_cfam_172,
Dasypus novemcinctus	ENSDNOG00000000072	1 retrocopy	retro_dnov_50,
Echinops telfairi	ENSETEG00000001007	1 retrocopy	retro_etel_1882,
Felis catus	ENSFCAG00000004392	1 retrocopy	retro_fcat_10,
Homo sapiens	ENSG00000101882	1 retrocopy	retro_hsap_15 ,
Loxodonta africana	ENSLAFG00000002962	1 retrocopy	retro_lafr_37,
Macaca mulatta	ENSMMUG00000012382	1 retrocopy	retro_mmul_121,
Mus musculus	ENSMUSG00000016409	1 retrocopy	retro_mmus_279,
Nomascus leucogenys	ENSNLEG00000014922	1 retrocopy	retro_nleu_88,
Otolemur garnettii	ENSOGAG00000001004	1 retrocopy	retro_ogar_239,
Pongo abelii	ENSPPYG00000020679	1 retrocopy	retro_pabe_198,
Pan troglodytes	ENSPTRG00000022233	1 retrocopy	retro_ptro_117,
Rattus norvegicus	ENSRNOG00000031169	1 retrocopy	retro_rnor_93,
Sus scrofa	ENSSSCG00000012613	1 retrocopy	retro_sscr_13,
Ictidomys tridecemlineatus	ENSSTOG00000001134	1 retrocopy	retro_itri_73,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.00 RPM
CEU_NA11843	0.06 RPM
CEU_NA11930	0.00 RPM
CEU_NA12004	0.00 RPM
CEU_NA12400	0.11 RPM
CEU_NA12751	0.05 RPM
CEU_NA12760	0.09 RPM
CEU_NA12827	0.05 RPM
CEU_NA12872	0.00 RPM
CEU_NA12873	0.03 RPM
FIN_HG00183	0.27 RPM
FIN_HG00277	0.11 RPM
FIN_HG00315	0.44 RPM
FIN_HG00321	0.09 RPM
FIN_HG00328	0.05 RPM
FIN_HG00338	0.13 RPM
FIN_HG00349	0.28 RPM
FIN_HG00375	0.24 RPM
FIN_HG00377	0.25 RPM
FIN_HG00378	0.13 RPM
GBR_HG00099	0.03 RPM
GBR_HG00111	0.21 RPM
GBR_HG00114	0.21 RPM
GBR_HG00119	0.43 RPM
GBR_HG00131	0.46 RPM
GBR_HG00133	0.31 RPM
GBR_HG00134	0.24 RPM
GBR_HG00137	0.11 RPM
GBR_HG00142	0.42 RPM
GBR_HG00143	0.16 RPM
TSI_NA20512	0.14 RPM
TSI_NA20513	0.02 RPM
TSI_NA20518	0.19 RPM
TSI_NA20532	0.10 RPM
TSI_NA20538	0.14 RPM
TSI_NA20756	0.20 RPM
TSI_NA20765	1.12 RPM
TSI_NA20771	0.20 RPM
TSI_NA20786	0.00 RPM
TSI_NA20798	0.19 RPM
YRI_NA18870	0.07 RPM
YRI_NA18907	0.42 RPM
YRI_NA18916	0.21 RPM
YRI_NA19093	0.05 RPM
YRI_NA19099	0.03 RPM
YRI_NA19114	0.10 RPM
YRI_NA19118	0.02 RPM
YRI_NA19213	0.69 RPM
YRI_NA19214	0.02 RPM
YRI_NA19223	0.06 RPM

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Indel association:

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