RetrogeneDB ID: retro_hsap_69

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 17:51900394..51902416(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000141200
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: KIF2A
• Ensembl ID: ENSG00000068796
• Aliases: None
• Description: kinesin heavy chain member 2A [Source:HGNC Symbol;Acc:6318]

Sequence

>retro_hsap_69
ATGGCCAGCCAGTTCTGCCTCCCTGAATCCCCATGTCTCTCGCCCCTGAAACCCTTGAAGCCACATTTCGGAGACATCCA
AGAGGGCATCTACGTGGCGATCCAGCGCAGTGACAAGCGGATCCACCTCGCTGTGGTCACGGAGATCAACAGAGAAAACT
ATTGGGTCACGGTAGAGTGGGTGGAGAAAGCAGTCAAAAAAGGCAAGAAGATTGACCTGGAGACCATACTCCTGCTGAAT
CCAGCTCTGGACTCTGCTGAACACCCCATGCCGCCCCCGCCCTTATCCCCCTTGGCTCTGGCGCCCTCTTCGGCCATCAG
GGACCAGCGTACCGCCACGAAATGGGTTGCGATGATCCCCCAGAAAAACCAAACAGCCTCAGGGGACAGCCTGGATGTGA
GGGTCCCCAGCAAACCTTGTCTGATGAAGCAGAAAAAGTCTCCCTGCCTCTGGGAAATCCAGAAACTGCAGGAGCAGCGG
GAAAAGCGCAGGCGGCTGCAGCAGGAGATCCGAGCTAGACGCGCCCTCGATGTCAATACCAGAAACCCCAACTACGAAAT
CATGCACATGATCGAAGAGTATCGCAGGCACCTGGACAGCAGCAAGATCTCAGTCCTGGAGCCCCCGCAAGAACATCGCA
TCTGCGTCTGCGTGAGGAAGCGGCCTCTCAACCAGCGAGAGACAACCTTAAAGGACCTGGATATCATCACCGTCCCCTCG
GACAATGTGGTTATGGTGCATGAGTCCAAGCAAAAGGTGGACCTCACTCGCTACCTGCAGAACCAGACCTTCTGCTTCGA
CCATGCCTTCGATGACAAAGCCTCCAACGAGTTGGTGTACCAGTTCACCGCCCAGCCACTGGTGGAGTCCATCTTCCGCA
AGGGCATGGCCACCTGCTTTGCCTATGGGCAGACGGGAAGTGGGAAGACGTACACCATGGGTGGAGACTTTTCAGGAACG
GCCCAAGATTGTTCTAAGGGCATTTATGCTCTGGTGGCACAGGATGTCTTTCTCCTGCTCAGAAACTCCACATATGAGAA
GCTGGACCTCAAAGTCTATGGGACATTTTTTGAGATTTATGGGGGCAAGGTGTATGATTTGTTGAACTGGAAGAAGAAGC
TGCAAGTCCTTGAGGATGGCAATCAGCAAATCCAAGTGGTCGGGCTGCAGGAGAAAGAGGTGTGTTGTGTGGAGGAAGTG
CTGAACCTGGTGGAAATAGGGAATAGCTGTCGGACTTCCAGGCAAACACCTGTCAACGCTCACTCATCCAGGAGCCATGC
AGTGTTCCAGATCATCCTGAAGTCAGGACGGATAATGCATGGCAAGTTTTCCCTCGTTGATTTAGCTGGGAATGAAAGAG
GAGCAGATACAACCAAGGCCAGCCGGAAAAGGCAGCTGGAAGGGGCAGAGATTAACAAGAGTCTTCTAGCCCTCAAAGAA
TGTATTCTGGCTTTGGGTCAGAACAAGCCTCACACCCCATTCAGAGCCAGCAAACTCACACTGGTGCTCCGGGACTCCTT
TATAGGCCAGAACTCCTCCACTTGCATGATTGCTACCATCTCTCCGGGGATGACCTCTTGTGAAAACACTCTCAACACTT
TAAGATATGCAAACAGAGTAAAAAAATTAAATGTAGATGTAAGGCCCTACCATCGTGGCCACTATCCGATTGGACATGAG
GCACCAAGGATGTTAAAAAGTCACATCGGAAATTCAGAAATGTCCCTTCAGAGGGATGAATTTATTAAAATACCTTATGT
ACAGAGTGAGGAGCAGAAAGAGATTGAAGAGGTTGAAACATTACCCACTCTGTTAGGGAAGGATACCACAATTTCAGGGA
AGGGATCTAGCCAATGGCTGGAAAACATCCAGGAGAGAGCTGGTGGAGTACACCATGATATTGATTTTTGCATTGCCCGG
TCTTTGTCCATTTTGGAGCAGAAAATTGATGCTCTGACCGAGATCCAAAAGAAACTGAAATTATTACTAGCTGACCTCCA
CGTGAAGAGCAAGGTAGAGTGA

Alignment

ORF - retro_hsap_69 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.19 %
• Parental protein coverage: 57.08 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RRKSNCVKEVEKLQEKREKRRLQQQELREKRAQDVDATNPNYEIMCMIRDFRGSLDYRPLTTADPIDEHR
          ..KS.C..E..KLQE.REKRR..QQE.R..RA.DV...NPNYEIM.MI...R..LD........P..EHR
Retrocopy QKKSPCLWEIQKLQEQREKRRRLQQEIRARRALDVNTRNPNYEIMHMIEEYRRHLDSSKISVLEPPQEHR

Parental  ICVCVRKRPLNKKETQMKDLDVITIPSKDVVMVHEPKQKVDLTRYLENQTFRFDYAFDDSAPNEMVYRFT
          ICVCVRKRPLN..ET..KDLD.IT.PS..VVMVHE.KQKVDLTRYL.NQTF.FD.AFDD.A.NE.VY.FT
Retrocopy ICVCVRKRPLNQRETTLKDLDIITVPSDNVVMVHESKQKVDLTRYLQNQTFCFDHAFDDKASNELVYQFT

Parental  ARPLVETIFERGMATCFAYGQTGSGKTHTMGGDFSGKNQDCSKGIYALAARDVFLMLKKPNYKKLELQVY
          A.PLVE.IF..GMATCFAYGQTGSGKT.TMGGDFSG..QDCSKGIYAL.A.DVFL.L....Y.KL.L.VY
Retrocopy AQPLVESIFRKGMATCFAYGQTGSGKTYTMGGDFSGTAQDCSKGIYALVAQDVFLLLRNSTYEKLDLKVY

Parental  ATFFEIYSGKVFDLLNRKTKLRVLEDGKQQVQVVGLQEREVKCVEDVLKLIDIGNSCRTSGQTSANAHSS
          .TFFEIY.GKV.DLLN.K.KL.VLEDG.QQ.QVVGLQE.EV.CVE.VL.L..IGNSCRTS.QT..NAHSS
Retrocopy GTFFEIYGGKVYDLLNWKKKLQVLEDGNQQIQVVGLQEKEVCCVEEVLNLVEIGNSCRTSRQTPVNAHSS

Parental  RSHAVFQIILRRKGKLHGKFSLIDLAGNERGADTSSADRQTRLEGAEINKSLLALKECIRALGRNKPHTP
          RSHAVFQIIL......HGKFSL.DLAGNERGADT..A.R...LEGAEINKSLLALKECI.ALG.NKPHTP
Retrocopy RSHAVFQIILKSGRIMHGKFSLVDLAGNERGADTTKASRKRQLEGAEINKSLLALKECILALGQNKPHTP

Parental  FRASKLTQVLRDSFIGENSRTCMIATISPGMASCENTLNTLRYANRVKELTVD
          FRASKLT.VLRDSFIG.NS.TCMIATISPGM.SCENTLNTLRYANRVK.L.VD
Retrocopy FRASKLTLVLRDSFIGQNSSTCMIATISPGMTSCENTLNTLRYANRVKKLNVD

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	0.12 RPM	25.94 RPM
bodymap2_adrenal	0.08 RPM	28.53 RPM
bodymap2_brain	0.00 RPM	98.96 RPM
bodymap2_breast	0.00 RPM	22.90 RPM
bodymap2_colon	0.00 RPM	27.69 RPM
bodymap2_heart	0.00 RPM	8.62 RPM
bodymap2_kidney	0.00 RPM	18.26 RPM
bodymap2_liver	0.00 RPM	4.39 RPM
bodymap2_lung	0.00 RPM	25.79 RPM
bodymap2_lymph_node	0.00 RPM	34.85 RPM
bodymap2_ovary	0.00 RPM	46.63 RPM
bodymap2_prostate	0.00 RPM	23.16 RPM
bodymap2_skeletal_muscle	0.00 RPM	7.75 RPM
bodymap2_testis	78.98 RPM	95.02 RPM
bodymap2_thyroid	0.00 RPM	28.21 RPM
bodymap2_white_blood_cells	0.00 RPM	126.40 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_hsap_69 was not detected

EST

105 EST(s) were mapped to retro_hsap_69 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
BF979470	51900290	51900993	97.4	672	3	651
BG717678	51900302	51900944	98.6	637	4	630
BG719749	51900306	51900942	99.6	631	3	626
BG721597	51900287	51901029	99.6	738	2	734
BG771992	51900306	51901110	99.2	788	6	775
BG772495	51900266	51901053	96.4	776	10	754
BI461290	51900306	51901088	97.9	772	5	758
BI462018	51900283	51900974	98.4	680	5	663
BI462901	51900290	51901142	97.9	806	13	786
BI463904	51900292	51900970	99.6	675	3	672
BI464561	51900306	51900907	98	593	4	580
BI561657	51900306	51901162	96	829	16	796
BI829106	51900300	51901019	99.6	719	0	718
BM560261	51900276	51901169	97.2	883	6	864
BP371564	51900289	51901010	99.9	581	1	579
BP371589	51900936	51901604	99.9	567	1	565
CD171892	51900328	51901130	98.6	799	3	792
CD244601	51900427	51901269	97.9	840	2	829
CD299965	51900313	51901159	98.4	844	2	836
CD634108	51900475	51901008	99.9	532	1	531
CD634109	51900299	51901008	99.2	708	1	705
CD634110	51900299	51901008	99.8	706	2	703
CD634111	51900299	51901008	99.9	708	1	707
CD634112	51900299	51900978	99	672	4	662
CD634113	51900288	51901008	99.4	718	1	714
CD634114	51900288	51901008	98.7	717	2	710
CD634115	51900299	51901008	99.5	708	1	706
CD634116	51900288	51901008	98.9	716	3	710
CD634117	51900299	51900922	99.9	622	1	621
CV030651	51900394	51901003	100	609	0	609
DB020022	51900481	51901036	99.9	554	1	553
DB020310	51900269	51900900	99.7	571	1	568
DB022664	51900287	51900843	99.3	555	1	553
DB022991	51900287	51900853	99.9	565	1	564
DB024150	51900287	51900835	100	548	0	548
DB024991	51900291	51900848	99.9	556	1	555
DB026207	51900283	51900839	100	556	0	556
DB027113	51900296	51900834	99.9	537	1	536
DB027216	51900288	51901057	99.9	600	1	598
DB027224	51900306	51900904	100	598	0	598
DB027590	51900307	51900884	100	577	0	577
DB028384	51900296	51900839	99.9	542	1	541
DB028704	51900289	51900870	99.9	580	1	579
DB029624	51900289	51900880	100	591	0	591
DB029947	51900277	51900880	100	603	0	603
DB030135	51900306	51900903	99.7	571	1	568
DB031001	51900306	51900873	99.9	566	1	565
DB031046	51900552	51901124	99.7	570	2	568
DB031435	51900275	51900884	99.7	607	2	605
DB031441	51900306	51900929	100	623	0	623
DB033974	51900296	51900866	99.7	568	2	566
DB034169	51900287	51900881	100	594	0	594
DB034667	51900306	51900886	99.9	579	1	578
DB035029	51900306	51900858	99.9	551	1	550
DB035419	51900301	51900851	99.9	549	1	548
DB035778	51900287	51900862	99.9	574	1	573
DB036627	51900287	51900863	100	576	0	576
DB038024	51900306	51900881	99.9	574	1	573
DB038823	51900306	51900881	100	574	0	574
DB040581	51900306	51900868	99.7	559	1	556
DB040676	51900306	51900868	99.9	561	1	560
DB041512	51900287	51900840	99.7	551	2	549
DB041680	51900287	51900835	99.9	547	1	546
DB042083	51900619	51901199	98.8	578	2	574
DB042261	51900306	51900897	99.7	589	2	587
DB042755	51900306	51900858	99.5	552	0	551
DB042765	51900287	51900843	99.7	554	2	552
DB043236	51900287	51900862	99.9	574	1	573
DB043273	51900287	51900863	100	576	0	576
DB043535	51900306	51900865	99.9	558	1	557
DB044392	51900289	51900845	99.9	555	1	554
DB044824	51900301	51900853	99.9	551	1	550
DB044886	51900287	51900850	99.5	560	3	557
DB045217	51900287	51900848	100	561	0	561
DB045293	51900927	51901498	99.9	570	1	569
DB045885	51900306	51900859	99.9	552	1	551
DB045896	51900306	51900864	100	558	0	558
DB045982	51900306	51900877	99.9	570	1	569
DB046738	51900287	51900852	99.9	564	1	563
DB047467	51900289	51900855	100	566	0	566
DB047630	51900306	51900883	99.9	576	1	575
DB047718	51900296	51900845	99.9	548	1	547
DB048033	51900306	51900856	100	550	0	550
DB048739	51900287	51900871	99.9	583	1	582
DB049910	51900283	51900847	99.9	563	1	562
DB050148	51900287	51900863	99.7	574	2	572
DB050845	51900300	51900858	99.9	557	1	556
DB051208	51900306	51900889	99.9	582	1	581
DB052193	51900306	51900866	99.9	559	1	558
DB053072	51900306	51900875	100	569	0	569
DB053423	51900287	51900841	100	554	0	554
DB056105	51900304	51900860	99.7	554	2	552
DB056441	51900296	51900817	99.9	520	1	519
DB057938	51900306	51900838	99.9	531	1	530
DB058724	51900289	51900832	100	543	0	543
DB060434	51900287	51900839	99.9	551	1	550
DB089298	51900306	51900868	99.9	561	1	560
DB093988	51900283	51900839	99.9	555	1	554
DB446880	51900323	51900761	99.6	436	1	433
DB456589	51900314	51900795	99.6	479	2	477
DB459465	51900306	51900793	99.2	486	1	484
DC396938	51900306	51901233	99.9	573	1	569
DC398892	51900306	51901088	99.9	550	1	548
HY012274	51900306	51900828	98.9	515	6	509
HY212815	51901082	51901565	99.6	481	2	479

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_60775	1811 libraries	13 libraries	2 libraries	0 libraries	3 libraries
TSS #2	TSS_60776	1824 libraries	3 libraries	2 libraries	0 libraries	0 libraries
TSS #3	TSS_60777	1825 libraries	1 library	2 libraries	1 library	0 libraries

The graphical summary, for retro_hsap_69 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_69 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_69 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pongo abelii	retro_pabe_88
Equus caballus	retro_ecab_32

---

Parental genes homology:

Parental genes homology involve 24 parental genes, and 30 retrocopies.

Species	Parental gene accession	Retrocopies number
Anas platyrhynchos	ENSAPLG00000009519	1 retrocopy	retro_apla_3,
Bos taurus	ENSBTAG00000015022	1 retrocopy	retro_btau_180,
Choloepus hoffmanni	ENSCHOG00000007888	1 retrocopy	retro_chof_1348,
Cavia porcellus	ENSCPOG00000009393	1 retrocopy	retro_cpor_72,
Dipodomys ordii	ENSDORG00000006335	1 retrocopy	retro_dord_763,
Equus caballus	ENSECAG00000019810	1 retrocopy	retro_ecab_32,
Homo sapiens	ENSG00000068796	1 retrocopy	retro_hsap_69 ,
Gorilla gorilla	ENSGGOG00000004774	1 retrocopy	retro_ggor_68,
Macaca mulatta	ENSMMUG00000000399	1 retrocopy	retro_mmul_145,
Monodelphis domestica	ENSMODG00000019605	1 retrocopy	retro_mdom_242,
Mus musculus	ENSMUSG00000021693	1 retrocopy	retro_mmus_68,
Nomascus leucogenys	ENSNLEG00000002865	1 retrocopy	retro_nleu_2329,
Oryctolagus cuniculus	ENSOCUG00000010466	1 retrocopy	retro_ocun_156,
Otolemur garnettii	ENSOGAG00000000527	5 retrocopies	retro_ogar_126, retro_ogar_3166, retro_ogar_3498, retro_ogar_3501, retro_ogar_672,
Ochotona princeps	ENSOPRG00000011768	1 retrocopy	retro_opri_815,
Procavia capensis	ENSPCAG00000005089	1 retrocopy	retro_pcap_22,
Rattus norvegicus	ENSRNOG00000014000	2 retrocopies	retro_rnor_1284, retro_rnor_47,
Sorex araneus	ENSSARG00000007768	1 retrocopy	retro_sara_457,
Sarcophilus harrisii	ENSSHAG00000001950	1 retrocopy	retro_shar_30,
Ictidomys tridecemlineatus	ENSSTOG00000012710	1 retrocopy	retro_itri_40,
Tupaia belangeri	ENSTBEG00000009396	1 retrocopy	retro_tbel_761,
Tarsius syrichta	ENSTSYG00000002115	1 retrocopy	retro_tsyr_1791,
Vicugna pacos	ENSVPAG00000008864	1 retrocopy	retro_vpac_572,
Drosophila melanogaster	FBgn0030268	2 retrocopies	retro_dmel_1, retro_dmel_2,