RetrogeneDB ID: retro_hsap_1760

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 17:43663236..43664292(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000264070
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: DND1
• Ensembl ID: ENSG00000256453
• Aliases: DND1, RBMS4
• Description: dead end homolog 1 (zebrafish) [Source:HGNC Symbol;Acc:23799]

Sequence

>retro_hsap_1760
ATGCAGTCCACGCGGGATTGTGAGCTGTGGTGTGAGAGGGTGAAGCCAGAGAACAAGGCGGCGCTGGAGGCGTGGGTCAG
GCAGACAGGCATCGCCTGGTGCAGGTGAACGGGCAGAGGAAGTATGGCGGGCCACCCCCAGGCTGGGTGGGCAGCCCGCC
GCCGGCTGGGTCAGAGGTGTTCATCGGGCGGCTGCCTCAGGAAGTGTATGAGCACCAGCTATCCTGCTGTTCCAGCGCGT
GGGCCGCCTCTACGAGTTCCGCCTGATGATGACCTTCAGCGGCCTGAACCGCGGCTTCGCATATGCCCGCTGCAGCTCGC
GGCGCGGCGCGCAGGCCGCCATCGCCCGCTGCACAACCACCCGCTGCGGCCGTCCTGCCCGCTGCTTCTGTGCCGCAGCA
CCGGGAAGTGTGAGCTGAGCGTTGACTGCCTGCCGCCGAATCTGACCCGCACCGCGCTGCAGCCCGCGCTGCAGCCGCTG
GGTCCCGGCCTGCAGGAGGCGCGGCTGCTGCCCAGCCCCGGACCGGCGCCCGGGCAGATCGCTCTGCTCAAATTCAGCTC
GCACTGGACCGCTGCCATGGCCAAAAAGGCCCTGGAGGAAGGGCAGCCACACCTCTGTGGAGAGCAGGTGGCTGTGGAGT
GGCTCAAGCCAGAACTGAAGCAGCGACTTCGCCAGCAGCTTGTGGGTCCCTCCTTGTGGTCCCCACAGCCAGACGGCAGC
CAGTTGGCCTTGGCAAGGGACAAGTTAGGGTCCCAAGGGGCTCGGGCTACCCTGCAGTTGCTGTGCCAACGAATGAAGCT
GGGCAGCTCTGTGTTCCTCACCAAGTGTTTGGGCATAGGACCTGCTGGCTGGCACCGCTTCTGGTACCAGGTGGTGATTC
CTGGGCATCCGGTGCCCTTCAGCGGCCTCATCTGGGTTGTGCTGATCCTAGATGGCCGGGATGGGCATGAGGTGGCCAAG
GATGCTGTGTCTGTACGGCTGCTGCAGGCACTCATTGAGTCTGGGGCCAACCTCCTGTGGTCTGCTGGGGCTGAGGCAGG
TAGCATGGTTAAACAG

Alignment

ORF - retro_hsap_1760 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.17 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MQSKRDCELWCERVNPENKAALEAWVRETGI-RLVQVNGQRKYGGPPPGWVGSPPPAGSEVFIGRLPQDV
          MQS.RDCELWCERV.PENKAALEAWVR.TGI.RLVQVNGQRKYGGPPPGWVGSPPPAGSEVFIGRLPQ.V
Retrocopy MQSTRDCELWCERVKPENKAALEAWVRQTGI<RLVQVNGQRKYGGPPPGWVGSPPPAGSEVFIGRLPQEV

Parental  YEHQL-IPLFQRVGRLYEFRLMMTFSGLNRGFAYARYSSRRGAQAAIAT-LHNHPLRPSCPLLVCRSTEK
          YEHQL.I.LFQRVGRLYEFRLMMTFSGLNRGFAYAR.SSRRGAQAAIA..LHNHPLRPSCPLL.CRST.K
Retrocopy YEHQL<ILLFQRVGRLYEFRLMMTFSGLNRGFAYARCSSRRGAQAAIAR<LHNHPLRPSCPLLLCRSTGK

Parental  CELSVDGLPPNLTRSALLLALQPLGPGLQEARLLPSPGPAPGQIALLKFSSHRAAAMAKKALVEGQSHLC
          CELSVD.LPPNLTR.........LGPGLQEARLLPSPGPAPGQIALLKFSSH..AAMAKKAL.EGQ.HLC
Retrocopy CELSVDCLPPNLTRXXXXXXXXXLGPGLQEARLLPSPGPAPGQIALLKFSSHWTAAMAKKALEEGQPHLC

Parental  GEQVAVEWLKPDLKQRLRQQLVGPFLRSPQPEGSQLALARDKLGFQGARATLQLLCQRMKLGSPVFLTKC
          GEQVAVEWLKP.LKQRLRQQLVGP.L.SPQP.GSQLALARDKLG.QGARATLQLLCQRMKLGS.VFLTKC
Retrocopy GEQVAVEWLKPELKQRLRQQLVGPSLWSPQPDGSQLALARDKLGSQGARATLQLLCQRMKLGSSVFLTKC

Parental  LGIGPAGWHRFWYQVVIPGHPVPFSGLIWVVLTLDGRDGHEVAKDAVSVRLLQALSESGANLLWSAGAEA
          LGIGPAGWHRFWYQVVIPGHPVPFSGLIWVVL.LDGRDGHEVAKDAVSVRLLQAL.ESGANLLWSAGAEA
Retrocopy LGIGPAGWHRFWYQVVIPGHPVPFSGLIWVVLILDGRDGHEVAKDAVSVRLLQALIESGANLLWSAGAEA

Parental  GTMVKQ
          G.MVKQ
Retrocopy GSMVKQ

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	0.42 RPM	0.00 RPM
bodymap2_adrenal	0.47 RPM	0.00 RPM
bodymap2_brain	0.21 RPM	0.00 RPM
bodymap2_breast	0.16 RPM	0.00 RPM
bodymap2_colon	0.02 RPM	0.00 RPM
bodymap2_heart	0.15 RPM	0.00 RPM
bodymap2_kidney	0.14 RPM	0.00 RPM
bodymap2_liver	0.02 RPM	0.00 RPM
bodymap2_lung	0.18 RPM	0.00 RPM
bodymap2_lymph_node	0.37 RPM	0.00 RPM
bodymap2_ovary	0.37 RPM	0.00 RPM
bodymap2_prostate	0.24 RPM	0.00 RPM
bodymap2_skeletal_muscle	0.00 RPM	0.00 RPM
bodymap2_testis	0.60 RPM	0.00 RPM
bodymap2_thyroid	0.53 RPM	0.00 RPM
bodymap2_white_blood_cells	0.81 RPM	0.00 RPM

ChIP-Seq

RNA Polymerase II actvity may be related with retro_hsap_1760 in 38 libraries

ENCODE library ID	Target	ChIP-Seq Peak coordinates
ENCFF002CFW	POLR2A	17:43662329..43662890
ENCFF002CFW	POLR2A	17:43661617..43662414
ENCFF002CFX	POLR2A	17:43661638..43662883
ENCFF002CGN	POLR2A	17:43662435..43662673
ENCFF002CHO	POLR2A	17:43661573..43662948
ENCFF002CIH	POLR2A	17:43662423..43662707
ENCFF002CIO	POLR2A	17:43662351..43662889
ENCFF002CIO	POLR2A	17:43662008..43662332
ENCFF002CJE	POLR2A	17:43661506..43662451
ENCFF002CJZ	POLR2A	17:43662352..43662882
ENCFF002CJZ	POLR2A	17:43661549..43662329
ENCFF002CKX	POLR2A	17:43662351..43662846
ENCFF002CMI	POLR2A	17:43662312..43662897
ENCFF002COJ	POLR2A	17:43662301..43662737
ENCFF002COJ	POLR2A	17:43661938..43662374
ENCFF002CPG	POLR2A	17:43662492..43662692
ENCFF002CQC	POLR2A	17:43661854..43662243
ENCFF002CQC	POLR2A	17:43662433..43662823
ENCFF002CQC	POLR2A	17:43662167..43662306
ENCFF002CQE	POLR2A	17:43662378..43662826
ENCFF002CQE	POLR2A	17:43661826..43662369
ENCFF002CQG	POLR2A	17:43662469..43662784
ENCFF002CQG	POLR2A	17:43661968..43662492
ENCFF002CQI	POLR2A	17:43662443..43662800
ENCFF002CQK	POLR2A	17:43662415..43662830
ENCFF002CQK	POLR2A	17:43661824..43662389
ENCFF002CQM	POLR2A	17:43662445..43662783
ENCFF002CQM	POLR2A	17:43662059..43662320
ENCFF002CQO	POLR2A	17:43662430..43662826
ENCFF002CQO	POLR2A	17:43661838..43662334
ENCFF002CRK	POLR2A	17:43661934..43662458
ENCFF002CRK	POLR2A	17:43662312..43662836
ENCFF002CRO	POLR2A	17:43662321..43662741
ENCFF002CSY	POLR2A	17:43661541..43662933
ENCFF002CUP	POLR2A	17:43662537..43662625
ENCFF002CUP	POLR2A	17:43662003..43662319
ENCFF002CUQ	POLR2A	17:43662276..43662780
ENCFF002CXM	POLR2A	17:43662282..43662772
ENCFF002CXO	POLR2A	17:43662312..43662736
ENCFF002CXO	POLR2A	17:43662517..43662941
ENCFF002CXP	POLR2A	17:43662284..43662764
ENCFF002CXR	POLR2A	17:43662305..43662741
ENCFF002CZC	POLR2A	17:43662413..43662779
ENCFF002CZD	POLR2A	17:43662429..43662686
ENCFF002CZQ	POLR2A	17:43661952..43662402
ENCFF002CZQ	POLR2A	17:43662438..43662741
ENCFF002CZY	POLR2A	17:43662368..43662847
ENCFF002CZY	POLR2A	17:43662007..43662285
ENCFF002DAE	POLR2A	17:43661996..43662306
ENCFF002DAE	POLR2A	17:43662371..43662681
ENCFF002DAH	POLR2A	17:43662401..43662685
ENCFF002DAK	POLR2A	17:43661910..43662410
ENCFF002DAK	POLR2A	17:43662280..43662780
ENCFF002DAV	POLR2A	17:43662262..43662806
ENCFF002DBB	POLR2A	17:43662152..43662352
ENCFF002DBT	POLR2A	17:43662310..43662680
ENCFF002CFW	POLR2A	17:43663526..43663786
ENCFF002CFX	POLR2A	17:43663479..43663778
ENCFF002CHO	POLR2A	17:43663488..43663798
ENCFF002CKX	POLR2A	17:43663393..43663813
ENCFF002CQC	POLR2A	17:43663363..43663843
ENCFF002CQE	POLR2A	17:43663400..43663836
ENCFF002CUP	POLR2A	17:43663485..43663801
ENCFF002DAE	POLR2A	17:43663503..43663813
ENCFF002CFW	POLR2A	17:43663122..43663552
ENCFF002CFX	POLR2A	17:43663250..43663409
ENCFF002CJE	POLR2A	17:43663337..43663973
ENCFF002CKX	POLR2A	17:43663141..43663561
ENCFF002CQC	POLR2A	17:43663098..43663578
ENCFF002CQE	POLR2A	17:43663130..43663566
ENCFF002CQG	POLR2A	17:43663336..43663860
ENCFF002CQK	POLR2A	17:43663358..43663848
ENCFF002CSY	POLR2A	17:43663259..43663949
ENCFF002CZY	POLR2A	17:43663342..43663858

EST

1 EST(s) were mapped to retro_hsap_1760 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
BF738271	43663304	43663470	97.5	152	2	145

TSS

No TSS is located nearby retro_hsap_1760 retrocopy 5' end.

Lab

retro_hsap_1760 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_1760 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000016345	1 retrocopy	retro_cjac_557,
Homo sapiens	ENSG00000125944	1 retrocopy	retro_hsap_651,
Homo sapiens	ENSG00000135316	1 retrocopy	retro_hsap_2410,
Homo sapiens	ENSG00000256453	1 retrocopy	retro_hsap_1760 ,
Macropus eugenii	ENSMEUG00000016276	2 retrocopies	retro_meug_1326, retro_meug_614,
Mus musculus	ENSMUSG00000044595	1 retrocopy	retro_mmus_2548,
Pongo abelii	ENSPPYG00000015863	1 retrocopy	retro_pabe_1502,
Rattus norvegicus	ENSRNOG00000016894	1 retrocopy	retro_rnor_2782,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.88 RPM
CEU_NA11843	0.54 RPM
CEU_NA11930	0.95 RPM
CEU_NA12004	0.65 RPM
CEU_NA12400	0.74 RPM
CEU_NA12751	0.46 RPM
CEU_NA12760	1.17 RPM
CEU_NA12827	0.85 RPM
CEU_NA12872	1.28 RPM
CEU_NA12873	1.24 RPM
FIN_HG00183	0.77 RPM
FIN_HG00277	1.11 RPM
FIN_HG00315	0.94 RPM
FIN_HG00321	1.30 RPM
FIN_HG00328	1.30 RPM
FIN_HG00338	0.87 RPM
FIN_HG00349	0.71 RPM
FIN_HG00375	0.83 RPM
FIN_HG00377	1.41 RPM
FIN_HG00378	0.55 RPM
GBR_HG00099	0.78 RPM
GBR_HG00111	0.84 RPM
GBR_HG00114	2.31 RPM
GBR_HG00119	0.65 RPM
GBR_HG00131	0.80 RPM
GBR_HG00133	1.91 RPM
GBR_HG00134	2.07 RPM
GBR_HG00137	2.39 RPM
GBR_HG00142	0.72 RPM
GBR_HG00143	0.99 RPM
TSI_NA20512	1.53 RPM
TSI_NA20513	2.03 RPM
TSI_NA20518	0.69 RPM
TSI_NA20532	1.53 RPM
TSI_NA20538	1.01 RPM
TSI_NA20756	0.76 RPM
TSI_NA20765	1.35 RPM
TSI_NA20771	1.45 RPM
TSI_NA20786	1.12 RPM
TSI_NA20798	1.15 RPM
YRI_NA18870	0.34 RPM
YRI_NA18907	1.04 RPM
YRI_NA18916	0.86 RPM
YRI_NA19093	1.48 RPM
YRI_NA19099	0.59 RPM
YRI_NA19114	0.63 RPM
YRI_NA19118	0.83 RPM
YRI_NA19213	0.45 RPM
YRI_NA19214	1.33 RPM
YRI_NA19223	0.97 RPM

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Indel association:

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