RetrogeneDB ID: retro_hsap_1618

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 16:3890566..3891011(+)
• Located in intron of: ENSG00000005339

Retrocopy information

• Ensembl ID: ENSG00000262516
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: DPPA3
• Ensembl ID: ENSG00000187569
• Aliases: DPPA3, STELLA
• Description: developmental pluripotency associated 3 [Source:HGNC Symbol;Acc:19199]

Sequence

>retro_hsap_1618
TCTTCAAAAATGCTCACTGAAGAAAATTCCCAGGACGATTCAGGGGCCTCTCAAAACTTCTGCTCTGAGATGTTGATAAA
GAACCTTAGTAACTTGACTATCAACCCTAGTACCAAATTCTCTTCCCCTCTACCAGAAGGCTCACCCCAACAACAGTATA
CGGGAGCAATGATCCTCAGGGAAATCAGAGATGACTTGCTTTACAGGAGAAGATTTAAGAACACTCCTGTCTATGCAGAA
AGAAAGGATGGCAAAATTGAGATACCTGTTACTCGGCAGAGTTCCTAGACTTGAACGAGAACTAACAAACACTGGGCTTA
AGGGAGTTCAGAATGAATCAAGAAGTGGACATTTCAGATGCTGCTGCAGTTTCTGCATGTGTAACAGATGGGGTACTTTT
GAGAGTGCTAGAATAGGGAATTACAACACTGAGCCACTTCAGCCA

Alignment

ORF - retro_hsap_1618 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.33 %
• Parental protein coverage: 91.82 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SPQMLTEENSRDDSGASQ-ISSETLIKNLSNLTINASSESVSPLSEALLRRESVGAAVLREIEDEWLYSR
          S..MLTEENS.DDSGASQ...SE.LIKNLSNLTIN.S....SPL.E........GA..LREI.D..LY.R
Retrocopy SSKMLTEENSQDDSGASQNFCSEMLIKNLSNLTINPSTKFSSPLPEGSPQQQYTGAMILREIRDDLLY-R

Parental  R-GVRTLLSVQREKMARLRYMLLGGVRTHERRPTNKEPKGVKKESRP--FKCPCSFCVSNGWDPSENARI
          R...RTLLS.Q.E.MA.LRY.LLG.V...ER..TN...KGV..ESR...F.C.CSFC..N.W...E.ARI
Retrocopy R>DLRTLLSMQKERMAKLRYLLLGRVPRLERELTNTGLKGVQNESRSGHFRCCCSFCMCNRWGTFESARI

Parental  GNQDTKPLQP
          GN..T.PLQP
Retrocopy GNYNTEPLQP

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	0.00 RPM	0.00 RPM
bodymap2_adrenal	0.16 RPM	0.00 RPM
bodymap2_brain	0.07 RPM	0.00 RPM
bodymap2_breast	0.02 RPM	0.00 RPM
bodymap2_colon	0.00 RPM	0.00 RPM
bodymap2_heart	0.07 RPM	0.02 RPM
bodymap2_kidney	0.00 RPM	0.00 RPM
bodymap2_liver	0.00 RPM	0.00 RPM
bodymap2_lung	0.00 RPM	0.00 RPM
bodymap2_lymph_node	0.00 RPM	0.00 RPM
bodymap2_ovary	0.08 RPM	0.00 RPM
bodymap2_prostate	0.00 RPM	0.00 RPM
bodymap2_skeletal_muscle	0.00 RPM	0.00 RPM
bodymap2_testis	0.00 RPM	0.47 RPM
bodymap2_thyroid	0.15 RPM	0.00 RPM
bodymap2_white_blood_cells	0.00 RPM	0.00 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_1618 was not detected

EST

No EST(s) were mapped for retro_hsap_1618 retrocopy.

TSS

No TSS is located nearby retro_hsap_1618 retrocopy 5' end.

Lab

retro_hsap_1618 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_1618 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_1085
Pongo abelii	retro_pabe_1338

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 58 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000046609	1 retrocopy	retro_btau_1001,
Canis familiaris	ENSCAFG00000032092	1 retrocopy	retro_cfam_1926,
Callithrix jacchus	ENSCJAG00000005409	10 retrocopies	retro_cjac_1329, retro_cjac_1446, retro_cjac_1465, retro_cjac_1474, retro_cjac_2052, retro_cjac_2628, retro_cjac_3162, retro_cjac_4006, retro_cjac_622, retro_cjac_730,
Homo sapiens	ENSG00000187569	6 retrocopies	retro_hsap_1043, retro_hsap_1323, retro_hsap_1618 , retro_hsap_2648, retro_hsap_4010, retro_hsap_4887,
Gorilla gorilla	ENSGGOG00000013040	4 retrocopies	retro_ggor_1849, retro_ggor_2693, retro_ggor_3052, retro_ggor_823,
Mustela putorius furo	ENSMPUG00000017530	3 retrocopies	retro_mputfur_1220, retro_mputfur_1452, retro_mputfur_520,
Mus musculus	ENSMUSG00000046323	4 retrocopies	retro_mmus_1186, retro_mmus_1682, retro_mmus_1838, retro_mmus_3598,
Nomascus leucogenys	ENSNLEG00000026887	2 retrocopies	retro_nleu_2041, retro_nleu_914,
Otolemur garnettii	ENSOGAG00000024813	7 retrocopies	retro_ogar_1514, retro_ogar_1618, retro_ogar_1775, retro_ogar_1780, retro_ogar_1964, retro_ogar_2538, retro_ogar_3406,
Pongo abelii	ENSPPYG00000004230	6 retrocopies	retro_pabe_1338, retro_pabe_1962, retro_pabe_2323, retro_pabe_3586, retro_pabe_873, retro_pabe_975,
Pan troglodytes	ENSPTRG00000004617	7 retrocopies	retro_ptro_1085, retro_ptro_1783, retro_ptro_2701, retro_ptro_2722, retro_ptro_3148, retro_ptro_711, retro_ptro_904,
Rattus norvegicus	ENSRNOG00000022950	4 retrocopies	retro_rnor_1249, retro_rnor_1816, retro_rnor_2234, retro_rnor_395,
Tursiops truncatus	ENSTTRG00000000751	3 retrocopies	retro_ttru_1293, retro_ttru_1911, retro_ttru_84,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.02 RPM
CEU_NA11843	0.00 RPM
CEU_NA11930	0.03 RPM
CEU_NA12004	0.00 RPM
CEU_NA12400	0.00 RPM
CEU_NA12751	0.02 RPM
CEU_NA12760	0.00 RPM
CEU_NA12827	0.05 RPM
CEU_NA12872	0.00 RPM
CEU_NA12873	0.00 RPM
FIN_HG00183	0.03 RPM
FIN_HG00277	0.00 RPM
FIN_HG00315	0.00 RPM
FIN_HG00321	0.03 RPM
FIN_HG00328	0.00 RPM
FIN_HG00338	0.02 RPM
FIN_HG00349	0.00 RPM
FIN_HG00375	0.02 RPM
FIN_HG00377	0.00 RPM
FIN_HG00378	0.00 RPM
GBR_HG00099	0.00 RPM
GBR_HG00111	0.00 RPM
GBR_HG00114	0.03 RPM
GBR_HG00119	0.02 RPM
GBR_HG00131	0.03 RPM
GBR_HG00133	0.05 RPM
GBR_HG00134	0.04 RPM
GBR_HG00137	0.03 RPM
GBR_HG00142	0.03 RPM
GBR_HG00143	0.00 RPM
TSI_NA20512	0.03 RPM
TSI_NA20513	0.02 RPM
TSI_NA20518	0.00 RPM
TSI_NA20532	0.03 RPM
TSI_NA20538	0.05 RPM
TSI_NA20756	0.00 RPM
TSI_NA20765	0.02 RPM
TSI_NA20771	0.00 RPM
TSI_NA20786	0.00 RPM
TSI_NA20798	0.00 RPM
YRI_NA18870	0.00 RPM
YRI_NA18907	0.00 RPM
YRI_NA18916	0.02 RPM
YRI_NA19093	0.03 RPM
YRI_NA19099	0.00 RPM
YRI_NA19114	0.03 RPM
YRI_NA19118	0.00 RPM
YRI_NA19213	0.02 RPM
YRI_NA19214	0.00 RPM
YRI_NA19223	0.08 RPM

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Indel association:

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