RetrogeneDB ID: retro_hsap_1479

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 15:35529526..35530024(+)
• Located in intron of: ENSG00000134146

Retrocopy information

• Ensembl ID: ENSG00000259516
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: ANP32A
• Ensembl ID: ENSG00000140350
• Aliases: ANP32A, C15orf1, HPPCn, I1PP2A, LANP, MAPM, PHAP1, PHAPI, PP32
• Description: acidic (leucine-rich) nuclear phosphoprotein 32 family, member A [Source:HGNC Symbol;Acc:13233]

Sequence

>retro_hsap_1479
ATGAAGATGGGCAGACGGATTCATTTAGAGCTGCGGAACAGGACGCCCTCTGATGTGAAAGAACTTGTCCTGGACAACAG
TCGGTCGAATGAAGGCAAACTCGAAGGCCTCACAGATGAATCTGAATAACTGGAATTCTTCAGTGCAACCAACGTAGGCC
TCACCTCAACTGCAAACTTACCGAAGTTAAACAAACTTAAGAAGCTTGAACTAAGCGATAACAGAGTCTCGGGGGGCGTG
GAAGCATTGGCAGAAAAGTGTCCGAACCTCACGCATCTAAATTTATGTGGCAACAAAATTAAAGACCTCAGCACAACAGA
GCCACTGAAAAACTTAGAAAACCTCAAGAGCTTAGACCTTTTCAATTGCGAGGTAACCAACCTGAACGACTACCGAGAAA
ATGTGTTCAAGCTCCTCCTGCAACTCACATATCTTGACGGCTATGACCGGGACGACAAGGAGGCCCCTAACTTGGATGCT
GAGGGCTACGTGGAGGGC

Alignment

ORF - retro_hsap_1479 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.96 %
• Parental protein coverage: 93.79 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MEMGRRIHLELRNRTPSDVKELVLDNSRSNEGKLEGLTDEFEELEFLSTINVGLTSIANLPKLNKLKKLE
          M.MGRRIHLELRNRTPSDVKELVLDNSRSNEGKLEGLTDE.E.LEF.S..NVGLTS.ANLPKLNKLKKLE
Retrocopy MKMGRRIHLELRNRTPSDVKELVLDNSRSNEGKLEGLTDESE*LEFFSATNVGLTSTANLPKLNKLKKLE

Parental  LSDNRVSGGLEVLAEKCPNLTHLNLSGNKIKDLSTIEPLKKLENLKSLDLFNCEVTNLNDYRENVFKLLP
          LSDNRVSGG.E.LAEKCPNLTHLNL.GNKIKDLST.EPLK.LENLKSLDLFNCEVTNLNDYRENVFKLL.
Retrocopy LSDNRVSGGVEALAEKCPNLTHLNLCGNKIKDLSTTEPLKNLENLKSLDLFNCEVTNLNDYRENVFKLLL

Parental  QLTYLDGYDRDDKEAPDSDAEGYVEG
          QLTYLDGYDRDDKEAP..DAEGYVEG
Retrocopy QLTYLDGYDRDDKEAPNLDAEGYVEG

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	111.28 RPM
bodymap2_adrenal	0.02 RPM	103.21 RPM
bodymap2_brain	0.07 RPM	120.25 RPM
bodymap2_breast	0.00 RPM	89.85 RPM
bodymap2_colon	0.04 RPM	129.99 RPM
bodymap2_heart	0.06 RPM	62.14 RPM
bodymap2_kidney	0.04 RPM	94.65 RPM
bodymap2_liver	0.04 RPM	50.51 RPM
bodymap2_lung	0.00 RPM	102.99 RPM
bodymap2_lymph_node	0.00 RPM	104.69 RPM
bodymap2_ovary	0.08 RPM	131.20 RPM
bodymap2_prostate	0.00 RPM	104.99 RPM
bodymap2_skeletal_muscle	0.00 RPM	55.73 RPM
bodymap2_testis	0.02 RPM	62.52 RPM
bodymap2_thyroid	0.00 RPM	107.56 RPM
bodymap2_white_blood_cells	0.00 RPM	222.89 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_1479 was not detected

EST

No EST(s) were mapped for retro_hsap_1479 retrocopy.

TSS

No TSS is located nearby retro_hsap_1479 retrocopy 5' end.

Lab

retro_hsap_1479 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_1479 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pongo abelii	retro_pabe_210

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000002339	2 retrocopies	retro_cjac_3305, retro_cjac_3799,
Dasypus novemcinctus	ENSDNOG00000015360	5 retrocopies	retro_dnov_1199, retro_dnov_1250, retro_dnov_1696, retro_dnov_836, retro_dnov_956,
Dipodomys ordii	ENSDORG00000008611	1 retrocopy	retro_dord_240,
Felis catus	ENSFCAG00000015773	1 retrocopy	retro_fcat_1188,
Homo sapiens	ENSG00000136938	2 retrocopies	retro_hsap_1597, retro_hsap_1603,
Homo sapiens	ENSG00000140350	3 retrocopies	retro_hsap_1479 , retro_hsap_3117, retro_hsap_48,
Gorilla gorilla	ENSGGOG00000015417	1 retrocopy	retro_ggor_1134,
Loxodonta africana	ENSLAFG00000022560	1 retrocopy	retro_lafr_679,
Nomascus leucogenys	ENSNLEG00000013347	2 retrocopies	retro_nleu_15, retro_nleu_2383,
Otolemur garnettii	ENSOGAG00000003058	1 retrocopy	retro_ogar_2596,
Ochotona princeps	ENSOPRG00000015394	2 retrocopies	retro_opri_302, retro_opri_563,
Pan troglodytes	ENSPTRG00000007219	2 retrocopies	retro_ptro_2108, retro_ptro_758,
Rattus norvegicus	ENSRNOG00000045651	1 retrocopy	retro_rnor_1043,
Sarcophilus harrisii	ENSSHAG00000010906	1 retrocopy	retro_shar_540,
Tupaia belangeri	ENSTBEG00000016417	2 retrocopies	retro_tbel_4078, retro_tbel_4595,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.02 RPM
CEU_NA11843	0.00 RPM
CEU_NA11930	0.00 RPM
CEU_NA12004	0.00 RPM
CEU_NA12400	0.00 RPM
CEU_NA12751	0.00 RPM
CEU_NA12760	0.09 RPM
CEU_NA12827	0.05 RPM
CEU_NA12872	0.00 RPM
CEU_NA12873	0.00 RPM
FIN_HG00183	0.82 RPM
FIN_HG00277	0.04 RPM
FIN_HG00315	0.03 RPM
FIN_HG00321	0.09 RPM
FIN_HG00328	0.00 RPM
FIN_HG00338	0.02 RPM
FIN_HG00349	0.00 RPM
FIN_HG00375	0.02 RPM
FIN_HG00377	0.03 RPM
FIN_HG00378	0.02 RPM
GBR_HG00099	0.06 RPM
GBR_HG00111	0.02 RPM
GBR_HG00114	0.03 RPM
GBR_HG00119	0.00 RPM
GBR_HG00131	0.00 RPM
GBR_HG00133	0.00 RPM
GBR_HG00134	0.02 RPM
GBR_HG00137	0.03 RPM
GBR_HG00142	0.06 RPM
GBR_HG00143	0.00 RPM
TSI_NA20512	0.00 RPM
TSI_NA20513	0.02 RPM
TSI_NA20518	0.11 RPM
TSI_NA20532	0.03 RPM
TSI_NA20538	0.00 RPM
TSI_NA20756	0.06 RPM
TSI_NA20765	0.06 RPM
TSI_NA20771	0.00 RPM
TSI_NA20786	0.00 RPM
TSI_NA20798	0.00 RPM
YRI_NA18870	0.07 RPM
YRI_NA18907	0.03 RPM
YRI_NA18916	0.04 RPM
YRI_NA19093	0.00 RPM
YRI_NA19099	0.05 RPM
YRI_NA19114	0.00 RPM
YRI_NA19118	0.00 RPM
YRI_NA19213	0.00 RPM
YRI_NA19214	0.00 RPM
YRI_NA19223	0.00 RPM

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Indel association:

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