RetrogeneDB ID: retro_hsap_1849

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 17:58179597..58179942(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: AP1S2
• Ensembl ID: ENSG00000182287
• Aliases: AP1S2, MGC:1902, MRX59, MRXS21, MRXS5, MRXSF, PGS, SIGMA1B
• Description: adaptor-related protein complex 1, sigma 2 subunit [Source:HGNC Symbol;Acc:560]

Sequence

>retro_hsap_1849
AAAAAGATCACAAGAGAACTTGTTCAGACCGTTTTAGCACGGAAACCTAAAATGTGCAGCTTCCTTGAGTGGCGAGATCT
GAAGATTGTTTACAAAAGATATGCTAGTCTGTATTTTTGCTGTGCTATTGAGGATCAGGACAATGAACTAATTACCCTGG
AAATAATTCATCGTTATGTGGAATTACTTGACAAGTATTTCGGCAGTGTCTGTGAACTAGATATCATCTTTAATTTTGAG
AAGGCTTATTTTATTTTGGATGAGTTTCTTTTGGGAGGGGAAGTTCAGGAAACATCCAAGAAAAATGTCCTTAAAGCAAT
TGAGCAGGCCGATCTACTGCAGGAG

Alignment

ORF - retro_hsap_1849 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 100. %
• Parental protein coverage: 75.16 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KKITRELVQTVLARKPKMCSFLEWRDLKIVYKRYASLYFCCAIEDQDNELITLEIIHRYVELLDKYFGSV
          KKITRELVQTVLARKPKMCSFLEWRDLKIVYKRYASLYFCCAIEDQDNELITLEIIHRYVELLDKYFGSV
Retrocopy KKITRELVQTVLARKPKMCSFLEWRDLKIVYKRYASLYFCCAIEDQDNELITLEIIHRYVELLDKYFGSV

Parental  CELDIIFNFEKAYFILDEFLLGGEVQETSKKNVLKAIEQADLLQE
          CELDIIFNFEKAYFILDEFLLGGEVQETSKKNVLKAIEQADLLQE
Retrocopy CELDIIFNFEKAYFILDEFLLGGEVQETSKKNVLKAIEQADLLQE

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	0.02 RPM	56.49 RPM
bodymap2_adrenal	0.02 RPM	51.93 RPM
bodymap2_brain	0.05 RPM	71.49 RPM
bodymap2_breast	0.14 RPM	44.09 RPM
bodymap2_colon	0.08 RPM	105.96 RPM
bodymap2_heart	0.06 RPM	130.50 RPM
bodymap2_kidney	0.14 RPM	31.99 RPM
bodymap2_liver	0.00 RPM	9.89 RPM
bodymap2_lung	0.00 RPM	36.87 RPM
bodymap2_lymph_node	0.04 RPM	66.97 RPM
bodymap2_ovary	0.02 RPM	36.36 RPM
bodymap2_prostate	0.00 RPM	47.86 RPM
bodymap2_skeletal_muscle	0.05 RPM	64.95 RPM
bodymap2_testis	0.04 RPM	121.00 RPM
bodymap2_thyroid	0.00 RPM	60.41 RPM
bodymap2_white_blood_cells	0.22 RPM	350.15 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_1849 was not detected

EST

No EST(s) were mapped for retro_hsap_1849 retrocopy.

TSS

No TSS is located nearby retro_hsap_1849 retrocopy 5' end.

Lab

retro_hsap_1849 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_1849 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_1234

---

Parental genes homology:

Parental genes homology involve 11 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000004393	1 retrocopy	retro_cjac_2312,
Dasypus novemcinctus	ENSDNOG00000013888	1 retrocopy	retro_dnov_1786,
Homo sapiens	ENSG00000100478	1 retrocopy	retro_hsap_3496,
Homo sapiens	ENSG00000106367	1 retrocopy	retro_hsap_3765,
Homo sapiens	ENSG00000182287	1 retrocopy	retro_hsap_1849 ,
Macaca mulatta	ENSMMUG00000014055	1 retrocopy	retro_mmul_1716,
Monodelphis domestica	ENSMODG00000017197	7 retrocopies	retro_mdom_1189, retro_mdom_1329, retro_mdom_1441, retro_mdom_1470, retro_mdom_1616, retro_mdom_1987, retro_mdom_903,
Otolemur garnettii	ENSOGAG00000011342	3 retrocopies	retro_ogar_2038, retro_ogar_265, retro_ogar_3453,
Procavia capensis	ENSPCAG00000000733	1 retrocopy	retro_pcap_386,
Sarcophilus harrisii	ENSSHAG00000013119	2 retrocopies	retro_shar_651, retro_shar_690,
Ictidomys tridecemlineatus	ENSSTOG00000008517	1 retrocopy	retro_itri_131,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.04 RPM
CEU_NA11843	0.00 RPM
CEU_NA11930	0.07 RPM
CEU_NA12004	0.00 RPM
CEU_NA12400	0.04 RPM
CEU_NA12751	0.05 RPM
CEU_NA12760	0.04 RPM
CEU_NA12827	0.05 RPM
CEU_NA12872	0.05 RPM
CEU_NA12873	0.00 RPM
FIN_HG00183	0.00 RPM
FIN_HG00277	0.07 RPM
FIN_HG00315	0.06 RPM
FIN_HG00321	0.15 RPM
FIN_HG00328	0.05 RPM
FIN_HG00338	0.11 RPM
FIN_HG00349	0.03 RPM
FIN_HG00375	0.05 RPM
FIN_HG00377	0.05 RPM
FIN_HG00378	0.08 RPM
GBR_HG00099	0.12 RPM
GBR_HG00111	0.06 RPM
GBR_HG00114	0.08 RPM
GBR_HG00119	0.02 RPM
GBR_HG00131	0.03 RPM
GBR_HG00133	0.05 RPM
GBR_HG00134	0.11 RPM
GBR_HG00137	0.14 RPM
GBR_HG00142	0.03 RPM
GBR_HG00143	0.00 RPM
TSI_NA20512	0.00 RPM
TSI_NA20513	0.05 RPM
TSI_NA20518	0.53 RPM
TSI_NA20532	0.03 RPM
TSI_NA20538	0.05 RPM
TSI_NA20756	0.09 RPM
TSI_NA20765	0.04 RPM
TSI_NA20771	0.03 RPM
TSI_NA20786	0.03 RPM
TSI_NA20798	0.03 RPM
YRI_NA18870	0.17 RPM
YRI_NA18907	0.00 RPM
YRI_NA18916	0.04 RPM
YRI_NA19093	0.05 RPM
YRI_NA19099	0.03 RPM
YRI_NA19114	0.03 RPM
YRI_NA19118	0.02 RPM
YRI_NA19213	0.05 RPM
YRI_NA19214	0.02 RPM
YRI_NA19223	0.08 RPM

---

Indel association:

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