RetrogeneDB ID: retro_hsap_3075

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 4:110474497..110475250(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000225094
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SET
• Ensembl ID: ENSG00000119335
• Aliases: SET, 2PP2A, I2PP2A, IGAAD, IPP2A2, PHAPII, TAF-I, TAF-IBETA
• Description: SET nuclear oncogene [Source:HGNC Symbol;Acc:10760]

Sequence

>retro_hsap_3075
CTGGCCCCCAAATGCCAGTCTTCCCTCCTGTCTCGAAAGAAGACACCAAGACCACCTCCTGTTCTGAGACCAGAGGAGAC
TTCGGCCTCTGTAGGCTTGCCAAAGAAGGGCGAAAAAGAACAGCAAGAAGCAATTGAACACATTGATGAAATACAAAATG
AAATAGACAGACTTAATGAACAAGACAATGAGGAGATTTTGAAAGTAGAACAGAAATATAACAAACTCCGCCAACCATTT
TTTCAGAAGAGGTCAGAATTGATCTCTAAAATCCTAAATTTGGGGGTAACAACATTTGGCAATCATTTACAAGTGTCTGC
ACTGCTTGGGAAGGAAAACGAAGAGACATTGCATTATTTGACCAGAGTTGAAGTGACAGAATTTGAAGATATTAAATCAG
GTTACAGAGTAGATTTTTATTTTGATGAAAATCCTTACTTTGAAAATAAAGTTCTCTCCAAAGAATTTCATCTGAATGAG
AGTGGTAATCCATCTTCAAAATCCACTGAAATCAAATGGAAATCTGGAAAGGATGTGACGAAACGTTTAAGTCAAATGCA
GAATAAAGCCAGCAGGAAGAGGCAGCATGAGGCACCAGAGAGCTTCTTGACCTGGTTTACTGACCATTCTGATGCAGGGG
CCGATGACTTAGGAGAGGACATCAAAGATGATATTTGGCCAAACCCATTACAGTACTACTTGGTTCCCCATATGGATGAT
GAAGAAGGAGAAGATGATAATGAGGAGGAGGAG

Alignment

ORF - retro_hsap_3075 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.1 %
• Parental protein coverage: 87.93 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAPKRQSPLPPQKKKPRPPPALGPEETSASAGLPKKGEKEQQEAIEHIDEVQNEIDRLNEQASEEILKVE
          .APK.QS.L...KK.PRPPP.L.PEETSAS.GLPKKGEKEQQEAIEHIDE.QNEIDRLNEQ..EEILKVE
Retrocopy LAPKCQSSLLSRKKTPRPPPVLRPEETSASVGLPKKGEKEQQEAIEHIDEIQNEIDRLNEQDNEEILKVE

Parental  QKYNKLRQPFFQKRSELIAKIPNFWVTTFVNHPQVSALLGEEDEEALHYLTRVEVTEFEDIKSGYRIDFY
          QKYNKLRQPFFQKRSELI.KI.N..VTTF.NH.QVSALLG.E.EE.LHYLTRVEVTEFEDIKSGYR.DFY
Retrocopy QKYNKLRQPFFQKRSELISKILNLGVTTFGNHLQVSALLGKENEETLHYLTRVEVTEFEDIKSGYRVDFY

Parental  FDENPYFENKVLSKEFHLNESGDPSSKSTEIKWKSGKDLTKRSSQTQNKASRKRQHEEPESFFTWFTDHS
          FDENPYFENKVLSKEFHLNESG.PSSKSTEIKWKSGKD.TKR.SQ.QNKASRKRQHE.PESF.TWFTDHS
Retrocopy FDENPYFENKVLSKEFHLNESGNPSSKSTEIKWKSGKDVTKRLSQMQNKASRKRQHEAPESFLTWFTDHS

Parental  DAGADELGEVIKDDIWPNPLQYYLVPDMDDEEGEGEEDDDDDEEE
          DAGAD.LGE.IKDDIWPNPLQYYLVP.MDDEEGE....DD..EEE
Retrocopy DAGADDLGEDIKDDIWPNPLQYYLVPHMDDEEGE----DDNEEEE

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	278.75 RPM
bodymap2_adrenal	0.04 RPM	304.11 RPM
bodymap2_brain	0.05 RPM	228.68 RPM
bodymap2_breast	0.00 RPM	196.89 RPM
bodymap2_colon	0.02 RPM	411.87 RPM
bodymap2_heart	0.04 RPM	153.49 RPM
bodymap2_kidney	0.12 RPM	226.29 RPM
bodymap2_liver	0.00 RPM	103.30 RPM
bodymap2_lung	0.21 RPM	285.23 RPM
bodymap2_lymph_node	0.15 RPM	229.77 RPM
bodymap2_ovary	0.21 RPM	454.22 RPM
bodymap2_prostate	0.00 RPM	279.46 RPM
bodymap2_skeletal_muscle	0.00 RPM	293.35 RPM
bodymap2_testis	0.08 RPM	324.90 RPM
bodymap2_thyroid	0.08 RPM	345.95 RPM
bodymap2_white_blood_cells	0.08 RPM	357.77 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_hsap_3075 was not detected

EST

No EST(s) were mapped for retro_hsap_3075 retrocopy.

TSS

No TSS is located nearby retro_hsap_3075 retrocopy 5' end.

Lab

retro_hsap_3075 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_3075 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_2073
Pongo abelii	retro_pabe_2549

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 117 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000015686	7 retrocopies	retro_amel_1093, retro_amel_1201, retro_amel_1459, retro_amel_1675, retro_amel_530, retro_amel_631, retro_amel_634,
Bos taurus	ENSBTAG00000020959	8 retrocopies	retro_btau_1179, retro_btau_1490, retro_btau_1519, retro_btau_1556, retro_btau_464, retro_btau_469, retro_btau_749, retro_btau_955,
Canis familiaris	ENSCAFG00000032728	2 retrocopies	retro_cfam_47, retro_cfam_83,
Felis catus	ENSFCAG00000005848	2 retrocopies	retro_fcat_130, retro_fcat_89,
Homo sapiens	ENSG00000119335	14 retrocopies	retro_hsap_1336, retro_hsap_1389, retro_hsap_1847, retro_hsap_241, retro_hsap_269, retro_hsap_2719, retro_hsap_2721, retro_hsap_3075 , retro_hsap_3088, retro_hsap_3326, retro_hsap_3358, retro_hsap_420, retro_hsap_4722, retro_hsap_806,
Myotis lucifugus	ENSMLUG00000014291	13 retrocopies	retro_mluc_1026, retro_mluc_1120, retro_mluc_1673, retro_mluc_1977, retro_mluc_2098, retro_mluc_2188, retro_mluc_2361, retro_mluc_2412, retro_mluc_2584, retro_mluc_419, retro_mluc_524, retro_mluc_855, retro_mluc_881,
Macaca mulatta	ENSMMUG00000008532	11 retrocopies	retro_mmul_1133, retro_mmul_1261, retro_mmul_1534, retro_mmul_2096, retro_mmul_2175, retro_mmul_2241, retro_mmul_2262, retro_mmul_2614, retro_mmul_362, retro_mmul_419, retro_mmul_569,
Mustela putorius furo	ENSMPUG00000013069	10 retrocopies	retro_mputfur_1330, retro_mputfur_1556, retro_mputfur_1581, retro_mputfur_1605, retro_mputfur_221, retro_mputfur_274, retro_mputfur_286, retro_mputfur_723, retro_mputfur_785, retro_mputfur_799,
Nomascus leucogenys	ENSNLEG00000017595	2 retrocopies	retro_nleu_108, retro_nleu_870,
Oryctolagus cuniculus	ENSOCUG00000007501	12 retrocopies	retro_ocun_1107, retro_ocun_1110, retro_ocun_1234, retro_ocun_1311, retro_ocun_1563, retro_ocun_276, retro_ocun_407, retro_ocun_421, retro_ocun_423, retro_ocun_476, retro_ocun_859, retro_ocun_923,
Otolemur garnettii	ENSOGAG00000007635	13 retrocopies	retro_ogar_115, retro_ogar_1370, retro_ogar_3084, retro_ogar_3186, retro_ogar_3195, retro_ogar_3289, retro_ogar_447, retro_ogar_465, retro_ogar_543, retro_ogar_565, retro_ogar_806, retro_ogar_899, retro_ogar_934,
Pongo abelii	ENSPPYG00000019659	17 retrocopies	retro_pabe_1076, retro_pabe_1110, retro_pabe_1150, retro_pabe_1218, retro_pabe_1452, retro_pabe_1717, retro_pabe_1771, retro_pabe_2549, retro_pabe_2557, retro_pabe_2740, retro_pabe_299, retro_pabe_3667, retro_pabe_400, retro_pabe_414, retro_pabe_470, retro_pabe_720, retro_pabe_838,
Ictidomys tridecemlineatus	ENSSTOG00000010546	6 retrocopies	retro_itri_1204, retro_itri_1588, retro_itri_477, retro_itri_529, retro_itri_603, retro_itri_876,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.02 RPM
CEU_NA11843	0.09 RPM
CEU_NA11930	0.16 RPM
CEU_NA12004	0.08 RPM
CEU_NA12400	0.11 RPM
CEU_NA12751	0.02 RPM
CEU_NA12760	0.00 RPM
CEU_NA12827	0.19 RPM
CEU_NA12872	0.14 RPM
CEU_NA12873	0.10 RPM
FIN_HG00183	0.25 RPM
FIN_HG00277	0.11 RPM
FIN_HG00315	0.06 RPM
FIN_HG00321	0.09 RPM
FIN_HG00328	0.21 RPM
FIN_HG00338	0.04 RPM
FIN_HG00349	0.00 RPM
FIN_HG00375	0.02 RPM
FIN_HG00377	0.05 RPM
FIN_HG00378	0.00 RPM
GBR_HG00099	0.12 RPM
GBR_HG00111	0.11 RPM
GBR_HG00114	0.03 RPM
GBR_HG00119	0.22 RPM
GBR_HG00131	0.06 RPM
GBR_HG00133	0.12 RPM
GBR_HG00134	0.09 RPM
GBR_HG00137	0.03 RPM
GBR_HG00142	0.19 RPM
GBR_HG00143	0.00 RPM
TSI_NA20512	0.06 RPM
TSI_NA20513	0.00 RPM
TSI_NA20518	0.06 RPM
TSI_NA20532	0.14 RPM
TSI_NA20538	0.14 RPM
TSI_NA20756	0.03 RPM
TSI_NA20765	0.10 RPM
TSI_NA20771	0.03 RPM
TSI_NA20786	0.08 RPM
TSI_NA20798	0.06 RPM
YRI_NA18870	0.03 RPM
YRI_NA18907	0.07 RPM
YRI_NA18916	0.06 RPM
YRI_NA19093	0.03 RPM
YRI_NA19099	0.08 RPM
YRI_NA19114	0.05 RPM
YRI_NA19118	0.12 RPM
YRI_NA19213	0.12 RPM
YRI_NA19214	0.02 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).