RetrogeneDB ID: retro_hsap_2011

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 19:53945115..53945857(+)
• Located in intron of: ENSG00000160336

Retrocopy information

• Ensembl ID: ENSG00000241015
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: TPM3
• Ensembl ID: ENSG00000143549
• Aliases: TPM3, CAPM1, CFTD, HEL-189, HEL-S-82p, NEM1, OK/SW-cl.5, TM-5, TM3, TM30, TM30nm, TM5, TPMsk3, TRK, hscp30
• Description: tropomyosin 3 [Source:HGNC Symbol;Acc:12012]

Sequence

>retro_hsap_2011
ATGGCTGGGATCACCACCATCGAGGCAGTGAAGCGCAAGATCCAGGTTCTGCAGCACCAGGCAGATGATGCAGAGGAGTG
AGCTGAGCACCTCCAGTGAGAAGCTGAGGGAAAAAGGTGGGCCTGGGAACAGGCAGAGGCTGAAGTGGCCTCCGTGAACG
GTAGGATCCAGCTGGTTGAAGAGGAGCTGGACTGTGCTCAGGAGCGCCTGGCCACTGCCCTGCAAAAGCTGGAAGAAGCG
GGAAAAGCTGCTGATGAGAGTGAGAGAGATACAAAGGTTATTGAAATCTGGGCCTTAAAAGATGAAGAAGATGGAACTCC
AGGAAATCCAACTCAAAGAAGCTAAGCACATTGCAGATGAGGCAGATGGGAAGTATGAAGAGGTGGCTCGTAAGTTGGTG
ATCATTGAAGGAGACATGGGATGCACAGAGGAACGAGCTGAGCTGGCAGAGTCCCGTTGCTGAGAGATGGATGAGCAGAT
CAGACTGATGGACCAGAACCTGAAGTGTCTGAGTGCAGCTGAAGAAAAGTACTCTCAAAAAGAAGACAAATGTGAGGAAG
AGATGAAGATTCTTACTGATAATCTCAAGGAGGCAGAGACCCATGCTGAGTTGGCTGAGAGATCAGTAGCCAAGCTGGAA
AAGACAATTGATGACTTGGAAGATAAACTGAAATGCACCAAAGAGGAACACCTCTGTACACAAAGGATGCTGGACCAGAC
TTTGCTTGACCTGAATGAGATG

Alignment

ORF - retro_hsap_2011 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.2 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAGITTIEAVKRKIQVLQQQADDAEERAERLQREVEGERRAREQAEAEVASLNRRIQLVEEELDRAQERL
          MAGITTIEAVKRKIQVLQ.QADDAEE.AE.LQ.E.EG.R.A.EQAEAEVAS.N.RIQLVEEELD.AQERL
Retrocopy MAGITTIEAVKRKIQVLQHQADDAEE*AEHLQ*EAEGKRWAWEQAEAEVASVNGRIQLVEEELDCAQERL

Parental  ATALQKLEEAEKAADESERGMKVIE-NRALK-DEEKMELQEIQLKEAKHIAEEADRKYEEVARKLVIIEG
          ATALQKLEEA.KAADESER..KVIE.N..LK....KMELQEIQLKEAKHIA.EAD.KYEEVARKLVIIEG
Retrocopy ATALQKLEEAGKAADESERDTKVIE<NLGLK<KMKKMELQEIQLKEAKHIADEADGKYEEVARKLVIIEG

Parental  DLERTEERAELAESRCREMDEQIRLMDQNLKCLSAAEEKYSQKEDKYEEEIKILTDKLKEAETRAEFAER
          D...TEERAELAESRC.EMDEQIRLMDQNLKCLSAAEEKYSQKEDK.EEE.KILTD.LKEAET.AE.AER
Retrocopy DMGCTEERAELAESRC*EMDEQIRLMDQNLKCLSAAEEKYSQKEDKCEEEMKILTDNLKEAETHAELAER

Parental  SVAKLEKTIDDLEDKLKCTKEEHLCTQRMLDQTLLDLNEM
          SVAKLEKTIDDLEDKLKCTKEEHLCTQRMLDQTLLDLNEM
Retrocopy SVAKLEKTIDDLEDKLKCTKEEHLCTQRMLDQTLLDLNEM

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	1.21 RPM	404.93 RPM
bodymap2_adrenal	2.80 RPM	369.51 RPM
bodymap2_brain	1.03 RPM	214.17 RPM
bodymap2_breast	0.68 RPM	275.26 RPM
bodymap2_colon	0.79 RPM	177.60 RPM
bodymap2_heart	0.41 RPM	174.40 RPM
bodymap2_kidney	2.54 RPM	210.94 RPM
bodymap2_liver	0.49 RPM	92.56 RPM
bodymap2_lung	1.32 RPM	466.61 RPM
bodymap2_lymph_node	1.75 RPM	264.49 RPM
bodymap2_ovary	0.94 RPM	156.91 RPM
bodymap2_prostate	3.46 RPM	137.16 RPM
bodymap2_skeletal_muscle	0.13 RPM	495.87 RPM
bodymap2_testis	0.94 RPM	238.91 RPM
bodymap2_thyroid	1.22 RPM	446.09 RPM
bodymap2_white_blood_cells	1.40 RPM	781.04 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_2011 was not detected

EST

No EST(s) were mapped for retro_hsap_2011 retrocopy.

TSS

No TSS is located nearby retro_hsap_2011 retrocopy 5' end.

Lab

• Experiment type: PCR amplification
• Forward primer: ACCAGGCAGATGATGCAGAGGAGT (24 nt long)
• Reverse primer: TCGTTCCTCTGTGCATCCCAT (21 nt long)
• Anneling temperature: 60 °C
• (Expected) product size: 381
• Electrophoresis gel image:
• Additional comment: Black arrows indicate PCR products of retrogenes undergoing deletions in various human populations (A-J). Lane 1 –GeneRuler Low Range DNA Ladder (Thermo Scientific); 2 –Heart; 3 –Brain; 4 –Placenta; 5 –Lung; 6 –Liver; 7 –Skeletal Muscle; 8 –Kidney; 9 –Pancreas; 10 –Spleen; 11 –Thymus; 12 –Prostate; 13 –Testis; 14 –Ovary, 15 –Small intestine 16 –Colon; 17 –Leukocyte; NTC—No template control (water instead of cDNA).

Homology

Retrocopy orthology:

Retrocopy retro_hsap_2011 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 45 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011877	2 retrocopies	retro_amel_1017, retro_amel_1212,
Bos taurus	ENSBTAG00000033217	3 retrocopies	retro_btau_1166, retro_btau_210, retro_btau_933,
Canis familiaris	ENSCAFG00000017311	4 retrocopies	retro_cfam_1278, retro_cfam_1678, retro_cfam_2089, retro_cfam_983,
Cavia porcellus	ENSCPOG00000007279	1 retrocopy	retro_cpor_150,
Dasypus novemcinctus	ENSDNOG00000019156	7 retrocopies	retro_dnov_1322, retro_dnov_1767, retro_dnov_329, retro_dnov_451, retro_dnov_848, retro_dnov_878, retro_dnov_944,
Equus caballus	ENSECAG00000010942	1 retrocopy	retro_ecab_390,
Felis catus	ENSFCAG00000012596	1 retrocopy	retro_fcat_1441,
Homo sapiens	ENSG00000143549	9 retrocopies	retro_hsap_1482, retro_hsap_1639, retro_hsap_2001, retro_hsap_2011 , retro_hsap_2012, retro_hsap_2237, retro_hsap_2395, retro_hsap_3711, retro_hsap_3893,
Homo sapiens	ENSG00000167460	2 retrocopies	retro_hsap_2623, retro_hsap_3969,
Myotis lucifugus	ENSMLUG00000013331	1 retrocopy	retro_mluc_1038,
Macaca mulatta	ENSMMUG00000010805	10 retrocopies	retro_mmul_1019, retro_mmul_1240, retro_mmul_1384, retro_mmul_1385, retro_mmul_1703, retro_mmul_1829, retro_mmul_2128, retro_mmul_2354, retro_mmul_314, retro_mmul_880,
Mustela putorius furo	ENSMPUG00000007875	1 retrocopy	retro_mputfur_604,
Mus musculus	ENSMUSG00000027940	1 retrocopy	retro_mmus_21,
Oryctolagus cuniculus	ENSOCUG00000011821	2 retrocopies	retro_ocun_699, retro_ocun_8,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	3.04 RPM
CEU_NA11843	5.32 RPM
CEU_NA11930	3.29 RPM
CEU_NA12004	4.37 RPM
CEU_NA12400	4.59 RPM
CEU_NA12751	5.71 RPM
CEU_NA12760	4.54 RPM
CEU_NA12827	3.73 RPM
CEU_NA12872	3.59 RPM
CEU_NA12873	4.56 RPM
FIN_HG00183	3.18 RPM
FIN_HG00277	3.55 RPM
FIN_HG00315	5.60 RPM
FIN_HG00321	5.44 RPM
FIN_HG00328	2.89 RPM
FIN_HG00338	2.11 RPM
FIN_HG00349	3.10 RPM
FIN_HG00375	4.28 RPM
FIN_HG00377	3.35 RPM
FIN_HG00378	3.46 RPM
GBR_HG00099	3.37 RPM
GBR_HG00111	2.84 RPM
GBR_HG00114	3.31 RPM
GBR_HG00119	3.62 RPM
GBR_HG00131	3.71 RPM
GBR_HG00133	3.67 RPM
GBR_HG00134	4.02 RPM
GBR_HG00137	5.75 RPM
GBR_HG00142	3.11 RPM
GBR_HG00143	2.52 RPM
TSI_NA20512	2.32 RPM
TSI_NA20513	8.25 RPM
TSI_NA20518	4.66 RPM
TSI_NA20532	6.60 RPM
TSI_NA20538	2.99 RPM
TSI_NA20756	3.35 RPM
TSI_NA20765	3.75 RPM
TSI_NA20771	3.09 RPM
TSI_NA20786	3.45 RPM
TSI_NA20798	3.59 RPM
YRI_NA18870	5.25 RPM
YRI_NA18907	5.20 RPM
YRI_NA18916	3.73 RPM
YRI_NA19093	2.50 RPM
YRI_NA19099	2.90 RPM
YRI_NA19114	2.78 RPM
YRI_NA19118	3.85 RPM
YRI_NA19213	2.94 RPM
YRI_NA19214	5.14 RPM
YRI_NA19223	4.74 RPM

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Indel association:

The presence of retro_hsap_2011 across human populations is associated with 1 indel. The percentage values indicate the frequencies of retro_hsap_2011 presence in various populations. Based on Kabza et al. 2015 (PubMed).

#	Indel coordinates	AFR, African			AMR, Ad Mixed American			EUR, European					EAS, East Asian
		ASW	YRI	LWK	MXL	PUR	CLM	CEU	IBS	GBR	FIN	TSI	JPT	CHB	CHS
1.	19:53936258..53973000	100	100	100	100	100	100	100	100	100	98.92	100	100	100	100

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Indel #1, located at the genomic coordinates 19:53936258..53973000.