RetrogeneDB ID: retro_hsap_2533

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 21:45275773..45276201(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000226543
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: MYL6
• Ensembl ID: ENSG00000092841
• Aliases: MYL6, ESMLC, LC17, LC17-GI, LC17-NM, LC17A, LC17B, MLC-3, MLC1SM, MLC3NM, MLC3SM
• Description: myosin, light chain 6, alkali, smooth muscle and non-muscle [Source:HGNC Symbol;Acc:7587]

Sequence

>retro_hsap_2533
AGCACAGAGTTCAAGGCTGCCTTCCGGCTGTTTGACTGAACAGGTGATGGCAAGGTCCTTCCAGCCCCTGTGGGGGCGTG
ATGAGGGCCCTGGGCCAGAACCCCACCAATGCCACGGCGCTCGAGGTCCTGGGGAACCCCAAGAGTGATGAGATGAACGT
GAAGGTGCTGGACTTTGAGCACTTCCTGCCCCTGCTGCAGACAGTGGCAGGGAACAGGGACCAGGGCACCTAAGAGGATT
ATGTGGAAAGACTTCAGGTGTTTGACAAGGAAGAGAATGGCACCGTCATGAGCGCGGAAATCCAGCATGTTCTTGTCTCA
CTGGGTGAGGAGATGACAGAGAGAGGAGGAGAGATGCTGGTGGCAGGGCATGAGGACAGCAGTGGTTGCATTGACTCCGA
AGTGCTTGTCCGCAGGCTGCTGAATGGC

Alignment

ORF - retro_hsap_2533 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.08 %
• Parental protein coverage: 94.7 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  TAEFKEAFQLFDRTGDGKIL-YSQCGDVMRALGQNPTNAEVLKVLGNPKSDEMNVKVLDFEHFLPMLQTV
          ..EFK.AF.LFD.TGDGK.L..S.CG.VMRALGQNPTNA..L.VLGNPKSDEMNVKVLDFEHFLP.LQTV
Retrocopy STEFKAAFRLFD*TGDGKVL<SSPCGGVMRALGQNPTNATALEVLGNPKSDEMNVKVLDFEHFLPLLQTV

Parental  AKNKDQGTYEDYVEGLRVFDKEGNGTVMGAEIRHVLVTLGEKMTEEEVEMLVAGHEDSNGCINYEELVRM
          A.N.DQGT.EDYVE.L.VFDKE.NGTVM.AEI.HVLV.LGE.MTE...EMLVAGHEDS.GCI..E.LVR.
Retrocopy AGNRDQGT*EDYVERLQVFDKEENGTVMSAEIQHVLVSLGEEMTERGGEMLVAGHEDSSGCIDSEVLVRR

Parental  VLNG
          .LNG
Retrocopy LLNG

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	536.57 RPM
bodymap2_adrenal	0.00 RPM	701.04 RPM
bodymap2_brain	0.42 RPM	133.14 RPM
bodymap2_breast	0.00 RPM	645.44 RPM
bodymap2_colon	0.00 RPM	1385.51 RPM
bodymap2_heart	0.00 RPM	131.33 RPM
bodymap2_kidney	0.00 RPM	695.20 RPM
bodymap2_liver	0.00 RPM	193.85 RPM
bodymap2_lung	0.00 RPM	1003.83 RPM
bodymap2_lymph_node	0.00 RPM	524.67 RPM
bodymap2_ovary	0.04 RPM	384.48 RPM
bodymap2_prostate	0.00 RPM	1328.99 RPM
bodymap2_skeletal_muscle	0.00 RPM	60.51 RPM
bodymap2_testis	0.00 RPM	545.74 RPM
bodymap2_thyroid	0.15 RPM	349.49 RPM
bodymap2_white_blood_cells	0.00 RPM	510.88 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_2533 was not detected

EST

No EST(s) were mapped for retro_hsap_2533 retrocopy.

TSS

TSS No.	TSS Name	TSS expression level (Expr) in TPM range:
		no expression	0 < Expr ≤ 1	1 < Expr ≤ 5	5 < Expr ≤ 10	Expr > 10
TSS #1	TSS_105779	647 libraries	818 libraries	356 libraries	7 libraries	1 library

The graphical summary, for retro_hsap_2533 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1829 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)

Lab

retro_hsap_2533 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_2533 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_1476
Pongo abelii	retro_pabe_1864

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000092841	2 retrocopies	retro_hsap_1786, retro_hsap_2533 ,
Homo sapiens	ENSG00000196465	1 retrocopy	retro_hsap_2383,
Macropus eugenii	ENSMEUG00000001272	1 retrocopy	retro_meug_2172,
Macaca mulatta	ENSMMUG00000031838	6 retrocopies	retro_mmul_1633, retro_mmul_1663, retro_mmul_211, retro_mmul_2221, retro_mmul_2410, retro_mmul_96,
Nomascus leucogenys	ENSNLEG00000000205	2 retrocopies	retro_nleu_2736, retro_nleu_779,
Oryctolagus cuniculus	ENSOCUG00000017371	1 retrocopy	retro_ocun_1300,
Otolemur garnettii	ENSOGAG00000034596	1 retrocopy	retro_ogar_2549,
Pan troglodytes	ENSPTRG00000005080	2 retrocopies	retro_ptro_1196, retro_ptro_1476,
Sarcophilus harrisii	ENSSHAG00000004472	6 retrocopies	retro_shar_137, retro_shar_318, retro_shar_452, retro_shar_510, retro_shar_719, retro_shar_765,
Sus scrofa	ENSSSCG00000025467	1 retrocopy	retro_sscr_829,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.00 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	0.00 RPM
CEU_NA12827	0.00 RPM
CEU_NA12872	0.03 RPM
CEU_NA12873	0.00 RPM
FIN_HG00183	0.00 RPM
FIN_HG00277	0.00 RPM
FIN_HG00315	0.00 RPM
FIN_HG00321	0.00 RPM
FIN_HG00328	0.00 RPM
FIN_HG00338	0.00 RPM
FIN_HG00349	0.00 RPM
FIN_HG00375	0.00 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	0.00 RPM
GBR_HG00133	0.00 RPM
GBR_HG00134	0.02 RPM
GBR_HG00137	0.03 RPM
GBR_HG00142	0.00 RPM
GBR_HG00143	0.00 RPM
TSI_NA20512	0.00 RPM
TSI_NA20513	0.00 RPM
TSI_NA20518	0.00 RPM
TSI_NA20532	0.00 RPM
TSI_NA20538	0.00 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	0.03 RPM
YRI_NA18916	0.00 RPM
YRI_NA19093	0.00 RPM
YRI_NA19099	0.03 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).