RetrogeneDB ID: retro_sscr_829

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 5:104152674..104153118(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MYL6
• Ensembl ID: ENSSSCG00000025467
• Aliases: None
• Description: Sus scrofa myosin, light chain 6, alkali, smooth muscle and non-muscle (MYL6), mRNA. [Source:RefSeq mRNA;Acc:NM_001163997]

Sequence

>retro_sscr_829
GAGTTTAACAAGGACCAGCTGGAGGAGTTGAAAGATGCCTTCCAGCTGCTTGACTGAGTAGGCGATGGCAAGACCCTGTA
CAGCCAGTGTGCAGACATGGTGAGGGCCCTGGGCCAAAACCTCTCAAATGCCAAAATGCTTAAGGTCCTGGTGAACCTCA
AAAGTGATGAGCTGAAGTCCCAGCATATGGACTTCGAGATTTTCCTACCCATCCTCCAGGCAGCGACCAAGAACCTGGAC
AAAGGCACATACCAGGACTACCTGGAGGGGCTTCTGGTGTTTGACAAAGAGAGGAACAGCAAAGCCATGGGAGCAGAGCT
CAGACGTATCCTCACCACCACAGGGGAGAAGATACCTGAGCAGGAGGCGGTGGCAGGTCTGGCAGGTCATGAGGACAGCA
AAGACTGCATCATCTATGAAGACTTCTGGAAGCACATCCTAAGC

Alignment

ORF - retro_sscr_829 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.14 %
• Parental protein coverage: 98.01 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DFTEDQTAEFKEAFQLFDRTGDGKILYSQCGDVMRALGQNPTNAEVLKVLGNPKSDEMNVKVLDFEHFLP
          .F..DQ..E.K.AFQL.D..GDGK.LYSQC.D..RALGQN..NA..LKVL.N.KSDE......DFE.FLP
Retrocopy EFNKDQLEELKDAFQLLD*VGDGKTLYSQCADMVRALGQNLSNAKMLKVLVNLKSDELKSQHMDFEIFLP

Parental  MLQTVAKNKDQGTYEDYVEGLRVFDKEGNGTVMGAEIRHVLVTLGEKMTEEEVEMLVAGHEDSNGCINYE
          .LQ...KN.D.GTY.DY.EGL.VFDKE.N...MGAE.R..L.T.GEK..E.E.....AGHEDS..CI.YE
Retrocopy ILQAATKNLDKGTYQDYLEGLLVFDKERNSKAMGAELRRILTTTGEKIPEQEAVAGLAGHEDSKDCIIYE

Parental  AFVRHILS
          .F..HILS
Retrocopy DFWKHILS

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
SRP014902_placenta	0.00 RPM	137.91 RPM
SRP014902_testis	0.14 RPM	41.44 RPM
SRP018288_heart	0.00 RPM	12.73 RPM
SRP018288_kidney	0.00 RPM	21.57 RPM
SRP018288_liver	0.00 RPM	5.60 RPM
SRP018288_lung	0.00 RPM	38.18 RPM
SRP018856_adipose	0.00 RPM	130.68 RPM
SRP035408_brain	0.00 RPM	13.94 RPM
SRP035408_liver	0.00 RPM	5.90 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_829 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_829 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_829 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 41 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000092841	2 retrocopies	retro_hsap_1786, retro_hsap_2533,
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,
Mus musculus	ENSMUSG00000090841	7 retrocopies	retro_mmus_1281, retro_mmus_1504, retro_mmus_2328, retro_mmus_3231, retro_mmus_3333, retro_mmus_3358, retro_mmus_434,
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,
Pongo abelii	ENSPPYG00000004647	3 retrocopies	retro_pabe_1467, retro_pabe_1864, retro_pabe_538,
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 ,
Ictidomys tridecemlineatus	ENSSTOG00000023318	1 retrocopy	retro_itri_1478,
Tupaia belangeri	ENSTBEG00000000485	8 retrocopies	retro_tbel_130, retro_tbel_1715, retro_tbel_2980, retro_tbel_332, retro_tbel_3515, retro_tbel_3545, retro_tbel_3707, retro_tbel_4075,