RetrogeneDB ID: retro_ptro_1196

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 17:70428087..70428537(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MYL6
• Ensembl ID: ENSPTRG00000005080
• Aliases: None
• Description: myosin, light chain 6, alkali, smooth muscle and non-muscle [Source:HGNC Symbol;Acc:7587]

Sequence

>retro_ptro_1196
TGTGACTTCACCGAGGACCAGACCGCAGAGTTCAAGGAGGCCTTCCAGCTGTTTGATCGAACAGGTGATGGCAAGATCCT
GTACAACCAATGTGCGGATGTGATGAGGGCCCTAGGTCAGAATCCCACTAACACTGAGGTGGTCAAGTTTCTGAGGAACC
CCAAGAGTAATGAGATGAATGTGAAGTTGCTGGACTTTGAGCACTTTCTGCCTATGCTGCAGACAGTGGCCAAGAACAAG
GACCAAGGCACCTATGAAGATTACATAGAAGGACTTCAGGTGTTTGACAAGGAAGGAAATGGCACTATCATGGGTGTTGA
ATTCTGGCATGTTCTTGTCACACTGGGTGAGAAGATAACAGAGGAAGAAGTAGAGGTGTTGGTGGCAGGGAACGAGGGCA
GCAATGGTTGTATCGACTATGAAGCATTTGTGAGGCATATCCTGTCGGGG

Alignment

ORF - retro_ptro_1196 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.33 %
• Parental protein coverage: 99.34 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  CDFTEDQTAEFKEAFQLFDRTGDGKILYSQCGDVMRALGQNPTNAEVLKVLGNPKSDEMNVKVLDFEHFL
          CDFTEDQTAEFKEAFQLFDRTGDGKILY.QC.DVMRALGQNPTN.EV.K.L.NPKS.EMNVK.LDFEHFL
Retrocopy CDFTEDQTAEFKEAFQLFDRTGDGKILYNQCADVMRALGQNPTNTEVVKFLRNPKSNEMNVKLLDFEHFL

Parental  PMLQTVAKNKDQGTYEDYVEGLRVFDKEGNGTVMGAEIRHVLVTLGEKMTEEEVEMLVAGHEDSNGCINY
          PMLQTVAKNKDQGTYEDY.EGL.VFDKEGNGT.MG.E..HVLVTLGEK.TEEEVE.LVAG.E.SNGCI.Y
Retrocopy PMLQTVAKNKDQGTYEDYIEGLQVFDKEGNGTIMGVEFWHVLVTLGEKITEEEVEVLVAGNEGSNGCIDY

Parental  EAFVRHILSG
          EAFVRHILSG
Retrocopy EAFVRHILSG

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
SRP007412_brain_prefrontal_cortex	0.25 RPM	278.04 RPM
SRP007412_cerebellum	5.99 RPM	194.80 RPM
SRP007412_heart	4.63 RPM	205.71 RPM
SRP007412_kidney	33.71 RPM	841.02 RPM
SRP007412_liver	16.24 RPM	484.63 RPM
SRP007412_testis	5.06 RPM	116.76 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1196 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1196 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1196 has 5 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1786
Gorilla gorilla	retro_ggor_2233
Pongo abelii	retro_pabe_1467
Macaca mulatta	retro_mmul_211
Callithrix jacchus	retro_cjac_2566

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 24 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,
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,
Pan troglodytes	ENSPTRG00000023043	2 retrocopies	retro_ptro_1741, retro_ptro_2579,
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,