RetrogeneDB ID: retro_ptro_1476

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 21:29851201..29851629(-)
• 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_1476
AGCACAGAGTTCAAGGCTGCCTTCCGGCTGTTTGACTGAACAGGTGACGGCAAGGTCCTTCCAGCCCCTGTGGGGACGTG
ATGAGGGCCCTGGGCCAGAACCCCACCAATGCCACGGCGCTCGAGGTCCTGGGGAACCCCAAGAGTGATGAGATGAACGT
GAAGGTGCTGGACTTTGAGCACTTCCTGCCCCTGCTGCAGACAGTGGCAGGGAACAGGGACCAGGGCACCTAAGAGGATT
ATGTGGAAAGACTTCAGGTGTTTGACAAGGAAGAGAATGGCACCGTCATGAGCACGGAAATCCAGCATGTTCTTGTCTCA
CTGGGTGAGGAGATGACAGAGAGAGGAGGAGAGATGCTGGTGGCAGGGCATGAGGACAGCAGTGGTTGCACTGACTCTGA
AGTGCTTGTCCGCAGGCTGCTGAAAGGC

Alignment

ORF - retro_ptro_1476 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.0 %
• 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.CGDVMRALGQNPTNA..L.VLGNPKSDEMNVKVLDFEHFLP.LQTV
Retrocopy STEFKAAFRLFD*TGDGKVL<SSPCGDVMRALGQNPTNATALEVLGNPKSDEMNVKVLDFEHFLPLLQTV

Parental  AKNKDQGTYEDYVEGLRVFDKEGNGTVMGAEIRHVLVTLGEKMTEEEVEMLVAGHEDSNGCINYEAFVRH
          A.N.DQGT.EDYVE.L.VFDKE.NGTVM..EI.HVLV.LGE.MTE...EMLVAGHEDS.GC...E..VR.
Retrocopy AGNRDQGT*EDYVERLQVFDKEENGTVMSTEIQHVLVSLGEEMTERGGEMLVAGHEDSSGCTDSEVLVRR

Parental  ILSG
          .L.G
Retrocopy LLKG

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	0.04 RPM	278.04 RPM
SRP007412_cerebellum	0.14 RPM	194.80 RPM
SRP007412_heart	0.00 RPM	205.71 RPM
SRP007412_kidney	0.03 RPM	841.02 RPM
SRP007412_liver	0.00 RPM	484.63 RPM
SRP007412_testis	0.00 RPM	116.76 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1476 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1476 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1476 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2533
Pongo abelii	retro_pabe_1864

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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,