RetrogeneDB ID: retro_pabe_538

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 10:70507403..70507858(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MYL6
• Ensembl ID: ENSPPYG00000004647
• Aliases: None
• Description: myosin light polypeptide 6 [Source:RefSeq peptide;Acc:NP_001126203]

Sequence

>retro_pabe_538
ATGTGTGGCTTCACCGAGGACCACACTGCAGAGTTCAAGGAGGCCTTCCAGCTGTTTGACTGAACAGATGATGGCAAGAT
CCTGTACAGCCAGCATGGGGACATGATGAGGCCCCTTGGCCAGAAATTCACCAACACTGAGGTGCCCAAAGTCCTGGGGA
ACTCTATGAGTGATGAAATGAATGTGAAGGTGCTGAACTTTGAGCACTTTCTGCCCATGCTGCAGATGGTGGTGGCCAAA
AACAAGGACCAGGGCACCTATGAGGATTATGTCAAAAGACTTAGGTGTTTGACAAGGAAGGAAATGGCACTGTCATGGGT
GCTGAAATCTGGCATGTTCTTGTCACACTGGGTGAGAAGATGACAGAGGAAGAAATAGAGATGCTAGGGGCAGGGCAAGA
GGACAACAATGGTTGTATTAACTATGAAGAGCTCATCTGCACGGTGCCGAATGGC

Alignment

ORF - retro_pabe_538 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.7 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MCDFTEDQTAEFKEAFQLFDRTGDGKILYSQCGDVMRALGQNPTNAEVLKVLGNPKSDEMNVKVLDFEHF
          MC.FTED.TAEFKEAFQLFD.T.DGKILYSQ.GD.MR.LGQ..TN.EV.KVLGN..SDEMNVKVL.FEHF
Retrocopy MCGFTEDHTAEFKEAFQLFD*TDDGKILYSQHGDMMRPLGQKFTNTEVPKVLGNSMSDEMNVKVLNFEHF

Parental  LPMLQ-TVAKNKDQGTYEDYVEGLR-VFDKEGNGTVMGAEIRHVLVTLGEKMTEEEVEMLVAGHEDSNGC
          LPMLQ..VAKNKDQGTYEDYV..LR.VFDKEGNGTVMGAEI.HVLVTLGEKMTEEE.EML.AG.ED.NGC
Retrocopy LPMLQMVVAKNKDQGTYEDYVKRLR<VFDKEGNGTVMGAEIWHVLVTLGEKMTEEEIEMLGAGQEDNNGC

Parental  INYEELVRMVLNG
          INYEEL...V.NG
Retrocopy INYEELICTVPNG

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	0.00 RPM	140.94 RPM
SRP007412_cerebellum	0.00 RPM	193.71 RPM
SRP007412_heart	0.00 RPM	149.37 RPM
SRP007412_kidney	0.00 RPM	341.88 RPM
SRP007412_liver	0.03 RPM	295.80 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_538 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_538 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_538 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Macaca mulatta	retro_mmul_2410

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 30 retrocopies.

Species	Parental gene accession	Retrocopies number
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	ENSPPYG00000004646	1 retrocopy	retro_pabe_2150,
Pongo abelii	ENSPPYG00000004647	3 retrocopies	retro_pabe_1467, retro_pabe_1864, retro_pabe_538 ,
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,