RetrogeneDB ID: retro_tbel_2980

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_125728:168888..169314(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MYL6
• Ensembl ID: ENSTBEG00000000485
• Aliases: None
• Description: myosin, light chain 6, alkali, smooth muscle and non-muscle [Source:HGNC Symbol;Acc:7587]

Sequence

>retro_tbel_2980
ACCACAGAGTTCAAGGAGGTCTTCCAGCTGTTTGACCAGACAGGGTATGGCAAAATCCTGAACAACCTGGGTAGAGATGT
GATGAGGGCCCTAGGCCAGAACCCCACCAACACTGAGGTGTTCAAGGTCCTGGGGAACCCCAATAGTGATGAGATGAATG
TCAAGGTGCTGGACTTTGAGCACGTCCTGCCCATGCTGGCAGCGACCAAGAACAAGGACCAAGGCACCTATGAGGATTAT
GTTGAAGGCCTTCGGGTATTTGACAAGGAAGGGAATGGTGCTGTAATAGATGCTGAAATCCAGCATGTCCTTGTCACTTT
AGGGGAGAAGATGACAGAGAAAGAAGTAGAGATGTTGATGGCAGGACACGAGGACAGCAATGGTTGTATCAACTATGAAG
AGCTCGTCCATGTGGTGCTGAATGGC

Alignment

ORF - retro_tbel_2980 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.02 %
• Parental protein coverage: 91.67 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  STGFKEAFQLFDRTGDGKILYSQCGDVMRALGQNPTNAEVLKVLGNPKSDEMNVKVLDFEHFLPMLQTVA
          .T.FKE.FQLFD.TG.GKIL.....DVMRALGQNPTN.EV.KVLGNP.SDEMNVKVLDFEH.LPML....
Retrocopy TTEFKEVFQLFDQTGYGKILNNLGRDVMRALGQNPTNTEVFKVLGNPNSDEMNVKVLDFEHVLPML-AAT

Parental  KNKDQGTYEDYVEGLRVFDKEGNGTVMGAEIRHVLVTLGEKMTEEEVEMLVAGHEDSNGCINYEAFVRHI
          KNKDQGTYEDYVEGLRVFDKEGNG.V..AEI.HVLVTLGEKMTE.EVEML.AGHEDSNGCINYE..V...
Retrocopy KNKDQGTYEDYVEGLRVFDKEGNGAVIDAEIQHVLVTLGEKMTEKEVEMLMAGHEDSNGCINYEELVHVV

Parental  LSG
          L.G
Retrocopy LNG

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Tupaia belangeri was not studied using RNA-Seq expression data.

ChIP-Seq

Tupaia belangeri was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_tbel_2980 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_2980 was not experimentally validated.

Homology

Retrocopy orthology:

Tupaia belangeri does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 26 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,
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,
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,
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,