RetrogeneDB ID: retro_itri_1478

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393501.1:807190..807513(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSTOG00000020893
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: MYL6
• Ensembl ID: ENSSTOG00000023318
• Aliases: None
• Description: myosin, light chain 6, alkali, smooth muscle and non-muscle [Source:HGNC Symbol;Acc:7587]

Sequence

>retro_itri_1478
ACCAATGCTGTGGTGCTCGGTATCCTGGGGAACTCCAAGAGTGATGAGATGAATATGAAGGTGCTGGACTTGGAGCAGTT
CCTGCCCATCCTGCAGTCAGTGGCCAAGAACAAGAACCAGGGAATCTATGAGGATTATGCCAAAGGTCTTTGGGTGTTTG
ACAAGGAAGGAATGGTATTATCATGGGCACTGAAATCCATAATCTCCTTGTCACACTGGATAAAAACATGACAGAGGAAG
AAGTAGAGATACTGGTGACAAGGTATGAGGGTACCGGTGGTTGTATCAACTATGACAAGCTTGCCCAGATGGTGGTGAAT
GGC

Alignment

ORF - retro_itri_1478 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.97 %
• Parental protein coverage: 54. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  TNAEVLKVLGNPKSDEMNVKVLDFEHFLPMLQTVAKNKDQGTYEDYVEGLRVFDKEG-NGTVMGAEIRHV
          TNA.VL..LGN.KSDEMN.KVLD.E.FLP.LQ.VAKNK.QG.YEDY..GL.VFDKEG.NG..MG.EI...
Retrocopy TNAVVLGILGNSKSDEMNMKVLDLEQFLPILQSVAKNKNQGIYEDYAKGLWVFDKEG<NGIIMGTEIHNL

Parental  LVTLGEKMTEEEVEMLVAGHEDSNGCINYEELVRMVLNG
          LVTL...MTEEEVE.LV...E...GCINY..L..MV.NG
Retrocopy LVTLDKNMTEEEVEILVTRYEGTGGCINYDKLAQMVVNG

Legend:

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

Expression

RNA-Seq

Ictidomys tridecemlineatus was not studied using RNA-Seq expression data.

ChIP-Seq

Ictidomys tridecemlineatus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_itri_1478 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1478 was not experimentally validated.

Homology

Retrocopy orthology:

Ictidomys tridecemlineatus 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 10 parental genes, and 29 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	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 ,