RetrogeneDB ID: retro_itri_578

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393302.1:15416044..15416250(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SEPW1
• Ensembl ID: ENSSTOG00000001294
• Aliases: None
• Description: selenoprotein W, 1 [Source:HGNC Symbol;Acc:10752]

Sequence

>retro_itri_578
TATTTTCAGCCCGAGAAGACATCAGGAGATAAGTTCCCCGGATGCCCAGACATCTGCAACAAGAGGATTCCCCAGGCCAC
CAGGTTACTGAACTGATGGTAGCACGGTAGTTGGTTCACTCCAAGAAGAAAGGTGATGGATTTGTGGATAGAGAGAACAA
GTCTCCGAACCTGGTGGCCAACATCAAAGCTACCTTGTCTCAGGGC

Alignment

ORF - retro_itri_578 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.14 %
• Parental protein coverage: 93.24 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  YLQLKKKLEDEFPGCLDICGEGTPQVTGFF-EVMVAGKLVHSKKRGDGYVDTESKFLKLVAAIKAALAQG
          Y.Q..K...D.FPGC.DIC....PQ.T....E.MVA..LVHSKK.GDG.VD.E.K...LVA.IKA.L.QG
Retrocopy YFQPEKTSGDKFPGCPDICNKRIPQATRLL<ELMVAR*LVHSKKKGDGFVDRENKSPNLVANIKATLSQG

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_578 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_578 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 8 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000015208	1 retrocopy	retro_amel_1135,
Bos taurus	ENSBTAG00000008203	2 retrocopies	retro_btau_1527, retro_btau_756,
Canis familiaris	ENSCAFG00000004074	1 retrocopy	retro_cfam_1368,
Choloepus hoffmanni	ENSCHOG00000013206	2 retrocopies	retro_chof_1486, retro_chof_61,
Felis catus	ENSFCAG00000015176	2 retrocopies	retro_fcat_108, retro_fcat_186,
Mustela putorius furo	ENSMPUG00000004433	1 retrocopy	retro_mputfur_326,
Rattus norvegicus	ENSRNOG00000013548	2 retrocopies	retro_rnor_1819, retro_rnor_688,
Ictidomys tridecemlineatus	ENSSTOG00000001294	1 retrocopy	retro_itri_578 ,