RetrogeneDB ID: retro_itri_295

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393282.1:30934040..30934371(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSTOG00000004006
• Aliases: None
• Description: None

Sequence

>retro_itri_295
AATCCCATCCATGCCAGTTTACCCTAAGCGATCCTCACAGAGGCCATCTACTCTTTTATCTTCCACAGCACTCTGCTGCA
CTTCCAGAAGGTCTGAACCAAGATTCCTATCCACATGATGGTTCCACGCATCATTCTTTAGCCTATGCAGGGGGAAATCT
AACATGTGCAGTTATTTAAAACAGCAGTGGCATTTTTACTTCATTTAATGTGTTTTGATGCACTTTCCCTCAATTTTTTT
ATAGTATATTGGCTGGCTCCTTCTTTAGGTATTTTGTTGATGATTTTCAATGTTCAGCTTTTTCCTCGAATGGCTTCATG
AAAACAATACA

Alignment

ORF - retro_itri_295 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.6 %
• Parental protein coverage: 55. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  NPINSDLPQAIITEAICSFIFHSALLQFQEVRTKLRIHLLAALITF-LAYAGGSITGAV-FNPALALSLH
          NPI...LP.AI.TEAI.SFIFHS.LL.FQ.V.TK..IH.....I...LAYAGG..T.AV.F..A.A..LH
Retrocopy NPIHASLP*AILTEAIYSFIFHSTLLHFQKV*TKIPIHMMVPRIIL<LAYAGGNLTCAV>FKTAVAFLLH

Parental  FMCFDEAFPQFFIVYWLAPSVGILLMIL-MFSFFLPWLHNNNT
          .MCFD.....FFIVYWLAPS.GILLMI..MFSFFL.WLH.NNT
Retrocopy LMCFDALSLNFFIVYWLAPSLGILLMIF>MFSFFLEWLHENNT

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_295 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_295 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 1 parental gene, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Ictidomys tridecemlineatus	ENSSTOG00000004006	2 retrocopies	retro_itri_164, retro_itri_295 ,