RetrogeneDB ID: retro_itri_1225

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393406.1:5374824..5375416(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NIT1
• Ensembl ID: ENSSTOG00000006372
• Aliases: None
• Description: nitrilase 1 [Source:HGNC Symbol;Acc:7828]

Sequence

>retro_itri_1225
GCATTTGATTTCACTGCACAAGACCCTACAGAGACACTGTGCCTGTCTGAGCCTGTGGGTGGGAACCTTCTGGGGGAATA
CACCCAGCTTTAAAGGAATGTGTGGACTCTGGCTGTCCTTGGGTGGTTTCCATGAGCGTGGCCAAGACTGGGAGCAGACT
CAGAGAATCTACAACTGTCATGTGCTTCTGAACAGCAAGGGATCAAGAGTGGTACCTATAGGAAGTCGTATCTGTGTGAT
GTAGAGATTCTAGGGCAGGAGCCTATCCAAGAAAGCAATTTTACCATGCCTGGGCCCAGTCTTGAGTCACCGTCAGCACA
CCAGCAGGCAAGATTGATCTAGCTGTCTGTGGTTCCCTCAACTCTCTAGCATTGGCTCACACTGGAGCAGAAATATTCAC
CTACCCTTCAGCTTTTGGATCTGCTACAGGCCCTATCCACTGGGAAGTATTGCTGAGCTATGCTATTGAAACCCAGTGCT
ATGTTGTGGCAGCTGCATAGTGTGGACACCACCATGAGAAGAGAGCAAGTTATGGCCACAGCATGGTAGTAGCCCTTGGG
GAACAGTGGTGGCCCATTGCTCTGAAGAGCCT

Alignment

ORF - retro_itri_1225 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.33 %
• Parental protein coverage: 67.67 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  AFDYIARDPAESLSLSEPLSGNLLGEYTQLARE-CGIWLSLGGFHERGQDWEQTQKIYNCHVLLNSKGSI
          AFD..A.DP.E.L.LSEP..GNLLGEYTQL.R..CG.WLSLGGFHERGQDWEQTQ.IYNCHVLLNSKGS.
Retrocopy AFDFTAQDPTETLCLSEPVGGNLLGEYTQL*RN>CGLWLSLGGFHERGQDWEQTQRIYNCHVLLNSKGSR

Parental  V-ATYRKTHLCDIEIPGQEPMRESNSTLPGSSLESP-VSTPAGKIGLAVCYDIRFPELSLALAQAGAEIL
          V..TYRK..LCD.EI.GQEP..ESN.T.PG.SLESP.VSTPAGKI.LAVC........SLALA..GAEI.
Retrocopy V<GTYRKSYLCDVEILGQEPIQESNFTMPGPSLESP<VSTPAGKIDLAVCGSLN----SLALAHTGAEIF

Parental  TYPSAFGSVTGPAHWEVLLRARAIETQCYVVAAAQCGRHHEKRASYGHSMVV-DPWGTVVARCSEGP
          TYPSAFGS.TGP.HWEVLL...AIETQCYVVAAA.CG.HHEKRASYGHSMVV..PWGTVVA.CSE.P
Retrocopy TYPSAFGSATGPIHWEVLL-SYAIETQCYVVAAA*CGHHHEKRASYGHSMVV<SPWGTVVAHCSEEP

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_1225 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1225 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.

---

Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Ictidomys tridecemlineatus	ENSSTOG00000006372	1 retrocopy	retro_itri_1225 ,