RetrogeneDB ID: retro_itri_1265

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393418.1:20134..20559(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FXR1
• Ensembl ID: ENSSTOG00000010612
• Aliases: None
• Description: fragile X mental retardation, autosomal homolog 1 [Source:HGNC Symbol;Acc:4023]

Sequence

>retro_itri_1265
TTCTTCAAGTGCACAGTTGATGTTCTTGAGGATTTGAGAGAGGCTTTTTGCTAATGAAAATGCACATAAAGATTTTAAAA
AAGCAGTAGGAGCATGCAGAATTTTTTACCCTCTAGAAACCATGCAGCTAAGGATACTGTCTGCCAGTGAAGCAACTGTG
AAGAGAGTAAATATTCTAAGTGACATGCATTTGTGAAGTATTCGTACAAAGTTGATGCTAATGTCCAGTTATGAAGAGGC
CAGTAAGCATTTAGAATGCACGGAACAACTTACAGCAGCATTTCATGACAAATTTGTTGTGAGAGAAGATTTAATGGGAC
TGGCAATAGGAACACATGGTAGTAATATCCAACAAGCTAAGGTTTCTTAAGTTACCTTAAGTTGAACTAGATGAAGATGC
TGGAACATTTAGAGTCTATGGAGAA

Alignment

ORF - retro_itri_1265 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.03 %
• Parental protein coverage: 53.18 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  FFKCTVDVPEDLREAC-ANENAHKDFKKAVGACRIFYHPETTQLMILSASEATVKRVNILSDMHLRSIRT
          FFKCTVDV.EDLREA..ANENAHKDFKKAVGACRIFY..ET.QL.ILSASEATVKRVNILSDMHL.SIRT
Retrocopy FFKCTVDVLEDLREAF>ANENAHKDFKKAVGACRIFYPLETMQLRILSASEATVKRVNILSDMHL*SIRT

Parental  KLMLMSRNEEATKHLECTKQLAAAFHEEFVVREDLMGLAIGTHGSNIQQARKVPGVTA-IELDEDTGTFR
          KLMLMS..EEA.KHLECT.QL.AAFH..FVVREDLMGLAIGTHGSNIQQA.KV..VT...ELDED.GTFR
Retrocopy KLMLMSSYEEASKHLECTEQLTAAFHDKFVVREDLMGLAIGTHGSNIQQA-KVS*VTL>VELDEDAGTFR

Parental  IYGE
          .YGE
Retrocopy VYGE

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_1265 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1265 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	ENSSTOG00000010612	1 retrocopy	retro_itri_1265 ,