RetrogeneDB ID: retro_itri_45

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393986.1:151085..151694(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSTOG00000019940
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: FGF4
• Ensembl ID: ENSSTOG00000019792
• Aliases: None
• Description: fibroblast growth factor 4 [Source:HGNC Symbol;Acc:3682]

Sequence

>retro_itri_45
GGGCCCGGGACGGCCGCGGCGGCTCTGCTCCTGGCAGTCCTGCTGGCCCTGCTGGCGCCCTGGGCGGGCCAAGGGGGCGC
CGCCGCACCCACAGCACCCAACGGCACGCTGGAGGCCGAGCCGGAGCACCACTGGGAGAGCCTGCTGGTGCGCTCGCTGG
TGCGCTTGCCCGTGGCCTCACAGCCCAAGGAGGCTGCTGTCCAGAGCGGCGCTGGGGATTACCTGTTGGGCATCAAGCGG
CTGCGGAGGCTCTACTGCAACGTGGGCATCGGCTTCCACCTGCAAGTGCTCCCCGATGGTCGCATCGGCGGCGTGCACGC
GGACATGAGCGACAGTCTGCTGGAGCTCTCCCCCGTGGAGCGGGGCGTCGTGAGCATCTTCGGAGTGGCCAGCAGGTTCT
TTTTGGCCATGAGCAGCAAGGGCAAGCTCTATGGCTCGCCCTTCTTTGCGGATGACTGCAAGTTCAAGGAGATTCTGCTC
CCCAACAACTACAACGCCTACGAGCCCCAGGAGCACCCCGGCATGTTCATCGCACTAAGAATGGTTCCCAAGAAGGGGAA
CCGAGTGCCACCCACCATGAAGGTCACCCACTTCCTCCCCAGGCTGTGA

Alignment

ORF - retro_itri_45 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.69 %
• Parental protein coverage: 99.03 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GPGTATASLLPAVLLALLAPWAGRGGAAAPTAPNGTLEAEPEHRWESLLARSLARLPVASQPKEAAVQSG
          GPGTA.A.LL.AVLLALLAPWAG.GGAAAPTAPNGTLEAEPEH.WESLL.RSL.RLPVASQPKEAAVQSG
Retrocopy GPGTAAAALLLAVLLALLAPWAGQGGAAAPTAPNGTLEAEPEHHWESLLVRSLVRLPVASQPKEAAVQSG

Parental  AGDYLLGIKRLRRLYCNVGIGFHLQVLPDGRIGGVHADTSDSLLELSPVERGVVSIFGVASRFFVAMSSK
          AGDYLLGIKRLRRLYCNVGIGFHLQVLPDGRIGGVHAD.SDSLLELSPVERGVVSIFGVASRFF.AMSSK
Retrocopy AGDYLLGIKRLRRLYCNVGIGFHLQVLPDGRIGGVHADMSDSLLELSPVERGVVSIFGVASRFFLAMSSK

Parental  GKLYGSPFFADECKFKEILLPNNYNAYESQEHPGMFIALSKNGRAKKGNRVSPTMKVTHFLPRL
          GKLYGSPFFAD.CKFKEILLPNNYNAYE.QEHPGMFIAL.......KGNRV.PTMKVTHFLPRL
Retrocopy GKLYGSPFFADDCKFKEILLPNNYNAYEPQEHPGMFIALRMVPK--KGNRVPPTMKVTHFLPRL

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_45 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_45 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000010247	1 retrocopy	retro_etel_892,
Ictidomys tridecemlineatus	ENSSTOG00000019792	1 retrocopy	retro_itri_45 ,