RetrogeneDB ID: retro_itri_1804

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393835.1:239359..240089(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSTOG00000024236
• Aliases: None
• Description: None

Sequence

>retro_itri_1804
CACGCAGACTGGTTCTTCCCTGAAGAGGTGGAGTTTAATGTATCAGAAGTGTTCGTGCCTCTCGCCACCCCAAATTCCGA
TTACTCATCTGACACTGGAAACGACTCTGACTCGGAGACTCTGGAGAGGTAGCAGCTGGCCAGCATGGCGGTGATGGAAA
GGGACTTGGTGAAGAAGGAGAGCTTTGGTGTGAAGCTTATGGACTTCCAGGCCCTCCGGTGGGGTGGCACTCTAAATAGA
AAGCACATATCCCCCGCTTTCCAGCCACCGCTCCCGCCCATGGATGGTAGCGCCTCCGCTCCAGCAAGGCCCAGAGCCCC
CTTCCCAGAGCTCTAGGGCTGAAAGCAGCTCAGGGGGTGGGACAGCCCCCTCCCCTGCGAGCATACTGGAGCAGGGGCTG
AGCCCAGGTGACAGCAGTTCTCCAAAACCCAAGGATTCTGTATCTGCAGCTGTCTCTGCACCAAGGAGAAATAGCAGTCA
AATGACCAGTGGCCAAAGCCAGGCCCAGGAAGGTGCCAGCTTCCATTAGCTCCCTGTCGGCCCAGCTCACAACGCTGCTG
GTCCCAGCCCTCACACGCTGCGCCGGGCAGTTAAAAAACCTGCTCCAGGGCCCCCAAACCCGGGAAAACCGCCTCCTGGC
CATTACGGGGACCCGAGTGCTCCAGGAGCGTTTCAGCTTCCACCCAGCCTGTCACCAAAGCCATCTGCTCGAAGTCCATC
TCCTCCCCCA

Alignment

ORF - retro_itri_1804 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.27 %
• Parental protein coverage: 51.8 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  HADWFFPEEVEFNVSEAFVPLATPNSNHSSHTGNDSDSGTLERKRPASMAVMEGDLVKKESFGVKLMDFQ
          HADWFFPEEVEFNVSE.FVPLATPNS..SS.TGNDSDS.TLER...ASMAVME.DLVKKESFGVKLMDFQ
Retrocopy HADWFFPEEVEFNVSEVFVPLATPNSDYSSDTGNDSDSETLER*QLASMAVMERDLVKKESFGVKLMDFQ

Parental  AHRRGGTLNRKHISPAFQPPLPPMDGSTSAPA-GPEPPSQSSRAESSSGGGTVPSPASILEQGLSPGDSS
          A.R.GGTLNRKHISPAFQPPLPPMDGS.SAPA.GPEPPSQSSRAESSSGGGT.PSPASILEQGLSPGDSS
Retrocopy ALRWGGTLNRKHISPAFQPPLPPMDGSASAPA>GPEPPSQSSRAESSSGGGTAPSPASILEQGLSPGDSS

Parental  PPKPKDSVSAAVPAPGRNSSQMTSGQSQAQAGASSHQLSVGLAHNAAGPSPHTLRRAVKKPAPAPPKPGN
          .PKPKDSVSAAV.AP.RNSSQMTSGQSQAQ.GAS.H.L.VG.AHNAAGPSPHTLRRAVKKPAP.PP.PG.
Retrocopy SPKPKDSVSAAVSAPRRNSSQMTSGQSQAQEGASFH*LPVGPAHNAAGPSPHTLRRAVKKPAPGPPNPGK

Parental  PPPGHHGGPSAPGALSPKPSARSPSPPPQHTGPAP
          PPPGH.G.PSAPGA....PS..SP.P......P.P
Retrocopy PPPGHYGDPSAPGAFQLPPSL-SPKPSARSPSPPP

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_1804 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1804 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
Ictidomys tridecemlineatus	ENSSTOG00000024236	1 retrocopy	retro_itri_1804 ,
Tarsius syrichta	ENSTSYG00000012109	1 retrocopy	retro_tsyr_505,