RetrogeneDB ID: retro_itri_1365

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393459.1:184219..184588(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: STYX
• Ensembl ID: ENSSTOG00000014504
• Aliases: None
• Description: serine/threonine/tyrosine interacting protein [Source:HGNC Symbol;Acc:11447]

Sequence

>retro_itri_1365
TATAATGTGACTAATGGATTTATTGATGGGAGCTCACAAACTGGAGGGAATGTTCTGCATGGAGATGCAGGGATCTGCCA
AAGTGCTGCCTTTACTATTGCATACATTATGGAAACATTTGGAACAAAGTACAAAGATGCCTTTTTCTTATGTCCAAGAA
ATAATATTTTGCATTAATCCAAATTCTGGATTTGTTCATCAGCTTCAGGAATATGAAGTCATCTACTAGCAAAATTGACA
ATATAGATAACATTGCCATTCTAGATAGAAAAGTCTTTATCTATTCATTCTGGTACGTCAGGCAGTCTGAAGAGAACACA
TAAAGAAGATGATTTTAGAAACCTGCAATTGGTAACTTCACAGAAGGGC

Alignment

ORF - retro_itri_1365 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.29 %
• Parental protein coverage: 56.05 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  FPMSKEFIDGSLQTGGKVLVHGNAGISRSAAFVIAYIMETFGVKYRDAF-AYVQERRFCINPNAGFVHQL
          ......FIDGS.QTGG.VL.HG.AGI..SAAF.IAYIMETFG.KY.DAF..YVQE..FCINPN.GFVHQL
Retrocopy YNVTNGFIDGSSQTGGNVL-HGDAGICQSAAFTIAYIMETFGTKYKDAF>SYVQEIIFCINPNSGFVHQL

Parental  QEYEAIY-LAKLTIQMMSPLQIERSLSVHSGTTGSLKRTHEEEDDFGNMQVATAQNG
          QEYE.IY.LAKLTI....P..IE.SLS.HSGT.GSLKRTH..EDDF.N.Q..T.Q.G
Retrocopy QEYEVIY<LAKLTI*ITLPF*IEKSLSIHSGTSGSLKRTH-KEDDFRNLQLVTSQKG

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_1365 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1365 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 10 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000016631	9 retrocopies	retro_dnov_1713, retro_dnov_1720, retro_dnov_1914, retro_dnov_2138, retro_dnov_2186, retro_dnov_2218, retro_dnov_2221, retro_dnov_461, retro_dnov_66,
Echinops telfairi	ENSETEG00000000561	1 retrocopy	retro_etel_1881,
Monodelphis domestica	ENSMODG00000029372	1 retrocopy	retro_mdom_44,
Mus musculus	ENSMUSG00000053205	1 retrocopy	retro_mmus_96,
Oryctolagus cuniculus	ENSOCUG00000029442	1 retrocopy	retro_ocun_1555,
Ochotona princeps	ENSOPRG00000016123	1 retrocopy	retro_opri_976,
Rattus norvegicus	ENSRNOG00000007956	1 retrocopy	retro_rnor_256,
Ictidomys tridecemlineatus	ENSSTOG00000014504	1 retrocopy	retro_itri_1365 ,
Ictidomys tridecemlineatus	ENSSTOG00000025153	1 retrocopy	retro_itri_1224,
Vicugna pacos	ENSVPAG00000012229	1 retrocopy	retro_vpac_464,