RetrogeneDB ID: retro_itri_1247

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393411.1:2321683..2322087(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CDIPT
• Ensembl ID: ENSSTOG00000001488
• Aliases: None
• Description: CDP-diacylglycerol--inositol 3-phosphatidyltransferase [Source:HGNC Symbol;Acc:1769]

Sequence

>retro_itri_1247
TTGGTCAACCTGACCCTGCTGTACCCTTGCCCTACCCTTTTCTTCCAGCTCAGCATGAGTTTGGAGGTGGCCAGTCACTG
GATGCACCATTGCAGTTCTGTGATTGGAGGCAGTGAGAGTCACAAGATGATGGACCTGTTAGGGAATCCAGTGCTTTGGA
TCTATATAGTTCCAGGCCTGCTCTGTTCACCCTCTGTGCTGCAAATGAGCTCTTTTCCTGCCTCCTGTACCTATTCAATT
TCTCTGAAGGACCATGAGTTGGCTCCAGCTCTGTGGGGCTTTTCTGAATGGGCCTCTGGGTCACTGCCCCATTCGCCTTG
GTCAAGTCCCTAATCAGCATTATCCACCTGATCACAGCTGCTGATAACATGGCTGCCCTGGACCCAGCAAACTGTGCCAA
GAAA

Alignment

ORF - retro_itri_1247 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.41 %
• Parental protein coverage: 99.25 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LVNLALLYPRATLLFQLSMSLDVASHWLHLHSSVVRGSESHKMIDLSGNPVLRIY-YTSRPALFTLCAGN
          LVNL.LLYP..TL.FQLSMSL.VASHW.H..SSV..GSESHKM.DL.GNPVL.IY.Y.SRPALFTLCA.N
Retrocopy LVNLTLLYPCPTLFFQLSMSLEVASHWMHHCSSVIGGSESHKMMDLLGNPVLWIY<YSSRPALFTLCAAN

Parental  ELFYCLLYLFNFSEGPLVG--SVGLFRMGLWVTAPIALLKSLISVIHLITAARNMAALDAADRAKK
          ELF.CLLYLFNFSEGP.VG..SVGLF.MGLWVTAP.AL.KSLIS.IHLITAA.NMAALD.A..AKK
Retrocopy ELFSCLLYLFNFSEGP*VGSSSVGLF*MGLWVTAPFALVKSLISIIHLITAADNMAALDPANCAKK

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_1247 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1247 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 1 parental gene, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Ictidomys tridecemlineatus	ENSSTOG00000001488	2 retrocopies	retro_itri_1247 , retro_itri_851,