RetrogeneDB ID: retro_itri_1217

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393404.1:1781867..1782128(+)
• Located in intron of: ENSSTOG00000001451

Retrocopy information

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

Parental gene information

• Parental gene symbol: HSPB11
• Ensembl ID: ENSSTOG00000002643
• Aliases: None
• Description: heat shock protein family B (small), member 11 [Source:HGNC Symbol;Acc:25019]

Sequence

>retro_itri_1217
CATATGTTTTCACATATAATAAAGCTTATAATACAAAGTTACTTAGCGTGGACCTTGAAGATTGAAAAGACCGCATCTAA
AGAGCCTGTCAGTTTTGAGCATTGGATTGAAAAAGATTTTGTACACACAGAGGGGCAGCTTCAAAATGAAGAAATTGTGG
CTCATGATGGCTTCTGTACAAACTTGAGATTCATAATTACATCAGCTTTTAGTCATTTTATATCTGTGCATAGTATTTCT
GCAAAGAGAATAGTAGTCTCA

Alignment

ORF - retro_itri_1217 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.56 %
• Parental protein coverage: 60.84 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  HKHVKVEKLIIQSYLVRTLKIEKTKSKEPVDFERWIERDFVHTEGQLQNEEILVHDGYCTYLRFIITKAF
          H......KLIIQSYL..TLKIEKT.SKEPV.FE.WIE.DFVHTEGQLQNEEI..HDG.CT.LRFIIT.AF
Retrocopy HMFSHIIKLIIQSYLAWTLKIEKTASKEPVSFEHWIEKDFVHTEGQLQNEEIVAHDGFCTNLRFIITSAF

Parental  DHFISVHCVSAEGLVVS
          .HFISVH..SA...VVS
Retrocopy SHFISVHSISAKRIVVS

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_1217 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1217 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 4 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000000284	3 retrocopies	retro_dnov_2439, retro_dnov_386, retro_dnov_514,
Rattus norvegicus	ENSRNOG00000010241	2 retrocopies	retro_rnor_849, retro_rnor_850,
Ictidomys tridecemlineatus	ENSSTOG00000002643	1 retrocopy	retro_itri_1217 ,
Tarsius syrichta	ENSTSYG00000012499	2 retrocopies	retro_tsyr_1813, retro_tsyr_697,