RetrogeneDB ID: retro_itri_1117

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393379.1:4595106..4595394(+)
• Located in intron of: ENSSTOG00000016169

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSTOG00000004124
• Aliases: None
• Description: None

Sequence

>retro_itri_1117
CAAAGAAATCAAAAGTGTACTGGGTCAGCATATGCAAGAAAAAAGGAGGATGAGCTCTGGGCCAGATTCCTCAATGACAC
CAGACCAAAATTAGAACTGCCTTGTACACAGTTAAGACAGCAGAGGAGACTGAAGAAATGGGATCAGGTAAACTGCTGGT
CAAAGCAGAAGAACTAGAGAAACCTAAAGAACTGAAAAAGTTAAAAATCACCCACGTGTTTGATTTGGCTGAAGTAAGAT
GACAAAGAAAGTGGATACTCATCTAAAGAAGCCAAATCCTTCCCAAAA

Alignment

ORF - retro_itri_1117 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.27 %
• Parental protein coverage: 51.53 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  EEQEKGTGSEDARKKKEDELWASFLNDVGPKSKLPSSTQ-VKTGEETEEMSSSKLLVKAEELEKPKETEK
          ....K.TGS..ARKK.EDELWA.FLND..PK..LP..TQ.VKT.EETEEM.S.KLLVKAEELEKPKE..K
Retrocopy QRNQKCTGSAYARKK-EDELWARFLNDTRPKLELPC-TQ<VKTAEETEEMGSGKLLVKAEELEKPKELKK

Parental  VKITKVFDFAGEEVR-VTKEVDA-TSKEAKSFFK
          .KIT.VFD.A..EVR..TK.VD...SKEAKSF.K
Retrocopy LKITHVFDLA--EVR<MTKKVDT<SSKEAKSFPK

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_1117 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1117 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 8 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000000695	1 retrocopy	retro_cpor_465,
Dasypus novemcinctus	ENSDNOG00000013266	2 retrocopies	retro_dnov_2442, retro_dnov_2546,
Echinops telfairi	ENSETEG00000016429	1 retrocopy	retro_etel_1574,
Myotis lucifugus	ENSMLUG00000000890	1 retrocopy	retro_mluc_2525,
Rattus norvegicus	ENSRNOG00000019326	1 retrocopy	retro_rnor_2289,
Ictidomys tridecemlineatus	ENSSTOG00000004124	2 retrocopies	retro_itri_1117 , retro_itri_1815,
Tupaia belangeri	ENSTBEG00000015362	2 retrocopies	retro_tbel_1305, retro_tbel_2189,
Tursiops truncatus	ENSTTRG00000001215	1 retrocopy	retro_ttru_1385,