RetrogeneDB ID: retro_itri_686

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393311.1:7031090..7031384(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: LIN52
• Ensembl ID: ENSSTOG00000008100
• Aliases: None
• Description: lin-52 homolog (C. elegans) [Source:HGNC Symbol;Acc:19856]

Sequence

>retro_itri_686
ATGGGTTGGAAGATGGAGTCTCCCACAGACAGGACAGATTTGGAAGCATCTTTGCTAAGTTTTGAAAAACTTGACCGTGC
CTCACCAGATCTTTGACCAGAACAATTATCAGGTGTTGCTGAATTTGCAGCTTCCTTCAAAAGTCCTATTACTAGCTCTC
CACCCAAATGGATGGCTGAAATAGAACGGGATGACAATGACATGTTGAAAGAATTGGGAAGTCTCACTACAGCTAATTTG
ATGGAGAAGGTATGAGGCCTACAGAACCTGGCCTATCAACTGGGGCTGGATGAG

Alignment

ORF - retro_itri_686 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.86 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGRKMASPTDGTDLEASLLSFEKLDRASPDLWPEQLPGVAEFAASFKSPITSSPPKWMAEIERDDIDMLK
          MG.KM.SPTD.TDLEASLLSFEKLDRASPDL.PEQL.GVAEFAASFKSPITSSPPKWMAEIERDD.DMLK
Retrocopy MGWKMESPTDRTDLEASLLSFEKLDRASPDL*PEQLSGVAEFAASFKSPITSSPPKWMAEIERDDNDMLK

Parental  ELGSLTTANLMEKVRGLQNLAYQLGLDE
          ELGSLTTANLMEKV.GLQNLAYQLGLDE
Retrocopy ELGSLTTANLMEKV*GLQNLAYQLGLDE

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_686 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_686 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 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Loxodonta africana	ENSLAFG00000002534	1 retrocopy	retro_lafr_1097,
Macropus eugenii	ENSMEUG00000007891	1 retrocopy	retro_meug_286,
Mus musculus	ENSMUSG00000085793	1 retrocopy	retro_mmus_750,
Oryctolagus cuniculus	ENSOCUG00000017491	1 retrocopy	retro_ocun_294,
Otolemur garnettii	ENSOGAG00000003009	1 retrocopy	retro_ogar_2580,
Ictidomys tridecemlineatus	ENSSTOG00000008100	1 retrocopy	retro_itri_686 ,
Tupaia belangeri	ENSTBEG00000005405	1 retrocopy	retro_tbel_388,