RetrogeneDB ID: retro_itri_837

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393331.1:5814018..5814580(+)
• Located in intron of: ENSSTOG00000002142

Retrocopy information

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

Parental gene information

• Parental gene symbol: TMEM165
• Ensembl ID: ENSSTOG00000025897
• Aliases: None
• Description: transmembrane protein 165 [Source:HGNC Symbol;Acc:30760]

Sequence

>retro_itri_837
CTATGCTTGACCCTGATGACTTGCTTATCAGTTCTCTTTGGCTATGCTACCACCGTCATCCCCAGGGTGTACAGGTATTA
TGTCTTAACTGCATTATTTGTCATTTTTGGCATTAGAATGCTTCGGGAAGGCTTAAAGATAAGCCCAGATGCAGGTCAAG
AGGAACTGGAAGAAGTTCTGCAGAACTAAAGAAGAAGGATGAAGGATTTCAATGAACCAAACTCTTAAATGGATCAGGAG
ATGTTGAAACAGGTACAAGCACAACAATACCTCAGAAAACGTTGCATGTTATTTCACCCATTTTTGTTCAAGCTCTTATA
CTAACATCCTTAGCAGAATGGGGAGATCACTCTCATCTCACTACAATTGTTCTGGCAGCTAGAGAGGATCCCTAGGGTGT
AGTGGTGGGTGGAACAGTGGGACACTGATTATACACTGGATTGGCAGTAATTGGAGGAAGGAATGATAACAAAAAATCTC
TGTCAGAACTGTGATAATAGGAGGTGTTGTGTTTTTGGCGTTTGCATTTTCTGCACTATTTATGTGTCCTGATTCTGGTT
TT

Alignment

ORF - retro_itri_837 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.85 %
• Parental protein coverage: 59.01 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LALALMTCLSVLFGYATTVIPRVYTYYVSTALFAIFGIRMLREGLKMSPDEGQEELEEV-QAELKKKDEE
          L.L.LMTCLSVLFGYATTVIPRVY.YYV.TALF.IFGIRMLREGLK.SPD.GQEELEEV..AELKKKDE.
Retrocopy LCLTLMTCLSVLFGYATTVIPRVYRYYVLTALFVIFGIRMLREGLKISPDAGQEELEEV<SAELKKKDEG

Parental  FQRTKLLNGPGDVETGTSTTIPQKKWLHFISPIFVQALTLTFLAEWGDRSQLTTIVLAAREDPYGVAVGG
          FQ.TKLLNG.GDVETGTSTTIPQK..LH.ISPIFVQAL.LT.LAEWGD.S.LTTIVLAAREDP.GV.VGG
Retrocopy FQ*TKLLNGSGDVETGTSTTIPQKT-LHVISPIFVQALILTSLAEWGDHSHLTTIVLAAREDP*GVVVGG

Parental  TVGHCLCTGLAVIGGRMIAQK-ISVRTVTIIGGVVFLAFAFSALFISPDSGF
          TVGH.L.TGLAVIGGR....K.ISVRTV.IIGGVVFLAFAFSALF..PDSGF
Retrocopy TVGH*LYTGLAVIGGRNDNKK<ISVRTV-IIGGVVFLAFAFSALFMCPDSGF

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_837 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_837 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000018339	1 retrocopy	retro_cjac_574,
Ictidomys tridecemlineatus	ENSSTOG00000025897	1 retrocopy	retro_itri_837 ,