RetrogeneDB ID: retro_itri_193

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393279.1:23381365..23381810(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSTOG00000024999
• Aliases: None
• Description: None

Sequence

>retro_itri_193
TTTCTTCAGAAAATGCTGCAAGAGACTTTTCAGAAATTGTCTCCAAACACCTTGTGACATCCCACAAGAAGAGTATGCTG
GGAAATGGGACCTATAATATAAATGTCATTATGGCTGCACTTCAGACCAAAGGTTATGAAGCTGTTTCGTGGGCAAAACA
CAGGATGTCATTGTCATTGGTCTCACTAATATCATGGGCTTCATCATGAATCTGCTTTCCACCCTGTGCTGGGGTACACT
CGAGTTTTTGCCTATCAAAAGGCAGCCCTGGATCTGTGTTCAAGAGATGAGCAAGGCATGCTACAACTTCAACTTACAAC
TCAAGATGCCCAAGTGGATTGGAGGCAAGAGCAAACTCAGGTAATTTCTAAAACATAATTTGCGAGCAGCGAATCATGAA
CTCCTGCTGATGGTACCTGAAGAGAAGGAAGCCCATCAAAGTTGG

Alignment

ORF - retro_itri_193 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.54 %
• Parental protein coverage: 73.27 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  FTRETLQEIFQRLSPNTM-VTPHKKSMLGNGNYDVNVIMAALQTKGYEAVWWDKRR-DVGVIALTNVMGF
          F....LQE.FQ.LSPNT..VT.HKKSMLGNG.Y..NVIMAALQTKGYEAV.W.K.R.DV.VI.LTN.MGF
Retrocopy FLQKMLQETFQKLSPNTL<VTSHKKSMLGNGTYNINVIMAALQTKGYEAVSWAKHR<DVIVIGLTNIMGF

Parental  IMNLPSSLCWGPLK-LPLKRQHWICVREVGGAYYNLDSKLKMPEWIGGESELRKFLKHHLRGKNCELLLV
          IMNL.S.LCWG.L..LP.KRQ.WICV.E...A.YN....LKMP.WIGG.S.LR.FLKH.LR..N.ELLL.
Retrocopy IMNLLSTLCWGTLEFLPIKRQPWICVQEMSKACYNFNLQLKMPKWIGGKSKLR*FLKHNLRAANHELLLM

Parental  VAEEVEAHQSW
          V.EE.EAHQSW
Retrocopy VPEEKEAHQSW

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_193 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_193 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 16 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000010171	1 retrocopy	retro_btau_1508,
Canis familiaris	ENSCAFG00000001379	1 retrocopy	retro_cfam_1500,
Choloepus hoffmanni	ENSCHOG00000001723	2 retrocopies	retro_chof_1576, retro_chof_233,
Dasypus novemcinctus	ENSDNOG00000016015	1 retrocopy	retro_dnov_128,
Equus caballus	ENSECAG00000015546	1 retrocopy	retro_ecab_251,
Felis catus	ENSFCAG00000002821	1 retrocopy	retro_fcat_565,
Macropus eugenii	ENSMEUG00000002899	2 retrocopies	retro_meug_1507, retro_meug_531,
Microcebus murinus	ENSMICG00000011798	1 retrocopy	retro_mmur_1202,
Myotis lucifugus	ENSMLUG00000003764	1 retrocopy	retro_mluc_1868,
Mus musculus	ENSMUSG00000022426	1 retrocopy	retro_mmus_3014,
Otolemur garnettii	ENSOGAG00000007520	3 retrocopies	retro_ogar_1462, retro_ogar_2911, retro_ogar_3487,
Pteropus vampyrus	ENSPVAG00000010148	1 retrocopy	retro_pvam_181,
Rattus norvegicus	ENSRNOG00000014440	2 retrocopies	retro_rnor_2954, retro_rnor_906,
Sarcophilus harrisii	ENSSHAG00000015931	1 retrocopy	retro_shar_643,
Ictidomys tridecemlineatus	ENSSTOG00000024999	1 retrocopy	retro_itri_193 ,
Tarsius syrichta	ENSTSYG00000008846	1 retrocopy	retro_tsyr_1076,