RetrogeneDB ID: retro_itri_166

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393519.1:315670..316387(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSTOG00000028404
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSTOG00000009955
• Aliases: None
• Description: None

Sequence

>retro_itri_166
ATGGTGGCGAGCAGCTCGCTGGAGGCGGTGCGGAGAAAGATCCGGAGCCTACAGGAGCATGCGGACGCAGCGGAGGAGCG
GGCGGACAGTCTGCAGCACGAGCTGGACCTTGAAAGGAAGCTGAGGGAGACCGCTGAAGCTGATGTAGCTTCTCTGAACA
GACGCATCCAGCTGGTTGAGGAAGAGTTGGATCCTGCTCAGAAGCGTCTGGCAACAGCTTTGCAGAAGCTGGTGGAGGCT
GAAAGAGCAGCAGATGAAAGCGAGAGAGGCATGAAAGTCATTGAAAGAAGAGCCCAAAAGGATGAAGAAAAAAGGGAAAT
TCAGGAGATCCAACTGAAAGAGGCCAAGCACATTGCTGAAGATGCCGACCGAAAATATGAAGAGGTGGCCGGTAAGCTGG
TCATCATTGAAAGTGACCTGGAACGTGCAGAGGAGCGGGCTGAGTTCTCAGAAGGCCAAGTTCAACAGCTGGAAGAGCAA
TTAAGAATGATGGATCAGACCTTGACAACATTAATGGCTGCAGAGGATAAGTACTCTCAGAAGGAAGACAAATATGAGGA
AGAGATCAAGGTCCTTTCTGACAAGCTGAAGGAGAGGTCAGTAACTAAATTGGAGAAAAGCATTGATGACTTAGAAGAGA
AAGTGGCTCATGCCAAAGAAGAAAACCTTAGTATGCATCAGATGCTGGATCAGACTTTCCTGGAGTTAAACAACATG

Alignment

ORF - retro_itri_166 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.44 %
• Parental protein coverage: 66.56 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LVSLQKKLKGTEDELDKYSEALKDAQEKLELAEKKATDAEADVASLNRRIQLVEEELDRAQERLATALQK
          L.....K........D...E.....Q..L.L..K....AEADVASLNRRIQLVEEELD.AQ.RLATALQK
Retrocopy LEAVRRKIRSLQEHADAAEERADSLQHELDLERKLRETAEADVASLNRRIQLVEEELDPAQKRLATALQK

Parental  LEEAEKAADESERGMKVIESRAQKDEEKMEIQEIQLKEAKHIAEDADRKYEEVARKLVIIESDLERAEER
          L.EAE.AADESERGMKVIE.RAQKDEEK.EIQEIQLKEAKHIAEDADRKYEEVA.KLVIIESDLERAEER
Retrocopy LVEAERAADESERGMKVIERRAQKDEEKREIQEIQLKEAKHIAEDADRKYEEVAGKLVIIESDLERAEER

Parental  AELSEGKCAELEEELKTVTNNLKSLEAQAEKYSQKEDKYEEEIKVLSDKLKEAETRAEFAERSVTKLEKS
          AE.SEG....LEE.L......L..L.A...KYSQKEDKYEEEIKVLSDKLKE........E.S...LE..
Retrocopy AEFSEGQVQQLEEQLRMMDQTLTTLMAAEDKYSQKEDKYEEEIKVLSDKLKERSVTK--LEKSIDDLEEK

Parental  IDDLEEK
          .....E.
Retrocopy VAHAKEE

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_166 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_166 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 11 parental genes, and 28 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000016966	1 retrocopy	retro_cfam_2167,
Choloepus hoffmanni	ENSCHOG00000012788	11 retrocopies	retro_chof_1194, retro_chof_1272, retro_chof_1360, retro_chof_1789, retro_chof_1829, retro_chof_2309, retro_chof_346, retro_chof_399, retro_chof_412, retro_chof_770, retro_chof_967,
Callithrix jacchus	ENSCJAG00000004355	2 retrocopies	retro_cjac_2200, retro_cjac_691,
Macropus eugenii	ENSMEUG00000014581	2 retrocopies	retro_meug_1944, retro_meug_2161,
Pongo abelii	ENSPPYG00000006534	1 retrocopy	retro_pabe_624,
Rattus norvegicus	ENSRNOG00000018184	1 retrocopy	retro_rnor_734,
Ictidomys tridecemlineatus	ENSSTOG00000009955	1 retrocopy	retro_itri_166 ,
Ictidomys tridecemlineatus	ENSSTOG00000023525	6 retrocopies	retro_itri_1453, retro_itri_1558, retro_itri_1837, retro_itri_231, retro_itri_674, retro_itri_709,
Ictidomys tridecemlineatus	ENSSTOG00000024252	1 retrocopy	retro_itri_1858,
Tursiops truncatus	ENSTTRG00000003762	1 retrocopy	retro_ttru_446,
Vicugna pacos	ENSVPAG00000003277	1 retrocopy	retro_vpac_424,