RetrogeneDB ID: retro_itri_151

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393443.1:1820247..1821087(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSTOG00000005964
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: HUS1
• Ensembl ID: ENSSTOG00000027204
• Aliases: None
• Description: HUS1 checkpoint homolog (S. pombe) [Source:HGNC Symbol;Acc:5309]

Sequence

>retro_itri_151
ATGAAGTTTCGTGCCAAGATCACCAACAAGGGCTTTATAGAGCTCTTCATTCAGGTCAGTGGCACCATAGCAAAGCTGGC
AAAGGTCTGCGTGCTCCATGTGTGCCAAGACAAACTGTGCTTTGGTCCCACAGGCCCCAGGGCCACCCGAGAGGCCAGGC
TGTGGTGCGAAGTGATGCGGGGAGCCTCCTTCTACCAGTTTAACATGGAAGGTGTTTCTGAAGAGCTCAGTGAGATTTAT
CTAGAGCTGATATCAGAGCATTTGTACAGAGCTGTAAGAAGTGCAGGAAATGCTGCCTCCCTGAAAATCCAGCTGACCAA
CAAGCGTCGCCCTTGCCTCACAGTGGCGATAGAGCTGGCATCGCGCACTGGGCACACCCATGTGATGGTCCATGATCTAC
CTGTGAGGGTGCTTCCCAGAAGATGGTGGAAAGAGTACCCAGAGCCCAGTATTCAAGTCTCTGATGTGAGTGTTTATCTG
CCAGCTTTGAAGACCCTGAAGAGCATTGTGGAAAGGATGGCCAACATGGGCGATAACGTGCTGGTGGAAGCAAATCTAAA
TGGTAAAATGAACTTGAGTATAGAAACTGATGTAGTATCTATTAAAAGTTATTTTGAAAATCTTGGAAATCCTTTAAAGT
CTGCTCATAGCGTGACCCAAGACAGAGACCCGGAGAACATGGTGCAAGTGCGGGTAGAGAACAGGAAACTTCTGCAGTTT
TTTGAGGGACAGCAGATAAATCCCAAAACGGCTTTATGCAATATTTTGAGCAATACTCTTCTTCATCTTGTTTTGGTTCA
TGAAGATGTCTCTCTTCAGTATTTCATTCCTGCCTTATAA

Alignment

ORF - retro_itri_151 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 50.36 %
• Parental protein coverage: 99.64 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MKFRAKIVDAACLNQFTRVSNMIAKLAKTCTLRISPNKLNFILSDKLASGGVSMWCELEQENFFSEFQME
          MKFRAKI........F..VS..IAKLAK.C.L.....KL.F......A......WCE......F..F.ME
Retrocopy MKFRAKITNKGFIELFIQVSGTIAKLAKVCVLHVCQDKLCFGPTGPRATREARLWCEVMRGASFYQFNME

Parental  GVSAENNEIYLELTSENLSRALKTTQNARSLKIKLTNKHFPCLTISVELQLSVSSSSRIVTHDIPITIIP
          GVS.E..EIYLEL.SE.L.RA.....NA.SLKI.LTNK..PCLT...EL..S.........HD.P....P
Retrocopy GVSEELSEIYLELISEHLYRAVRSAGNAASLKIQLTNKRRPCLTVAIELA-SRTGHTHVMVHDLPVRVLP

Parental  RRLWKDLREPSVPDSDVSIYLPVLKTMRSVVEKMKNISNHLIIEANLNGDLNLKIETELVCITTHFKDLG
          RR.WK...EPS...SDVS.YLP.LKT..S.VE.M.N.......EANLNG..NL.IET..V.I...F..LG
Retrocopy RRWWKEYPEPSIQVSDVSVYLPALKTLKSIVERMANMGDNVLVEANLNGKMNLSIETDVVSIKSYFENLG

Parental  NPPLASENTSQNRNPEEMAEVHIDIKKLLQFLAGQQVNPTKAICNIVNNRIVHFDLLHEDVSLQYFIPAL
          NP........Q.R.PE.M..V.....KLLQF..GQQ.NP..A.CNI..N...H..L.HEDVSLQYFIPAL
Retrocopy NPLKSAHSVTQDRDPENMVQVRVENRKLLQFFEGQQINPKTALCNILSNTLLHLVLVHEDVSLQYFIPAL

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_151 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_151 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 9 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000001764	4 retrocopies	retro_chof_1438, retro_chof_1958, retro_chof_2084, retro_chof_898,
Dipodomys ordii	ENSDORG00000006582	1 retrocopy	retro_dord_182,
Echinops telfairi	ENSETEG00000009941	2 retrocopies	retro_etel_1764, retro_etel_1797,
Nomascus leucogenys	ENSNLEG00000004497	1 retrocopy	retro_nleu_2321,
Oryctolagus cuniculus	ENSOCUG00000027263	1 retrocopy	retro_ocun_761,
Otolemur garnettii	ENSOGAG00000012683	1 retrocopy	retro_ogar_1,
Pongo abelii	ENSPPYG00000025821	1 retrocopy	retro_pabe_151,
Sorex araneus	ENSSARG00000012348	1 retrocopy	retro_sara_391,
Ictidomys tridecemlineatus	ENSSTOG00000027204	1 retrocopy	retro_itri_151 ,