RetrogeneDB ID: retro_itri_1318

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393439.1:2494698..2495781(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: UBAP1
• Ensembl ID: ENSSTOG00000028294
• Aliases: None
• Description: ubiquitin associated protein 1 [Source:HGNC Symbol;Acc:12461]

Sequence

>retro_itri_1318
AGCAGAGTGCCACGAAACAAAGTTCTCAGCCCACCCCACACAGAGGCAGGTTTCAGTCCTGCTGATTTCGAGTGTGAAGA
AGACCCATTTGATAATGTGGAGTTGAAAACCATTGATGAGAGGGAAGAGCTGAGAAATACTCTGGTAGGAACCACTGGAC
CCATTATGGCTCAGTGACTGGACGGCAACTTGCCCAGAGGAGGCTCTGGGTCTGTGTTACAGGATGCGGAGGTCTTGGCA
TCCTTGGAACGGGCAACCCTAGGTTTCAAGCCTCTTCATAAACCCAAGGGCTTCATAACCTTACCACAGTTGGGCAACTG
TGAAAAGATGCCGCTGTCTTCCAGAGTGTCCCTGCTCCCTATCCCTGCAGTCAGCAGTATCAAATCTCTGTCCTTCCCGA
CTCTGGTGACAGCAACCAGAAGACAGTCCAGCTGGCAAGCCCTTTCCATAGCACATCCTGCCTCCGCAGTGGCATGTTCC
GGAATTCCCTAAAGCCTTCCACCCAAAGCAGTGCCAGTGAGCTCAATGGCTTTGAACTTGGACAGTGGCACCGAGGTGCC
AACCCTGACGTCCTCTCAGATGCCTTCCCTGTCTGTCCTGTCTGTGAGAAGGAGTGAGGGTGTGAATGAGGTGTGAAGAC
CATCACCTCCAAGTACAGGCCCCACAGTTACCCCTCCAGGTTTCCCAGTGTCACAAGTGCCCAACGTGCCCAGCTGTCCC
CAGGCCTACTCTGAACCGCAAACACTATCTCCAAGTGAGCGGCAGTGTGTGGAGACGTGGTTAACATGGGTACTCAGAGG
AGCGTGGCCTGAGAGCCATGAAGAAGGGAGAGAATATCGAGCAGATTCTCGACTATCTCTTTGCACATGGTCAGCTTTTG
AGAAGGGCTTCGACCCTCTCCTAGTGGCAGAGGCCCTGGAAATGCACTGATGTTCAGAAGACAAGATGATGAAGTTTCTC
CAGTTAATGAGCACATTTAAGGAAACGGGCTTTGAAGTGAAAGACATTAAGGAAGTTTTGCTGTCACACAACAATGACTG
GGACAATGCTTTGGAAGACGTCATGGCTCGGGCTGGAGCCAGC

Alignment

ORF - retro_itri_1318 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.03 %
• Parental protein coverage: 72.91 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  SSATKQKVLSPPHTKADFNPADFECEEDPFDNLELKTIDEKEELRNILVGTTGPIMAQLLDNNLPRGGSG
          S.....KVLSPPHT.A.F.PADFECEEDPFDN.ELKTIDE.EELRN.LVGTTGPIMAQ.LD.NLPRGGSG
Retrocopy SRVPRNKVLSPPHTEAGFSPADFECEEDPFDNVELKTIDEREELRNTLVGTTGPIMAQ*LDGNLPRGGSG

Parental  SVLQDEEVLASLERATLDFKPLHKPNGFITLPQLGNCEKMSLSSKVSLPPIPAVSNIKSLSFPKLDSDDS
          SVLQD.EVLASLERATL.FKPLHKP.GFITLPQLGNCEKM.LSS.VSL.PIPAVS.IKSLSFP.L.....
Retrocopy SVLQDAEVLASLERATLGFKPLHKPKGFITLPQLGNCEKMPLSSRVSLLPIPAVSSIKSLSFPTLVTATR

Parental  NQKTVKLASTFHSTSCLRSGMFRNSLKP-STQSSASELNGDHTLGLSALNLDSGTEVPTLTSSQMPSLSV
          .Q......S..H..S.........SL.P.....S...LN.D.......L..........L..........
Retrocopy RQSSWQALSIAHPASAVACSGIP*SLPPKAVPVSSMALNLDSGTEVPTLTSSQMPSLSVLSVRRSEGVNE

Parental  LSVCTEESSPPNTGPTVTPPNFSVSQVPNMPSCPQVYSELQTLSPSERQCVET-VVNM-GYSYERVLRAM
          .......S..P...P...P....VSQVPN.PSCPQ.YSE.QTLSPSERQCVET.VVNM.GYS.ER.LRAM
Retrocopy V*RPSPPSTGPTVTPPGFP----VSQVPNVPSCPQAYSEPQTLSPSERQCVET<VVNM<GYSEERGLRAM

Parental  KKKGENIEQILDYLFAHGQLC-EKGFDPLLVEEALEMHQCSEEKMMEFLQLMSKFKEMGFELKDIKEVLL
          .KKGENIEQILDYLFAHGQL..EKGFDPLLV.EALEMH.CSE.KMM.FLQLMS.FKE.GFE.KDIKEVLL
Retrocopy -KKGENIEQILDYLFAHGQLL<EKGFDPLLVAEALEMH*CSEDKMMKFLQLMSTFKETGFEVKDIKEVLL

Parental  LHNNDQDNALEDLMARAGAS
          .HNND.DNALED.MARAGAS
Retrocopy SHNNDWDNALEDVMARAGAS

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_1318 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1318 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 6 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Erinaceus europaeus	ENSEEUG00000011672	1 retrocopy	retro_eeur_466,
Myotis lucifugus	ENSMLUG00000013063	1 retrocopy	retro_mluc_2305,
Otolemur garnettii	ENSOGAG00000015802	1 retrocopy	retro_ogar_557,
Ochotona princeps	ENSOPRG00000009100	3 retrocopies	retro_opri_355, retro_opri_477, retro_opri_680,
Ictidomys tridecemlineatus	ENSSTOG00000028294	1 retrocopy	retro_itri_1318 ,
Tarsius syrichta	ENSTSYG00000013035	2 retrocopies	retro_tsyr_1908, retro_tsyr_846,