RetrogeneDB ID: retro_itri_990

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393357.1:2181097..2181848(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NUP43
• Ensembl ID: ENSSTOG00000013449
• Aliases: None
• Description: nucleoporin 43kDa [Source:HGNC Symbol;Acc:21182]

Sequence

>retro_itri_990
ATAGAGGAAATTTATGCCAAGTTTGTGTTTCAGAAAATCAGCAAAACCCACTGGCAACCAGTGTCTCCAGGAAGCCTGCA
GAGCACACATCCTTTGCTACTGGCTCTTGGGACAATGAGAAAAATTATGTTTCATTGTGGTCTATTGGAGATTTGGGAAA
TTTGATGGAGGATTCAAAAGAGACGATCAATTATTTTGTGATATCAAACACCATGGTGATGTCATGAGTTTACAGTTTTT
TTGACCAGGAAAGAATTATAGCTGCTTCATCAATAGGATGTGTAACAGTTTTTCTCCATCATCCAAATAACCAGACTGTC
AGTCAACCAGCAGTGGACAGCAGCCCACTACCATATGGGGCTTTGCAGTCCTTCCTACAACAATGCCCCACATACAGGCA
TTGTATGCAACAACCCAGAAATTGTCATGTTTGGAGAGGATCGTTGAATAAATCTTTTCAGAGTTGATCACATGGAAGCT
ATAAGAACTATAGATAATGCAGATAGCAGTACACTACATGCTCTGAGCTTCCTTCAAATTCCTGAGATACTTACAGTAGA
ATCAGGTGGACAGTTAAAAATATGGAACTTCAGAAAACAAGGAAATGAACTTTCTCAGATATTATCATTGACTGGTGACT
GAACGCCACTTCATTGTGTTGACAAACATCTCAACCATTAGCAGTGTTGTAGCTATTGGTGTCCAGGATGGAAGGCTGAG
TATTTGTGATAGACAAGATATTATGTGTGTA

Alignment

ORF - retro_itri_990 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.46 %
• Parental protein coverage: 66.93 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  MEEIYAKFVSQKISKTRWRPVPPGSLQTAE-TFATGSWDNEENYVSLWSIGD-FGNLDSDGGFEGDHQLL
          .EEIYAKFV.QKISKT.W.PV.PGSLQ.....FATGSWDNE.NYVSLWSIGD.FG..D..GGF..D.QL.
Retrocopy IEEIYAKFVFQKISKTHWQPVSPGSLQSTH<SFATGSWDNEKNYVSLWSIGD<FGKFD--GGFKRDDQLF

Parental  CDIKHHGDVMDLQFF-DQERIVAASSTGCVTVFLHHPNNQT-LSVNQQWTAAHYHTGPGSPSYSSAPCTG
          CDIKHHGDVM.LQFF.DQERI.AASS.GCVTVFL.H..N...LSVNQQWTAAHYH.G..SPSY..AP.TG
Retrocopy CDIKHHGDVMSLQFF>DQERIIAASSIGCVTVFL-HHPNNQ>LSVNQQWTAAHYHMGLCSPSYNNAPHTG

Parental  IVCDNPEIVTVGEDGRINLFRVDHKEAVRTIDNADSSTLHAVTFLRTPEILTVNSIGQLKIWDFRQQGNE
          IVC.NPEIV..GED..INLFRVDH.EA.RTIDNADSSTLHA..FL..PEILTV.S.GQLKIW.FR.QGNE
Retrocopy IVCNNPEIVMFGEDR*INLFRVDHMEAIRTIDNADSSTLHALSFLQIPEILTVESGGQLKIWNFRKQGNE

Parental  PSQILSLRTGDRVPLHCVDRHPNQ-QHVVATGGQDGMLSIWDVRQGTMPV
          .SQILSL.TGD..PLHCVD.H.N....VVA.G.QDG.LSI.D.RQ..M.V
Retrocopy LSQILSL-TGD*TPLHCVDKHLNH>SSVVAIGVQDGRLSICD-RQDIMCV

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_990 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_990 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 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000009426	1 retrocopy	retro_chof_1765,
Cavia porcellus	ENSCPOG00000010815	1 retrocopy	retro_cpor_481,
Macaca mulatta	ENSMMUG00000009830	1 retrocopy	retro_mmul_1962,
Monodelphis domestica	ENSMODG00000016808	2 retrocopies	retro_mdom_199, retro_mdom_353,
Ictidomys tridecemlineatus	ENSSTOG00000013449	1 retrocopy	retro_itri_990 ,
Tarsius syrichta	ENSTSYG00000000944	1 retrocopy	retro_tsyr_267,