RetrogeneDB ID: retro_itri_1286

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393428.1:2472220..2473081(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: BZW2
• Ensembl ID: ENSSTOG00000002506
• Aliases: None
• Description: basic leucine zipper and W2 domains 2 [Source:HGNC Symbol;Acc:18808]

Sequence

>retro_itri_1286
GTAAAAAAGCTGCTGCTGTTCTTAAAGGGTTTTTCAGAGTCGGAGAGGAACAAGCTGGCTATGTTGACTGGTGTTCTTCT
GGCTAATGGAACACTTAATGCATCCATTCTTAATAGCCTTTATAATGAGAATTTGGTTAAAGAAGGAGTTTCAGCAGCTT
TTGCTGTAAAACTCTTTAAAAAATCATGGATAAATGAAAAAGACATCAACGCAGTATCTGCAAGTCTTCGGAAAGTCAGC
ATGGATAACAGACTGATGGAACTTTTTCCTGCCAACAAGCAAAGCGTTGAACACTTCACAAAGTATTTTACTGAGGCAGG
CTTGAAAGAGCTTTCAGAGTATGTTCGGAATCAACAGACCATAGGAGCGCGCAAGGAGCTCCAGAAAGAACTTCAAGAAC
AGATGTCCCGTGGCGATCCATTTAAGGATATAATTTTATATGTCAAGGAAGAGATGAAAAGAAACAACATTCCAGAACCA
GTTGTCATTGGGATAGTCTGGTCAAGTGTAATGAGCACCGTGGAGTGGAACAAAAAAGAGGAGCTTGTAGCAGAGCAAGC
CATCAAGCACTTAAAGCAATACAGCCCTCTACTTGCTGCCTTTACTACTCAAGGTCAGTTTGAGCTGACTCTGTTACTGA
AGATTCAGGAGTATTGTTATGACAACATTCATTTCATGAAAGCCTTCCAGAAAATAGTGGTGCTTTTTTATAAAGCTGAA
GTCCTGAGTGAAGAGCCGATTCTGAAGTGGTATAAAGATGCACATGTTGCAAAGGGGAAAAGTGTCTTCCTTGAACAAAT
GAAAAAGTTTGTTGAATGGCTCAAAAATGCTGAAGAAGAATCTGAGTCTGAAGCTGAAGAA

Alignment

ORF - retro_itri_1286 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.17 %
• Parental protein coverage: 99.65 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MKKLLLFLKAFSETEQTKLAMLSGILLGNGTLPATILTSLFTDSLVKEGIAASFAVKLFK-AWMAEKDAN
          .KKLLLFLK.FSE.E..KLAML.G.LL.NGTL.A.IL.SL....LVKEG..A.FAVKLFK..W..EKD.N
Retrocopy VKKLLLFLKGFSESERNKLAMLTGVLLANGTLNASILNSLYNENLVKEGVSAAFAVKLFKKSWINEKDIN

Parental  SVTSSLRKANLDKRLLELFPVNRQSVDHFAKYFTDAGLKELSDFLRVQQSLGTRKELQKELQERLSQECP
          .V..SLRK...D.RL.ELFP.N.QSV.HF.KYFT.AGLKELS...R.QQ..G.RKELQKELQE..S...P
Retrocopy AVSASLRKVSMDNRLMELFPANKQSVEHFTKYFTEAGLKELSEYVRNQQTIGARKELQKELQEQMSRGDP

Parental  IKEVVLYVKEEMKRNDIPETAVIGLLWTCIMNAVEWNKKEELVAEQALKHLKQYAPLLAVFSSQGQSELI
          .K...LYVKEEMKRN.IPE..VIG..W...M..VEWNKKEELVAEQA.KHLKQY.PLLA.F..QGQ.EL.
Retrocopy FKDIILYVKEEMKRNNIPEPVVIGIVWSSVMSTVEWNKKEELVAEQAIKHLKQYSPLLAAFTTQGQFELT

Parental  LLQKVQEYCYDNIHFMKAFQKIVVLFYKADVLSEEAILKWYKEAHVAKGKSVFLDQMKKFVEWLQNAEEE
          LL.K.QEYCYDNIHFMKAFQKIVVLFYKA.VLSEE.ILKWYK.AHVAKGKSVFL.QMKKFVEWL.NAEEE
Retrocopy LLLKIQEYCYDNIHFMKAFQKIVVLFYKAEVLSEEPILKWYKDAHVAKGKSVFLEQMKKFVEWLKNAEEE

Parental  SESEGEE
          SESE.EE
Retrocopy SESEAEE

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_1286 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1286 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
Dasypus novemcinctus	ENSDNOG00000001663	4 retrocopies	retro_dnov_2177, retro_dnov_2422, retro_dnov_2649, retro_dnov_575,
Equus caballus	ENSECAG00000022038	1 retrocopy	retro_ecab_1121,
Macaca mulatta	ENSMMUG00000017045	1 retrocopy	retro_mmul_1457,
Ochotona princeps	ENSOPRG00000005256	2 retrocopies	retro_opri_665, retro_opri_9,
Pongo abelii	ENSPPYG00000017763	1 retrocopy	retro_pabe_2385,
Pteropus vampyrus	ENSPVAG00000014571	1 retrocopy	retro_pvam_481,
Ictidomys tridecemlineatus	ENSSTOG00000002506	1 retrocopy	retro_itri_1286 ,
Tarsius syrichta	ENSTSYG00000009806	1 retrocopy	retro_tsyr_1923,
Tursiops truncatus	ENSTTRG00000009867	1 retrocopy	retro_ttru_162,