RetrogeneDB ID: retro_itri_396

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393289.1:838617..839429(+)
• Located in intron of: ENSSTOG00000001402

Retrocopy information

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

Parental gene information

• Parental gene symbol: TOR1B
• Ensembl ID: ENSSTOG00000004915
• Aliases: None
• Description: torsin family 1, member B (torsin B) [Source:HGNC Symbol;Acc:11995]

Sequence

>retro_itri_396
CTCATCGCCTCGACTCTCAAGTTGGATTTGGAACAGAAGCTGTTTGGACAGCATCTGGCCACGGAAGTGATTCTCAAGGC
ACTGATAGGCTTCAAGAAAGCAGAAATCCCAAGAAATCACTGACCCTGTCTTTGCATGGCCAGGCTGGCACAGGCAAGAA
TTTTGTTAGTTAAATTGTGGCTGAAAATCTTCACCCAAAAGGCCTGAAGAGCGACTTTGTCCACCTGTTTGTATCAACTC
TGCACTTCCCTCATGAGCAGAAGATTAAACTGTACCAGTAGCAGCTACAGAAGTGGATTCATGGAAATGTGAGTGCCTGC
ACCAGCTTGGCTTTCATATTTGAGAAGATTCATAAGTTGCATCCTGGGATCATCGATTCCATCAAGCCCTTCCTAGACTA
CTATGAGCAGTTGGATAGGGTATTCTACTGCAAAGCCATCTTCATCTTTCTCAGCAATGCAGGTGGAGACCTCATAACTA
AGATGGTTCTGGACTTCTGGAGGGCAGGAAGAAAGAGGGAAGACATCCAGCTGAAGGACCTGGAACCTGTGCTGTCTGTT
GGAGTCTTCAACAATAAACACAGTGGCCTGTGGCACAGTGGGCTAATAGAAAGAAACCTTATCAACTACTTCATCCCCTT
GGAGTACAGACACATGAAGATGTATGTGAGGGCAGAGATGCAGTCCTGTGGTGTTGCTGTAGATGAAGACATATTCACCA
GGGTGGCAGAGGAAATGACGTTTTTCCCCAAAGATGAGAAAATCTATTCAGACAAGGGCTGTAAGAGCGTGCAGTCCCGG
CTAGATTTCCAC

Alignment

ORF - retro_itri_396 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.0 %
• Parental protein coverage: 98.92 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LAPAALKLDLEQKLFGQHLATEVILKALTGFKN-NKNPKKPLTLSLHGWAGTGKNFVSQIVAENLHPKGL
          L....LKLDLEQKLFGQHLATEVILKAL.GFK....NPKK.LTLSLHG.AGTGKNFVS.IVAENLHPKGL
Retrocopy LIASTLKLDLEQKLFGQHLATEVILKALIGFKK<SRNPKKSLTLSLHGQAGTGKNFVS*IVAENLHPKGL

Parental  KSNFVHLFVSTLHFPHEQKIKLYQEQLQKWIRGNVSACASSVFIFDEMDKLHPGIIDAIKPFLDYYEQVD
          KS.FVHLFVSTLHFPHEQKIKLYQ.QLQKWI.GNVSAC.S..FIF....KLHPGIID.IKPFLDYYEQ.D
Retrocopy KSDFVHLFVSTLHFPHEQKIKLYQ*QLQKWIHGNVSACTSLAFIFEKIHKLHPGIIDSIKPFLDYYEQLD

Parental  GVSYCKAIFIFLSNAGGDLITKTALDFWRAGRKREDIQLKDLEPVLSVGVFNNKHSGLWRSGLIDRNLID
          .V.YCKAIFIFLSNAGGDLITK..LDFWRAGRKREDIQLKDLEPVLSVGVFNNKHSGLW.SGLI.RNLI.
Retrocopy RVFYCKAIFIFLSNAGGDLITKMVLDFWRAGRKREDIQLKDLEPVLSVGVFNNKHSGLWHSGLIERNLIN

Parental  YFVPFLPLEYKHVKMCVRAEMRARGAAVDEDIVTRVAEEMTFFPKDEKIYSDKGCKTVQSRLDFH
          YF.P...LEY.H.KM.VRAEM...G.AVDEDI.TRVAEEMTFFPKDEKIYSDKGCK.VQSRLDFH
Retrocopy YFIP---LEYRHMKMYVRAEMQSCGVAVDEDIFTRVAEEMTFFPKDEKIYSDKGCKSVQSRLDFH

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_396 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_396 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000020343	1 retrocopy	retro_cjac_1349,
Otolemur garnettii	ENSOGAG00000009763	1 retrocopy	retro_ogar_602,
Ictidomys tridecemlineatus	ENSSTOG00000004915	1 retrocopy	retro_itri_396 ,