RetrogeneDB ID: retro_itri_1686

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393640.1:313226..314460(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HSPA5
• Ensembl ID: ENSSTOG00000011243
• Aliases: None
• Description: heat shock 70kDa protein 5 (glucose-regulated protein, 78kDa) [Source:HGNC Symbol;Acc:5238]

Sequence

>retro_itri_1686
GTCTTCAAAGTCATAGCCACCAATAGAGATACTCATCGAGGTGAAGAAGACTTTGACTAGCGTGTTATAGAACATTTCAT
CAGGCTGTACAAAAAGAAGACTGGCAAATATGGTAGGAAAGAAAACAGAGCTGTGAAGAAACTCCAGCATAAATTAGAAA
AGGCCAAGTGGGCCCTGTCTGCCCAACATTAAGCAAGAATTAGAATTGAGTTCTTCTATGAAGGAGAAGACTTTTCTGAA
ATCCTGACTCAGGCAAAATTTGAAGAAAAAACATGGTCCTGTTCTGGTCTACCATGAAGCCTGTTCAGAAAGTACTGGAG
GATTCTGACTTGTAGAAGTCTAATATTGATAAGATTGTTCTTGTTGGTGTCTCTAGTCAAATTCCAAAGATTCAGCAACT
TGTTAAAGAGTTCTTTAATGGCAAGGAGCCATTCTGTGGCATAAACCCAGATGAGGCTGTTGCATATGGTGACACTGTCC
AGGCTGGTGTACTCTCTGATGATCAAGATACAGGTGACCTTGATCTGCTTGATGTATGTCCCCTGACATTTGGTATTGAA
ACTGTGGAAGGTGTTATGACCAAAGTGATACCAAGGAACACTGTGGTACCCACCAAGTAGTCTCAGATCTTTTCTACAGC
TTCTGATAAGCAACCTACCATTCCAATCAAGGTCTATGAAGGTAAAGGACCCCTGAAAAAGAACAACCACCTTCCGGGTA
CATTTGATCTCACTGGAATTCCTCCTGTGGGGTCCCCCAGATTGAAGTCACTTTTGAGATACATGTCAATGCTATTCTTT
GGGTGATAGCTAAAGACAAAGGTACAGAGAACAAAAATAACATTACAATTACCAATGATCAAAATTGCCTGACACTTGAA
GAAATTAAAAAGATAGTTAATGATGTTGAGAAGTTTGCTGAGGGAGACAAAAGTCTGAAGGAGCTCACTGATAGTAGGAA
TGAGTTGAAAAGCTATGCCTACTCTCTAAAGTATCAGATTGAAGATAAAGAAAAGTTGAGAGGCAAACTTTCCACTGAAG
ATAAGGGGACTATTGAAAAAGATGTAGAGGAAAAGATTGAATGGCTGGAAAGCCACCAAGAAGCTGACATTGAAGACTTC
AAAACTAAAAAGAAAAAACTAGAAGAAATTGTTCATCCAATTAGCAGCAAATTCTATGGAAGTGTAGGCCCTCCCCCAAC
TGGTGAAGAGAATAGAGCAGAAAGAGATGAGTTG

Alignment

ORF - retro_itri_1686 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.92 %
• Parental protein coverage: 63.3 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VFEVVATNGDTHLGGEDFDQRVMEHFIKLYKKKTGKDVRKDNRAVQKLRREVEKAKRALSSQHQARIEIE
          VF.V.ATN.DTH.G.EDFD.RV.EHFI.LYKKKTGK..RK.NRAV.KL....EKAK.ALS.QH.ARI.IE
Retrocopy VFKVIATNRDTHRGEEDFD*RVIEHFIRLYKKKTGKYGRKENRAVKKLQHKLEKAKWALSAQH*ARIRIE

Parental  SFYEGEDFSETLTRAKFEEL-NMDLFRSTMKPVQKVLEDSDLKKSDIDEIVLVGGSTRIPKIQQLVKEFF
          .FYEGEDFSE.LT.AKFEE..NM.LF.STMKPVQKVLEDSDL.KS.ID.IVLVG.S..IPKIQQLVKEFF
Retrocopy FFYEGEDFSEILTQAKFEEK<NMVLFWSTMKPVQKVLEDSDL*KSNIDKIVLVGVSSQIPKIQQLVKEFF

Parental  NGKEPSRGINPDEAVAYGAAVQAGVLSGDQDTGDLVLLDVCPLTLGIETVGGVMTKLIPRNTVVPTKKSQ
          NGKEP..GINPDEAVAYG..VQAGVLS.DQDTGDL.LLDVCPLT.GIETV.GVMTK.IPRNTVVPTK.SQ
Retrocopy NGKEPFCGINPDEAVAYGDTVQAGVLSDDQDTGDLDLLDVCPLTFGIETVEGVMTKVIPRNTVVPTK*SQ

Parental  IFSTASDNQPTVTIKVYEGERPLTKDNHLLGTFDLTGIPPAPRGVP-QIEVTFEIDVNGILRVTAEDKGT
          IFSTASD.QPT..IKVYEG..PL.K.NHL.GTFDLTGIPP...G.P.QIEVTFEI.VN.IL.V.A.DKGT
Retrocopy IFSTASDKQPTIPIKVYEGKGPLKKNNHLPGTFDLTGIPPV--GSP<QIEVTFEIHVNAILWVIAKDKGT

Parental  GNKNKITITNDQNRLTPEEIERMVNDAEKFAEEDKRLKERIDTRNELESYAYSLKNQIGDKEKLGGKLSS
          .NKN.ITITNDQN.LT.EEI...VND.EKFAE.DK.LKE..D.RNEL.SYAYSLK.QI.DKEKL.GKLS.
Retrocopy ENKNNITITNDQNCLTLEEIKKIVNDVEKFAEGDKSLKELTDSRNELKSYAYSLKYQIEDKEKLRGKLST

Parental  EDKETMEKAVEEKIEWLESHQDADIEDFKAKKKELEEIVQPIISKLYGSAGPPPTGEEDTSERDEL
          EDK.T.EK.VEEKIEWLESHQ.ADIEDF......LEEIV.PI.SK.YGS.GPPPTGEE...ERDEL
Retrocopy EDKGTIEKDVEEKIEWLESHQEADIEDFXXXXXXLEEIVHPISSKFYGSVGPPPTGEENRAERDEL

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_1686 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1686 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 12 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000006880	1 retrocopy	retro_cjac_2221,
Homo sapiens	ENSG00000044574	1 retrocopy	retro_hsap_3005,
Gallus gallus	ENSGALG00000001000	1 retrocopy	retro_ggal_21,
Gorilla gorilla	ENSGGOG00000026879	1 retrocopy	retro_ggor_2082,
Macropus eugenii	ENSMEUG00000016702	1 retrocopy	retro_meug_522,
Mus musculus	ENSMUSG00000026864	1 retrocopy	retro_mmus_1299,
Nomascus leucogenys	ENSNLEG00000017348	1 retrocopy	retro_nleu_751,
Otolemur garnettii	ENSOGAG00000006786	1 retrocopy	retro_ogar_2901,
Pongo abelii	ENSPPYG00000019609	1 retrocopy	retro_pabe_2491,
Pan troglodytes	ENSPTRG00000000563	1 retrocopy	retro_ptro_2033,
Ictidomys tridecemlineatus	ENSSTOG00000003756	1 retrocopy	retro_itri_51,
Ictidomys tridecemlineatus	ENSSTOG00000011243	4 retrocopies	retro_itri_1686 , retro_itri_1687, retro_itri_1689, retro_itri_1879,