RetrogeneDB ID: retro_itri_1689

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393640.1:904246..905480(+)
• 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_1689
GTCTTCAAAGTCATGGCCACCAATAGAGATACTCATCGAGGTGAAGAAGACTTTGACCAGCGTGTTATGGAACATTTCAT
CAGGCTGTACAAAAAGAAGACTGGCAAATATGGTAGGAAAAAAAAAGAGCTGTGCAGAAACTCCAGCATGAAATAGAAAA
GGCCAAGTGGGCCCTGTCTGCCCAACATTAAGCAAGAATTAAAATTGAGTTTTTCTATGAAGGAGAAGACTTTTCTGAAA
TCCTGACTAAGGCAAAATTTGAAGAGAAAACATGGTCCTGTTCTGGTCTACCATAAAGCCTGTTCAGAAAGTACTAGAGG
ATTCTGACTTGTAGAAGTCTAATATTGATAAGATTGTTCTTGTTGGTGGCTGTAGTCAAATTCCAAAGATTCAGCAACTT
GTTAAAGAGTTCTTCAATGGCAAGGAGCCATTCTGTGGCATAAACCCAGATGAGGCTGTTGCATATGGCGACACTGTCCA
GGTTGGTGTACTCTTTGATAATCAAGATACAGGTGACCTTGCTCTGCTTGATGTATGTCCCCTAACATTTGGTATTGAAA
CTGTGGGAGGTGTCATGACCAAAGTGATACCAAGGAACACTGTGGTACCCACCAAGTAGTCTCAGATCTTTTCTACAGCT
TCTGATAAGCAACCTACCATTCCAATCAAGGTCTATGAAAGTAAAGGACCCCTGAATAAAGACAACCACCTTCCGGGTAC
ATTTGATCTCACTGGAATTCCTCCTGTGGGGTCCCCCAGATTGAAGTCACTTTTGAGATACATGTCAATGCTATTCTTTG
GGTGACAGCTGAAGACAAAGGTACAGAGAACAAAAATAAAATTACAATTATCAATGACCAAAATTGCCTGACACTTGAAA
AAATTGAAAAGATGGTTAATGATGTTGAGAAGTTTGCTGAGGGAGACAAAAGTCTCAAGGAGCACACTGATAGTAGGAAT
GAGTTGAAAAGCTATGCCTACTCTCTAAAGTAGCAGATTGGAGATAAAGAAAAGTTGAGAGGCAAACTTTAATCTGAAGA
TAAGGGGACCATGGAAAAAGCTGTAGAGGAAAAAATTGAATGGCTCGAAAGCCACCAAAAAGCTGACATTGAAGACTTCA
AAACTAAAAAAGAAGGAACTAGAAGAAATTGTTCATCCAATTAGCAGCAAATTCTGTGGAAGTGTAGGCCCTCCCCCAAC
TGGTGAAGAGGATAGAGCAAAAAGAGATGAGTTG

Alignment

ORF - retro_itri_1689 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.47 %
• Parental protein coverage: 63.3 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  VFEVVATNGDTHLGGEDFDQRVMEHFIKLYKKKTGKDVRKDNR-AVQKLRREVEKAKRALSSQHQARIEI
          VF.V.ATN.DTH.G.EDFDQRVMEHFI.LYKKKTGK..R.....AVQKL..E.EKAK.ALS.QH.ARI.I
Retrocopy VFKVMATNRDTHRGEEDFDQRVMEHFIRLYKKKTGKYGRXXXE<AVQKLQHEIEKAKWALSAQH*ARIKI

Parental  ESFYEGEDFSETLTRAKFEEL-NMDLFRSTMKPVQKVLEDSDLKKSDIDEIVLVGGSTRIPKIQQLVKEF
          E.FYEGEDFSE.LT.AKFEE..NM.LF.ST.KPVQKVLEDSDL.KS.ID.IVLVGG...IPKIQQLVKEF
Retrocopy EFFYEGEDFSEILTKAKFEEK<NMVLFWSTIKPVQKVLEDSDL*KSNIDKIVLVGGCSQIPKIQQLVKEF

Parental  FNGKEPSRGINPDEAVAYGAAVQAGVLSGDQDTGDLVLLDVCPLTLGIETVGGVMTKLIPRNTVVPTKKS
          FNGKEP..GINPDEAVAYG..VQ.GVL...QDTGDL.LLDVCPLT.GIETVGGVMTK.IPRNTVVPTK.S
Retrocopy FNGKEPFCGINPDEAVAYGDTVQVGVLFDNQDTGDLALLDVCPLTFGIETVGGVMTKVIPRNTVVPTK*S

Parental  QIFSTASDNQPTVTIKVYEGERPLTKDNHLLGTFDLTGIPPAPRGVP-QIEVTFEIDVNGILRVTAEDKG
          QIFSTASD.QPT..IKVYE...PL.KDNHL.GTFDLTGIPP...G.P.QIEVTFEI.VN.IL.VTAEDKG
Retrocopy QIFSTASDKQPTIPIKVYESKGPLNKDNHLPGTFDLTGIPPV--GSP<QIEVTFEIHVNAILWVTAEDKG

Parental  TGNKNKITITNDQNRLTPEEIERMVNDAEKFAEEDKRLKERIDTRNELESYAYSLKNQIGDKEKLGGKLS
          T.NKNKITI.NDQN.LT.E.IE.MVND.EKFAE.DK.LKE..D.RNEL.SYAYSLK.QIGDKEKL.GKL.
Retrocopy TENKNKITIINDQNCLTLEKIEKMVNDVEKFAEGDKSLKEHTDSRNELKSYAYSLK*QIGDKEKLRGKL*

Parental  SEDKETMEKAVEEKIEWLESHQDADIEDFKA-KKKELEEIVQPIISKLYGSAGPPPTGEEDTSERDEL
          SEDK.TMEKAVEEKIEWLESHQ.ADIEDFK..KKKELEEIV.PI.SK..GS.GPPPTGEED...RDEL
Retrocopy SEDKGTMEKAVEEKIEWLESHQKADIEDFKT>KKKELEEIVHPISSKFCGSVGPPPTGEEDRAKRDEL

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_1689 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1689 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,