RetrogeneDB ID: retro_itri_1879

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH394458.1:13353..14585(+)
• 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_1879
GTCTTCAAATTCATGCCCACCAATAGAGATACTCATCAAGGTGAAGAAGACTTTGACCAGCATGTTATGAAAAATTTCAT
CAGGCTGTACAAAAAGAAGACTGGCAAATATGTTAGGAAAAAAAACAGAGCTGTGCAGAAACTCCAGCATGAAGTAGAAA
AGGCCAAGTGGGCCCTGTCTGCCCAACATTAAGCAAGAATTAAAATTGAGTTCTTCTATGAAGGAGAAGACTTTTCTGAA
ACCCTGACTCAGGCAAAATTTGAAGAGAAAACATGGACCTGTTCTGGTCTACCATGAAACCTGTTCAGAAAGTACTGCAG
GATTCTGACTTGTAGAAGTCTGATATTGATGAGATTGTTCTTGTTGGTGGCTCTAGTCAAATTCCAAATATTCAGCAACT
TGTTAAAGAGTTATTCAATGGCAAGGAACCATTCTGTGGCATAAACCCAGATGAGGCTGTTGCATATGGCGACACTGTCC
AGGCTGGTGTACTCTCTGATGATCCAGATACAGGTGACCTTGCTCTGCTTGATGTATTTCCCCTGACATTTGGTATTGAA
ACTGTGGGAGGTGTCATGACCAAAGTGATACCAAGGAACACAGTGGTACCCACCAAGAGCCTCAGATCTTTTCTCAGCTT
CTGATAAGCAACCTACTGTTCCAATCAATGTCTATGAAGGTAATGGACCCCTGAAAAACGACAACCACCTTCTGGGTACA
TTTGATCTCACTGGAATTCCTCCTGTGGGGTCCCCCAGATTGAAGTCACTTTTGAGATACATATGAATGCTATTCTTTGG
GTTACAGCTGTAGACAAAGGTACAGAGAACAAAAATAAGACTACAATTACTAATGACCAAAATTGCTTGACACTTGAAGA
AATTGAAAAGATGATTAATGATGTTAAGAAGTTTGCTGAGGAAAACAAAAGACTCAAGGAGCATACTGATAGTAGGAATT
AGTTGAAAAGCTATGCCTACTCTATAAAGTATCAAATTGGAGATAAAGAAAAGTTGAGAGGCAAACTTTCCTCTGAAGAT
AAGGAGACCATGGAAAAAGCTGTAGAGGAAAAGACTGAATGGCTGGAAAGCCGCCAAGAAGCTGACATTGAAGACTTCAA
AACTGAAAAGAAGAAACTAAAATAAATTGTTCAGCCAATTAGCAGCAAATTCTATGGAAGTGTAGGCCCTCCCCCAACTG
GTGAAGAGGATAAAGCAGAAAGAGATGAGTTG

Alignment

ORF - retro_itri_1879 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.51 %
• Parental protein coverage: 63.3 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  VFEVVATNGDTHLGGEDFDQRVMEHFIKLYKKKTGKDVRKDNRAVQKLRREVEKAKRALSSQHQARIEIE
          VF....TN.DTH.G.EDFDQ.VM..FI.LYKKKTGK.VR...RAVQKL..EVEKAK.ALS.QH.ARI.IE
Retrocopy VFKFMPTNRDTHQGEEDFDQHVMKNFIRLYKKKTGKYVRXXXRAVQKLQHEVEKAKWALSAQH*ARIKIE

Parental  SFYEGEDFSETLTRAKFEEL-NMDLFRSTMKPVQKVLEDSDLKKSDIDEIVLVGGSTRIPKIQQLVKEFF
          .FYEGEDFSETLT.AKFEE..NMDLF.STMKPVQKVL.DSDL.KSDIDEIVLVGGS..IP.IQQLVKE.F
Retrocopy FFYEGEDFSETLTQAKFEEK<NMDLFWSTMKPVQKVLQDSDL*KSDIDEIVLVGGSSQIPNIQQLVKELF

Parental  NGKEPSRGINPDEAVAYGAAVQAGVLSGDQDTGDLVLLDVCPLTLGIETVGGVMTKLIPRNTVVPTK-KS
          NGKEP..GINPDEAVAYG..VQAGVLS.D.DTGDL.LLDV.PLT.GIETVGGVMTK.IPRNTVVPTK...
Retrocopy NGKEPFCGINPDEAVAYGDTVQAGVLSDDPDTGDLALLDVFPLTFGIETVGGVMTKVIPRNTVVPTK<EP

Parental  QIFS-TASDNQPTVTIKVYEGERPLTKDNHLLGTFDLTGIPPAPRGVP-QIEVTFEIDVNGILRVTAEDK
          QIFS..ASD.QPTV.I.VYEG..PL..DNHLLGTFDLTGIPP...G.P.QIEVTFEI..N.IL.VTA.DK
Retrocopy QIFS<SASDKQPTVPINVYEGNGPLKNDNHLLGTFDLTGIPPV--GSP<QIEVTFEIHMNAILWVTAVDK

Parental  GTGNKNKITITNDQNRLTPEEIERMVNDAEKFAEEDKRLKERIDTRNELESYAYSLKNQIGDKEKLGGKL
          GT.NKNK.TITNDQN.LT.EEIE.M.ND..KFAEE.KRLKE..D.RN.L.SYAYS.K.QIGDKEKL.GKL
Retrocopy GTENKNKTTITNDQNCLTLEEIEKMINDVKKFAEENKRLKEHTDSRN*LKSYAYSIKYQIGDKEKLRGKL

Parental  SSEDKETMEKAVEEKIEWLESHQDADIEDFKAKKKELEEIVQPIISKLYGSAGPPPTGEEDTSERDEL
          SSEDKETMEKAVEEK.EWLES.Q.ADIEDFK..KK.L..IVQPI.SK.YGS.GPPPTGEED..ERDEL
Retrocopy SSEDKETMEKAVEEKTEWLESRQEADIEDFKTEKKKLK*IVQPISSKFYGSVGPPPTGEEDKAERDEL

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_1879 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1879 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 ,