RetrogeneDB ID: retro_itri_328

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393284.1:29678873..29679930(+)
• Located in intron of: ENSSTOG00000006972

Retrocopy information

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

Parental gene information

• Parental gene symbol: CDC37
• Ensembl ID: ENSSTOG00000015962
• Aliases: None
• Description: cell division cycle 37 [Source:HGNC Symbol;Acc:1735]

Sequence

>retro_itri_328
GACTACAGTGTGTGGGACCACATCGAAATGTCTGACAATGAGGATGAGAAGCACCCCAGCATTGACTTGGCCAGCCTCTT
CTGCTGGTGGCACCAAGCCAGGTGGAATACATGGAGCAGTTCTAGAAGGAGAAGGAGGAGCTGGACAGGGGTTGCCACGA
TTGCAGGCACAGGGGGGCCAAGTGCCAACGGAACCTGAAGGAGCTGGAGGTGGATGAATGTGACCAGGTGGAGTTGGAGT
GACTGCAGACTAAGGCACAGCAACTGCGCAAGGAAGAGCAGAGCTGGGAGCAGAGGCTGGAGGAGAGGCGCAAGAACGAA
AAGAGCATGCCCTGGAATGTGGATATGCTCAGCAAAGATGGCTTCAGCAAGAGCATGGTCAAGACCAAGCCTGAGAAGGC
AGACGAGGATTTGAAAGAAGTGAGGAAGCAGAAACACAAAACCTTTGTGGCGAAGTACGAGAAACAGATCAAGCACTTTG
GAATGCTCTGTCACTGGGAAGACAGCTAGAAATACCCGTCAGACAATGTCCACTTGGTTTGTGAGCAGACAGCCACTACT
TGGTTATCTGGTGCACTGACCTAGAGATGGAGGAAAACTGTGCACTGATGGAGTAGGTGGCCCACCAGACCATTGTCTTG
CAGTTTATCCTGGAGCTAGCCAAGAGTCTGAAGGTGGACCCCCATGCCTGCTTCAGACAGTCATTCACTAAGATTAAGAT
GGCTGACTGCTAGTATATGGAAGGCTTCAATGAAGAGCTGAAGGGTTTCAAGGAGCGCCTGTGGGATGGTGCCAAGCTGC
TCATTGAGAAGACCATGAAGGATGAGGCAGAAGAACACAAGCCTGGTGGCCTGGACCTCATAGAGGTCTATGAGTCCCTC
CCTGAGGAACTTCAAAAGAGGTTTGAAATGAAGGATGTGCAGATGCTCCAAGATTCCATCAGCGAGATGGTCCCTACTGA
TGAGAAGTACCACATGCAGTGTTGCATTGACTCTGGCCTCTGGGTCCCCAACTACAAGTCCATCGAGGCCAAGAATGGGG
AAGAGCCAGGTCTAGGG

Alignment

ORF - retro_itri_328 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.39 %
• Parental protein coverage: 94.71 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  DYSVWDHIEVSDDEDETHPNIDTASLFRWRHQAR-VERMEQFQKEKEELDRGCRECKRKVAECQRKLKEL
          DYSVWDHIE.SD.EDE.HP.ID.ASLF.W.HQAR.VE.MEQF.KEKEELDRGC..C....A.CQR.LKEL
Retrocopy DYSVWDHIEMSDNEDEKHPSIDLASLFCWWHQAR<VEYMEQF*KEKEELDRGCHDCRHRGAKCQRNLKEL

Parental  EVAEGGQAELERLQAEAQQLRKEERSWEQKLEEMRKKEKSMPWNVDTLSKDGFSKSMVNTKPEKAEEDSE
          EV.E..Q.ELE.LQ..AQQLRKEE.SWEQ.LEE.RK.EKSMPWNVD.LSKDGFSKSMV.TKPEKA.ED..
Retrocopy EVDECDQVELE*LQTKAQQLRKEEQSWEQRLEERRKNEKSMPWNVDMLSKDGFSKSMVKTKPEKADEDLK

Parental  EVREQKHKTFVEKYEKQIKHFGMLRRWDDSQKYLSDNVHLVCEETA-NYLVIWCIDLEVEEKCALMEQVA
          EVR.QKHKTFV.KYEKQIKHFGML..W.DS.KY.SDNVHLVCE.TA..YLVIWC.DLE.EE.CALME.VA
Retrocopy EVRKQKHKTFVAKYEKQIKHFGMLCHWEDS*KYPSDNVHLVCEQTA<HYLVIWCTDLEMEENCALME*VA

Parental  HQTIVMQFILELAKSLKVDPRACFRQFFTKIKTADRQYMEGFNDELEAFKERVRGRAKLRIEKAMKEYEA
          HQTIV.QFILELAKSLKVDP.ACFRQ.FTKIK.AD..YMEGFN.EL..FKER....AKL.IEK.MK..EA
Retrocopy HQTIVLQFILELAKSLKVDPHACFRQSFTKIKMADC*YMEGFNEELKGFKERLWDGAKLLIEKTMKD-EA

Parental  EERKKRLGPGGLDPVEVYESLPEELQKCFDVKDVQMLQDAISKMDPTDAKYHMQRCIDSGLWVPNSKSSE
          EE.K....PGGLD..EVYESLPEELQK.F..KDVQMLQD.IS.M.PTD.KYHMQ.CIDSGLWVPN.KS.E
Retrocopy EEHK----PGGLDLIEVYESLPEELQKRFEMKDVQMLQDSISEMVPTDEKYHMQCCIDSGLWVPNYKSIE

Parental  AKEGEEAGPG
          AK.GEE.G.G
Retrocopy AKNGEEPGLG

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_328 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_328 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 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000105401	1 retrocopy	retro_hsap_3396,
Gorilla gorilla	ENSGGOG00000008098	1 retrocopy	retro_ggor_2299,
Macropus eugenii	ENSMEUG00000002278	1 retrocopy	retro_meug_1373,
Macaca mulatta	ENSMMUG00000003111	1 retrocopy	retro_mmul_2113,
Pongo abelii	ENSPPYG00000009551	1 retrocopy	retro_pabe_2790,
Ictidomys tridecemlineatus	ENSSTOG00000015962	1 retrocopy	retro_itri_328 ,