RetrogeneDB ID: retro_itri_95

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393385.1:1216713..1218822(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSTOG00000020094
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSTOG00000015890
• Aliases: None
• Description: None

Sequence

>retro_itri_95
TCTGAAATAATTGAGGAAAAATGTAGACTACTTGAAAAAGTCAGTCTTGTTCAAAAAGAATATGAAGACTTAGAGTCATC
TTTAAAGAATGCCATTTTGGAGAAGGAGTCAATACAAGTGGAAAATTTGGAGGCAATACACACAAACCTGGATAGGTCCA
TATCTAAATTTGAGGATGAAATACTCTTTCTAGAAAATGAGCTAAAAGAAGAGAAAATTAAAGATTCTCAACAGAATGAA
TTGATAGAGTATATATCAAAAACGATTAAGTCCCTAGAAGAGGAATTAAAATCTGTCAGATCACATATACCTGAAGCTGC
AACAACCTTAACAATATTTCAACTGAATGCAGAAGGATTGAAGGTACCAATCAAAGAAGTTTCAAATGAAAATTCCCAAC
TCCTGGAAAGTCCGAAACAGCTTTTACATGAAGCGGAAGTATGGGAAGAAGAAGTGAATGGCCTTAATAAACAGAAAACA
ATACTGGAAGACCCCAAAGAACATGAAGAACAAGTTCTAAGAGAGAAAGAAAATCACATTAAGTCTCTGTCTGAACACTT
GCTGAAAGATTGTGCTCCTGGGCTTGAAGAAGCCCTAACAGACGACGGTAACTTGGACTTGGAAATGAAAAGTGAGTCAG
AAATCAGTGCTCACTTAGAGGATCAGCCAAATGGAGATTTGAAGAAACAGCTTTATGCTGATAAGTTAAATTCCTCTTTT
AAAATCTTAGAAGGAGAAAGAAATCAAGTTTTTACTTTAGTATCTGAAGTCGTTGAAACAAAGGAAGACCTTATAGAAGA
GATTAAAAATCTTAAGACAGAACAAGCATCTTTGCAGTCCAAAAATACACAACTTGAAAGTGAGAATCAGCATCTTGAGC
AGAAACTTAAACTCATCGTTGAAGTATATGAACCCATTGTAAGGAAACTCCAGAGGAAAGTAACAGAAGAGGAAAATGAC
CGGGTAGTGCAAGAGGAGAAACTTTTCAAAATGGAGGAAAACATCAGCCATGCAAGTGAACAGCTTAAGACCTATAGAAA
GCAGGTCAAATACCTTGAAGAAGAATTAGAGAGAACCACTTATTTTTATCAGGGGCAGATTACACATTATGAGGAAAAAG
CACAAGATAATGAGTGGGCCGCTCAGAGGGCTGAAAGATACCTCCATGATTTAGAGAAACAAGAGGCTCACGACAGTCAA
AACTTCACCAAAAATGAGTTTAAATTTAAAAAAGATCCTTCTGCACTTCATGTTTCAAATACAGCCATTGGCAGAGAGCA
TTTCCCAAATGGTCCCTCACCATTGGGTCGACCTTCATCTGAAATGAGAGCTCCACTTCTGGGAAAGGAGGGTCCACTCA
GACTCTCACCTTTGCTTCCAGGGGTAGGAGGAAGAGGCTCAAGAGGCCCAGAGAATCCTCTGGGCCCTCAAATTATCAAT
GAAAGAAGAGAATCCGGCTATGATGGGATAACTGATCATCAGAGAGTGCCTTGTAACATTAGGCCCCTGTCATCTCCATG
GGAACAGAACCCTAAGATGATGATGGCTCCACCAGGCCAACCATATTGTGATCCACGTCTTCCTCTGCCAAGGCAAGATG
GATGTTTCTCTAACTATGGTGGACCATCAGGACCAGCAGAACTCAGAAGTTCTACTCTGCCGCCTTTGGATCAAATGGAT
GGGCCTAAGCTTTCTGAAATGGAATCCAGTAGAAATGATTCCAAAGTGGATCTTGATAATTCCAAAGTGCCCGAGTCATC
TCACCCTGCTGAAAACCAAGAAACTGCCTCTGGCTTTGCTTTCCCTCCAATCAGAGGTCCATTGTTTCCAGTGGATCCAA
GGAATCAGTTCATGAGAAGAGGCCCTTTTTTTCCTCCACCTCCTCCAGGAAACATGTATGGAGCATCTCGAGAATATTTT
CCATGGGGCCCACCACCCCCTCCATTCCCAATGGAGCCATGGTGTTTTCCTCATTATCTCCCCCCAAGAGCTGAATTCCC
CCCCCTCCCTCCCGTGCATTCTGAAAGTAGAAGTGAGTTCCCCTCAGGGTTGAGTCCAGCTTCAAATGAGCCTACTACCC
AACATACAGAACCACAACAAGAAATTTGA

Alignment

ORF - retro_itri_95 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.04 %
• Parental protein coverage: 58.72 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SGLIKEKCELLEKVSLVQKEYEGLESSLKDASFEKESTEAQSLEATYEKLDRSKSKLEDEILFLEKELKE
          S..I.EKC.LLEKVSLVQKEYE.LESSLK.A..EKES.....LEA....LDRS.SK.EDEILFLE.ELKE
Retrocopy SEIIEEKCRLLEKVSLVQKEYEDLESSLKNAILEKESIQVENLEAIHTNLDRSISKFEDEILFLENELKE

Parental  EKSKHSEQDELMADISKRIQSLEDESKSLKSQIAEAKTTFKIYQMNEERLKVVIKEALNENSQLQESQKQ
          EK.K.S.Q.EL...ISK.I.SLE.E.KS..S.I.EA.TT..I.Q.N.E.LKV.IKE..NENSQL.ES.KQ
Retrocopy EKIKDSQQNELIEYISKTIKSLEEELKSVRSHIPEAATTLTIFQLNAEGLKVPIKEVSNENSQLLESPKQ

Parental  LLQEAEVWKEQVSDLNKQKITFEESKVHAEQVLNDKENHIKSLIERLLKMEDWGAVLGEDPTDDDNSELE
          LL.EAEVW.E.V..LNKQK...E..K.H.EQVL..KENHIKSL.E.LLK..D....L.E..TDD.N..LE
Retrocopy LLHEAEVWEEEVNGLNKQKTILEDPKEHEEQVLREKENHIKSLSEHLLK--DCAPGLEEALTDDGNLDLE

Parental  MNSESEVGAYLDNQPKGALKKVVYAAKLNASLKTLEGERNQIYTQLSEVDKTKEDLIEHIKNLQTEQASL
          M.SESE..A.L..QP.G.LKK..YA.KLN.S.K.LEGERNQ..T..SEV..TKEDLIE.IKNL.TEQASL
Retrocopy MKSESEISAHLEDQPNGDLKKQLYADKLNSSFKILEGERNQVFTLVSEVVETKEDLIEEIKNLKTEQASL

Parental  QSEYTQFESENQKLQQKLKVMTELYQENEMKLHRKLTVEENYRLEKEEKLSKVDEKISHAAEELETYRKR
          QS..TQ.ESENQ.L.QKLK...E.Y.....KL.RK.T.EEN.R...EEKL.K..E.ISHA.E.L.TYRK.
Retrocopy QSKNTQLESENQHLEQKLKLIVEVYEPIVRKLQRKVTEEENDRVVQEEKLFKMEENISHASEQLKTYRKQ

Parental  AKDLEEELERTIHSYQGQIISHEKKAHDNWLAARAAERNLNDLKKENAHNRQKLTETEFKFELLEKDPYA
          .K.LEEELERT...YQGQI...E.KA.DN..AA..AER.L.DL.K..AH..Q..T..EFKF....KDP.A
Retrocopy VKYLEEELERTTYFYQGQITHYEEKAQDNEWAAQRAERYLHDLEKQEAHDSQNFTKNEFKF---KKDPSA

Parental  LDVPNTAFGREHSPYGASPLGRPSSETRAFLSPPTLLEGPLRLSPLLPGGGGRGSRGPENPLDHQFSNER
          L.V.NTA.GREH.P.G.SPLGRPSSE.RA...P....EGPLRLSPLLPG.GGRGSRGPENPL..Q..NER
Retrocopy LHVSNTAIGREHFPNGPSPLGRPSSEMRA---PLLGKEGPLRLSPLLPGVGGRGSRGPENPLGPQIINER

Parental  GESSYDRLTDPHRAPSDTGSLSPPWEQDRRMMIPPPGQPYSDPPLPPQRQDRYYSNSGRLSGPAELRSFN
          .ES.YD..TD..R.P.....LS.PWEQ...MM..PPGQPY.DP.LP..RQD...SN.G..SGPAELRS..
Retrocopy RESGYDGITDHQRVPCNIRPLSSPWEQNPKMMMAPPGQPYCDPRLPLPRQDGCFSNYGGPSGPAELRSST

Parental  MPSLDKVDGPMSLEMESSTNDTKDDLDNSNVPDSSLPAENQATGSRFGFSPLPPIRGPLFPVDPRSHFMR
          .P.LD..DGP...EMESS.ND.K.DLDNS.VP.SS.PAENQ.T.S.F.F...PPIRGPLFPVDPR..FMR
Retrocopy LPPLDQMDGPKLSEMESSRNDSKVDLDNSKVPESSHPAENQETASGFAF---PPIRGPLFPVDPRNQFMR

Parental  RGPSFPPPPPPPGNMYGASRDYFLPGPPPPLFPMRNAYSPRGFPHFLPPRAGFFPSPP-HSESRSEFPSG
          RGP.F..PPPPPGNMYGASR.YF..GPPPP.FPM.....P..FPH.LPPRA.F.P.PP.HSESRSEFPSG
Retrocopy RGPFF--PPPPPGNMYGASREYFPWGPPPPPFPM----EPWCFPHYLPPRAEFPPLPPVHSESRSEFPSG

Parental  LIPPSNEPATEHPEPQQE
          L.P.SNEP.T.H.EPQQE
Retrocopy LSPASNEPTTQHTEPQQE

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_95 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_95 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 9 parental genes, and 41 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000016105	4 retrocopies	retro_cjac_1747, retro_cjac_2711, retro_cjac_3217, retro_cjac_921,
Cavia porcellus	ENSCPOG00000026514	2 retrocopies	retro_cpor_189, retro_cpor_727,
Homo sapiens	ENSG00000150527	3 retrocopies	retro_hsap_1201, retro_hsap_3691, retro_hsap_640,
Homo sapiens	ENSG00000258941	1 retrocopy	retro_hsap_78,
Gorilla gorilla	ENSGGOG00000011990	1 retrocopy	retro_ggor_936,
Nomascus leucogenys	ENSNLEG00000004121	10 retrocopies	retro_nleu_1218, retro_nleu_1690, retro_nleu_2087, retro_nleu_2103, retro_nleu_2148, retro_nleu_2600, retro_nleu_2951, retro_nleu_3017, retro_nleu_3077, retro_nleu_688,
Pongo abelii	ENSPPYG00000005768	9 retrocopies	retro_pabe_1001, retro_pabe_1002, retro_pabe_1007, retro_pabe_1055, retro_pabe_1060, retro_pabe_1588, retro_pabe_2119, retro_pabe_29, retro_pabe_3024,
Pan troglodytes	ENSPTRG00000006297	10 retrocopies	retro_ptro_1286, retro_ptro_1712, retro_ptro_2503, retro_ptro_2580, retro_ptro_2880, retro_ptro_466, retro_ptro_821, retro_ptro_826, retro_ptro_868, retro_ptro_876,
Ictidomys tridecemlineatus	ENSSTOG00000015890	1 retrocopy	retro_itri_95 ,