RetrogeneDB ID: retro_itri_1559

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393540.1:1452381..1453800(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSTOG00000028864
• Aliases: None
• Description: None

Sequence

>retro_itri_1559
TATGGGACCTCTTCACATGGATATTTTAAGAAGCTGGGAATTCCAGGGCCAACACCTCTGCCTTTTGGGGGGACTCTTCT
TAATTGTCGCCAGGGTTTGTTTAATTTTGATACAGAATGTTATAAAAAGTATGGAAAAACATGGGGCCTGTTTGATGGTT
CACAACCTGTTTTGTCTATTATGGAGCCAACAGTTCTCATCAAAGAATGTTATTCTGTCTTCACCAACCTGCGGGATGTT
GGTCCAATGGGATTTATGAAAAAATCCATCTCCTTGTCTGAGGATGAAGAGTGGAAGAGAATAAGAACACTGCTGTCTCC
AACCTTCACCACTGGAAAACTCAAGGAGATGTTCCCCATCATTAACCAGTATGGAGAAATGTTGGTGAAAAGCATGAGAC
TGAGACGGGAATCAGAGAAGGGCAAGTTTATCAACTTGAAAGACATCTTTGGGGCCTACAGCATTGATGTGATCACTGTG
ACATCATTTGGAGTGAACATTGATTCCCTCAAAAACCCACAAGATCCCTTTGTGGAGAAAGTCAAGAAGCTCTTAAGATT
TGATTTCTTTGACCTTTGCTCCTCTCAATAACTATCTTTCCATTCCTTACTCCAATTTATGAGGCAATGAATATCTCTAT
GTTTCCAAAGGATGTCACATTTTTTTTAAGAAAGCTATAAACAGAATGAAGGAAAGTCACCTTCAGGAGAAACAACAGCA
TCGGGTGTTGTTTATCAGCTTATGATAAATTCTCAGAATTCTAAAGATGTGGAATCTCATAAAGCCCAGTCTGATCTGGA
GCTTGTGGCCCAATCAATTATCTTCATTTTTTGCTGGCTGTGAGACCACTAGCAGTGCTCTTTCCTTCATTTTGTATGAA
CTGCCACCCATCCTGATGTCCAGACCAAACTGCAGCAGGAGATTGATGCGGCTTTGCCCAATGAGGCACCTGCTACCTAT
GATACCCTGATGCAGATGAAGTACCTGGACATAGTGGTGAATGAAACTCTCAGGTTGTATCCAGTTGGTGCCAGAATTGA
GAGAATCTTTAAGAAAGATATTGAAATCCATGGAGTATTCATTAGTAAGGGGACGCTGGTGGTGATACCAATCTTTGTTC
TACATCAAGACCCAAAGTATTGGCCAGAGCCTGAGGAGTTCCACCCTGAAAGGTTCAATAAGAACAAGAAAGCATTGATC
CTTATGTGTACATGCCCTTTGGAAATGGCCCCTGAAACTGCATTGGCATGAAGTTTGCTCTCATGAACATGAAACTTGCT
CTTGTCAATACAGAACTTCTCCTTCCAAATTTGTAAGGAAACGCAGATTCCTCTGAAATTAAGCAATCAAGGACTTCTTC
AACCTGAAAAGCCTATTATTCTGAAGGTTTTGTGCAGAGATGGGACAATTAGTGGAGCC

Alignment

ORF - retro_itri_1559 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.61 %
• Parental protein coverage: 95.25 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  YGTYSHGYFKKLGIPGPTPVPFFGTLLNYRRGFFNFDVECYKKYGKTWGIYDGRRPVLVITEPSIIKTVL
          YGT.SHGYFKKLGIPGPTP.PF.GTLLN.R.G.FNFD.ECYKKYGKTWG..DG..PVL.I.EP....TVL
Retrocopy YGTSSHGYFKKLGIPGPTPLPFGGTLLNCRQGLFNFDTECYKKYGKTWGLFDGSQPVLSIMEP----TVL

Parental  IKECYSAFTNRRDFGPVGFMKKAISLSEDEEWKRIRTLLSPTFTSGKLKEMFPIINQYGDVLVKNMRL--
          IKECYS.FTN.RD.GP.GFMKK.ISLSEDEEWKRIRTLLSPTFT.GKLKEMFPIINQYG..LVK.MRL..
Retrocopy IKECYSVFTNLRDVGPMGFMKKSISLSEDEEWKRIRTLLSPTFTTGKLKEMFPIINQYGEMLVKSMRLRR

Parental  ESEKGKFINLKDIFGAYSMDVITATSFGVNIDSLNNPQDPFVEKVKKLLKFDFFD-PLLLSITIFPFLTP
          ESEKGKFINLKDIFGAYS.DVIT.TSFGVNIDSL.NPQDPFVEKVKKLL.FDFFD.PLLLSITIFPFLTP
Retrocopy ESEKGKFINLKDIFGAYSIDVITVTSFGVNIDSLKNPQDPFVEKVKKLLRFDFFD<PLLLSITIFPFLTP

Parental  IFEAMNISMFPKDVTNFL-KKAISRMKESRLQEKQQHRVDFL-QLMINSQNSKDVESHKALSDLELVAQS
          I.EAMNISMFPKDVT....KKAI.RMKES.LQEKQQHRV.F..QLMINSQNSKDVESHKA.SDLELVAQS
Retrocopy IYEAMNISMFPKDVTXXX<KKAINRMKESHLQEKQQHRVLFI<QLMINSQNSKDVESHKAQSDLELVAQS

Parental  IIFIF-AGYETTSSALSFILYEL-ATNPDAQTKLQQEIDAALPNKAPATYDTVLQMEYLDMVVNETLRLF
          IIFIF.AG.ETTSSALSFILYEL.AT.PD.QTKLQQEIDAALPN.APATYDT..QM.YLD.VVNETLRL.
Retrocopy IIFIF>AGCETTSSALSFILYEL<ATHPDVQTKLQQEIDAALPNEAPATYDTLMQMKYLDIVVNETLRLY

Parental  PIAGRIERVCKKDVEINGVPIRKGTVVMIPSYVLHRDPQHWPEPEEFHPERTRFSKKNK-DSIDPYIYMP
          P...RIER..KKD.EI.GV.I.KGT.V.IP..VLH.DP..WPEPEEFHPER.....KNK..SIDPY.YMP
Retrocopy PVGARIERIFKKDIEIHGVFISKGTLVVIPIFVLHQDPKYWPEPEEFHPERFN---KNK<ESIDPYVYMP

Parental  FGNGPRNCIGMRFALMNMKLALVKV-MQNFSFQLCKETQIPLKLADQGLLQPEKPIILKAVCRDGTISGA
          FGNGP.NCIGM.FAL..M...L..V..QNFSFQ.CKETQIPLKL..QGLLQPEKPIILK..CRDGTISGA
Retrocopy FGNGP*NCIGMKFAL--MNMKLALV>IQNFSFQICKETQIPLKLSNQGLLQPEKPIILKVLCRDGTISGA

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_1559 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1559 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000035708	1 retrocopy	retro_cjac_1135,
Procavia capensis	ENSPCAG00000001718	1 retrocopy	retro_pcap_234,
Ictidomys tridecemlineatus	ENSSTOG00000028864	1 retrocopy	retro_itri_1559 ,