AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1139670

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1139670 MtrunA17_Chr7g0220631 93.382 136 5 3 1 133 1 135 2.59e-83 240
Msa1139670 MtrunA17_Chr7g0220691 44.860 107 51 3 1 101 1 105 2.15e-25 92.8
Msa1139670 MtrunA17_Chr4g0072911 46.835 79 41 1 21 98 25 103 3.44e-19 78.6
Msa1139670 MtrunA17_Chr6g0456221 43.750 80 39 2 23 101 14 88 2.67e-18 74.3
Msa1139670 MtrunA17_Chr1g0150501 43.023 86 48 1 20 104 24 109 2.89e-17 72.8
Msa1139670 MtrunA17_Chr3g0136681 41.509 106 56 1 7 106 14 119 4.44e-17 72.8
Msa1139670 MtrunA17_Chr4g0061911 40.000 80 47 1 21 100 25 103 5.60e-13 60.8
Msa1139670 MtrunA17_Chr1g0150491 37.363 91 46 2 20 104 24 109 3.61e-12 59.7
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1139670 AT4G31730.1 40.800 125 59 4 1 115 1 120 1.06e-23 90.1
Msa1139670 AT4G25760.1 48.936 94 45 2 21 113 28 119 5.89e-22 84.7
Msa1139670 AT2G24762.1 44.000 100 50 2 18 116 30 124 3.43e-20 81.3
Msa1139670 AT5G57685.1 45.918 98 42 3 21 112 28 120 4.45e-19 78.2
Msa1139670 AT5G24920.1 41.975 81 42 1 21 101 28 103 6.64e-13 61.6

Find 20 sgRNAs with CRISPR-Local

Find 23 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATTAATCTTCTCTATGTTCT+TGG 0.218840 7_4:+10306086 None:intergenic
TCTCCAATTCCATATCTATT+TGG 0.228950 7_4:-10306234 Msa1139670:CDS
AAAGAAGTAGTGATAATAAT+TGG 0.275831 7_4:+10306003 None:intergenic
GCCATAATCACAAGTACTTC+TGG 0.351204 7_4:+10306057 None:intergenic
ATTAGTTAATGTTTGGTCAT+TGG 0.359783 7_4:+10305924 None:intergenic
TTGCCATATCTTAATCTCAT+TGG 0.363415 7_4:+10306257 None:intergenic
TAATGTTTGGTCATTGGTTA+AGG 0.364149 7_4:+10305930 None:intergenic
CAACTTAATTAGTTAATGTT+TGG 0.367551 7_4:+10305917 None:intergenic
CCTCCAAATAGATATGGAAT+TGG 0.395109 7_4:+10306231 None:intergenic
GCCAGAAGTACTTGTGATTA+TGG 0.399181 7_4:-10306058 Msa1139670:CDS
GCTAAGCCTCCAAATAGATA+TGG 0.402398 7_4:+10306225 None:intergenic
AGTAGTGATAATAATTGGTT+TGG 0.410163 7_4:+10306008 None:intergenic
ATTGGTTTGGCTATGTAAGT+TGG 0.431103 7_4:+10306021 None:intergenic
TTCAGATGAAGAAATGAAAC+AGG 0.432931 7_4:-10306115 Msa1139670:CDS
CCAATTCCATATCTATTTGG+AGG 0.435839 7_4:-10306231 Msa1139670:CDS
TCTTTACCTTACTGCACTTG+TGG 0.450831 7_4:-10305985 Msa1139670:CDS
AAACCAATGAGATTAAGATA+TGG 0.476091 7_4:-10306260 Msa1139670:CDS
GAAGTACTTGTGATTATGGC+TGG 0.486766 7_4:-10306054 Msa1139670:CDS
GATGATGATAAAGTGTTGAT+TGG 0.502596 7_4:+10306294 None:intergenic
TCAGCTCCACAAGTGCAGTA+AGG 0.569478 7_4:+10305979 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! AATTTTAATTTCAGTTGCAT+TGG - chr7_4:10306028-10306047 Msa1139670:CDS 20.0%
!! AAAGAAGTAGTGATAATAAT+TGG + chr7_4:10306221-10306240 None:intergenic 20.0%
! AAACCAATGAGATTAAGATA+TGG - chr7_4:10305961-10305980 Msa1139670:CDS 25.0%
! ATTAATCTTCTCTATGTTCT+TGG + chr7_4:10306138-10306157 None:intergenic 25.0%
! AGTAGTGATAATAATTGGTT+TGG + chr7_4:10306216-10306235 None:intergenic 25.0%
! ATTAGTTAATGTTTGGTCAT+TGG + chr7_4:10306300-10306319 None:intergenic 25.0%
!! GATGATGATAAAGTGTTGAT+TGG + chr7_4:10305930-10305949 None:intergenic 30.0%
TTGCCATATCTTAATCTCAT+TGG + chr7_4:10305967-10305986 None:intergenic 30.0%
TCTCCAATTCCATATCTATT+TGG - chr7_4:10305987-10306006 Msa1139670:CDS 30.0%
TTCAGATGAAGAAATGAAAC+AGG - chr7_4:10306106-10306125 Msa1139670:CDS 30.0%
! TAATGTTTGGTCATTGGTTA+AGG + chr7_4:10306294-10306313 None:intergenic 30.0%
CCTCCAAATAGATATGGAAT+TGG + chr7_4:10305993-10306012 None:intergenic 35.0%
CCAATTCCATATCTATTTGG+AGG - chr7_4:10305990-10306009 Msa1139670:CDS 35.0%
!!! GTTTTTTGTAGGAGCATACA+AGG + chr7_4:10306058-10306077 None:intergenic 35.0%
!!! AGAAGAACCACGTTTTTTGT+AGG + chr7_4:10306069-10306088 None:intergenic 35.0%
!! ATTGGTTTGGCTATGTAAGT+TGG + chr7_4:10306203-10306222 None:intergenic 35.0%
GCTAAGCCTCCAAATAGATA+TGG + chr7_4:10305999-10306018 None:intergenic 40.0%
GTATGCTCCTACAAAAAACG+TGG - chr7_4:10306059-10306078 Msa1139670:CDS 40.0%
!! GCCAGAAGTACTTGTGATTA+TGG - chr7_4:10306163-10306182 Msa1139670:CDS 40.0%
GCCATAATCACAAGTACTTC+TGG + chr7_4:10306167-10306186 None:intergenic 40.0%
! GAAGTACTTGTGATTATGGC+TGG - chr7_4:10306167-10306186 Msa1139670:CDS 40.0%
TCTTTACCTTACTGCACTTG+TGG - chr7_4:10306236-10306255 Msa1139670:CDS 40.0%
TCAGCTCCACAAGTGCAGTA+AGG + chr7_4:10306245-10306264 None:intergenic 50.0%
Chromosome Type Strat End Strand Name
chr7_4 gene 10305921 10306322 10305921 ID=Msa1139670;Name=Msa1139670
chr7_4 mRNA 10305921 10306322 10305921 ID=Msa1139670-mRNA-1;Parent=Msa1139670;Name=Msa1139670-mRNA-1;_AED=0.00;_eAED=0.00;_QI=0|-1|0|1|-1|1|1|0|133
chr7_4 exon 10305921 10306322 10305921 ID=Msa1139670-mRNA-1:exon:2546;Parent=Msa1139670-mRNA-1
chr7_4 CDS 10305921 10306322 10305921 ID=Msa1139670-mRNA-1:cds;Parent=Msa1139670-mRNA-1
Gene Sequence

>Msa1139670

ATGAGGCCAATCAACACTTTATCATCATCATCAACAACTCAAACCAATGAGATTAAGATATGGCAATCTCCAATTCCATATCTATTTGGAGGCTTAGCTATAATGCTAATTTTAATTTCAGTTGCATTGGTGATCCTTGTATGCTCCTACAAAAAACGTGGTTCTTCTCAATCATCATCAAATAATTCAGATGAAGAAATGAAACAGGTAATGTCCAAGAACATAGAGAAGATTAATTCTGAGCCAGAAGTACTTGTGATTATGGCTGGAGAAGATAAACCAACTTACATAGCCAAACCAATTATTATCACTACTTCTTTACCTTACTGCACTTGTGGAGCTGAATCAACTTCAACAACATCTTCATCAACCTTAACCAATGACCAAACATTAACTAATTAA
Protein sequence

>Msa1139670

MRPINTLSSSSTTQTNEIKIWQSPIPYLFGGLAIMLILISVALVILVCSYKKRGSSQSSSNNSDEEMKQVMSKNIEKINSEPEVLVIMAGEDKPTYIAKPIIITTSLPYCTCGAESTSTTSSSTLTNDQTLTN*