AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1444660


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1444660 MtrunA17_Chr6g0478031 98.089 157 3 0 1 157 1 157 1.06e-110 311
Msa1444660 MtrunA17_Chr2g0303931 75.524 143 35 0 1 143 6 148 6.63e-71 210
Msa1444660 MtrunA17_Chr4g0065951 45.985 137 74 0 16 152 21 157 2.97e-35 120
Msa1444660 MtrunA17_Chr1g0199041 42.857 154 73 5 2 154 6 145 3.00e-27 100
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1444660 AT5G46530.1 71.812 149 42 0 1 149 6 154 1.85e-76 225
Msa1444660 AT1G29520.1 78.523 149 32 0 1 149 6 154 1.71e-75 222
Msa1444660 AT5G18970.1 43.506 154 87 0 2 155 7 160 1.11e-37 127
Msa1444660 AT1G04560.1 43.590 156 74 4 2 156 7 149 8.40e-31 110

Find 29 sgRNAs with CRISPR-Local

Find 121 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATTTCCCATTGGGAAGAAAA+TGG 0.238328 tig0030776:-38258 Msa1444660:intergenic
TGCATGTATGTCATTGTTCT+AGG 0.248721 tig0030776:+37984 Msa1444660:CDS
CTCTACATAGTTGCAATTCA+TGG 0.294119 tig0030776:+39101 Msa1444660:CDS
GGTGCTGCATCGACAATTTC+AGG 0.318250 tig0030776:+38329 Msa1444660:CDS
TGCTGCTTCAATTGCTACTT+TGG 0.334645 tig0030776:+38394 Msa1444660:CDS
CCAATGGGAAATGCTTCAAC+TGG 0.374176 tig0030776:+38269 Msa1444660:CDS
CTTCAATTGCTACTTTGGCT+TGG 0.384442 tig0030776:+38399 Msa1444660:CDS
GACTCTTACACTGCTTGCCA+TGG 0.388463 tig0030776:+38421 Msa1444660:CDS
GTTACGATTTCTTTGTTAGC+TGG 0.398205 tig0030776:+38299 Msa1444660:CDS
TCTTTGTTAGCTGGAGTAGT+TGG 0.415192 tig0030776:+38308 Msa1444660:CDS
TTGTTCTAGGCATTGGTGCA+TGG 0.424644 tig0030776:+37997 Msa1444660:CDS
CAGTTGAAGCATTTCCCATT+GGG 0.433142 tig0030776:-38268 Msa1444660:intergenic
TGAGCTGGAAGATTTAATTC+CGG 0.439380 tig0030776:-38227 Msa1444660:intergenic
TGTTCTAGGCATTGGTGCAT+GGG 0.449144 tig0030776:+37998 Msa1444660:CDS
ACTCTTACACTGCTTGCCAT+GGG 0.453490 tig0030776:+38422 Msa1444660:CDS
ACAAAATACATAGTTCGGTT+AGG 0.457892 tig0030776:+37917 None:intergenic
TTTCCCATTGGGAAGAAAAT+GGG 0.461124 tig0030776:-38257 Msa1444660:intergenic
GAGTCAAACATATCTGTTCA+TGG 0.465531 tig0030776:+38351 Msa1444660:CDS
TCAAATTAGAAATGCACGTC+TGG 0.465623 tig0030776:+38948 Msa1444660:CDS
CCAGTTGAAGCATTTCCCAT+TGG 0.492597 tig0030776:-38269 Msa1444660:intergenic
GATAATTATGAAAGCCTCCA+TGG 0.495765 tig0030776:-39060 Msa1444660:intergenic
TATGTCATTGTTCTAGGCAT+TGG 0.506725 tig0030776:+37990 Msa1444660:CDS
GTCCATAGCAACACTTCTCT+TGG 0.510981 tig0030776:+37950 Msa1444660:CDS
CACCAAGAGAAGTGTTGCTA+TGG 0.525202 tig0030776:-37952 Msa1444660:intergenic
TTAACTTCTGCAGATTTGCA+TGG 0.530112 tig0030776:+38911 Msa1444660:intron
ATGAATAGAGCAATAGATCA+TGG 0.550315 tig0030776:+38023 Msa1444660:CDS
AGAGAAGTTGTGTAACTGAA+AGG 0.568727 tig0030776:-39082 Msa1444660:intergenic
GTAGCAATTGAAGCAGCAGA+TGG 0.611432 tig0030776:-38389 Msa1444660:intergenic
CTCTTACACTGCTTGCCATG+GGG 0.615745 tig0030776:+38423 Msa1444660:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTTTTATTACTATTATTTAG+AGG - tig0030776:38489-38508 Msa1444660:intergenic 10.0%
!! AATAAAACTATAAAAATCAA+AGG + tig0030776:38622-38641 Msa1444660:intron 10.0%
!! CATATAATATATATATTTGA+CGG + tig0030776:39132-39151 Msa1444660:CDS 10.0%
!!! TTTTTATTACTATTATTTAG+AGG - tig0030776:38489-38508 Msa1444660:intergenic 10.0%
!! AATAAAACTATAAAAATCAA+AGG + tig0030776:38622-38641 Msa1444660:intron 10.0%
!!! GTTTTAATTGAAAACAAATT+TGG - tig0030776:38844-38863 Msa1444660:intergenic 15.0%
!! GAATCATTTAATAAATTTCT+TGG + tig0030776:38984-39003 Msa1444660:intron 15.0%
!!! GTTTTAATTGAAAACAAATT+TGG - tig0030776:38844-38863 Msa1444660:intergenic 15.0%
!! GAATCATTTAATAAATTTCT+TGG + tig0030776:38984-39003 Msa1444660:intron 15.0%
!!! TTCTGACATTCTAAAATATT+TGG - tig0030776:38091-38110 Msa1444660:intergenic 20.0%
!!! ATTTTGTTATGAAATTATGC+AGG + tig0030776:38203-38222 Msa1444660:intron 20.0%
!! ATTACTATTATTTAGAGGTA+TGG - tig0030776:38484-38503 Msa1444660:intergenic 20.0%
!!! TTCTGACATTCTAAAATATT+TGG - tig0030776:38091-38110 Msa1444660:intergenic 20.0%
!!! ATTTTGTTATGAAATTATGC+AGG + tig0030776:38203-38222 Msa1444660:intron 20.0%
!! ATTACTATTATTTAGAGGTA+TGG - tig0030776:38484-38503 Msa1444660:intergenic 20.0%
!!! ATAGATCATGGTTTTATCAT+AGG + tig0030776:38035-38054 Msa1444660:CDS 25.0%
! TTAGAATGTCAGAAAAACAA+TGG + tig0030776:38097-38116 Msa1444660:intron 25.0%
!! TTGATTTTATCCATTCCTAT+AGG + tig0030776:38553-38572 Msa1444660:intron 25.0%
! CAATGAATTTCGTAAAATCA+TGG + tig0030776:38757-38776 Msa1444660:intron 25.0%
!! TGTAACTTTTGTCAAAATCA+CGG + tig0030776:38810-38829 Msa1444660:intron 25.0%
!!! ATAGATCATGGTTTTATCAT+AGG + tig0030776:38035-38054 Msa1444660:CDS 25.0%
! TTAGAATGTCAGAAAAACAA+TGG + tig0030776:38097-38116 Msa1444660:intron 25.0%
!! TTGATTTTATCCATTCCTAT+AGG + tig0030776:38553-38572 Msa1444660:intron 25.0%
! CAATGAATTTCGTAAAATCA+TGG + tig0030776:38757-38776 Msa1444660:intron 25.0%
!! TGTAACTTTTGTCAAAATCA+CGG + tig0030776:38810-38829 Msa1444660:intron 25.0%
ATGAATAGAGCAATAGATCA+TGG + tig0030776:38023-38042 Msa1444660:CDS 30.0%
ATTTGGCAAATGTGAAAGAT+AGG - tig0030776:38074-38093 Msa1444660:intergenic 30.0%
!!! GTATGCTGAAGTTTTAATTC+CGG - tig0030776:38181-38200 Msa1444660:intergenic 30.0%
TAAGTCTATCAATCACCTAT+AGG - tig0030776:38571-38590 Msa1444660:intergenic 30.0%
! AAATCAAAGGAGCGTATTAA+AGG + tig0030776:38635-38654 Msa1444660:intron 30.0%
! AATCAAAGGAGCGTATTAAA+GGG + tig0030776:38636-38655 Msa1444660:intron 30.0%
!!! TCTATTTTTGCAGAAAACCA+TGG + tig0030776:39043-39062 Msa1444660:intron 30.0%
ATGAATAGAGCAATAGATCA+TGG + tig0030776:38023-38042 Msa1444660:CDS 30.0%
ATTTGGCAAATGTGAAAGAT+AGG - tig0030776:38074-38093 Msa1444660:intergenic 30.0%
!!! GTATGCTGAAGTTTTAATTC+CGG - tig0030776:38181-38200 Msa1444660:intergenic 30.0%
TAAGTCTATCAATCACCTAT+AGG - tig0030776:38571-38590 Msa1444660:intergenic 30.0%
! AAATCAAAGGAGCGTATTAA+AGG + tig0030776:38635-38654 Msa1444660:intron 30.0%
! AATCAAAGGAGCGTATTAAA+GGG + tig0030776:38636-38655 Msa1444660:intron 30.0%
!!! TCTATTTTTGCAGAAAACCA+TGG + tig0030776:39043-39062 Msa1444660:intron 30.0%
TGCATGTATGTCATTGTTCT+AGG + tig0030776:37984-38003 Msa1444660:CDS 35.0%
! TATGTCATTGTTCTAGGCAT+TGG + tig0030776:37990-38009 Msa1444660:CDS 35.0%
GTTATGAAATTATGCAGGTC+CGG + tig0030776:38208-38227 Msa1444660:intron 35.0%
TGAGCTGGAAGATTTAATTC+CGG - tig0030776:38230-38249 Msa1444660:intergenic 35.0%
AAAATGGGTGAAAAATGAGC+TGG - tig0030776:38245-38264 Msa1444660:intergenic 35.0%
TTTCCCATTGGGAAGAAAAT+GGG - tig0030776:38260-38279 Msa1444660:intergenic 35.0%
ATTTCCCATTGGGAAGAAAA+TGG - tig0030776:38261-38280 Msa1444660:intergenic 35.0%
GTTACGATTTCTTTGTTAGC+TGG + tig0030776:38299-38318 Msa1444660:CDS 35.0%
GAGTCAAACATATCTGTTCA+TGG + tig0030776:38351-38370 Msa1444660:CDS 35.0%
AAAGAGAGAAATTTACCCCA+TGG - tig0030776:38441-38460 Msa1444660:intergenic 35.0%
CTATCAATCACCTATAGGAA+TGG - tig0030776:38566-38585 Msa1444660:intergenic 35.0%
! TGCTCTTCTTTTATCTTACC+AGG + tig0030776:38718-38737 Msa1444660:intron 35.0%
TTAACTTCTGCAGATTTGCA+TGG + tig0030776:38911-38930 Msa1444660:intron 35.0%
TCAAATTAGAAATGCACGTC+TGG + tig0030776:38948-38967 Msa1444660:CDS 35.0%
! ATTTTTGCAGAAAACCATGG+AGG + tig0030776:39046-39065 Msa1444660:intron 35.0%
GATAATTATGAAAGCCTCCA+TGG - tig0030776:39063-39082 Msa1444660:intergenic 35.0%
AGAGAAGTTGTGTAACTGAA+AGG - tig0030776:39085-39104 Msa1444660:intergenic 35.0%
CTCTACATAGTTGCAATTCA+TGG + tig0030776:39101-39120 Msa1444660:CDS 35.0%
TGCATGTATGTCATTGTTCT+AGG + tig0030776:37984-38003 Msa1444660:CDS 35.0%
! TATGTCATTGTTCTAGGCAT+TGG + tig0030776:37990-38009 Msa1444660:CDS 35.0%
GTTATGAAATTATGCAGGTC+CGG + tig0030776:38208-38227 Msa1444660:intron 35.0%
TGAGCTGGAAGATTTAATTC+CGG - tig0030776:38230-38249 Msa1444660:intergenic 35.0%
AAAATGGGTGAAAAATGAGC+TGG - tig0030776:38245-38264 Msa1444660:intergenic 35.0%
TTTCCCATTGGGAAGAAAAT+GGG - tig0030776:38260-38279 Msa1444660:intergenic 35.0%
ATTTCCCATTGGGAAGAAAA+TGG - tig0030776:38261-38280 Msa1444660:intergenic 35.0%
GTTACGATTTCTTTGTTAGC+TGG + tig0030776:38299-38318 Msa1444660:CDS 35.0%
GAGTCAAACATATCTGTTCA+TGG + tig0030776:38351-38370 Msa1444660:CDS 35.0%
AAAGAGAGAAATTTACCCCA+TGG - tig0030776:38441-38460 Msa1444660:intergenic 35.0%
CTATCAATCACCTATAGGAA+TGG - tig0030776:38566-38585 Msa1444660:intergenic 35.0%
! TGCTCTTCTTTTATCTTACC+AGG + tig0030776:38718-38737 Msa1444660:intron 35.0%
TTAACTTCTGCAGATTTGCA+TGG + tig0030776:38911-38930 Msa1444660:intron 35.0%
TCAAATTAGAAATGCACGTC+TGG + tig0030776:38948-38967 Msa1444660:CDS 35.0%
! ATTTTTGCAGAAAACCATGG+AGG + tig0030776:39046-39065 Msa1444660:intron 35.0%
GATAATTATGAAAGCCTCCA+TGG - tig0030776:39063-39082 Msa1444660:intergenic 35.0%
AGAGAAGTTGTGTAACTGAA+AGG - tig0030776:39085-39104 Msa1444660:intergenic 35.0%
CTCTACATAGTTGCAATTCA+TGG + tig0030776:39101-39120 Msa1444660:CDS 35.0%
AACGTGTGAGTTAGGTTTAC+CGG + tig0030776:38154-38173 Msa1444660:intron 40.0%
!!! CTGAAGTTTTAATTCCGGTC+CGG - tig0030776:38176-38195 Msa1444660:intergenic 40.0%
! TTCACCCATTTTCTTCCCAA+TGG + tig0030776:38253-38272 Msa1444660:CDS 40.0%
! TCACCCATTTTCTTCCCAAT+GGG + tig0030776:38254-38273 Msa1444660:CDS 40.0%
! CAGTTGAAGCATTTCCCATT+GGG - tig0030776:38271-38290 Msa1444660:intergenic 40.0%
TCTTTGTTAGCTGGAGTAGT+TGG + tig0030776:38308-38327 Msa1444660:CDS 40.0%
! TGCTGCTTCAATTGCTACTT+TGG + tig0030776:38394-38413 Msa1444660:CDS 40.0%
!! CTTCAATTGCTACTTTGGCT+TGG + tig0030776:38399-38418 Msa1444660:CDS 40.0%
TATCTTACCAGGTGCATGTT+TGG + tig0030776:38729-38748 Msa1444660:intron 40.0%
AACGTGTGAGTTAGGTTTAC+CGG + tig0030776:38154-38173 Msa1444660:intron 40.0%
!!! CTGAAGTTTTAATTCCGGTC+CGG - tig0030776:38176-38195 Msa1444660:intergenic 40.0%
! TTCACCCATTTTCTTCCCAA+TGG + tig0030776:38253-38272 Msa1444660:CDS 40.0%
! TCACCCATTTTCTTCCCAAT+GGG + tig0030776:38254-38273 Msa1444660:CDS 40.0%
! CAGTTGAAGCATTTCCCATT+GGG - tig0030776:38271-38290 Msa1444660:intergenic 40.0%
TCTTTGTTAGCTGGAGTAGT+TGG + tig0030776:38308-38327 Msa1444660:CDS 40.0%
! TGCTGCTTCAATTGCTACTT+TGG + tig0030776:38394-38413 Msa1444660:CDS 40.0%
!! CTTCAATTGCTACTTTGGCT+TGG + tig0030776:38399-38418 Msa1444660:CDS 40.0%
TATCTTACCAGGTGCATGTT+TGG + tig0030776:38729-38748 Msa1444660:intron 40.0%
GTCCATAGCAACACTTCTCT+TGG + tig0030776:37950-37969 Msa1444660:CDS 45.0%
!! CACCAAGAGAAGTGTTGCTA+TGG - tig0030776:37955-37974 Msa1444660:intergenic 45.0%
!! TTGTTCTAGGCATTGGTGCA+TGG + tig0030776:37997-38016 Msa1444660:CDS 45.0%
!! TGTTCTAGGCATTGGTGCAT+GGG + tig0030776:37998-38017 Msa1444660:CDS 45.0%
TGCGTAGTAACGTGTGAGTT+AGG + tig0030776:38146-38165 Msa1444660:intron 45.0%
! CCAGTTGAAGCATTTCCCAT+TGG - tig0030776:38272-38291 Msa1444660:intergenic 45.0%
CCAATGGGAAATGCTTCAAC+TGG + tig0030776:38269-38288 Msa1444660:CDS 45.0%
GTAGCAATTGAAGCAGCAGA+TGG - tig0030776:38392-38411 Msa1444660:intergenic 45.0%
ACTCTTACACTGCTTGCCAT+GGG + tig0030776:38422-38441 Msa1444660:CDS 45.0%
TGTCAATCCAAACATGCACC+TGG - tig0030776:38739-38758 Msa1444660:intergenic 45.0%
GTCCATAGCAACACTTCTCT+TGG + tig0030776:37950-37969 Msa1444660:CDS 45.0%
!! CACCAAGAGAAGTGTTGCTA+TGG - tig0030776:37955-37974 Msa1444660:intergenic 45.0%
!! TTGTTCTAGGCATTGGTGCA+TGG + tig0030776:37997-38016 Msa1444660:CDS 45.0%
!! TGTTCTAGGCATTGGTGCAT+GGG + tig0030776:37998-38017 Msa1444660:CDS 45.0%
TGCGTAGTAACGTGTGAGTT+AGG + tig0030776:38146-38165 Msa1444660:intron 45.0%
! CCAGTTGAAGCATTTCCCAT+TGG - tig0030776:38272-38291 Msa1444660:intergenic 45.0%
CCAATGGGAAATGCTTCAAC+TGG + tig0030776:38269-38288 Msa1444660:CDS 45.0%
GTAGCAATTGAAGCAGCAGA+TGG - tig0030776:38392-38411 Msa1444660:intergenic 45.0%
ACTCTTACACTGCTTGCCAT+GGG + tig0030776:38422-38441 Msa1444660:CDS 45.0%
TGTCAATCCAAACATGCACC+TGG - tig0030776:38739-38758 Msa1444660:intergenic 45.0%
GTGAGTTAGGTTTACCGGAC+CGG + tig0030776:38159-38178 Msa1444660:intron 50.0%
! GGTGCTGCATCGACAATTTC+AGG + tig0030776:38329-38348 Msa1444660:CDS 50.0%
GACTCTTACACTGCTTGCCA+TGG + tig0030776:38421-38440 Msa1444660:CDS 50.0%
CTCTTACACTGCTTGCCATG+GGG + tig0030776:38423-38442 Msa1444660:CDS 50.0%
GTGAGTTAGGTTTACCGGAC+CGG + tig0030776:38159-38178 Msa1444660:intron 50.0%
! GGTGCTGCATCGACAATTTC+AGG + tig0030776:38329-38348 Msa1444660:CDS 50.0%
GACTCTTACACTGCTTGCCA+TGG + tig0030776:38421-38440 Msa1444660:CDS 50.0%
CTCTTACACTGCTTGCCATG+GGG + tig0030776:38423-38442 Msa1444660:CDS 50.0%
Chromosome Type Strat End Strand Name
tig0030776 gene 37932 39151 37932 ID=Msa1444660;Name=Msa1444660
tig0030776 mRNA 37932 39151 37932 ID=Msa1444660-mRNA-1;Parent=Msa1444660;Name=Msa1444660-mRNA-1;_AED=0.14;_eAED=0.14;_QI=13|1|0.75|1|1|1|4|0|157
tig0030776 exon 37932 38056 37932 ID=Msa1444660-mRNA-1:exon:14597;Parent=Msa1444660-mRNA-1
tig0030776 exon 38225 38444 38225 ID=Msa1444660-mRNA-1:exon:14598;Parent=Msa1444660-mRNA-1
tig0030776 exon 38924 38969 38924 ID=Msa1444660-mRNA-1:exon:14599;Parent=Msa1444660-mRNA-1
tig0030776 exon 39056 39151 39056 ID=Msa1444660-mRNA-1:exon:14600;Parent=Msa1444660-mRNA-1
tig0030776 five_prime_UTR 37932 37944 37932 ID=Msa1444660-mRNA-1:five_prime_utr;Parent=Msa1444660-mRNA-1
tig0030776 CDS 37945 38056 37945 ID=Msa1444660-mRNA-1:cds;Parent=Msa1444660-mRNA-1
tig0030776 CDS 38225 38444 38225 ID=Msa1444660-mRNA-1:cds;Parent=Msa1444660-mRNA-1
tig0030776 CDS 38924 38969 38924 ID=Msa1444660-mRNA-1:cds;Parent=Msa1444660-mRNA-1
tig0030776 CDS 39056 39151 39056 ID=Msa1444660-mRNA-1:cds;Parent=Msa1444660-mRNA-1
Gene Sequence

>Msa1444660

ATGAAGTCCATAGCAACACTTCTCTTGGTGCTCAACTTTTGCATGTATGTCATTGTTCTAGGCATTGGTGCATGGGCTATGAATAGAGCAATAGATCATGGTTTTATCATAGGTCCGGAATTAAATCTTCCAGCTCATTTTTCACCCATTTTCTTCCCAATGGGAAATGCTTCAACTGGATTCTTTGTTACGATTTCTTTGTTAGCTGGAGTAGTTGGTGCTGCATCGACAATTTCAGGAGTCAAACATATCTGTTCATGGACTGCAGAGAGCTTGCCATCTGCTGCTTCAATTGCTACTTTGGCTTGGACTCTTACACTGCTTGCCATGGGATTTGCATGGAAAGAGATTGAGCTTCAAATTAGAAATGCACGTCTGAAAACCATGGAGGCTTTCATAATTATCCTTTCAGTTACACAACTTCTCTACATAGTTGCAATTCATGGTGCTGCTGCATATAATATATATATTTGA

Protein sequence

>Msa1444660

MKSIATLLLVLNFCMYVIVLGIGAWAMNRAIDHGFIIGPELNLPAHFSPIFFPMGNASTGFFVTISLLAGVVGAASTISGVKHICSWTAESLPSAASIATLAWTLTLLAMGFAWKEIELQIRNARLKTMEAFIIILSVTQLLYIVAIHGAAAYNIYI*