AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0243100


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0243100 MtrunA17_Chr2g0295651 97.917 144 3 0 1 144 1 144 3.05e-103 291
Msa0243100 MtrunA17_Chr4g0067541 57.627 118 36 4 1 112 1 110 1.51e-32 111
Msa0243100 MtrunA17_Chr3g0115551 44.444 72 38 1 37 106 61 132 2.59e-16 71.2
Msa0243100 MtrunA17_Chr5g0400051 48.276 58 29 1 53 110 74 130 3.30e-13 63.2
Msa0243100 MtrunA17_Chr4g0055191 46.552 58 31 0 53 110 62 119 9.54e-13 62.0
Msa0243100 MtrunA17_Chr8g0344991 41.333 75 41 1 64 135 39 113 9.93e-13 60.8
Msa0243100 MtrunA17_Chr3g0124361 37.349 83 43 2 26 106 91 166 3.36e-12 61.2
Msa0243100 MtrunA17_Chr8g0336591 48.148 54 21 1 51 104 32 78 2.32e-11 57.4
Msa0243100 MtrunA17_Chr3g0138651 50.000 58 28 1 58 114 348 405 7.24e-11 58.9
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0243100 AT5G49120.1 40.132 152 81 4 1 144 1 150 1.14e-29 105
Msa0243100 AT1G78020.1 40.278 72 40 1 64 135 89 157 1.13e-13 64.7
Msa0243100 AT1G22160.1 51.852 54 23 1 53 106 70 120 1.48e-13 63.9
Msa0243100 AT5G47060.2 53.846 52 24 0 53 104 86 137 2.76e-13 63.9
Msa0243100 AT5G47060.1 53.846 52 24 0 53 104 86 137 2.76e-13 63.9
Msa0243100 AT4G39795.1 52.083 48 23 0 62 109 71 118 7.51e-13 61.6
Msa0243100 AT1G74940.1 42.169 83 40 3 62 144 148 222 4.27e-11 58.9
Msa0243100 AT4G17670.1 50.000 50 25 0 55 104 67 116 6.03e-11 57.4
Msa0243100 AT5G20700.1 55.319 47 20 1 60 106 178 223 7.90e-11 58.5

Find 25 sgRNAs with CRISPR-Local

Find 92 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GCTTCTTATCATCATGAAAA+AGG 0.300416 2_2:-19886513 Msa0243100:CDS
TTAATTAAGCAGGGTAAAAC+TGG 0.323409 2_2:+19886361 None:intergenic
GCTCCATTCTCCAACCTCTT+TGG 0.343871 2_2:-19886256 Msa0243100:three_prime_UTR
AATAAGCAAAACCACCGTTT+TGG 0.352315 2_2:+19886481 None:intergenic
TTGGTAATGTAGTGTGGTTT+TGG 0.361553 2_2:-19886237 Msa0243100:three_prime_UTR
TTAATTAATGTTGTTAGATA+AGG 0.409759 2_2:-19886346 Msa0243100:three_prime_UTR
TCTAACAACATTAATTAAGC+AGG 0.429786 2_2:+19886351 None:intergenic
GGCTAGTAGTTACTAGTGAA+TGG 0.502662 2_2:+19887111 None:intergenic
GTAGTGTTAGAATCTCAAAA+AGG 0.513194 2_2:-19887048 Msa0243100:CDS
ACCTCTTTGGTAATGTAGTG+TGG 0.517027 2_2:-19886243 Msa0243100:three_prime_UTR
TAGTGAATGGAAAGTGTATG+AGG 0.523850 2_2:+19887124 None:intergenic
ATTGATACATGAATGAAGAA+AGG 0.524095 2_2:-19886461 Msa0243100:exon
GGACGTTTCAGCTTCATACA+AGG 0.529104 2_2:+19886300 None:intergenic
CACTACATTACCAAAGAGGT+TGG 0.538254 2_2:+19886246 None:intergenic
TTTGGTTATTATAATTGACT+TGG 0.543260 2_2:-19886219 Msa0243100:three_prime_UTR
TTACCAAAGAGGTTGGAGAA+TGG 0.552783 2_2:+19886253 None:intergenic
ATGATGAAAATAAGAACTCA+AGG 0.565409 2_2:+19886927 None:intergenic
TATTAGCAATAGCAAGAAGA+AGG 0.566617 2_2:-19887019 Msa0243100:CDS
CTAACAACATTAATTAAGCA+GGG 0.589637 2_2:+19886352 None:intergenic
GGATAGAGCTTTCTGTAGTG+TGG 0.592385 2_2:-19886634 Msa0243100:CDS
ACCACACTACATTACCAAAG+AGG 0.594824 2_2:+19886242 None:intergenic
AAAGGAAGAAGAAACCAAAA+CGG 0.628233 2_2:-19886495 Msa0243100:CDS
TAGATGCAAGCATATTGTGA+TGG 0.653765 2_2:-19886607 Msa0243100:CDS
GGAAGAAGAAACCAAAACGG+TGG 0.688263 2_2:-19886492 Msa0243100:CDS
AAGATGAAGAAATTGCAGCA+TGG 0.688850 2_2:+19886544 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAAGTGATAGAATAAAAAAA+TGG - chr2_2:19886252-19886271 Msa0243100:three_prime_UTR 15.0%
!! AATATAAAGTTTCATAACAT+AGG + chr2_2:19886551-19886570 None:intergenic 15.0%
!! AAAAATAAAAACAAAGATCT+AGG + chr2_2:19886597-19886616 None:intergenic 15.0%
!! ATTGTGAGATAAAAAAAAAA+TGG - chr2_2:19886921-19886940 Msa0243100:CDS 15.0%
!! TTAATTAATGTTGTTAGATA+AGG - chr2_2:19886988-19887007 Msa0243100:CDS 15.0%
!!! CTTTCTACTTTTTATTTTAT+GGG - chr2_2:19887056-19887075 Msa0243100:CDS 15.0%
!! AAAGTGATAGAATAAAAAAA+TGG - chr2_2:19886252-19886271 Msa0243100:three_prime_UTR 15.0%
!! AATATAAAGTTTCATAACAT+AGG + chr2_2:19886551-19886570 None:intergenic 15.0%
!! AAAAATAAAAACAAAGATCT+AGG + chr2_2:19886597-19886616 None:intergenic 15.0%
!! ATTGTGAGATAAAAAAAAAA+TGG - chr2_2:19886921-19886940 Msa0243100:CDS 15.0%
!! TTAATTAATGTTGTTAGATA+AGG - chr2_2:19886988-19887007 Msa0243100:CDS 15.0%
!!! CTTTCTACTTTTTATTTTAT+GGG - chr2_2:19887056-19887075 Msa0243100:CDS 15.0%
!!! TTATTCTATCACTTTTTTTG+TGG + chr2_2:19886247-19886266 None:intergenic 20.0%
!! TGATAGAATAAAAAAATGGT+GGG - chr2_2:19886256-19886275 Msa0243100:three_prime_UTR 20.0%
!!! ATTGTTTTGTTAATCACTTT+TGG + chr2_2:19886346-19886365 None:intergenic 20.0%
!! CATAGGTTATAAAATATAGA+AGG + chr2_2:19886534-19886553 None:intergenic 20.0%
!!! TGTTTATTTTTTTGTGAAGA+GGG - chr2_2:19886678-19886697 Msa0243100:intron 20.0%
!! CCATAAAATAAAAAGTAGAA+AGG + chr2_2:19887058-19887077 None:intergenic 20.0%
!!! CCTTTCTACTTTTTATTTTA+TGG - chr2_2:19887055-19887074 Msa0243100:CDS 20.0%
!! TTTGGTTATTATAATTGACT+TGG - chr2_2:19887115-19887134 Msa0243100:five_prime_UTR 20.0%
!!! TTATTCTATCACTTTTTTTG+TGG + chr2_2:19886247-19886266 None:intergenic 20.0%
!! TGATAGAATAAAAAAATGGT+GGG - chr2_2:19886256-19886275 Msa0243100:three_prime_UTR 20.0%
!!! ATTGTTTTGTTAATCACTTT+TGG + chr2_2:19886346-19886365 None:intergenic 20.0%
!! CATAGGTTATAAAATATAGA+AGG + chr2_2:19886534-19886553 None:intergenic 20.0%
!!! TGTTTATTTTTTTGTGAAGA+GGG - chr2_2:19886678-19886697 Msa0243100:intron 20.0%
!! CCATAAAATAAAAAGTAGAA+AGG + chr2_2:19887058-19887077 None:intergenic 20.0%
!!! CCTTTCTACTTTTTATTTTA+TGG - chr2_2:19887055-19887074 Msa0243100:CDS 20.0%
!! TTTGGTTATTATAATTGACT+TGG - chr2_2:19887115-19887134 Msa0243100:five_prime_UTR 20.0%
! GTGATAGAATAAAAAAATGG+TGG - chr2_2:19886255-19886274 Msa0243100:three_prime_UTR 25.0%
! ATGATGAAAATAAGAACTCA+AGG + chr2_2:19886410-19886429 None:intergenic 25.0%
!!! GTGTTTATTTTTTTGTGAAG+AGG - chr2_2:19886677-19886696 Msa0243100:intron 25.0%
!!! GTTTATTTTTTTGTGAAGAG+GGG - chr2_2:19886679-19886698 Msa0243100:intron 25.0%
! ATTGATACATGAATGAAGAA+AGG - chr2_2:19886873-19886892 Msa0243100:CDS 25.0%
! CTAACAACATTAATTAAGCA+GGG + chr2_2:19886985-19887004 None:intergenic 25.0%
! TCTAACAACATTAATTAAGC+AGG + chr2_2:19886986-19887005 None:intergenic 25.0%
! GTGATAGAATAAAAAAATGG+TGG - chr2_2:19886255-19886274 Msa0243100:three_prime_UTR 25.0%
! ATGATGAAAATAAGAACTCA+AGG + chr2_2:19886410-19886429 None:intergenic 25.0%
!!! GTGTTTATTTTTTTGTGAAG+AGG - chr2_2:19886677-19886696 Msa0243100:intron 25.0%
!!! GTTTATTTTTTTGTGAAGAG+GGG - chr2_2:19886679-19886698 Msa0243100:intron 25.0%
! ATTGATACATGAATGAAGAA+AGG - chr2_2:19886873-19886892 Msa0243100:CDS 25.0%
! CTAACAACATTAATTAAGCA+GGG + chr2_2:19886985-19887004 None:intergenic 25.0%
! TCTAACAACATTAATTAAGC+AGG + chr2_2:19886986-19887005 None:intergenic 25.0%
GTAGTGTTAGAATCTCAAAA+AGG - chr2_2:19886286-19886305 Msa0243100:three_prime_UTR 30.0%
TATTAGCAATAGCAAGAAGA+AGG - chr2_2:19886315-19886334 Msa0243100:three_prime_UTR 30.0%
! TCATCATGAATCTCATTTTC+AGG - chr2_2:19886423-19886442 Msa0243100:three_prime_UTR 30.0%
GCTTCTTATCATCATGAAAA+AGG - chr2_2:19886821-19886840 Msa0243100:intron 30.0%
AAAGGAAGAAGAAACCAAAA+CGG - chr2_2:19886839-19886858 Msa0243100:CDS 30.0%
TTAATTAAGCAGGGTAAAAC+TGG + chr2_2:19886976-19886995 None:intergenic 30.0%
GTAGTGTTAGAATCTCAAAA+AGG - chr2_2:19886286-19886305 Msa0243100:three_prime_UTR 30.0%
TATTAGCAATAGCAAGAAGA+AGG - chr2_2:19886315-19886334 Msa0243100:three_prime_UTR 30.0%
! TCATCATGAATCTCATTTTC+AGG - chr2_2:19886423-19886442 Msa0243100:three_prime_UTR 30.0%
GCTTCTTATCATCATGAAAA+AGG - chr2_2:19886821-19886840 Msa0243100:intron 30.0%
AAAGGAAGAAGAAACCAAAA+CGG - chr2_2:19886839-19886858 Msa0243100:CDS 30.0%
TTAATTAAGCAGGGTAAAAC+TGG + chr2_2:19886976-19886995 None:intergenic 30.0%
! TAGTGAATGGAAAGTGTATG+AGG + chr2_2:19886213-19886232 None:intergenic 35.0%
GTGTTAGAATCTCAAAAAGG+TGG - chr2_2:19886289-19886308 Msa0243100:three_prime_UTR 35.0%
TTAGAATCTCAAAAAGGTGG+TGG - chr2_2:19886292-19886311 Msa0243100:three_prime_UTR 35.0%
!!! TTGAGCTTTGTTTTCTCTGT+AGG - chr2_2:19886464-19886483 Msa0243100:exon 35.0%
TGTAGGAAAAAGTTGTTACC+TGG - chr2_2:19886481-19886500 Msa0243100:CDS 35.0%
! TACATGTAGATGTCTTTTCC+AGG + chr2_2:19886502-19886521 None:intergenic 35.0%
TAGATGCAAGCATATTGTGA+TGG - chr2_2:19886727-19886746 Msa0243100:intron 35.0%
AAGATGAAGAAATTGCAGCA+TGG + chr2_2:19886793-19886812 None:intergenic 35.0%
! AATAAGCAAAACCACCGTTT+TGG + chr2_2:19886856-19886875 None:intergenic 35.0%
!!! TTGGTAATGTAGTGTGGTTT+TGG - chr2_2:19887097-19887116 Msa0243100:five_prime_UTR 35.0%
! TAGTGAATGGAAAGTGTATG+AGG + chr2_2:19886213-19886232 None:intergenic 35.0%
GTGTTAGAATCTCAAAAAGG+TGG - chr2_2:19886289-19886308 Msa0243100:three_prime_UTR 35.0%
TTAGAATCTCAAAAAGGTGG+TGG - chr2_2:19886292-19886311 Msa0243100:three_prime_UTR 35.0%
!!! TTGAGCTTTGTTTTCTCTGT+AGG - chr2_2:19886464-19886483 Msa0243100:exon 35.0%
TGTAGGAAAAAGTTGTTACC+TGG - chr2_2:19886481-19886500 Msa0243100:CDS 35.0%
! TACATGTAGATGTCTTTTCC+AGG + chr2_2:19886502-19886521 None:intergenic 35.0%
TAGATGCAAGCATATTGTGA+TGG - chr2_2:19886727-19886746 Msa0243100:intron 35.0%
AAGATGAAGAAATTGCAGCA+TGG + chr2_2:19886793-19886812 None:intergenic 35.0%
! AATAAGCAAAACCACCGTTT+TGG + chr2_2:19886856-19886875 None:intergenic 35.0%
!!! TTGGTAATGTAGTGTGGTTT+TGG - chr2_2:19887097-19887116 Msa0243100:five_prime_UTR 35.0%
GGCTAGTAGTTACTAGTGAA+TGG + chr2_2:19886226-19886245 None:intergenic 40.0%
TTACCAAAGAGGTTGGAGAA+TGG + chr2_2:19887084-19887103 None:intergenic 40.0%
CACTACATTACCAAAGAGGT+TGG + chr2_2:19887091-19887110 None:intergenic 40.0%
!! ACCTCTTTGGTAATGTAGTG+TGG - chr2_2:19887091-19887110 Msa0243100:five_prime_UTR 40.0%
ACCACACTACATTACCAAAG+AGG + chr2_2:19887095-19887114 None:intergenic 40.0%
GGCTAGTAGTTACTAGTGAA+TGG + chr2_2:19886226-19886245 None:intergenic 40.0%
TTACCAAAGAGGTTGGAGAA+TGG + chr2_2:19887084-19887103 None:intergenic 40.0%
CACTACATTACCAAAGAGGT+TGG + chr2_2:19887091-19887110 None:intergenic 40.0%
!! ACCTCTTTGGTAATGTAGTG+TGG - chr2_2:19887091-19887110 Msa0243100:five_prime_UTR 40.0%
ACCACACTACATTACCAAAG+AGG + chr2_2:19887095-19887114 None:intergenic 40.0%
GGATAGAGCTTTCTGTAGTG+TGG - chr2_2:19886700-19886719 Msa0243100:intron 45.0%
GGAAGAAGAAACCAAAACGG+TGG - chr2_2:19886842-19886861 Msa0243100:CDS 45.0%
GGACGTTTCAGCTTCATACA+AGG + chr2_2:19887037-19887056 None:intergenic 45.0%
GGATAGAGCTTTCTGTAGTG+TGG - chr2_2:19886700-19886719 Msa0243100:intron 45.0%
GGAAGAAGAAACCAAAACGG+TGG - chr2_2:19886842-19886861 Msa0243100:CDS 45.0%
GGACGTTTCAGCTTCATACA+AGG + chr2_2:19887037-19887056 None:intergenic 45.0%
GCTCCATTCTCCAACCTCTT+TGG - chr2_2:19887078-19887097 Msa0243100:exon 50.0%
GCTCCATTCTCCAACCTCTT+TGG - chr2_2:19887078-19887097 Msa0243100:exon 50.0%
Chromosome Type Strat End Strand Name
chr2_2 gene 19886204 19887152 19886204 ID=Msa0243100;Name=Msa0243100
chr2_2 mRNA 19886204 19887152 19886204 ID=Msa0243100-mRNA-1;Parent=Msa0243100;Name=Msa0243100-mRNA-1;_AED=0.01;_eAED=0.01;_QI=67|1|1|1|1|1|2|275|144
chr2_2 exon 19886204 19886659 19886204 ID=Msa0243100-mRNA-1:exon:8010;Parent=Msa0243100-mRNA-1
chr2_2 exon 19886832 19887152 19886832 ID=Msa0243100-mRNA-1:exon:8009;Parent=Msa0243100-mRNA-1
chr2_2 five_prime_UTR 19887086 19887152 19887086 ID=Msa0243100-mRNA-1:five_prime_utr;Parent=Msa0243100-mRNA-1
chr2_2 CDS 19886832 19887085 19886832 ID=Msa0243100-mRNA-1:cds;Parent=Msa0243100-mRNA-1
chr2_2 CDS 19886479 19886659 19886479 ID=Msa0243100-mRNA-1:cds;Parent=Msa0243100-mRNA-1
chr2_2 three_prime_UTR 19886204 19886478 19886204 ID=Msa0243100-mRNA-1:three_prime_utr;Parent=Msa0243100-mRNA-1
Gene Sequence

>Msa0243100

ATGGTGGGTTTGAGTGTAGTGTTAGAATCTCAAAAAGGTGGTGGTATTAGCAATAGCAAGAAGAAGGAAACTCCAAAAGTGATTAACAAAACAATGATGCTTAGTAGCAACAACAACAAACAATCTTCTATAGTTTCCTTGAGTTCTTATTTTCATCATGAATCTCATTTTCAGGAACAACAAACAACGTTTCTTGAGCTTTGTTTTCTCTGTAGGAAAAAGTTGTTACCTGGAAAAGACATCTACATGTACAAAGGGGATAGAGCTTTCTGTAGTGTGGAATGTAGATGCAAGCATATTGTGATGGATGAAGAAGAAAGTAACAATATTCAGAATGAGAACTGTTACCATGCTGCAATTTCTTCATCTTCTTCAGAAGCTTCTTATCATCATGAAAAAGGAAGAAGAAACCAAAACGGTGGTTTTGCTTATTGA

Protein sequence

>Msa0243100

MVGLSVVLESQKGGGISNSKKKETPKVINKTMMLSSNNNKQSSIVSLSSYFHHESHFQEQQTTFLELCFLCRKKLLPGKDIYMYKGDRAFCSVECRCKHIVMDEEESNNIQNENCYHAAISSSSSEASYHHEKGRRNQNGGFAY*