AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0238460


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0238460 MtrunA17_Chr2g0288361 97.403 77 2 0 1 77 1 77 4.48e-53 159
Msa0238460 MtrunA17_Chr4g0024181 49.333 75 35 2 1 74 1 73 3.57e-20 76.3
Msa0238460 MtrunA17_Chr2g0322831 59.184 49 20 0 27 75 32 80 9.03e-18 70.5
Msa0238460 MtrunA17_Chr5g0396771 42.647 68 36 1 7 74 20 84 7.08e-15 63.2
Msa0238460 MtrunA17_Chr3g0121241 51.111 45 22 0 28 72 99 143 1.78e-12 60.5
Msa0238460 MtrunA17_Chr4g0055981 51.163 43 21 0 29 71 113 155 6.65e-12 58.2
Msa0238460 MtrunA17_Chr7g0275911 51.163 43 21 0 30 72 71 113 1.19e-11 57.8
Msa0238460 MtrunA17_Chr7g0240821 47.727 44 23 0 29 72 59 102 1.20e-11 57.8
Msa0238460 MtrunA17_Chr8g0360111 47.727 44 23 0 29 72 83 126 1.78e-11 57.4
Msa0238460 MtrunA17_Chr4g0070641 44.444 45 25 0 28 72 69 113 1.98e-11 56.2
Msa0238460 MtrunA17_Chr7g0229101 45.455 44 24 0 28 71 29 72 2.60e-11 56.6
Msa0238460 MtrunA17_Chr5g0435101 48.837 43 22 0 29 71 69 111 2.98e-11 56.2
Msa0238460 MtrunA17_Chr7g0228991 46.000 50 24 1 18 67 79 125 6.08e-11 55.8
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0238460 AT2G46410.1 63.636 44 16 0 27 70 36 79 1.70e-17 70.5
Msa0238460 AT4G01060.1 50.000 64 29 1 7 70 16 76 5.71e-16 65.9
Msa0238460 AT1G01380.1 56.818 44 19 0 27 70 32 75 1.51e-15 65.1
Msa0238460 AT5G53200.1 52.000 50 24 0 27 76 31 80 2.03e-15 65.5
Msa0238460 AT4G01060.2 60.000 45 18 0 26 70 29 73 2.10e-15 64.3
Msa0238460 AT4G01060.3 60.000 45 18 0 26 70 30 74 2.71e-15 64.3
Msa0238460 AT2G30420.1 36.111 72 43 1 1 72 15 83 1.74e-12 58.2
Msa0238460 AT2G30424.1 50.000 44 22 0 27 70 34 77 4.93e-12 56.6
Msa0238460 AT5G52600.1 45.455 44 24 0 29 72 70 113 1.09e-11 57.8
Msa0238460 AT5G14750.4 43.182 44 25 0 29 72 13 56 2.21e-11 55.8
Msa0238460 AT5G14750.2 43.182 44 25 0 29 72 13 56 2.21e-11 55.8
Msa0238460 AT2G30432.1 44.262 61 31 2 10 70 19 76 4.10e-11 53.9
Msa0238460 AT3G13540.1 52.500 40 19 0 30 69 82 121 8.08e-11 55.8

Find 30 sgRNAs with CRISPR-Local

Find 114 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GCAACGATATCTTCCTCTTC+TGG 0.165562 2_2:+11997175 None:intergenic
ATATCTTCTGGGGTTCTTCC+AGG 0.255062 2_2:+11996963 None:intergenic
TGCATATGTATCAATATAAT+AGG 0.341014 2_2:+11996651 None:intergenic
GTATCAATATAATAGGAAAA+AGG 0.365949 2_2:+11996658 None:intergenic
CAACGATATCTTCCTCTTCT+GGG 0.371629 2_2:+11997176 None:intergenic
TGTAGATGGCATCTCATTGC+TGG 0.392405 2_2:-11996993 Msa0238460:intron
TTGTTATTACATCATATTTG+TGG 0.396920 2_2:+11996563 None:intergenic
CTCATTGCTGGGAGAATCCC+TGG 0.434907 2_2:-11996981 Msa0238460:CDS
CAGTTTATGTGTGCAGGCAT+TGG 0.436054 2_2:+11997500 None:intergenic
TTAACTCAGTTTATGTGTGC+AGG 0.437915 2_2:+11997494 None:intergenic
CAGAAGATATTGAAAAGTAT+TGG 0.446559 2_2:-11996950 Msa0238460:CDS
TATCTTCTGGGGTTCTTCCA+GGG 0.463656 2_2:+11996964 None:intergenic
ATTTGCTCAGGAACTTAGAA+TGG 0.468776 2_2:+11996874 None:intergenic
GATGAAACGTGAGGCTGTGC+TGG 0.475255 2_2:-11997206 Msa0238460:CDS
AATGGCCAGTATGTCTCTTC+AGG 0.479277 2_2:-11997411 Msa0238460:intron
TTGTTTAGAAATAGACATGT+AGG 0.497435 2_2:+11997579 None:intergenic
ATATTTGTGGATAAAGATGT+AGG 0.506418 2_2:+11996576 None:intergenic
AATTACACAATAATTTGCTC+AGG 0.510754 2_2:+11996862 None:intergenic
TGTTTAGATTGGTCGGAAAG+AGG 0.513739 2_2:-11997147 Msa0238460:intron
TGGTACCTGAAGAGACATAC+TGG 0.523534 2_2:+11997406 None:intergenic
AGGAACTTAGAATGGTACTT+AGG 0.533310 2_2:+11996882 None:intergenic
TGTTTAGAAATAGACATGTA+GGG 0.567975 2_2:+11997580 None:intergenic
GTAGATGGCATCTCATTGCT+GGG 0.572643 2_2:-11996992 Msa0238460:intron
ATTATATTGATACATATGCA+TGG 0.586546 2_2:-11996648 Msa0238460:three_prime_UTR
TATTTGTGGATAAAGATGTA+GGG 0.588008 2_2:+11996577 None:intergenic
AACGATATCTTCCTCTTCTG+GGG 0.611771 2_2:+11997177 None:intergenic
CATTGGTATTGAGATAAGCA+TGG 0.631499 2_2:+11997517 None:intergenic
TATGCAACCACTGCAAACAA+TGG 0.637268 2_2:-11997429 Msa0238460:CDS
ATACTGGCCATTGTTTGCAG+TGG 0.645184 2_2:+11997422 None:intergenic
CTCAGATCAGATGAAACGTG+AGG 0.650176 2_2:-11997215 Msa0238460:intron

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATATATATATATATATATAT+AGG - chr2_2:11996665-11996684 Msa0238460:three_prime_UTR 0.0%
!! TATATATATATATATATATA+GGG - chr2_2:11996664-11996683 Msa0238460:three_prime_UTR 0.0%
!! ATATATATATATATATATAT+AGG - chr2_2:11996665-11996684 Msa0238460:three_prime_UTR 0.0%
!! TATATATATATATATATATA+GGG - chr2_2:11996664-11996683 Msa0238460:three_prime_UTR 0.0%
!! TATACAGATTCATATGATTT+GGG + chr2_2:11996779-11996798 None:intergenic 20.0%
!! ATATACAGATTCATATGATT+TGG + chr2_2:11996780-11996799 None:intergenic 20.0%
!! TATATGTTAATTAACTTCGT+TGG - chr2_2:11996920-11996939 Msa0238460:CDS 20.0%
!!! AATACTTTTCAATATCTTCT+GGG + chr2_2:11997081-11997100 None:intergenic 20.0%
!!! TTTATATATGCATCTTTTGT+TGG - chr2_2:11997331-11997350 Msa0238460:intron 20.0%
!! GTATCAATATAATAGGAAAA+AGG + chr2_2:11997375-11997394 None:intergenic 20.0%
!! TGCATATGTATCAATATAAT+AGG + chr2_2:11997382-11997401 None:intergenic 20.0%
!! ATTATATTGATACATATGCA+TGG - chr2_2:11997382-11997401 Msa0238460:intron 20.0%
!!! TTGTTATTACATCATATTTG+TGG + chr2_2:11997470-11997489 None:intergenic 20.0%
!! TATACAGATTCATATGATTT+GGG + chr2_2:11996779-11996798 None:intergenic 20.0%
!! ATATACAGATTCATATGATT+TGG + chr2_2:11996780-11996799 None:intergenic 20.0%
!! TATATGTTAATTAACTTCGT+TGG - chr2_2:11996920-11996939 Msa0238460:CDS 20.0%
!!! AATACTTTTCAATATCTTCT+GGG + chr2_2:11997081-11997100 None:intergenic 20.0%
!!! TTTATATATGCATCTTTTGT+TGG - chr2_2:11997331-11997350 Msa0238460:intron 20.0%
!! GTATCAATATAATAGGAAAA+AGG + chr2_2:11997375-11997394 None:intergenic 20.0%
!! TGCATATGTATCAATATAAT+AGG + chr2_2:11997382-11997401 None:intergenic 20.0%
!! ATTATATTGATACATATGCA+TGG - chr2_2:11997382-11997401 Msa0238460:intron 20.0%
!!! TTGTTATTACATCATATTTG+TGG + chr2_2:11997470-11997489 None:intergenic 20.0%
! TGTTTAGAAATAGACATGTA+GGG + chr2_2:11996453-11996472 None:intergenic 25.0%
! TTGTTTAGAAATAGACATGT+AGG + chr2_2:11996454-11996473 None:intergenic 25.0%
! TTTGACATGTTAATTGTAGA+TGG - chr2_2:11997023-11997042 Msa0238460:intron 25.0%
!! ATACTTTTCAATATCTTCTG+GGG + chr2_2:11997080-11997099 None:intergenic 25.0%
!! CAATACTTTTCAATATCTTC+TGG + chr2_2:11997082-11997101 None:intergenic 25.0%
!! CAGAAGATATTGAAAAGTAT+TGG - chr2_2:11997080-11997099 Msa0238460:intron 25.0%
!!! AATTACACAATAATTTGCTC+AGG + chr2_2:11997171-11997190 None:intergenic 25.0%
! TTTATCCATCAACAAAAAGT+CGG - chr2_2:11997189-11997208 Msa0238460:CDS 25.0%
! TATTTGTGGATAAAGATGTA+GGG + chr2_2:11997456-11997475 None:intergenic 25.0%
! ATATTTGTGGATAAAGATGT+AGG + chr2_2:11997457-11997476 None:intergenic 25.0%
! TGTTTAGAAATAGACATGTA+GGG + chr2_2:11996453-11996472 None:intergenic 25.0%
! TTGTTTAGAAATAGACATGT+AGG + chr2_2:11996454-11996473 None:intergenic 25.0%
! TTTGACATGTTAATTGTAGA+TGG - chr2_2:11997023-11997042 Msa0238460:intron 25.0%
!! ATACTTTTCAATATCTTCTG+GGG + chr2_2:11997080-11997099 None:intergenic 25.0%
!! CAATACTTTTCAATATCTTC+TGG + chr2_2:11997082-11997101 None:intergenic 25.0%
!! CAGAAGATATTGAAAAGTAT+TGG - chr2_2:11997080-11997099 Msa0238460:intron 25.0%
!!! AATTACACAATAATTTGCTC+AGG + chr2_2:11997171-11997190 None:intergenic 25.0%
! TTTATCCATCAACAAAAAGT+CGG - chr2_2:11997189-11997208 Msa0238460:CDS 25.0%
! TATTTGTGGATAAAGATGTA+GGG + chr2_2:11997456-11997475 None:intergenic 25.0%
! ATATTTGTGGATAAAGATGT+AGG + chr2_2:11997457-11997476 None:intergenic 25.0%
! AGATTCATATGATTTGGGAA+GGG + chr2_2:11996774-11996793 None:intergenic 30.0%
CGTTGCAAAAATGTTTAGAT+TGG - chr2_2:11996872-11996891 Msa0238460:three_prime_UTR 30.0%
GCAAAAATGTTTAGATTGGT+CGG - chr2_2:11996876-11996895 Msa0238460:three_prime_UTR 30.0%
TCATGTGTTTGTATTGTAGA+AGG - chr2_2:11996985-11997004 Msa0238460:CDS 30.0%
! ATATATGCATCTTTTGTTGG+TGG - chr2_2:11997334-11997353 Msa0238460:intron 30.0%
! AGATTCATATGATTTGGGAA+GGG + chr2_2:11996774-11996793 None:intergenic 30.0%
CGTTGCAAAAATGTTTAGAT+TGG - chr2_2:11996872-11996891 Msa0238460:three_prime_UTR 30.0%
GCAAAAATGTTTAGATTGGT+CGG - chr2_2:11996876-11996895 Msa0238460:three_prime_UTR 30.0%
TCATGTGTTTGTATTGTAGA+AGG - chr2_2:11996985-11997004 Msa0238460:CDS 30.0%
! ATATATGCATCTTTTGTTGG+TGG - chr2_2:11997334-11997353 Msa0238460:intron 30.0%
! CATTGGTATTGAGATAAGCA+TGG + chr2_2:11996516-11996535 None:intergenic 35.0%
TTAACTCAGTTTATGTGTGC+AGG + chr2_2:11996539-11996558 None:intergenic 35.0%
!!! CACTCATGATTTTTTGAGGT+GGG + chr2_2:11996573-11996592 None:intergenic 35.0%
!!! TCACTCATGATTTTTTGAGG+TGG + chr2_2:11996574-11996593 None:intergenic 35.0%
!!! GAGTCACTCATGATTTTTTG+AGG + chr2_2:11996577-11996596 None:intergenic 35.0%
ATAAGATGGTCAACTTGAAG+TGG + chr2_2:11996647-11996666 None:intergenic 35.0%
! GATTCATATGATTTGGGAAG+GGG + chr2_2:11996773-11996792 None:intergenic 35.0%
! CAGATTCATATGATTTGGGA+AGG + chr2_2:11996775-11996794 None:intergenic 35.0%
AGGAACTTAGAATGGTACTT+AGG + chr2_2:11997151-11997170 None:intergenic 35.0%
ATTTGCTCAGGAACTTAGAA+TGG + chr2_2:11997159-11997178 None:intergenic 35.0%
! CATTGGTATTGAGATAAGCA+TGG + chr2_2:11996516-11996535 None:intergenic 35.0%
TTAACTCAGTTTATGTGTGC+AGG + chr2_2:11996539-11996558 None:intergenic 35.0%
!!! CACTCATGATTTTTTGAGGT+GGG + chr2_2:11996573-11996592 None:intergenic 35.0%
!!! TCACTCATGATTTTTTGAGG+TGG + chr2_2:11996574-11996593 None:intergenic 35.0%
!!! GAGTCACTCATGATTTTTTG+AGG + chr2_2:11996577-11996596 None:intergenic 35.0%
ATAAGATGGTCAACTTGAAG+TGG + chr2_2:11996647-11996666 None:intergenic 35.0%
! GATTCATATGATTTGGGAAG+GGG + chr2_2:11996773-11996792 None:intergenic 35.0%
! CAGATTCATATGATTTGGGA+AGG + chr2_2:11996775-11996794 None:intergenic 35.0%
AGGAACTTAGAATGGTACTT+AGG + chr2_2:11997151-11997170 None:intergenic 35.0%
ATTTGCTCAGGAACTTAGAA+TGG + chr2_2:11997159-11997178 None:intergenic 35.0%
TATGCAACCACTGCAAACAA+TGG - chr2_2:11996601-11996620 Msa0238460:three_prime_UTR 40.0%
AACGATATCTTCCTCTTCTG+GGG + chr2_2:11996856-11996875 None:intergenic 40.0%
CAACGATATCTTCCTCTTCT+GGG + chr2_2:11996857-11996876 None:intergenic 40.0%
! TGTTTAGATTGGTCGGAAAG+AGG - chr2_2:11996883-11996902 Msa0238460:three_prime_UTR 40.0%
GTCAAGTTTGTGCAAATGCA+AGG + chr2_2:11996952-11996971 None:intergenic 40.0%
!!! CTCTACCGACTTTTTGTTGA+TGG + chr2_2:11997197-11997216 None:intergenic 40.0%
TATGCAACCACTGCAAACAA+TGG - chr2_2:11996601-11996620 Msa0238460:three_prime_UTR 40.0%
AACGATATCTTCCTCTTCTG+GGG + chr2_2:11996856-11996875 None:intergenic 40.0%
CAACGATATCTTCCTCTTCT+GGG + chr2_2:11996857-11996876 None:intergenic 40.0%
! TGTTTAGATTGGTCGGAAAG+AGG - chr2_2:11996883-11996902 Msa0238460:three_prime_UTR 40.0%
GTCAAGTTTGTGCAAATGCA+AGG + chr2_2:11996952-11996971 None:intergenic 40.0%
!!! CTCTACCGACTTTTTGTTGA+TGG + chr2_2:11997197-11997216 None:intergenic 40.0%
CAGTTTATGTGTGCAGGCAT+TGG + chr2_2:11996533-11996552 None:intergenic 45.0%
ATACTGGCCATTGTTTGCAG+TGG + chr2_2:11996611-11996630 None:intergenic 45.0%
AATGGCCAGTATGTCTCTTC+AGG - chr2_2:11996619-11996638 Msa0238460:three_prime_UTR 45.0%
TGGTACCTGAAGAGACATAC+TGG + chr2_2:11996627-11996646 None:intergenic 45.0%
CTCAGATCAGATGAAACGTG+AGG - chr2_2:11996815-11996834 Msa0238460:three_prime_UTR 45.0%
GCAACGATATCTTCCTCTTC+TGG + chr2_2:11996858-11996877 None:intergenic 45.0%
GCATTTGCACAAACTTGACG+AGG - chr2_2:11996953-11996972 Msa0238460:CDS 45.0%
TGTAGATGGCATCTCATTGC+TGG - chr2_2:11997037-11997056 Msa0238460:intron 45.0%
GTAGATGGCATCTCATTGCT+GGG - chr2_2:11997038-11997057 Msa0238460:intron 45.0%
!! TATCTTCTGGGGTTCTTCCA+GGG + chr2_2:11997069-11997088 None:intergenic 45.0%
!! ATATCTTCTGGGGTTCTTCC+AGG + chr2_2:11997070-11997089 None:intergenic 45.0%
CAGTTTATGTGTGCAGGCAT+TGG + chr2_2:11996533-11996552 None:intergenic 45.0%
ATACTGGCCATTGTTTGCAG+TGG + chr2_2:11996611-11996630 None:intergenic 45.0%
AATGGCCAGTATGTCTCTTC+AGG - chr2_2:11996619-11996638 Msa0238460:three_prime_UTR 45.0%
TGGTACCTGAAGAGACATAC+TGG + chr2_2:11996627-11996646 None:intergenic 45.0%
CTCAGATCAGATGAAACGTG+AGG - chr2_2:11996815-11996834 Msa0238460:three_prime_UTR 45.0%
GCAACGATATCTTCCTCTTC+TGG + chr2_2:11996858-11996877 None:intergenic 45.0%
GCATTTGCACAAACTTGACG+AGG - chr2_2:11996953-11996972 Msa0238460:CDS 45.0%
TGTAGATGGCATCTCATTGC+TGG - chr2_2:11997037-11997056 Msa0238460:intron 45.0%
GTAGATGGCATCTCATTGCT+GGG - chr2_2:11997038-11997057 Msa0238460:intron 45.0%
!! TATCTTCTGGGGTTCTTCCA+GGG + chr2_2:11997069-11997088 None:intergenic 45.0%
!! ATATCTTCTGGGGTTCTTCC+AGG + chr2_2:11997070-11997089 None:intergenic 45.0%
!! ATATATATATATATATAAGA+TGG + chr2_2:11996661-11996680 None:intergenic 5.0%
!! ATATATATATATATATAAGA+TGG + chr2_2:11996661-11996680 None:intergenic 5.0%
! GCTGGAATTTTCCCCAGAAG+AGG - chr2_2:11996842-11996861 Msa0238460:three_prime_UTR 50.0%
! GCTGGAATTTTCCCCAGAAG+AGG - chr2_2:11996842-11996861 Msa0238460:three_prime_UTR 50.0%
GATGAAACGTGAGGCTGTGC+TGG - chr2_2:11996824-11996843 Msa0238460:three_prime_UTR 55.0%
CTCATTGCTGGGAGAATCCC+TGG - chr2_2:11997049-11997068 Msa0238460:intron 55.0%
GATGAAACGTGAGGCTGTGC+TGG - chr2_2:11996824-11996843 Msa0238460:three_prime_UTR 55.0%
CTCATTGCTGGGAGAATCCC+TGG - chr2_2:11997049-11997068 Msa0238460:intron 55.0%
Chromosome Type Strat End Strand Name
chr2_2 gene 11996444 11997608 11996444 ID=Msa0238460;Name=Msa0238460
chr2_2 mRNA 11996444 11997608 11996444 ID=Msa0238460-mRNA-1;Parent=Msa0238460;Name=Msa0238460-mRNA-1;_AED=0.01;_eAED=0.01;_QI=142|1|1|1|1|1|3|473|77
chr2_2 exon 11996444 11997010 11996444 ID=Msa0238460-mRNA-1:exon:5183;Parent=Msa0238460-mRNA-1
chr2_2 exon 11997148 11997232 11997148 ID=Msa0238460-mRNA-1:exon:5182;Parent=Msa0238460-mRNA-1
chr2_2 exon 11997412 11997608 11997412 ID=Msa0238460-mRNA-1:exon:5181;Parent=Msa0238460-mRNA-1
chr2_2 five_prime_UTR 11997467 11997608 11997467 ID=Msa0238460-mRNA-1:five_prime_utr;Parent=Msa0238460-mRNA-1
chr2_2 CDS 11997412 11997466 11997412 ID=Msa0238460-mRNA-1:cds;Parent=Msa0238460-mRNA-1
chr2_2 CDS 11997148 11997232 11997148 ID=Msa0238460-mRNA-1:cds;Parent=Msa0238460-mRNA-1
chr2_2 CDS 11996917 11997010 11996917 ID=Msa0238460-mRNA-1:cds;Parent=Msa0238460-mRNA-1
chr2_2 three_prime_UTR 11996444 11996916 11996444 ID=Msa0238460-mRNA-1:three_prime_utr;Parent=Msa0238460-mRNA-1
Gene Sequence

>Msa0238460

ATGAGTGACTCAAAGTATGCAACCACTGCAAACAATGGCCAGTATGTCTCTTCAGATCAGATGAAACGTGAGGCTGTGCTGGAATTTTCCCCAGAAGAGGAAGATATCGTTGCAAAAATGTTTAGATTGGTCGGAAAGAGATGGCATCTCATTGCTGGGAGAATCCCTGGAAGAACCCCAGAAGATATTGAAAAGTATTGGACATCAAAGTTCTCATCATCAACTGCATGCTAA

Protein sequence

>Msa0238460

MSDSKYATTANNGQYVSSDQMKREAVLEFSPEEEDIVAKMFRLVGKRWHLIAGRIPGRTPEDIEKYWTSKFSSSTAC*