AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0275980


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0275980 MtrunA17_Chr2g0288361 97.403 77 2 0 1 77 1 77 4.48e-53 159
Msa0275980 MtrunA17_Chr4g0024181 49.333 75 35 2 1 74 1 73 3.57e-20 76.3
Msa0275980 MtrunA17_Chr2g0322831 59.184 49 20 0 27 75 32 80 9.03e-18 70.5
Msa0275980 MtrunA17_Chr5g0396771 42.647 68 36 1 7 74 20 84 7.08e-15 63.2
Msa0275980 MtrunA17_Chr3g0121241 51.111 45 22 0 28 72 99 143 1.78e-12 60.5
Msa0275980 MtrunA17_Chr4g0055981 51.163 43 21 0 29 71 113 155 6.65e-12 58.2
Msa0275980 MtrunA17_Chr7g0275911 51.163 43 21 0 30 72 71 113 1.19e-11 57.8
Msa0275980 MtrunA17_Chr7g0240821 47.727 44 23 0 29 72 59 102 1.20e-11 57.8
Msa0275980 MtrunA17_Chr8g0360111 47.727 44 23 0 29 72 83 126 1.78e-11 57.4
Msa0275980 MtrunA17_Chr4g0070641 44.444 45 25 0 28 72 69 113 1.98e-11 56.2
Msa0275980 MtrunA17_Chr7g0229101 45.455 44 24 0 28 71 29 72 2.60e-11 56.6
Msa0275980 MtrunA17_Chr5g0435101 48.837 43 22 0 29 71 69 111 2.98e-11 56.2
Msa0275980 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
Msa0275980 AT2G46410.1 63.636 44 16 0 27 70 36 79 1.70e-17 70.5
Msa0275980 AT4G01060.1 50.000 64 29 1 7 70 16 76 5.71e-16 65.9
Msa0275980 AT1G01380.1 56.818 44 19 0 27 70 32 75 1.51e-15 65.1
Msa0275980 AT5G53200.1 52.000 50 24 0 27 76 31 80 2.03e-15 65.5
Msa0275980 AT4G01060.2 60.000 45 18 0 26 70 29 73 2.10e-15 64.3
Msa0275980 AT4G01060.3 60.000 45 18 0 26 70 30 74 2.71e-15 64.3
Msa0275980 AT2G30420.1 36.111 72 43 1 1 72 15 83 1.74e-12 58.2
Msa0275980 AT2G30424.1 50.000 44 22 0 27 70 34 77 4.93e-12 56.6
Msa0275980 AT5G52600.1 45.455 44 24 0 29 72 70 113 1.09e-11 57.8
Msa0275980 AT5G14750.4 43.182 44 25 0 29 72 13 56 2.21e-11 55.8
Msa0275980 AT5G14750.2 43.182 44 25 0 29 72 13 56 2.21e-11 55.8
Msa0275980 AT2G30432.1 44.262 61 31 2 10 70 19 76 4.10e-11 53.9
Msa0275980 AT3G13540.1 52.500 40 19 0 30 69 82 121 8.08e-11 55.8

Find 31 sgRNAs with CRISPR-Local

Find 112 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GCAACGATATCTTCCTCTTC+TGG 0.165562 2_3:+8143991 None:intergenic
ATATCTTCTGGGGTTCTTCC+AGG 0.255062 2_3:+8143779 None:intergenic
TGCATATGGATCAATATAAT+AGG 0.367574 2_3:+8143467 None:intergenic
CAACGATATCTTCCTCTTCT+GGG 0.371629 2_3:+8143992 None:intergenic
ATAATTTCAAACCATGCATA+TGG 0.386582 2_3:+8143453 None:intergenic
TGTAGATGGCATCTCATTGC+TGG 0.392405 2_3:-8143809 Msa0275980:intron
TTGTTATTACATCATATTTG+TGG 0.396920 2_3:+8143379 None:intergenic
CTCATTGCTGGGAGAATCCC+TGG 0.434907 2_3:-8143797 Msa0275980:CDS
CAGAAGATATTGAAAAGTAT+TGG 0.446559 2_3:-8143766 Msa0275980:CDS
TCAGTTTATGTGTGCAGTGC+AGG 0.449820 2_3:+8144283 None:intergenic
TATCTTCTGGGGTTCTTCCA+GGG 0.463656 2_3:+8143780 None:intergenic
ATTTGCTCAGGAACTTAGAA+TGG 0.468776 2_3:+8143690 None:intergenic
GATGAAACGTGAGGCTGTGC+TGG 0.475255 2_3:-8144022 Msa0275980:CDS
AATGGCCAGTATGTCTCTTC+AGG 0.479277 2_3:-8144195 Msa0275980:intron
TTGTTTAGAAATAGACATGT+AGG 0.497435 2_3:+8144368 None:intergenic
ATATTTGTGGATAAAGATGT+AGG 0.506418 2_3:+8143392 None:intergenic
AATTACACAATAATTTGCTC+AGG 0.510754 2_3:+8143678 None:intergenic
TGTTTAGATTGGTCGGAAAG+AGG 0.513739 2_3:-8143963 Msa0275980:intron
TGGTACCTGAAGAGACATAC+TGG 0.523534 2_3:+8144190 None:intergenic
AGGAACTTAGAATGGTACTT+AGG 0.533310 2_3:+8143698 None:intergenic
GGATCAATATAATAGGCAAA+AGG 0.539175 2_3:+8143474 None:intergenic
TGTTTAGAAATAGACATGTA+GGG 0.567975 2_3:+8144369 None:intergenic
GTAGATGGCATCTCATTGCT+GGG 0.572643 2_3:-8143808 Msa0275980:intron
ATTATATTGATCCATATGCA+TGG 0.574143 2_3:-8143464 Msa0275980:three_prime_UTR
TATGTGTGCAGTGCAGGCAT+TGG 0.585896 2_3:+8144289 None:intergenic
TATTTGTGGATAAAGATGTA+GGG 0.588008 2_3:+8143393 None:intergenic
CATTGGTATTGAGATAAGCA+TGG 0.590027 2_3:+8144306 None:intergenic
AACGATATCTTCCTCTTCTG+GGG 0.611771 2_3:+8143993 None:intergenic
TATGCAACCACTGCAAACAA+TGG 0.637268 2_3:-8144213 Msa0275980:CDS
ATACTGGCCATTGTTTGCAG+TGG 0.645184 2_3:+8144206 None:intergenic
CTCAGATCAGATGAAACGTG+AGG 0.650176 2_3:-8144031 Msa0275980:intron

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATCTTGTATATATATATATA+GGG - chr2_3:8143483-8143502 Msa0275980:three_prime_UTR 10.0%
!! ATCTTGTATATATATATATA+GGG - chr2_3:8143483-8143502 Msa0275980:three_prime_UTR 10.0%
!! CTATATATATATATACAAGA+TGG + chr2_3:8143484-8143503 None:intergenic 15.0%
!! CATCTTGTATATATATATAT+AGG - chr2_3:8143482-8143501 Msa0275980:three_prime_UTR 15.0%
!! CTATATATATATATACAAGA+TGG + chr2_3:8143484-8143503 None:intergenic 15.0%
!! CATCTTGTATATATATATAT+AGG - chr2_3:8143482-8143501 Msa0275980:three_prime_UTR 15.0%
!! TATACAGATTCATATGATTT+GGG + chr2_3:8143570-8143589 None:intergenic 20.0%
!! ATATACAGATTCATATGATT+TGG + chr2_3:8143571-8143590 None:intergenic 20.0%
!! TATATGTTAATTAACTTCGT+TGG - chr2_3:8143711-8143730 Msa0275980:three_prime_UTR 20.0%
!!! AATACTTTTCAATATCTTCT+GGG + chr2_3:8143872-8143891 None:intergenic 20.0%
!! TTTATCTATCAACAAAAAGT+CGG - chr2_3:8143980-8143999 Msa0275980:CDS 20.0%
!!! TTTATATATGCATCTTTTGT+TGG - chr2_3:8144122-8144141 Msa0275980:intron 20.0%
!!! TTGTTATTACATCATATTTG+TGG + chr2_3:8144261-8144280 None:intergenic 20.0%
!! TATACAGATTCATATGATTT+GGG + chr2_3:8143570-8143589 None:intergenic 20.0%
!! ATATACAGATTCATATGATT+TGG + chr2_3:8143571-8143590 None:intergenic 20.0%
!! TATATGTTAATTAACTTCGT+TGG - chr2_3:8143711-8143730 Msa0275980:three_prime_UTR 20.0%
!!! AATACTTTTCAATATCTTCT+GGG + chr2_3:8143872-8143891 None:intergenic 20.0%
!! TTTATCTATCAACAAAAAGT+CGG - chr2_3:8143980-8143999 Msa0275980:CDS 20.0%
!!! TTTATATATGCATCTTTTGT+TGG - chr2_3:8144122-8144141 Msa0275980:intron 20.0%
!!! TTGTTATTACATCATATTTG+TGG + chr2_3:8144261-8144280 None:intergenic 20.0%
! TGTTTAGAAATAGACATGTA+GGG + chr2_3:8143271-8143290 None:intergenic 25.0%
! TTGTTTAGAAATAGACATGT+AGG + chr2_3:8143272-8143291 None:intergenic 25.0%
! TTTGACATGTTAATTGTAGA+TGG - chr2_3:8143814-8143833 Msa0275980:intron 25.0%
!! ATACTTTTCAATATCTTCTG+GGG + chr2_3:8143871-8143890 None:intergenic 25.0%
!! CAATACTTTTCAATATCTTC+TGG + chr2_3:8143873-8143892 None:intergenic 25.0%
!! CAGAAGATATTGAAAAGTAT+TGG - chr2_3:8143871-8143890 Msa0275980:intron 25.0%
!!! AATTACACAATAATTTGCTC+AGG + chr2_3:8143962-8143981 None:intergenic 25.0%
! TGCATATGGATCAATATAAT+AGG + chr2_3:8144173-8144192 None:intergenic 25.0%
! ATTATATTGATCCATATGCA+TGG - chr2_3:8144173-8144192 Msa0275980:intron 25.0%
! ATAATTTCAAACCATGCATA+TGG + chr2_3:8144187-8144206 None:intergenic 25.0%
! TATTTGTGGATAAAGATGTA+GGG + chr2_3:8144247-8144266 None:intergenic 25.0%
! ATATTTGTGGATAAAGATGT+AGG + chr2_3:8144248-8144267 None:intergenic 25.0%
! TGTTTAGAAATAGACATGTA+GGG + chr2_3:8143271-8143290 None:intergenic 25.0%
! TTGTTTAGAAATAGACATGT+AGG + chr2_3:8143272-8143291 None:intergenic 25.0%
! TTTGACATGTTAATTGTAGA+TGG - chr2_3:8143814-8143833 Msa0275980:intron 25.0%
!! ATACTTTTCAATATCTTCTG+GGG + chr2_3:8143871-8143890 None:intergenic 25.0%
!! CAATACTTTTCAATATCTTC+TGG + chr2_3:8143873-8143892 None:intergenic 25.0%
!! CAGAAGATATTGAAAAGTAT+TGG - chr2_3:8143871-8143890 Msa0275980:intron 25.0%
!!! AATTACACAATAATTTGCTC+AGG + chr2_3:8143962-8143981 None:intergenic 25.0%
! TGCATATGGATCAATATAAT+AGG + chr2_3:8144173-8144192 None:intergenic 25.0%
! ATTATATTGATCCATATGCA+TGG - chr2_3:8144173-8144192 Msa0275980:intron 25.0%
! ATAATTTCAAACCATGCATA+TGG + chr2_3:8144187-8144206 None:intergenic 25.0%
! TATTTGTGGATAAAGATGTA+GGG + chr2_3:8144247-8144266 None:intergenic 25.0%
! ATATTTGTGGATAAAGATGT+AGG + chr2_3:8144248-8144267 None:intergenic 25.0%
! AGATTCATATGATTTGGGAA+GGG + chr2_3:8143565-8143584 None:intergenic 30.0%
CGTTGCAAAAATGTTTAGAT+TGG - chr2_3:8143663-8143682 Msa0275980:three_prime_UTR 30.0%
GCAAAAATGTTTAGATTGGT+CGG - chr2_3:8143667-8143686 Msa0275980:three_prime_UTR 30.0%
TCATGTGTTTGTATTGTAGA+AGG - chr2_3:8143776-8143795 Msa0275980:CDS 30.0%
! ATATATGCATCTTTTGTTGG+TGG - chr2_3:8144125-8144144 Msa0275980:intron 30.0%
GGATCAATATAATAGGCAAA+AGG + chr2_3:8144166-8144185 None:intergenic 30.0%
! AGATTCATATGATTTGGGAA+GGG + chr2_3:8143565-8143584 None:intergenic 30.0%
CGTTGCAAAAATGTTTAGAT+TGG - chr2_3:8143663-8143682 Msa0275980:three_prime_UTR 30.0%
GCAAAAATGTTTAGATTGGT+CGG - chr2_3:8143667-8143686 Msa0275980:three_prime_UTR 30.0%
TCATGTGTTTGTATTGTAGA+AGG - chr2_3:8143776-8143795 Msa0275980:CDS 30.0%
! ATATATGCATCTTTTGTTGG+TGG - chr2_3:8144125-8144144 Msa0275980:intron 30.0%
GGATCAATATAATAGGCAAA+AGG + chr2_3:8144166-8144185 None:intergenic 30.0%
! CATTGGTATTGAGATAAGCA+TGG + chr2_3:8143334-8143353 None:intergenic 35.0%
!!! CACTCATGATTTTTTGAGCT+GGG + chr2_3:8143396-8143415 None:intergenic 35.0%
!!! TCACTCATGATTTTTTGAGC+TGG + chr2_3:8143397-8143416 None:intergenic 35.0%
! GATTCATATGATTTGGGAAG+GGG + chr2_3:8143564-8143583 None:intergenic 35.0%
! CAGATTCATATGATTTGGGA+AGG + chr2_3:8143566-8143585 None:intergenic 35.0%
AGGAACTTAGAATGGTACTT+AGG + chr2_3:8143942-8143961 None:intergenic 35.0%
ATTTGCTCAGGAACTTAGAA+TGG + chr2_3:8143950-8143969 None:intergenic 35.0%
! CATTGGTATTGAGATAAGCA+TGG + chr2_3:8143334-8143353 None:intergenic 35.0%
!!! CACTCATGATTTTTTGAGCT+GGG + chr2_3:8143396-8143415 None:intergenic 35.0%
!!! TCACTCATGATTTTTTGAGC+TGG + chr2_3:8143397-8143416 None:intergenic 35.0%
! GATTCATATGATTTGGGAAG+GGG + chr2_3:8143564-8143583 None:intergenic 35.0%
! CAGATTCATATGATTTGGGA+AGG + chr2_3:8143566-8143585 None:intergenic 35.0%
AGGAACTTAGAATGGTACTT+AGG + chr2_3:8143942-8143961 None:intergenic 35.0%
ATTTGCTCAGGAACTTAGAA+TGG + chr2_3:8143950-8143969 None:intergenic 35.0%
TATGCAACCACTGCAAACAA+TGG - chr2_3:8143424-8143443 Msa0275980:three_prime_UTR 40.0%
ACAAGATGGTCAACTTGAAG+TGG + chr2_3:8143470-8143489 None:intergenic 40.0%
AACGATATCTTCCTCTTCTG+GGG + chr2_3:8143647-8143666 None:intergenic 40.0%
CAACGATATCTTCCTCTTCT+GGG + chr2_3:8143648-8143667 None:intergenic 40.0%
! TGTTTAGATTGGTCGGAAAG+AGG - chr2_3:8143674-8143693 Msa0275980:three_prime_UTR 40.0%
GTCAAGTTTGTGCAAATGCA+AGG + chr2_3:8143743-8143762 None:intergenic 40.0%
TATGCAACCACTGCAAACAA+TGG - chr2_3:8143424-8143443 Msa0275980:three_prime_UTR 40.0%
ACAAGATGGTCAACTTGAAG+TGG + chr2_3:8143470-8143489 None:intergenic 40.0%
AACGATATCTTCCTCTTCTG+GGG + chr2_3:8143647-8143666 None:intergenic 40.0%
CAACGATATCTTCCTCTTCT+GGG + chr2_3:8143648-8143667 None:intergenic 40.0%
! TGTTTAGATTGGTCGGAAAG+AGG - chr2_3:8143674-8143693 Msa0275980:three_prime_UTR 40.0%
GTCAAGTTTGTGCAAATGCA+AGG + chr2_3:8143743-8143762 None:intergenic 40.0%
TCAGTTTATGTGTGCAGTGC+AGG + chr2_3:8143357-8143376 None:intergenic 45.0%
ATACTGGCCATTGTTTGCAG+TGG + chr2_3:8143434-8143453 None:intergenic 45.0%
AATGGCCAGTATGTCTCTTC+AGG - chr2_3:8143442-8143461 Msa0275980:three_prime_UTR 45.0%
TGGTACCTGAAGAGACATAC+TGG + chr2_3:8143450-8143469 None:intergenic 45.0%
CTCAGATCAGATGAAACGTG+AGG - chr2_3:8143606-8143625 Msa0275980:three_prime_UTR 45.0%
GCAACGATATCTTCCTCTTC+TGG + chr2_3:8143649-8143668 None:intergenic 45.0%
GCATTTGCACAAACTTGACG+AGG - chr2_3:8143744-8143763 Msa0275980:CDS 45.0%
TGTAGATGGCATCTCATTGC+TGG - chr2_3:8143828-8143847 Msa0275980:intron 45.0%
GTAGATGGCATCTCATTGCT+GGG - chr2_3:8143829-8143848 Msa0275980:intron 45.0%
!! TATCTTCTGGGGTTCTTCCA+GGG + chr2_3:8143860-8143879 None:intergenic 45.0%
!! ATATCTTCTGGGGTTCTTCC+AGG + chr2_3:8143861-8143880 None:intergenic 45.0%
TCAGTTTATGTGTGCAGTGC+AGG + chr2_3:8143357-8143376 None:intergenic 45.0%
ATACTGGCCATTGTTTGCAG+TGG + chr2_3:8143434-8143453 None:intergenic 45.0%
AATGGCCAGTATGTCTCTTC+AGG - chr2_3:8143442-8143461 Msa0275980:three_prime_UTR 45.0%
TGGTACCTGAAGAGACATAC+TGG + chr2_3:8143450-8143469 None:intergenic 45.0%
CTCAGATCAGATGAAACGTG+AGG - chr2_3:8143606-8143625 Msa0275980:three_prime_UTR 45.0%
GCAACGATATCTTCCTCTTC+TGG + chr2_3:8143649-8143668 None:intergenic 45.0%
GCATTTGCACAAACTTGACG+AGG - chr2_3:8143744-8143763 Msa0275980:CDS 45.0%
TGTAGATGGCATCTCATTGC+TGG - chr2_3:8143828-8143847 Msa0275980:intron 45.0%
GTAGATGGCATCTCATTGCT+GGG - chr2_3:8143829-8143848 Msa0275980:intron 45.0%
!! TATCTTCTGGGGTTCTTCCA+GGG + chr2_3:8143860-8143879 None:intergenic 45.0%
!! ATATCTTCTGGGGTTCTTCC+AGG + chr2_3:8143861-8143880 None:intergenic 45.0%
TATGTGTGCAGTGCAGGCAT+TGG + chr2_3:8143351-8143370 None:intergenic 50.0%
! GCTGGAATTTTCCCCAGAAG+AGG - chr2_3:8143633-8143652 Msa0275980:three_prime_UTR 50.0%
TATGTGTGCAGTGCAGGCAT+TGG + chr2_3:8143351-8143370 None:intergenic 50.0%
! GCTGGAATTTTCCCCAGAAG+AGG - chr2_3:8143633-8143652 Msa0275980:three_prime_UTR 50.0%
GATGAAACGTGAGGCTGTGC+TGG - chr2_3:8143615-8143634 Msa0275980:three_prime_UTR 55.0%
CTCATTGCTGGGAGAATCCC+TGG - chr2_3:8143840-8143859 Msa0275980:intron 55.0%
GATGAAACGTGAGGCTGTGC+TGG - chr2_3:8143615-8143634 Msa0275980:three_prime_UTR 55.0%
CTCATTGCTGGGAGAATCCC+TGG - chr2_3:8143840-8143859 Msa0275980:intron 55.0%
Chromosome Type Strat End Strand Name
chr2_3 gene 8143262 8144397 8143262 ID=Msa0275980;Name=Msa0275980
chr2_3 mRNA 8143262 8144397 8143262 ID=Msa0275980-mRNA-1;Parent=Msa0275980;Name=Msa0275980-mRNA-1;_AED=0.01;_eAED=0.01;_QI=147|1|1|1|1|1|3|471|77
chr2_3 exon 8143262 8143826 8143262 ID=Msa0275980-mRNA-1:exon:3717;Parent=Msa0275980-mRNA-1
chr2_3 exon 8143964 8144048 8143964 ID=Msa0275980-mRNA-1:exon:3716;Parent=Msa0275980-mRNA-1
chr2_3 exon 8144196 8144397 8144196 ID=Msa0275980-mRNA-1:exon:3715;Parent=Msa0275980-mRNA-1
chr2_3 five_prime_UTR 8144251 8144397 8144251 ID=Msa0275980-mRNA-1:five_prime_utr;Parent=Msa0275980-mRNA-1
chr2_3 CDS 8144196 8144250 8144196 ID=Msa0275980-mRNA-1:cds;Parent=Msa0275980-mRNA-1
chr2_3 CDS 8143964 8144048 8143964 ID=Msa0275980-mRNA-1:cds;Parent=Msa0275980-mRNA-1
chr2_3 CDS 8143733 8143826 8143733 ID=Msa0275980-mRNA-1:cds;Parent=Msa0275980-mRNA-1
chr2_3 three_prime_UTR 8143262 8143732 8143262 ID=Msa0275980-mRNA-1:three_prime_utr;Parent=Msa0275980-mRNA-1
Gene Sequence

>Msa0275980

ATGAGTGACTCGAAGTATGCAACCACTGCAAACAATGGCCAGTATGTCTCTTCAGATCAGATGAAACGTGAGGCTGTGCTGGAATTTTCCCCAGAAGAGGAAGATATCGTTGCAAAAATGTTTAGATTGGTCGGAAAGAGATGGCATCTCATTGCTGGGAGAATCCCTGGAAGAACCCCAGAAGATATTGAAAAGTATTGGACATCAAAGTTCTCATCATCAACTGCATGCTAA

Protein sequence

>Msa0275980

MSDSKYATTANNGQYVSSDQMKREAVLEFSPEEEDIVAKMFRLVGKRWHLIAGRIPGRTPEDIEKYWTSKFSSSTAC*