AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0955210


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0955210 MtrunA17_Chr6g0471211 99.083 109 1 0 36 144 1 109 1.89e-62 187
Msa0955210 MtrunA17_Chr1g0203261 87.143 70 9 0 38 107 4 73 4.78e-26 94.4
Msa0955210 MtrunA17_Chr8g0387471 50.704 71 34 1 39 109 3 72 3.07e-17 72.8
Msa0955210 MtrunA17_Chr7g0233191 46.250 80 42 1 39 118 3 81 1.14e-15 68.2
Msa0955210 MtrunA17_Chr6g0469651 50.000 70 34 1 38 107 2 70 1.71e-15 68.6
Msa0955210 MtrunA17_Chr7g0233251 50.000 74 36 1 39 112 3 75 4.16e-15 67.0
Msa0955210 MtrunA17_Chr7g0233201 47.368 76 39 1 39 114 3 77 4.26e-15 66.6
Msa0955210 MtrunA17_Chr7g0248671 53.731 67 30 1 39 105 3 68 4.30e-15 68.2
Msa0955210 MtrunA17_Chr7g0233181 47.368 76 39 1 39 114 3 77 1.05e-14 65.5
Msa0955210 MtrunA17_Chr7g0233231 46.053 76 40 1 39 114 3 77 2.61e-14 64.7
Msa0955210 MtrunA17_Chr6g0469541 45.333 75 40 1 39 113 3 76 2.96e-14 64.7
Msa0955210 MtrunA17_Chr7g0233211 46.053 76 40 1 39 114 3 77 3.91e-14 64.3
Msa0955210 MtrunA17_Chr6g0469571 49.275 69 34 1 39 107 3 70 5.15e-14 64.3
Msa0955210 MtrunA17_Chr1g0202541 48.571 70 35 1 39 108 3 71 6.05e-14 64.3
Msa0955210 MtrunA17_Chr6g0469591 49.275 69 34 1 39 107 3 70 6.65e-14 63.9
Msa0955210 MtrunA17_Chr1g0202561 48.571 70 35 1 39 108 3 71 7.41e-14 64.3
Msa0955210 MtrunA17_Chr6g0469671 44.286 70 38 1 38 107 2 70 1.14e-13 63.2
Msa0955210 MtrunA17_Chr6g0469551 47.826 69 35 1 39 107 3 70 1.15e-13 63.5
Msa0955210 MtrunA17_Chr6g0469681 41.429 70 40 1 38 107 2 70 9.36e-13 61.2
Msa0955210 MtrunA17_Chr1g0202501 49.296 71 35 1 38 108 2 71 1.60e-11 58.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0955210 AT5G23760.1 86.111 72 10 0 36 107 1 72 1.78e-27 98.6
Msa0955210 AT5G23760.2 83.607 61 10 0 47 107 1 61 5.12e-20 79.3
Msa0955210 AT1G01490.4 44.186 86 46 2 23 107 14 98 2.68e-15 69.7
Msa0955210 AT1G01490.1 52.857 70 31 2 39 107 3 71 8.96e-15 67.8
Msa0955210 AT1G01490.2 52.857 70 31 2 39 107 3 71 8.96e-15 67.8

Find 21 sgRNAs with CRISPR-Local

Find 92 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AAAGCAGAAGGTTGTGTTAA+AGG 0.218749 6_3:-59000034 Msa0955210:intron
TATTACAGAAAGTAAATAAA+AGG 0.324086 6_3:+58999450 None:intergenic
GAGCAAAAGTTGACAGTGAT+TGG 0.373869 6_3:-58999811 Msa0955210:CDS
AGGAAAGAAAGAAGAGAAGA+AGG 0.404813 6_3:-58999695 Msa0955210:CDS
GTTGACAGTGATTGGTTCAA+TGG 0.405513 6_3:-58999803 Msa0955210:CDS
TTTACCCACTAATACTATAT+AGG 0.407590 6_3:-59000403 None:intergenic
AGAGAAGAAAGAAGAGAAGA+AGG 0.411074 6_3:-58999647 Msa0955210:CDS
CCATTTGAAGAGGAGTTTGA+AGG 0.428358 6_3:+59000285 None:intergenic
GAAGCAGCTGCAGATATCTA+TGG 0.439199 6_3:-58999970 Msa0955210:intron
ACTGAAGAAAGTAGGAAAAG+TGG 0.459459 6_3:-58999758 Msa0955210:CDS
CCTTCAAACTCCTCTTCAAA+TGG 0.460700 6_3:-59000285 Msa0955210:CDS
GAAGAAGGAGGAAAAGAAAG+AGG 0.464286 6_3:-58999632 Msa0955210:CDS
AACTCCTCTTCAAATGGCTC+AGG 0.480679 6_3:-59000279 Msa0955210:intron
TTCGATTGTGGCAGATGTAA+AGG 0.481595 6_3:-58999833 Msa0955210:CDS
GTGAAGAAACTGAAGAAAGT+AGG 0.505141 6_3:-58999766 Msa0955210:CDS
GAAGAAAGAAGAGAAGAAGG+AGG 0.516884 6_3:-58999644 Msa0955210:CDS
GCAAAAGAAGAGAAGAAAGA+AGG 0.526342 6_3:-58999715 Msa0955210:CDS
AAAGTGGATATTGTATCTGT+TGG 0.556535 6_3:-58999742 Msa0955210:CDS
GAAAACAAGAAAGAAAATGA+AGG 0.570844 6_3:+59000313 None:intergenic
AATAGGGGTTGATTCGATTG+TGG 0.591286 6_3:-58999845 Msa0955210:intron
TATACCTGAGCCATTTGAAG+AGG 0.613212 6_3:+59000275 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! GTCAAAAAAAATATATATAT+AGG - chr6_3:58999449-58999468 Msa0955210:three_prime_UTR 10.0%
!! AAAATTAAATTAAATAGGAT+AGG + chr6_3:58999587-58999606 None:intergenic 10.0%
!! TGAACAAAATTAAATTAAAT+AGG + chr6_3:58999592-58999611 None:intergenic 10.0%
!!! ATTTAATTTAATTTTGTTCA+TGG - chr6_3:58999592-58999611 Msa0955210:three_prime_UTR 10.0%
!!! AATGTTATTTAATAAATCAA+AGG - chr6_3:58999917-58999936 Msa0955210:intron 10.0%
!!! TTATTTTTCTAATTTTTCTT+TGG - chr6_3:59000271-59000290 Msa0955210:intron 10.0%
!!! AATTGTCAATAATTTTTTTT+TGG - chr6_3:59000340-59000359 Msa0955210:CDS 10.0%
!! GTCAAAAAAAATATATATAT+AGG - chr6_3:58999449-58999468 Msa0955210:three_prime_UTR 10.0%
!! AAAATTAAATTAAATAGGAT+AGG + chr6_3:58999587-58999606 None:intergenic 10.0%
!! TGAACAAAATTAAATTAAAT+AGG + chr6_3:58999592-58999611 None:intergenic 10.0%
!!! ATTTAATTTAATTTTGTTCA+TGG - chr6_3:58999592-58999611 Msa0955210:three_prime_UTR 10.0%
!!! AATGTTATTTAATAAATCAA+AGG - chr6_3:58999917-58999936 Msa0955210:intron 10.0%
!!! TTATTTTTCTAATTTTTCTT+TGG - chr6_3:59000271-59000290 Msa0955210:intron 10.0%
!!! AATTGTCAATAATTTTTTTT+TGG - chr6_3:59000340-59000359 Msa0955210:CDS 10.0%
!! ATAAGAGAATGAAAAAAAAA+AGG + chr6_3:58999743-58999762 None:intergenic 15.0%
!! TATTACAGAAAGTAAATAAA+AGG + chr6_3:59000369-59000388 None:intergenic 15.0%
!! ATAAGAGAATGAAAAAAAAA+AGG + chr6_3:58999743-58999762 None:intergenic 15.0%
!! TATTACAGAAAGTAAATAAA+AGG + chr6_3:59000369-59000388 None:intergenic 15.0%
!! TAAATTAAATAGGATAGGAT+AGG + chr6_3:58999582-58999601 None:intergenic 20.0%
!! AAATATATAGCTAAATCATG+AGG + chr6_3:58999658-58999677 None:intergenic 20.0%
!! TAAATTAAATAGGATAGGAT+AGG + chr6_3:58999582-58999601 None:intergenic 20.0%
!! AAATATATAGCTAAATCATG+AGG + chr6_3:58999658-58999677 None:intergenic 20.0%
! GAAAACAAGAAAGAAAATGA+AGG + chr6_3:58999506-58999525 None:intergenic 25.0%
! AATCATGAGGATTTACATAA+GGG + chr6_3:58999645-58999664 None:intergenic 25.0%
! AAATCATGAGGATTTACATA+AGG + chr6_3:58999646-58999665 None:intergenic 25.0%
! TCATTCTCTTATTCTTTCAT+TGG - chr6_3:58999751-58999770 Msa0955210:CDS 25.0%
!!! TGTTGTTGATTTTGATGAAT+AGG - chr6_3:58999954-58999973 Msa0955210:intron 25.0%
!!! GTTGTTGATTTTGATGAATA+GGG - chr6_3:58999955-58999974 Msa0955210:intron 25.0%
!!! TTGTTGATTTTGATGAATAG+GGG - chr6_3:58999956-58999975 Msa0955210:intron 25.0%
! GAAAGAGGAGAAAAAATAAA+AGG - chr6_3:59000199-59000218 Msa0955210:intron 25.0%
! GAAAACAAGAAAGAAAATGA+AGG + chr6_3:58999506-58999525 None:intergenic 25.0%
! AATCATGAGGATTTACATAA+GGG + chr6_3:58999645-58999664 None:intergenic 25.0%
! AAATCATGAGGATTTACATA+AGG + chr6_3:58999646-58999665 None:intergenic 25.0%
! TCATTCTCTTATTCTTTCAT+TGG - chr6_3:58999751-58999770 Msa0955210:CDS 25.0%
!!! TGTTGTTGATTTTGATGAAT+AGG - chr6_3:58999954-58999973 Msa0955210:intron 25.0%
!!! GTTGTTGATTTTGATGAATA+GGG - chr6_3:58999955-58999974 Msa0955210:intron 25.0%
!!! TTGTTGATTTTGATGAATAG+GGG - chr6_3:58999956-58999975 Msa0955210:intron 25.0%
! GAAAGAGGAGAAAAAATAAA+AGG - chr6_3:59000199-59000218 Msa0955210:intron 25.0%
AAAGTGGATATTGTATCTGT+TGG - chr6_3:59000074-59000093 Msa0955210:intron 30.0%
AGAGAAAAAAGAGGAGAAAA+AGG - chr6_3:59000145-59000164 Msa0955210:intron 30.0%
AAAGTGGATATTGTATCTGT+TGG - chr6_3:59000074-59000093 Msa0955210:intron 30.0%
AGAGAAAAAAGAGGAGAAAA+AGG - chr6_3:59000145-59000164 Msa0955210:intron 30.0%
!! AGGCTAAGAGAATTTTGATG+AGG + chr6_3:58999486-58999505 None:intergenic 35.0%
GATAGGATAGGATATGAAAG+AGG + chr6_3:58999570-58999589 None:intergenic 35.0%
ACATAAGGGATCTAAGAGAT+AGG + chr6_3:58999631-58999650 None:intergenic 35.0%
! TTGGATTGATTCAAAGCAGA+AGG - chr6_3:58999770-58999789 Msa0955210:CDS 35.0%
AAAGCAGAAGGTTGTGTTAA+AGG - chr6_3:58999782-58999801 Msa0955210:CDS 35.0%
! TGCTTCTATAGCTTTTTGCT+TGG + chr6_3:58999832-58999851 None:intergenic 35.0%
GTGAAGAAACTGAAGAAAGT+AGG - chr6_3:59000050-59000069 Msa0955210:intron 35.0%
ACTGAAGAAAGTAGGAAAAG+TGG - chr6_3:59000058-59000077 Msa0955210:intron 35.0%
! TCTTTCTTCTCTTCTTTTGC+AGG + chr6_3:59000101-59000120 None:intergenic 35.0%
GCAAAAGAAGAGAAGAAAGA+AGG - chr6_3:59000101-59000120 Msa0955210:intron 35.0%
AGGAAAGAAAGAAGAGAAGA+AGG - chr6_3:59000121-59000140 Msa0955210:intron 35.0%
GAAGAAGGAAGAGAAAAAAG+AGG - chr6_3:59000136-59000155 Msa0955210:intron 35.0%
AGAGAAGAAAGAAGAGAAGA+AGG - chr6_3:59000169-59000188 Msa0955210:intron 35.0%
! ACAATTTTTGCAGCTTACAC+TGG + chr6_3:59000326-59000345 None:intergenic 35.0%
!! AGGCTAAGAGAATTTTGATG+AGG + chr6_3:58999486-58999505 None:intergenic 35.0%
GATAGGATAGGATATGAAAG+AGG + chr6_3:58999570-58999589 None:intergenic 35.0%
ACATAAGGGATCTAAGAGAT+AGG + chr6_3:58999631-58999650 None:intergenic 35.0%
! TTGGATTGATTCAAAGCAGA+AGG - chr6_3:58999770-58999789 Msa0955210:CDS 35.0%
AAAGCAGAAGGTTGTGTTAA+AGG - chr6_3:58999782-58999801 Msa0955210:CDS 35.0%
! TGCTTCTATAGCTTTTTGCT+TGG + chr6_3:58999832-58999851 None:intergenic 35.0%
GTGAAGAAACTGAAGAAAGT+AGG - chr6_3:59000050-59000069 Msa0955210:intron 35.0%
ACTGAAGAAAGTAGGAAAAG+TGG - chr6_3:59000058-59000077 Msa0955210:intron 35.0%
! TCTTTCTTCTCTTCTTTTGC+AGG + chr6_3:59000101-59000120 None:intergenic 35.0%
GCAAAAGAAGAGAAGAAAGA+AGG - chr6_3:59000101-59000120 Msa0955210:intron 35.0%
AGGAAAGAAAGAAGAGAAGA+AGG - chr6_3:59000121-59000140 Msa0955210:intron 35.0%
GAAGAAGGAAGAGAAAAAAG+AGG - chr6_3:59000136-59000155 Msa0955210:intron 35.0%
AGAGAAGAAAGAAGAGAAGA+AGG - chr6_3:59000169-59000188 Msa0955210:intron 35.0%
! ACAATTTTTGCAGCTTACAC+TGG + chr6_3:59000326-59000345 None:intergenic 35.0%
CCATTTGAAGAGGAGTTTGA+AGG + chr6_3:58999534-58999553 None:intergenic 40.0%
CCTTCAAACTCCTCTTCAAA+TGG - chr6_3:58999531-58999550 Msa0955210:three_prime_UTR 40.0%
TATACCTGAGCCATTTGAAG+AGG + chr6_3:58999544-58999563 None:intergenic 40.0%
!! AATAGGGGTTGATTCGATTG+TGG - chr6_3:58999971-58999990 Msa0955210:CDS 40.0%
TTCGATTGTGGCAGATGTAA+AGG - chr6_3:58999983-59000002 Msa0955210:CDS 40.0%
GAGCAAAAGTTGACAGTGAT+TGG - chr6_3:59000005-59000024 Msa0955210:CDS 40.0%
! GTTGACAGTGATTGGTTCAA+TGG - chr6_3:59000013-59000032 Msa0955210:CDS 40.0%
GAAGAAAGAAGAGAAGAAGG+AGG - chr6_3:59000172-59000191 Msa0955210:intron 40.0%
GAAGAAGGAGGAAAAGAAAG+AGG - chr6_3:59000184-59000203 Msa0955210:intron 40.0%
CCATTTGAAGAGGAGTTTGA+AGG + chr6_3:58999534-58999553 None:intergenic 40.0%
CCTTCAAACTCCTCTTCAAA+TGG - chr6_3:58999531-58999550 Msa0955210:three_prime_UTR 40.0%
TATACCTGAGCCATTTGAAG+AGG + chr6_3:58999544-58999563 None:intergenic 40.0%
!! AATAGGGGTTGATTCGATTG+TGG - chr6_3:58999971-58999990 Msa0955210:CDS 40.0%
TTCGATTGTGGCAGATGTAA+AGG - chr6_3:58999983-59000002 Msa0955210:CDS 40.0%
GAGCAAAAGTTGACAGTGAT+TGG - chr6_3:59000005-59000024 Msa0955210:CDS 40.0%
! GTTGACAGTGATTGGTTCAA+TGG - chr6_3:59000013-59000032 Msa0955210:CDS 40.0%
GAAGAAAGAAGAGAAGAAGG+AGG - chr6_3:59000172-59000191 Msa0955210:intron 40.0%
GAAGAAGGAGGAAAAGAAAG+AGG - chr6_3:59000184-59000203 Msa0955210:intron 40.0%
AACTCCTCTTCAAATGGCTC+AGG - chr6_3:58999537-58999556 Msa0955210:three_prime_UTR 45.0%
GAAGCAGCTGCAGATATCTA+TGG - chr6_3:58999846-58999865 Msa0955210:intron 45.0%
AACTCCTCTTCAAATGGCTC+AGG - chr6_3:58999537-58999556 Msa0955210:three_prime_UTR 45.0%
GAAGCAGCTGCAGATATCTA+TGG - chr6_3:58999846-58999865 Msa0955210:intron 45.0%
Chromosome Type Strat End Strand Name
chr6_3 gene 58999427 59000411 58999427 ID=Msa0955210;Name=Msa0955210
chr6_3 mRNA 58999427 59000411 58999427 ID=Msa0955210-mRNA-1;Parent=Msa0955210;Name=Msa0955210-mRNA-1;_AED=0.16;_eAED=0.16;_QI=18|1|1|1|1|1|3|194|144
chr6_3 exon 58999427 58999862 58999427 ID=Msa0955210-mRNA-1:exon:11661;Parent=Msa0955210-mRNA-1
chr6_3 exon 58999971 59000049 58999971 ID=Msa0955210-mRNA-1:exon:11660;Parent=Msa0955210-mRNA-1
chr6_3 exon 59000280 59000411 59000280 ID=Msa0955210-mRNA-1:exon:11659;Parent=Msa0955210-mRNA-1
chr6_3 five_prime_UTR 59000394 59000411 59000394 ID=Msa0955210-mRNA-1:five_prime_utr;Parent=Msa0955210-mRNA-1
chr6_3 CDS 59000280 59000393 59000280 ID=Msa0955210-mRNA-1:cds;Parent=Msa0955210-mRNA-1
chr6_3 CDS 58999971 59000049 58999971 ID=Msa0955210-mRNA-1:cds;Parent=Msa0955210-mRNA-1
chr6_3 CDS 58999621 58999862 58999621 ID=Msa0955210-mRNA-1:cds;Parent=Msa0955210-mRNA-1
chr6_3 three_prime_UTR 58999427 58999620 58999427 ID=Msa0955210-mRNA-1:three_prime_utr;Parent=Msa0955210-mRNA-1
Gene Sequence

>Msa0955210

ATGTGTCAAAAAAAATATATATATAGGTACTACAAAAGCCTCATCAAAATTCTCTTAGCCTTCATTTTCTTTCTTGTTTTCATACTCCTTCAAACTCCTCTTCAAATGGCTCAGAAGGTTGTGTTAAAGGTGTTAACTATGACAGATGACAAAACCAAGCAAAAAGCTATAGAAGCAGCTGCAGATATCTATGGGGTTGATTCGATTGTGGCAGATGTAAAGGAGCAAAAGTTGACAGTGATTGGTTCAATGGATACAGTGAAAATTGTGAAGAAACTGAAGAAAGTAGGAAAAGTGGATATTGTATCTGTTGGTCCTGCAAAAGAAGAGAAGAAAGAAGGAAAGAAAGAAGAGAAGAAGGAAGAGAAAAAAGAGGAGAAAAAGGAAGAGAAGAAAGAAGAGAAGAAGGAGGAAAAGAAAGAGGAGAAAAAATAA

Protein sequence

>Msa0955210

MCQKKYIYRYYKSLIKILLAFIFFLVFILLQTPLQMAQKVVLKVLTMTDDKTKQKAIEAAADIYGVDSIVADVKEQKLTVIGSMDTVKIVKKLKKVGKVDIVSVGPAKEEKKEGKKEEKKEEKKEEKKEEKKEEKKEEKKEEKK*