AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene39198

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene39198.t1 MTR_6g043490 89.781 137 11 1 1 137 97 230 4.47e-88 256
MS.gene39198.t1 MTR_6g043480 88.321 137 13 1 1 137 97 230 4.25e-86 251
MS.gene39198.t1 MTR_8g072990 67.763 152 33 1 1 136 90 241 2.65e-70 211
MS.gene39198.t1 MTR_8g073050 61.765 136 45 5 3 137 95 224 5.19e-45 146
MS.gene39198.t1 MTR_5g027570 39.241 79 45 1 6 84 87 162 5.91e-13 63.9
MS.gene39198.t1 MTR_5g081860 38.462 78 43 2 11 88 125 197 4.48e-12 61.6
MS.gene39198.t1 MTR_1g048660 45.283 53 29 0 12 64 13 65 9.05e-12 57.8
MS.gene39198.t1 MTR_4g111975 35.802 81 43 2 8 83 135 211 1.38e-11 60.5
MS.gene39198.t1 MTR_3g462790 48.936 47 24 0 11 57 147 193 1.46e-11 60.5
MS.gene39198.t1 MTR_5g069710 48.936 47 24 0 11 57 132 178 1.68e-11 60.5
MS.gene39198.t1 MTR_8g063870 30.556 108 55 2 5 95 89 193 2.30e-11 59.7
MS.gene39198.t1 MTR_8g101650 35.135 74 43 1 4 77 98 166 8.74e-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
MS.gene39198.t1 AT5G05790 41.270 63 30 1 3 58 116 178 4.79e-12 61.6
MS.gene39198.t1 AT5G05790 41.270 63 30 1 3 58 116 178 4.79e-12 61.6
MS.gene39198.t1 AT5G58900 51.064 47 23 0 11 57 141 187 5.33e-12 61.6
MS.gene39198.t1 AT2G38090 40.909 66 35 1 11 76 141 202 8.70e-12 61.2
MS.gene39198.t1 AT5G01200 45.205 73 34 3 2 72 136 204 1.20e-11 60.5
MS.gene39198.t1 AT3G11280 45.833 48 26 0 11 58 127 174 1.64e-11 60.1
MS.gene39198.t1 AT3G11280 45.833 48 26 0 11 58 127 174 1.64e-11 60.1
MS.gene39198.t1 AT1G49010 43.396 53 30 0 8 60 131 183 2.36e-11 60.1
MS.gene39198.t1 AT5G08520 43.396 53 30 0 8 60 115 167 6.96e-11 58.5

Find 34 sgRNAs with CRISPR-Local

Find 51 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CCATAAAATGTTGGAACTTT+TGG 0.122390 1.2:+42388829 None:intergenic
ACACATATGTGCATGGTTTA+AGG 0.242121 1.2:-42388915 MS.gene39198:CDS
GTTGATTTGGAACTTCGTTT+AGG 0.363323 1.2:-42388718 MS.gene39198:CDS
GCTATGTTACTAGCTTCTTC+AGG 0.393017 1.2:-42388948 MS.gene39198:CDS
GTGATGGGGATGATTAAGTA+TGG 0.403039 1.2:-42389036 MS.gene39198:CDS
TGTCTTAGCTTATTAGTGAT+GGG 0.419172 1.2:-42389051 MS.gene39198:intron
CCATGTGCCTAGATCCATTT+GGG 0.419898 1.2:+42389655 None:intergenic
ACTCTTCCTGTTGTTTATGT+TGG 0.423320 1.2:-42388751 MS.gene39198:CDS
TGGTCATGGAGAAGTTGATT+TGG 0.426283 1.2:-42388731 MS.gene39198:CDS
TTAAGTATGGAAAAGGGAAA+TGG 0.433708 1.2:-42389023 MS.gene39198:CDS
GGGATGATTAAGTATGGAAA+AGG 0.439099 1.2:-42389030 MS.gene39198:CDS
ATGTGCATGGTTTAAGGAAA+AGG 0.449777 1.2:-42388909 MS.gene39198:CDS
ACCATGTGCCTAGATCCATT+TGG 0.461726 1.2:+42389654 None:intergenic
CCTGTTGTTTATGTTGGTCA+TGG 0.470311 1.2:-42388745 MS.gene39198:CDS
TTGTCTTAGCTTATTAGTGA+TGG 0.474565 1.2:-42389052 MS.gene39198:intron
AGTGCTTGCTTCATAGTTGT+TGG 0.477998 1.2:+42388780 None:intergenic
CCATGACCAACATAAACAAC+AGG 0.483887 1.2:+42388745 None:intergenic
TGCCATTCCCAAATGGATCT+AGG 0.485708 1.2:-42389662 MS.gene39198:CDS
ACATAGCTTTGAACTTGTTG+TGG 0.496796 1.2:+42388964 None:intergenic
AAACCATGCACATATGTGTC+TGG 0.497935 1.2:+42388919 None:intergenic
GTCTTAGCTTATTAGTGATG+GGG 0.500061 1.2:-42389050 MS.gene39198:intron
ATGGTTTAAGGAAAAGGAAA+AGG 0.505645 1.2:-42388903 MS.gene39198:CDS
GATCTAGGCACATGGTGCCT+TGG 0.510496 1.2:-42389647 MS.gene39198:CDS
TACACCATGCCATTCCCAAA+TGG 0.516510 1.2:-42389669 None:intergenic
GCTTCTCCTCCATAAAATGT+TGG 0.545997 1.2:+42388820 None:intergenic
GGATGATTAAGTATGGAAAA+GGG 0.561038 1.2:-42389029 MS.gene39198:CDS
TGCCTAGATCCATTTGGGAA+TGG 0.575429 1.2:+42389660 None:intergenic
TGTTAACAATGATCTTGCAA+AGG 0.578401 1.2:-42388869 MS.gene39198:CDS
CCCAAATGGATCTAGGCACA+TGG 0.598806 1.2:-42389655 MS.gene39198:CDS
CATGCACATATGTGTCTGGT+AGG 0.610902 1.2:+42388923 None:intergenic
ATAAACAACAGGAAGAGTCA+TGG 0.611118 1.2:+42388756 None:intergenic
TCATGCTCTAATTGACTCCA+AGG 0.619497 1.2:+42389630 None:intergenic
AGATCCATTTGGGAATGGCA+TGG 0.633238 1.2:+42389665 None:intergenic
CTACCAGACACATATGTGCA+TGG 0.648995 1.2:-42388922 MS.gene39198:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ACAATAAAAAAAAAGATTTA+AGG + chr1.2:42388784-42388803 None:intergenic 10.0%
!! AGAAATAAAAAAAAAAATTG+GGG + chr1.2:42388899-42388918 None:intergenic 10.0%
!! AGAGAAATAAAAAAAAAAAT+TGG + chr1.2:42388901-42388920 None:intergenic 10.0%
!! GAGAAATAAAAAAAAAAATT+GGG + chr1.2:42388900-42388919 None:intergenic 10.0%
!!! TTTGAATAATAAATTTTAAG+GGG + chr1.2:42389217-42389236 None:intergenic 10.0%
!!! GGTTATTAGATAATAAATTT+TGG - chr1.2:42389146-42389165 MS.gene39198:intron 15.0%
!!! TAATAAATTTTGGTCAAAAA+AGG - chr1.2:42389156-42389175 MS.gene39198:intron 15.0%
!!! TTTTTTTATTTCTCTAGTAT+TGG - chr1.2:42388906-42388925 MS.gene39198:CDS 15.0%
! TATTATCTAATAACCTACGA+AGG + chr1.2:42389141-42389160 None:intergenic 25.0%
! TCTATGATAAATTGTGAGTT+TGG + chr1.2:42389268-42389287 None:intergenic 25.0%
AATAAGTAGAAATGAGCGTA+TGG + chr1.2:42388991-42389010 None:intergenic 30.0%
ATAACCTACGAAGGTTTAAT+TGG + chr1.2:42389132-42389151 None:intergenic 30.0%
ATGGTTTAAGGAAAAGGAAA+AGG - chr1.2:42389468-42389487 MS.gene39198:intron 30.0%
GGATGATTAAGTATGGAAAA+GGG - chr1.2:42389342-42389361 MS.gene39198:intron 30.0%
TGTCTTAGCTTATTAGTGAT+GGG - chr1.2:42389320-42389339 MS.gene39198:intron 30.0%
TGTTAACAATGATCTTGCAA+AGG - chr1.2:42389502-42389521 MS.gene39198:intron 30.0%
TTAAGTATGGAAAAGGGAAA+TGG - chr1.2:42389348-42389367 MS.gene39198:intron 30.0%
TTGTCTTAGCTTATTAGTGA+TGG - chr1.2:42389319-42389338 MS.gene39198:intron 30.0%
! AAAGTTCCAACATTTTATGG+AGG - chr1.2:42389545-42389564 MS.gene39198:intron 30.0%
! CCAAAAGTTCCAACATTTTA+TGG - chr1.2:42389542-42389561 MS.gene39198:intron 30.0%
! CCATAAAATGTTGGAACTTT+TGG + chr1.2:42389545-42389564 None:intergenic 30.0%
AACTCCAATTAAACCTTCGT+AGG - chr1.2:42389125-42389144 MS.gene39198:intron 35.0%
ACACATATGTGCATGGTTTA+AGG - chr1.2:42389456-42389475 MS.gene39198:intron 35.0%
ATAAACAACAGGAAGAGTCA+TGG + chr1.2:42389618-42389637 None:intergenic 35.0%
ATGTGCATGGTTTAAGGAAA+AGG - chr1.2:42389462-42389481 MS.gene39198:intron 35.0%
GGGATGATTAAGTATGGAAA+AGG - chr1.2:42389341-42389360 MS.gene39198:intron 35.0%
GTCTTAGCTTATTAGTGATG+GGG - chr1.2:42389321-42389340 MS.gene39198:intron 35.0%
! ACTCTTCCTGTTGTTTATGT+TGG - chr1.2:42389620-42389639 MS.gene39198:intron 35.0%
!! ACATAGCTTTGAACTTGTTG+TGG + chr1.2:42389410-42389429 None:intergenic 35.0%
!! GTTGATTTGGAACTTCGTTT+AGG - chr1.2:42389653-42389672 MS.gene39198:CDS 35.0%
AAACCATGCACATATGTGTC+TGG + chr1.2:42389455-42389474 None:intergenic 40.0%
AGTGCTTGCTTCATAGTTGT+TGG + chr1.2:42389594-42389613 None:intergenic 40.0%
CCATGACCAACATAAACAAC+AGG + chr1.2:42389629-42389648 None:intergenic 40.0%
CTCACTTCTACACCATATGT+TGG - chr1.2:42388965-42388984 MS.gene39198:CDS 40.0%
GCTTCTCCTCCATAAAATGT+TGG + chr1.2:42389554-42389573 None:intergenic 40.0%
! CCTGTTGTTTATGTTGGTCA+TGG - chr1.2:42389626-42389645 MS.gene39198:intron 40.0%
! GCTATGTTACTAGCTTCTTC+AGG - chr1.2:42389423-42389442 MS.gene39198:intron 40.0%
! GTGATGGGGATGATTAAGTA+TGG - chr1.2:42389335-42389354 MS.gene39198:intron 40.0%
! TCATGCTCTAATTGACTCCA+AGG + chr1.2:42388744-42388763 None:intergenic 40.0%
! TGGTCATGGAGAAGTTGATT+TGG - chr1.2:42389640-42389659 MS.gene39198:CDS 40.0%
ACCATGTGCCTAGATCCATT+TGG + chr1.2:42388720-42388739 None:intergenic 45.0%
ATGAGCGTATGGCCAACATA+TGG + chr1.2:42388980-42388999 None:intergenic 45.0%
CATGCACATATGTGTCTGGT+AGG + chr1.2:42389451-42389470 None:intergenic 45.0%
CCATGTGCCTAGATCCATTT+GGG + chr1.2:42388719-42388738 None:intergenic 45.0%
CTACCAGACACATATGTGCA+TGG - chr1.2:42389449-42389468 MS.gene39198:intron 45.0%
TGCCATTCCCAAATGGATCT+AGG - chr1.2:42388709-42388728 MS.gene39198:CDS 45.0%
TGCCTAGATCCATTTGGGAA+TGG + chr1.2:42388714-42388733 None:intergenic 45.0%
!!! AATTTGAATAATAAATTTTA+AGG + chr1.2:42389219-42389238 None:intergenic 5.0%
!!! ATTTGAATAATAAATTTTAA+GGG + chr1.2:42389218-42389237 None:intergenic 5.0%
CCCAAATGGATCTAGGCACA+TGG - chr1.2:42388716-42388735 MS.gene39198:CDS 50.0%
GATCTAGGCACATGGTGCCT+TGG - chr1.2:42388724-42388743 MS.gene39198:CDS 55.0%


Chromosome Type Strat End Strand Name
chr1.2 gene 42388708 42389685 42388708 ID=MS.gene39198
chr1.2 mRNA 42388708 42389685 42388708 ID=MS.gene39198.t1;Parent=MS.gene39198
chr1.2 exon 42389630 42389685 42389630 ID=MS.gene39198.t1.exon1;Parent=MS.gene39198.t1
chr1.2 CDS 42389630 42389685 42389630 ID=cds.MS.gene39198.t1;Parent=MS.gene39198.t1
chr1.2 exon 42388708 42389065 42388708 ID=MS.gene39198.t1.exon2;Parent=MS.gene39198.t1
chr1.2 CDS 42388708 42389065 42388708 ID=cds.MS.gene39198.t1;Parent=MS.gene39198.t1
Gene Sequence

>MS.gene39198

ATGCCATTCCCAAATGGATCTAGGCACATGGTGCCTTGGAGTCAATTAGAGCATGAGTAATTTCTTCTCTCAGCCTTAAATCTTTTTTTTTATTGTTATGATATCACTTTACTTCTGCAAAAAATTAATTTTTTAAAGATAGAAAAATGCAAAATTTGTCTCTAATTTTTCAGTCAAATGTTAAAGAACCCCAATTTTTTTTTTTATTTCTCTAGTATTGGTAATTATTTTAACTTCTTTGTTGCACTTTTTACACTCTCACTTCTACACCATATGTTGGCCATACGCTCATTTCTACTTATTTTTTAGTAGAAAAAGTTGAAATAGAGACGTCAAATTTATTGATCATTTTTTATTTTCGTCTCTAATACTCGTTATTTCAACTTTTTAATGTAATGCTTTCTTAACTCTCATTTCAACTCCAATTAAACCTTCGTAGGTTATTAGATAATAAATTTTGGTCAAAAAAGGTTATTAAATAATGTGCAAGCATTGATTATTGATCTCCCCTTAAAATTTATTATTCAAATTTGTATTTACTTTTAAAAGCTTTGTGACCAAACTCACAATTTATCATAGATATTTAATTAATACATATGTTTATTTTATTTTTGTCTTAGCTTATTAGTGATGGGGATGATTAAGTATGGAAAAGGGAAATGGAGTGAAATTGCTAAGAACTTTGTGTGCAACAAGACTCCACAACAAGTTCAAAGCTATGTTACTAGCTTCTTCAGGTACCTACCAGACACATATGTGCATGGTTTAAGGAAAAGGAAAAGGAACAACATGATTGTTAACAATGATCTTGCAAAGGAAACTCTCACTCTTTTTCCAAAAGTTCCAACATTTTATGGAGGAGAAGCTAGCAGTAGCAAGAACACCAACAACTATGAAGCAAGCACTTCCATGACTCTTCCTGTTGTTTATGTTGGTCATGGAGAAGTTGATTTGGAACTTCGTTTAGGTTTAAATTAG
Protein sequence

>MS.gene39198.t1

MPFPNGSRHMVPWSQLEHDLLVMGMIKYGKGKWSEIAKNFVCNKTPQQVQSYVTSFFRYLPDTYVHGLRKRKRNNMIVNNDLAKETLTLFPKVPTFYGGEASSSKNTNNYEASTSMTLPVVYVGHGEVDLELRLGLN