AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene46477

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene46477.t1 MTR_6g043490 90.511 137 10 1 1 137 97 230 1.90e-88 257
MS.gene46477.t1 MTR_6g043480 89.051 137 12 1 1 137 97 230 1.41e-86 252
MS.gene46477.t1 MTR_8g072990 68.421 152 32 1 1 136 90 241 9.67e-72 215
MS.gene46477.t1 MTR_8g073050 63.504 137 41 6 3 137 95 224 5.39e-48 154
MS.gene46477.t1 MTR_5g027570 40.506 79 44 1 6 84 87 162 6.81e-14 66.2
MS.gene46477.t1 MTR_5g081860 38.272 81 45 2 8 88 122 197 3.98e-13 64.7
MS.gene46477.t1 MTR_1g048660 47.170 53 28 0 12 64 13 65 1.13e-12 60.1
MS.gene46477.t1 MTR_4g111975 37.037 81 42 2 8 83 135 211 1.32e-12 63.5
MS.gene46477.t1 MTR_3g462790 48.000 50 26 0 8 57 144 193 1.52e-12 63.5
MS.gene46477.t1 MTR_5g069710 48.000 50 26 0 8 57 129 178 1.84e-12 63.2
MS.gene46477.t1 MTR_8g101650 36.486 74 42 1 4 77 98 166 6.23e-12 61.6
MS.gene46477.t1 MTR_8g063870 31.000 100 52 1 13 95 94 193 6.99e-12 61.2
MS.gene46477.t1 MTR_2g100930 48.000 50 26 0 8 57 106 155 8.52e-12 61.2
MS.gene46477.t1 MTR_7g067080 42.857 56 32 0 2 57 131 186 1.48e-11 60.5
MS.gene46477.t1 MTR_1g111830 37.662 77 46 1 5 81 118 192 2.18e-11 59.7
MS.gene46477.t1 MTR_5g088010 42.308 52 30 0 8 59 57 108 2.52e-11 59.7
MS.gene46477.t1 MTR_5g037080 46.000 50 27 0 8 57 99 148 2.53e-11 60.1
MS.gene46477.t1 MTR_4g107230 44.000 50 28 0 8 57 81 130 6.39e-11 58.5
MS.gene46477.t1 MTR_5g027550 40.385 52 31 0 6 57 72 123 7.18e-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.gene46477.t1 AT5G58900 50.000 50 25 0 8 57 138 187 4.11e-13 64.7
MS.gene46477.t1 AT5G05790 44.643 56 31 0 3 58 123 178 4.51e-13 64.7
MS.gene46477.t1 AT5G05790 44.643 56 31 0 3 58 123 178 4.51e-13 64.7
MS.gene46477.t1 AT5G01200 49.206 63 30 2 2 62 136 198 1.11e-12 63.5
MS.gene46477.t1 AT2G38090 50.000 50 25 0 8 57 138 187 1.13e-12 63.5
MS.gene46477.t1 AT3G11280 41.935 62 29 1 4 58 113 174 1.33e-12 63.2
MS.gene46477.t1 AT3G11280 41.935 62 29 1 4 58 113 174 1.33e-12 63.2
MS.gene46477.t1 AT1G49010 45.283 53 29 0 8 60 131 183 1.45e-12 63.5
MS.gene46477.t1 AT5G08520 45.283 53 29 0 8 60 115 167 5.57e-12 61.6
MS.gene46477.t1 AT1G19000 46.154 52 28 0 6 57 97 148 1.34e-11 60.5
MS.gene46477.t1 AT1G19000 46.154 52 28 0 6 57 97 148 1.34e-11 60.5
MS.gene46477.t1 AT3G16350 46.000 50 27 0 8 57 134 183 1.61e-11 60.8
MS.gene46477.t1 AT5G04760 39.189 74 43 1 8 81 96 167 1.89e-11 59.7
MS.gene46477.t1 AT5G56840 33.333 81 54 0 8 88 88 168 2.86e-11 59.3
MS.gene46477.t1 AT1G70000 46.000 50 27 0 8 57 95 144 6.19e-11 58.5
MS.gene46477.t1 AT1G70000 46.000 50 27 0 8 57 95 144 6.19e-11 58.5

Find 34 sgRNAs with CRISPR-Local

Find 50 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CCATAAAATGTTGGAACTTC+TGG 0.186491 1.4:+45244310 None:intergenic
ACACATATGTGCATGGTTTA+AGG 0.242121 1.4:-45244396 MS.gene46477:CDS
AGTTGATGTGGAACTTCGTT+TGG 0.343928 1.4:-45244200 MS.gene46477:CDS
CCTGTTGTTTCTGTTGATGA+TGG 0.376916 1.4:-45244226 MS.gene46477:CDS
GTGATGGGGATGATTAAGTA+TGG 0.403039 1.4:-45244517 MS.gene46477:CDS
TGTCTTAGCTTATTAGTGAT+GGG 0.419172 1.4:-45244532 MS.gene46477:intron
GTTGATGTGGAACTTCGTTT+GGG 0.430893 1.4:-45244199 MS.gene46477:CDS
TTAAGTATGGAAAAGGGAAA+TGG 0.433708 1.4:-45244504 MS.gene46477:CDS
GGGATGATTAAGTATGGAAA+AGG 0.439099 1.4:-45244511 MS.gene46477:CDS
GCTATGCTAATAGCTTCTTC+AGG 0.441719 1.4:-45244429 MS.gene46477:CDS
ATGTGCATGGTTTAAGGAAA+AGG 0.449777 1.4:-45244390 MS.gene46477:CDS
CCATGCGCCTAGATCCATTT+GGG 0.454900 1.4:+45245166 None:intergenic
GATCTAGGCGCATGGTTCCT+TGG 0.456488 1.4:-45245158 MS.gene46477:CDS
CCATCATCAACAGAAACAAC+AGG 0.464747 1.4:+45244226 None:intergenic
TTGTCTTAGCTTATTAGTGA+TGG 0.474565 1.4:-45244533 MS.gene46477:intron
AGTGCTTGCTTCATAGTTGT+TGG 0.477998 1.4:+45244261 None:intergenic
TGCCATTCCCAAATGGATCT+AGG 0.484246 1.4:-45245173 MS.gene46477:CDS
ACCATGCGCCTAGATCCATT+TGG 0.492468 1.4:+45245165 None:intergenic
AAACCATGCACATATGTGTC+TGG 0.497935 1.4:+45244400 None:intergenic
GTCTTAGCTTATTAGTGATG+GGG 0.500061 1.4:-45244531 MS.gene46477:intron
ATGGTTTAAGGAAAAGGAAA+AGG 0.505645 1.4:-45244384 MS.gene46477:CDS
GCATAGCTTTGAACTTGTTG+TGG 0.507199 1.4:+45244445 None:intergenic
GACACCATGCCATTCCCAAA+TGG 0.525818 1.4:-45245180 None:intergenic
CGCCTAGATCCATTTGGGAA+TGG 0.533156 1.4:+45245171 None:intergenic
GCTTCTCCTCCATAAAATGT+TGG 0.545997 1.4:+45244301 None:intergenic
GGATGATTAAGTATGGAAAA+GGG 0.561038 1.4:-45244510 MS.gene46477:CDS
TGTTAACAATGATCTTGCAA+AGG 0.578401 1.4:-45244350 MS.gene46477:CDS
AGAAACAACAGGAAGAGTCA+TGG 0.595597 1.4:+45244237 None:intergenic
CCCAAATGGATCTAGGCGCA+TGG 0.601245 1.4:-45245166 MS.gene46477:CDS
TCATGCTCTAACTGACTCCA+AGG 0.609370 1.4:+45245141 None:intergenic
CATGCACATATGTGTCTGGT+AGG 0.610902 1.4:+45244404 None:intergenic
AGATCCATTTGGGAATGGCA+TGG 0.633238 1.4:+45245176 None:intergenic
TGATGATGGAAAAGTTGATG+TGG 0.639976 1.4:-45244212 MS.gene46477:CDS
CTACCAGACACATATGTGCA+TGG 0.648995 1.4:-45244403 MS.gene46477:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTTGAATAATAAATATTAAG+GGG + chr1.4:45244728-45244747 None:intergenic 10.0%
!! ACTAGAGAAATAAAAAAAAT+TGG + chr1.4:45244383-45244402 None:intergenic 15.0%
!! CTAGAGAAATAAAAAAAATT+GGG + chr1.4:45244382-45244401 None:intergenic 15.0%
!! TAGAGAAATAAAAAAAATTG+GGG + chr1.4:45244381-45244400 None:intergenic 15.0%
!!! AATAAATTTTGGTCAAAAAA+AGG - chr1.4:45244667-45244686 MS.gene46477:intron 15.0%
!!! GGTTATTAGATAATAAATTT+TGG - chr1.4:45244656-45244675 MS.gene46477:intron 15.0%
!! TATTATCTAATAACCTACAA+AGG + chr1.4:45244651-45244670 None:intergenic 20.0%
! ATAACCTACAAAGGTTTAAT+TGG + chr1.4:45244642-45244661 None:intergenic 25.0%
! TCTATGATAAATTGTGAGTT+TGG + chr1.4:45244779-45244798 None:intergenic 25.0%
!! TGCCAGAAAATTTGAAATAA+TGG + chr1.4:45244470-45244489 None:intergenic 25.0%
AACTCCAATTAAACCTTTGT+AGG - chr1.4:45244635-45244654 MS.gene46477:intron 30.0%
ATGGTTTAAGGAAAAGGAAA+AGG - chr1.4:45244979-45244998 MS.gene46477:intron 30.0%
GGATGATTAAGTATGGAAAA+GGG - chr1.4:45244853-45244872 MS.gene46477:intron 30.0%
TGTCTTAGCTTATTAGTGAT+GGG - chr1.4:45244831-45244850 MS.gene46477:intron 30.0%
TGTTAACAATGATCTTGCAA+AGG - chr1.4:45245013-45245032 MS.gene46477:intron 30.0%
TTAAGTATGGAAAAGGGAAA+TGG - chr1.4:45244859-45244878 MS.gene46477:intron 30.0%
TTGAAATAATGGCCAACATA+TGG + chr1.4:45244459-45244478 None:intergenic 30.0%
TTGTCTTAGCTTATTAGTGA+TGG - chr1.4:45244830-45244849 MS.gene46477:intron 30.0%
! GGCCATTATTTCAAATTTTC+TGG - chr1.4:45244465-45244484 MS.gene46477:CDS 30.0%
ACACATATGTGCATGGTTTA+AGG - chr1.4:45244967-45244986 MS.gene46477:intron 35.0%
ATGTGCATGGTTTAAGGAAA+AGG - chr1.4:45244973-45244992 MS.gene46477:intron 35.0%
CCATAAAATGTTGGAACTTC+TGG + chr1.4:45245056-45245075 None:intergenic 35.0%
GGGATGATTAAGTATGGAAA+AGG - chr1.4:45244852-45244871 MS.gene46477:intron 35.0%
GTCTTAGCTTATTAGTGATG+GGG - chr1.4:45244832-45244851 MS.gene46477:intron 35.0%
! CCAGAAGTTCCAACATTTTA+TGG - chr1.4:45245053-45245072 MS.gene46477:intron 35.0%
! GAAGTTCCAACATTTTATGG+AGG - chr1.4:45245056-45245075 MS.gene46477:intron 35.0%
!! TGATGATGGAAAAGTTGATG+TGG - chr1.4:45245151-45245170 MS.gene46477:CDS 35.0%
AAACCATGCACATATGTGTC+TGG + chr1.4:45244966-45244985 None:intergenic 40.0%
AGAAACAACAGGAAGAGTCA+TGG + chr1.4:45245129-45245148 None:intergenic 40.0%
AGTGCTTGCTTCATAGTTGT+TGG + chr1.4:45245105-45245124 None:intergenic 40.0%
CCATCATCAACAGAAACAAC+AGG + chr1.4:45245140-45245159 None:intergenic 40.0%
CTCACTTCTACACCATATGT+TGG - chr1.4:45244444-45244463 MS.gene46477:CDS 40.0%
GCTATGCTAATAGCTTCTTC+AGG - chr1.4:45244934-45244953 MS.gene46477:intron 40.0%
GCTTCTCCTCCATAAAATGT+TGG + chr1.4:45245065-45245084 None:intergenic 40.0%
GTTGATGTGGAACTTCGTTT+GGG - chr1.4:45245164-45245183 MS.gene46477:CDS 40.0%
! AGTTGATGTGGAACTTCGTT+TGG - chr1.4:45245163-45245182 MS.gene46477:CDS 40.0%
! GTGATGGGGATGATTAAGTA+TGG - chr1.4:45244846-45244865 MS.gene46477:intron 40.0%
!! CCTGTTGTTTCTGTTGATGA+TGG - chr1.4:45245137-45245156 MS.gene46477:intron 40.0%
!! GCATAGCTTTGAACTTGTTG+TGG + chr1.4:45244921-45244940 None:intergenic 40.0%
CATGCACATATGTGTCTGGT+AGG + chr1.4:45244962-45244981 None:intergenic 45.0%
CTACCAGACACATATGTGCA+TGG - chr1.4:45244960-45244979 MS.gene46477:intron 45.0%
TGCCATTCCCAAATGGATCT+AGG - chr1.4:45244190-45244209 MS.gene46477:CDS 45.0%
! TCATGCTCTAACTGACTCCA+AGG + chr1.4:45244225-45244244 None:intergenic 45.0%
!! AATTTGAATAATAAATATTA+AGG + chr1.4:45244730-45244749 None:intergenic 5.0%
!! ATTTGAATAATAAATATTAA+GGG + chr1.4:45244729-45244748 None:intergenic 5.0%
ACCATGCGCCTAGATCCATT+TGG + chr1.4:45244201-45244220 None:intergenic 50.0%
CCATGCGCCTAGATCCATTT+GGG + chr1.4:45244200-45244219 None:intergenic 50.0%
CGCCTAGATCCATTTGGGAA+TGG + chr1.4:45244195-45244214 None:intergenic 50.0%
CCCAAATGGATCTAGGCGCA+TGG - chr1.4:45244197-45244216 MS.gene46477:CDS 55.0%
GATCTAGGCGCATGGTTCCT+TGG - chr1.4:45244205-45244224 MS.gene46477:CDS 55.0%


Chromosome Type Strat End Strand Name
chr1.4 gene 45244189 45245196 45244189 ID=MS.gene46477
chr1.4 mRNA 45244189 45245196 45244189 ID=MS.gene46477.t1;Parent=MS.gene46477
chr1.4 exon 45245141 45245196 45245141 ID=MS.gene46477.t1.exon1;Parent=MS.gene46477.t1
chr1.4 CDS 45245141 45245196 45245141 ID=cds.MS.gene46477.t1;Parent=MS.gene46477.t1
chr1.4 exon 45244189 45244546 45244189 ID=MS.gene46477.t1.exon2;Parent=MS.gene46477.t1
chr1.4 CDS 45244189 45244546 45244189 ID=cds.MS.gene46477.t1;Parent=MS.gene46477.t1
Gene Sequence

>MS.gene46477

ATGCCATTCCCAAATGGATCTAGGCGCATGGTTCCTTGGAGTCAGTTAGAGCATGAGTAATTTCAACTCTCAGTCTTAAATCTTTTTTTTTTATTGTTATGATATCACTTTACTTCTGCAAAAAATTAATTTTTTAAAGATAGAAAAATGCAAAATTTGTCTCTAATTTTTCAGTCAAATGTTAAAGAACCCCAATTTTTTTTATTTCTCTAGTATTTATAATTATTTTAACTTCTTTGTTGCACTTTTTATACTCTCACTTCTACACCATATGTTGGCCATTATTTCAAATTTTCTGGCAATGATTTTCTTACGCTCATTTCTACTTATTTTTTAGTAGAAAAAGTTGAAATAGAGACGTCAAATTTATTGATCATTTTTTATTTTCGTCTCTAATACTCGTTGTTATTTCAACTTTTTAATGTAATGCTTTCTATACTCATTTCAACTCCAATTAAACCTTTGTAGGTTATTAGATAATAAATTTTGGTCAAAAAAAGGTTATTAAATAATGTGCAAGCATTGATTATTGTTCTCCCCTTAATATTTATTATTCAAATTTGTATTTAATTTTAAAAGCTTTGTGACCAAACTCACAATTTATCATAGATATTTAATTAATACATATTTTTATTTTATTTTTGTCTTAGCTTATTAGTGATGGGGATGATTAAGTATGGAAAAGGGAAATGGAGTGAAATTGCTAAGAACTTTGTGTGCAACAAGACTCCACAACAAGTTCAAAGCTATGCTAATAGCTTCTTCAGGTACCTACCAGACACATATGTGCATGGTTTAAGGAAAAGGAAAAGGAACAACATGATTGTTAACAATGATCTTGCAAAGGAAACTCTCACTCTTTTTCCAGAAGTTCCAACATTTTATGGAGGAGAAGCTAGCAGTAGCAAGAACACCAACAACTATGAAGCAAGCACTTCCATGACTCTTCCTGTTGTTTCTGTTGATGATGGAAAAGTTGATGTGGAACTTCGTTTGGGTTTAAATTAG
Protein sequence

>MS.gene46477.t1

MPFPNGSRRMVPWSQLEHDLLVMGMIKYGKGKWSEIAKNFVCNKTPQQVQSYANSFFRYLPDTYVHGLRKRKRNNMIVNNDLAKETLTLFPEVPTFYGGEASSSKNTNNYEASTSMTLPVVSVDDGKVDVELRLGLN