AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene040413


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene040413.t1 MTR_5g080150 62.411 282 100 4 1 280 1 278 4.01e-113 331
MS.gene040413.t1 MTR_2g048140 43.431 274 148 5 4 276 5 272 1.84e-59 196
MS.gene040413.t1 MTR_1g090907 42.701 274 150 5 4 276 5 272 4.87e-55 184
MS.gene040413.t1 MTR_3g448340 40.071 282 154 6 1 277 1 272 2.13e-52 177
MS.gene040413.t1 MTR_1g090903 40.625 224 127 5 31 252 30 249 9.92e-45 156
MS.gene040413.t1 MTR_3g049530 35.971 278 117 7 1 276 1 219 1.19e-33 127
MS.gene040413.t1 MTR_5g080110 62.687 67 25 0 1 67 1 67 2.81e-21 85.5
MS.gene040413.t1 MTR_5g066900 47.561 82 28 1 19 100 19 85 6.27e-16 71.6
MS.gene040413.t1 MTR_5g080160 64.912 57 19 1 1 56 1 57 6.53e-15 71.2
MS.gene040413.t1 MTR_5g038430 26.154 260 129 11 2 248 92 301 1.68e-13 70.5
MS.gene040413.t1 MTR_1g071060 38.889 90 54 1 38 127 7 95 3.77e-12 61.6
MS.gene040413.t1 MTR_8g015830 27.562 283 162 10 6 272 8 263 2.66e-11 63.9
MS.gene040413.t1 MTR_8g015830 27.562 283 162 10 6 272 8 263 2.94e-11 63.9
MS.gene040413.t1 MTR_1g013630 26.291 213 137 5 1 208 34 231 3.52e-11 63.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene040413.t1 AT1G56400 32.374 278 177 4 2 276 9 278 6.56e-37 137
MS.gene040413.t1 AT3G29830 34.397 282 160 10 6 277 8 274 6.58e-33 125
MS.gene040413.t1 AT3G29830 34.397 282 160 10 6 277 8 274 6.72e-33 125
MS.gene040413.t1 AT5G54820 31.930 285 173 8 2 277 3 275 1.20e-29 117
MS.gene040413.t1 AT1G56400 29.964 277 142 5 3 276 10 237 2.22e-25 104
MS.gene040413.t1 AT3G62230 29.137 278 190 4 2 276 4 277 3.68e-25 104
MS.gene040413.t1 AT3G59000 27.830 212 140 4 5 204 1 211 1.35e-14 73.2
MS.gene040413.t1 AT3G59000 32.308 130 87 1 5 134 1 129 2.33e-14 73.2
MS.gene040413.t1 AT3G58860 26.953 256 155 7 5 250 6 239 1.46e-12 67.8
MS.gene040413.t1 AT3G52680 28.235 255 154 9 6 253 21 253 2.74e-12 66.6
MS.gene040413.t1 AT3G58880 29.286 140 96 2 5 142 2 140 5.43e-12 65.9
MS.gene040413.t1 AT3G52680 28.235 255 154 9 6 253 21 253 8.72e-12 65.5
MS.gene040413.t1 AT4G13960 26.482 253 157 8 5 250 1 231 1.30e-11 65.1
MS.gene040413.t1 AT4G13960 26.482 253 157 8 5 250 1 231 1.30e-11 65.1
MS.gene040413.t1 AT3G58900 32.203 118 79 1 5 122 1 117 2.37e-11 64.3
MS.gene040413.t1 AT3G58900 32.203 118 79 1 5 122 1 117 2.84e-11 63.2
MS.gene040413.t1 AT3G58900 32.203 118 79 1 5 122 1 117 3.22e-11 63.2
MS.gene040413.t1 AT3G58900 32.203 118 79 1 5 122 1 117 3.22e-11 63.2
MS.gene040413.t1 AT5G41840 24.286 210 149 4 1 206 9 212 7.70e-11 62.8
MS.gene040413.t1 AT1G69630 25.962 208 124 6 5 206 17 200 7.99e-11 62.4

Find 32 sgRNAs with CRISPR-Local

Find 47 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTTTGAGCATCAACAATTTC+AGG 0.243731 7.3:+71397437 None:intergenic
ATGACCTGATTAAACATTTC+AGG 0.246755 7.3:+71397329 None:intergenic
CCTAGTTATGTTTATGACTA+TGG 0.249350 7.3:-71397185 MS.gene040413:CDS
GAAAGACAAATGGGAGAAAA+TGG 0.250720 7.3:+71397568 None:intergenic
TTCCCTCAAAGAAATATCTT+TGG 0.270717 7.3:-71397099 MS.gene040413:CDS
GAGAAATGGAGTTAAGTATT+TGG 0.273380 7.3:-71397282 MS.gene040413:CDS
AGTGAAGCTATGTGCTATTA+AGG 0.312329 7.3:-71397066 MS.gene040413:CDS
CCACTTCTTTGAAAGACAAA+TGG 0.342556 7.3:+71397558 None:intergenic
ATGGTTGATAACAATGAATT+AGG 0.345686 7.3:+71397587 None:intergenic
AGTGCCTGAAATGTTTAATC+AGG 0.350234 7.3:-71397333 MS.gene040413:CDS
CCATGGGAGTAAACATTGAT+AGG 0.355905 7.3:-71397622 MS.gene040413:CDS
TCCCTCAAAGAAATATCTTT+GGG 0.372400 7.3:-71397098 MS.gene040413:CDS
TTCCCTTGAGCATGGATGTC+AGG 0.403881 7.3:-71396802 None:intergenic
ACCCAAAGATATTTCTTTGA+GGG 0.417663 7.3:+71397097 None:intergenic
AGTTCATTGAACTCTATGTT+TGG 0.432595 7.3:+71397485 None:intergenic
CACTTCTTTGAAAGACAAAT+GGG 0.434762 7.3:+71397559 None:intergenic
GTTTGAGTTTGTTTAAGTGC+TGG 0.444803 7.3:-71397013 MS.gene040413:CDS
ATGTGCTATTAAGGCACTAT+TGG 0.446523 7.3:-71397057 MS.gene040413:CDS
AAACTATCTTTGATCCGAGT+TGG 0.455902 7.3:+71397242 None:intergenic
ATTGGCCAATTGTGAAAAGT+TGG 0.461528 7.3:-71397039 MS.gene040413:CDS
CCATTTGTCTTTCAAAGAAG+TGG 0.465077 7.3:-71397558 MS.gene040413:CDS
CCATAGTCATAAACATAACT+AGG 0.481893 7.3:+71397185 None:intergenic
GTTGCGTCAGCTGTGAGAAA+TGG 0.489194 7.3:-71397296 MS.gene040413:CDS
TGATATTCAATCAACTGCAT+TGG 0.494222 7.3:-71396844 MS.gene040413:CDS
AACCCAAAGATATTTCTTTG+AGG 0.497703 7.3:+71397096 None:intergenic
AAGTGCTGGAATTCAGATGC+TGG 0.524277 7.3:-71396999 MS.gene040413:CDS
CCTATCAATGTTTACTCCCA+TGG 0.527132 7.3:+71397622 None:intergenic
TGACCTGACATCCATGCTCA+AGG 0.552492 7.3:+71396799 None:intergenic
AGTTAATGCCCCAAATCTGA+AGG 0.566076 7.3:-71396904 MS.gene040413:CDS
GACCTGACATCCATGCTCAA+GGG 0.599854 7.3:+71396800 None:intergenic
TTGATTTCACTCATCCAACT+CGG 0.602313 7.3:-71397256 MS.gene040413:CDS
TTGGGTGAACATTAGCAAAG+TGG 0.666162 7.3:-71397510 MS.gene040413:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAATAAAAACCTTCAGATTT+GGG + chr7.3:71397531-71397550 None:intergenic 20.0%
!! TAAATAAAAACCTTCAGATT+TGG + chr7.3:71397532-71397551 None:intergenic 20.0%
!! TTCTATTCTCTCAAAAAATT+GGG - chr7.3:71396895-71396914 MS.gene040413:CDS 20.0%
!!! TGAAGGTTTTTATTTATCAA+GGG - chr7.3:71397536-71397555 MS.gene040413:CDS 20.0%
! AATAAAAACCTTCAGATTTG+GGG + chr7.3:71397530-71397549 None:intergenic 25.0%
! CTTCTATTCTCTCAAAAAAT+TGG - chr7.3:71396894-71396913 MS.gene040413:CDS 25.0%
!! ATATTCTGGGTTGAAAAAAT+TGG - chr7.3:71397465-71397484 MS.gene040413:CDS 25.0%
!! TTTTGGATTTCATGGAAAAA+TGG - chr7.3:71397017-71397036 MS.gene040413:CDS 25.0%
!!! AATAGCATTTTTGGATTTCA+TGG - chr7.3:71397009-71397028 MS.gene040413:CDS 25.0%
!!! ATGGTTGATAACAATGAATT+AGG + chr7.3:71396839-71396858 None:intergenic 25.0%
!!! ATTTTGAAGGAAGAATATTC+TGG - chr7.3:71397451-71397470 MS.gene040413:CDS 25.0%
!!! CTGAAGGTTTTTATTTATCA+AGG - chr7.3:71397535-71397554 MS.gene040413:CDS 25.0%
!!! TTTTGAAGGAAGAATATTCT+GGG - chr7.3:71397452-71397471 MS.gene040413:CDS 25.0%
AACCCAAAGATATTTCTTTG+AGG + chr7.3:71397330-71397349 None:intergenic 30.0%
ACCCAAAGATATTTCTTTGA+GGG + chr7.3:71397329-71397348 None:intergenic 30.0%
AGTTCATTGAACTCTATGTT+TGG + chr7.3:71396941-71396960 None:intergenic 30.0%
ATGACCTGATTAAACATTTC+AGG + chr7.3:71397097-71397116 None:intergenic 30.0%
CCATAGTCATAAACATAACT+AGG + chr7.3:71397241-71397260 None:intergenic 30.0%
CCTAGTTATGTTTATGACTA+TGG - chr7.3:71397238-71397257 MS.gene040413:CDS 30.0%
GAGAAATGGAGTTAAGTATT+TGG - chr7.3:71397141-71397160 MS.gene040413:CDS 30.0%
TCCCTCAAAGAAATATCTTT+GGG - chr7.3:71397325-71397344 MS.gene040413:CDS 30.0%
TGATATTCAATCAACTGCAT+TGG - chr7.3:71397579-71397598 MS.gene040413:CDS 30.0%
TTCCCTCAAAGAAATATCTT+TGG - chr7.3:71397324-71397343 MS.gene040413:CDS 30.0%
! CACTTCTTTGAAAGACAAAT+GGG + chr7.3:71396867-71396886 None:intergenic 30.0%
! TAGTTTTTCTCAAGATGAGT+TGG - chr7.3:71397198-71397217 MS.gene040413:CDS 30.0%
! TGCTCAAAGAATAGCATTTT+TGG - chr7.3:71397000-71397019 MS.gene040413:CDS 30.0%
!!! AGATGCTGGTTTTATTTTGA+AGG - chr7.3:71397438-71397457 MS.gene040413:CDS 30.0%
AAACTATCTTTGATCCGAGT+TGG + chr7.3:71397184-71397203 None:intergenic 35.0%
AGTGCCTGAAATGTTTAATC+AGG - chr7.3:71397090-71397109 MS.gene040413:CDS 35.0%
ATTGGCCAATTGTGAAAAGT+TGG - chr7.3:71397384-71397403 MS.gene040413:CDS 35.0%
CCATTTGTCTTTCAAAGAAG+TGG - chr7.3:71396865-71396884 MS.gene040413:CDS 35.0%
CTTTGAGCATCAACAATTTC+AGG + chr7.3:71396989-71397008 None:intergenic 35.0%
GAAAGACAAATGGGAGAAAA+TGG + chr7.3:71396858-71396877 None:intergenic 35.0%
TTGATTTCACTCATCCAACT+CGG - chr7.3:71397167-71397186 MS.gene040413:CDS 35.0%
! ACTCTCCAACTTTTCACAAT+TGG + chr7.3:71397392-71397411 None:intergenic 35.0%
! AGTGAAGCTATGTGCTATTA+AGG - chr7.3:71397357-71397376 MS.gene040413:CDS 35.0%
! ATGTGCTATTAAGGCACTAT+TGG - chr7.3:71397366-71397385 MS.gene040413:CDS 35.0%
! CAATTTTGTTGCTAGTGGAA+TGG - chr7.3:71397291-71397310 MS.gene040413:CDS 35.0%
! CCACTTCTTTGAAAGACAAA+TGG + chr7.3:71396868-71396887 None:intergenic 35.0%
! GTTTGAGTTTGTTTAAGTGC+TGG - chr7.3:71397410-71397429 MS.gene040413:CDS 35.0%
!! TTTTTCTCAAGATGAGTTGG+TGG - chr7.3:71397201-71397220 MS.gene040413:CDS 35.0%
AGTTAATGCCCCAAATCTGA+AGG - chr7.3:71397519-71397538 MS.gene040413:CDS 40.0%
TTGGGTGAACATTAGCAAAG+TGG - chr7.3:71396913-71396932 MS.gene040413:CDS 40.0%
! GCATGCAATTTTGTTGCTAG+TGG - chr7.3:71397286-71397305 MS.gene040413:CDS 40.0%
! CTTGACTTTTCCCTTGAGCA+TGG - chr7.3:71397613-71397632 MS.gene040413:CDS 45.0%
!! AAGTGCTGGAATTCAGATGC+TGG - chr7.3:71397424-71397443 MS.gene040413:CDS 45.0%
GTTGCGTCAGCTGTGAGAAA+TGG - chr7.3:71397127-71397146 MS.gene040413:CDS 50.0%


Chromosome Type Strat End Strand Name
chr7.3 gene 71396803 71397642 71396803 ID=MS.gene040413
chr7.3 mRNA 71396803 71397642 71396803 ID=MS.gene040413.t1;Parent=MS.gene040413
chr7.3 exon 71396803 71397642 71396803 ID=MS.gene040413.t1.exon1;Parent=MS.gene040413.t1
chr7.3 CDS 71396803 71397642 71396803 ID=cds.MS.gene040413.t1;Parent=MS.gene040413.t1
Gene Sequence

>MS.gene040413

ATGGGAGTAAACATTGATAGGTTTAGTTCGTTGCCTAATTCATTGTTATCAACCATTTTCTCCCATTTGTCTTTCAAAGAAGTGGCAAGAACTTCTATTCTCTCAAAAAATTGGGTGAACATTAGCAAAGTGGCACCAAACATAGAGTTCAATGAACTCTTCTTTGTTAAATTTGATCAATCTCCTGAAATTGTTGATGCTCAAAGAATAGCATTTTTGGATTTCATGGAAAAATGGATAAAAGATCGCGCAGAAAATGTCGTTAACAAATTGTCTTTAACAATTTCAGTGCCTGAAATGTTTAATCAGGTCATAGATCAATTTGTTGCGTCAGCTGTGAGAAATGGAGTTAAGTATTTGGAACTTGATTTCACTCATCCAACTCGGATCAAAGATAGTTTTTCTCAAGATGAGTTGGTGGCTTTGTTTGATTTGCCTAGTTATGTTTATGACTATGGTGAACTTGAATCTTTGAAATTGTATGCATGCAATTTTGTTGCTAGTGGAATGGTTAATTTTCATTCCCTCAAAGAAATATCTTTGGGTTGTATGAAAGTGAAGCTATGTGCTATTAAGGCACTATTGGCCAATTGTGAAAAGTTGGAGAGTTTGAGTTTGTTTAAGTGCTGGAATTCAGATGCTGGTTTTATTTTGAAGGAAGAATATTCTGGGTTGAAAAAATTGGTTATCAATAGATGTCAATTTAATACTCTCAAAGTTAATGCCCCAAATCTGAAGGTTTTTATTTATCAAGGGTTGATGACACTTTTTGTTGTTGATATTCAATCAACTGCATTGGATGAAGTTAATCTTGACTTTTCCCTTGAGCATGGATGTCAG

Protein sequence

>MS.gene040413.t1

MGVNIDRFSSLPNSLLSTIFSHLSFKEVARTSILSKNWVNISKVAPNIEFNELFFVKFDQSPEIVDAQRIAFLDFMEKWIKDRAENVVNKLSLTISVPEMFNQVIDQFVASAVRNGVKYLELDFTHPTRIKDSFSQDELVALFDLPSYVYDYGELESLKLYACNFVASGMVNFHSLKEISLGCMKVKLCAIKALLANCEKLESLSLFKCWNSDAGFILKEEYSGLKKLVINRCQFNTLKVNAPNLKVFIYQGLMTLFVVDIQSTALDEVNLDFSLEHGCQ