AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene017021

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene017021.t1 MTR_5g090250 94.286 70 4 0 1 70 1 70 1.62e-44 137
MS.gene017021.t1 MTR_5g090250 94.286 70 4 0 1 70 1 70 1.62e-44 137
MS.gene017021.t1 MTR_1g075410 89.706 68 7 0 3 70 5 72 1.02e-38 122
MS.gene017021.t1 MTR_1g075340 84.286 70 11 0 1 70 1 70 7.97e-38 120
MS.gene017021.t1 MTR_1g075340 84.286 70 11 0 1 70 1 70 7.97e-38 120
MS.gene017021.t1 MTR_1g075380 82.353 68 12 0 3 70 4 71 1.33e-33 110
MS.gene017021.t1 MTR_1g070335 60.000 70 28 0 1 70 1 70 8.17e-24 85.1
MS.gene017021.t1 MTR_5g045470 62.121 66 25 0 5 70 4 69 9.91e-24 85.1
MS.gene017021.t1 MTR_1g070330 59.259 54 22 0 17 70 1 54 1.31e-15 63.9
MS.gene017021.t1 MTR_3g020970 50.794 63 31 0 8 70 36 98 2.08e-14 62.4
MS.gene017021.t1 MTR_3g020930 42.857 63 36 0 8 70 32 94 3.43e-11 53.9
MS.gene017021.t1 MTR_3g020800 47.619 63 33 0 8 70 36 98 4.98e-11 53.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene017021.t1 AT2G38870 60.000 70 28 0 1 70 1 70 5.34e-24 85.9
MS.gene017021.t1 AT5G43580 54.688 64 29 0 7 70 36 99 6.50e-19 73.6
MS.gene017021.t1 AT2G38900 48.438 64 33 0 7 70 10 73 1.28e-16 67.0
MS.gene017021.t1 AT2G38900 48.438 64 33 0 7 70 25 88 1.91e-16 67.0
MS.gene017021.t1 AT3G46860 47.619 63 33 0 8 70 23 85 1.50e-13 59.7
MS.gene017021.t1 AT5G43570 45.946 74 34 1 1 68 1 74 4.49e-13 58.9
MS.gene017021.t1 AT5G43570 49.180 61 31 0 8 68 24 84 4.42e-12 56.6
MS.gene017021.t1 AT5G45277 47.170 53 28 0 8 60 2 54 7.58e-11 52.4

Find 28 sgRNAs with CRISPR-Local

Find 32 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GTCTATCAGGTTCCAGTAAT+TGG 0.190800 5.2:-76604050 MS.gene017021:CDS
CTGTGACAGGGTTAGGGTTT+GGG 0.262714 5.2:-76604090 MS.gene017021:CDS
GACACTTTCTATCCAATTAC+TGG 0.267846 5.2:+76604038 None:intergenic
ACTTCCGCTGTGACAGGGTT+AGG 0.276358 5.2:-76604097 MS.gene017021:CDS
TAAAGATGGAATTGTCTATC+AGG 0.346883 5.2:-76604063 MS.gene017021:CDS
GCTGTGACAGGGTTAGGGTT+TGG 0.358066 5.2:-76604091 MS.gene017021:CDS
AGGGTTTGGGTTGATAAAGA+TGG 0.412719 5.2:-76604077 MS.gene017021:CDS
CCGCCGACTTCCGCTGTGAC+AGG 0.421191 5.2:-76604103 MS.gene017021:CDS
CTTCCGCTGTGACAGGGTTA+GGG 0.422816 5.2:-76604096 MS.gene017021:CDS
CCTTCCACTCCAACCAACTC+TGG 0.454716 5.2:+76604203 None:intergenic
AGATCCTTCTGGCACAATGA+TGG 0.502286 5.2:+76604133 None:intergenic
CCAGAGTTGGTTGGAGTGGA+AGG 0.515293 5.2:-76604203 MS.gene017021:CDS
GTTGGTTGGAGTGGAAGGAA+AGG 0.527079 5.2:-76604198 MS.gene017021:CDS
GCGGTGACAAAAGATCCTTC+TGG 0.550057 5.2:+76604122 None:intergenic
TATGGTCAGGTAAGAGCTCA+TGG 0.552544 5.2:-76604226 MS.gene017021:intron
CGCCGACTTCCGCTGTGACA+GGG 0.553611 5.2:-76604102 MS.gene017021:CDS
ATGGCCAGAGTTGGTTGGAG+TGG 0.564909 5.2:-76604207 MS.gene017021:CDS
AATTGAGAGGGAGAATCCAT+TGG 0.570404 5.2:-76604162 MS.gene017021:CDS
AACCCTGTCACAGCGGAAGT+CGG 0.575336 5.2:+76604100 None:intergenic
AGCTCATGGCCAGAGTTGGT+TGG 0.578782 5.2:-76604212 MS.gene017021:CDS
TAAGAGCTCATGGCCAGAGT+TGG 0.585826 5.2:-76604216 MS.gene017021:CDS
AGCAGAAGCTACAATTGAGA+GGG 0.593359 5.2:-76604174 MS.gene017021:CDS
TAGCAGAAGCTACAATTGAG+AGG 0.609404 5.2:-76604175 MS.gene017021:CDS
AATGCCATCATTGTGCCAGA+AGG 0.618440 5.2:-76604137 MS.gene017021:CDS
ACAATGATGGCATTCACCAA+TGG 0.635361 5.2:+76604146 None:intergenic
CCTGTCACAGCGGAAGTCGG+CGG 0.661655 5.2:+76604103 None:intergenic
AAAATGTCTGATGAATGCAA+AGG 0.675933 5.2:-76604335 MS.gene017021:intron
AAACCCTAACCCTGTCACAG+CGG 0.735906 5.2:+76604093 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! GAATTTTAATTATAATTTGA+TGG - chr5.2:76604111-76604130 MS.gene017021:CDS 10.0%
!! TTGAATTAATCAATATTGTA+TGG - chr5.2:76604134-76604153 MS.gene017021:CDS 15.0%
!! TGTTTAAATTAAATGGTTTG+TGG - chr5.2:76604089-76604108 MS.gene017021:CDS 20.0%
! TTAATCAATATTGTATGGTC+AGG - chr5.2:76604139-76604158 MS.gene017021:CDS 25.0%
TAAAGATGGAATTGTCTATC+AGG - chr5.2:76604315-76604334 MS.gene017021:intron 30.0%
AATTGAGAGGGAGAATCCAT+TGG - chr5.2:76604216-76604235 MS.gene017021:CDS 40.0%
ACAATGATGGCATTCACCAA+TGG + chr5.2:76604235-76604254 None:intergenic 40.0%
AGCAGAAGCTACAATTGAGA+GGG - chr5.2:76604204-76604223 MS.gene017021:CDS 40.0%
GTCTATCAGGTTCCAGTAAT+TGG - chr5.2:76604328-76604347 MS.gene017021:intron 40.0%
GTCTGATGAATGCAAAGGTA+AGG - chr5.2:76604048-76604067 MS.gene017021:CDS 40.0%
TAGCAGAAGCTACAATTGAG+AGG - chr5.2:76604203-76604222 MS.gene017021:CDS 40.0%
!! AGGGTTTGGGTTGATAAAGA+TGG - chr5.2:76604301-76604320 MS.gene017021:intron 40.0%
AATGCCATCATTGTGCCAGA+AGG - chr5.2:76604241-76604260 MS.gene017021:intron 45.0%
AGATCCTTCTGGCACAATGA+TGG + chr5.2:76604248-76604267 None:intergenic 45.0%
TATGGTCAGGTAAGAGCTCA+TGG - chr5.2:76604152-76604171 MS.gene017021:CDS 45.0%
!! TATAATATGTTTAAATTAAA+TGG - chr5.2:76604082-76604101 MS.gene017021:CDS 5.0%
AAACCCTAACCCTGTCACAG+CGG + chr5.2:76604288-76604307 None:intergenic 50.0%
CTGTGACAGGGTTAGGGTTT+GGG - chr5.2:76604288-76604307 MS.gene017021:intron 50.0%
GCGGTGACAAAAGATCCTTC+TGG + chr5.2:76604259-76604278 None:intergenic 50.0%
GTTGGTTGGAGTGGAAGGAA+AGG - chr5.2:76604180-76604199 MS.gene017021:CDS 50.0%
TAAGAGCTCATGGCCAGAGT+TGG - chr5.2:76604162-76604181 MS.gene017021:CDS 50.0%
AACCCTGTCACAGCGGAAGT+CGG + chr5.2:76604281-76604300 None:intergenic 55.0%
ACTTCCGCTGTGACAGGGTT+AGG - chr5.2:76604281-76604300 MS.gene017021:intron 55.0%
CCTTCCACTCCAACCAACTC+TGG + chr5.2:76604178-76604197 None:intergenic 55.0%
CTTCCGCTGTGACAGGGTTA+GGG - chr5.2:76604282-76604301 MS.gene017021:intron 55.0%
GCTGTGACAGGGTTAGGGTT+TGG - chr5.2:76604287-76604306 MS.gene017021:intron 55.0%
! AGCTCATGGCCAGAGTTGGT+TGG - chr5.2:76604166-76604185 MS.gene017021:CDS 55.0%
! ATGGCCAGAGTTGGTTGGAG+TGG - chr5.2:76604171-76604190 MS.gene017021:CDS 55.0%
! CCAGAGTTGGTTGGAGTGGA+AGG - chr5.2:76604175-76604194 MS.gene017021:CDS 55.0%
CCTGTCACAGCGGAAGTCGG+CGG + chr5.2:76604278-76604297 None:intergenic 65.0%
!! CGCCGACTTCCGCTGTGACA+GGG - chr5.2:76604276-76604295 MS.gene017021:intron 65.0%
!! CCGCCGACTTCCGCTGTGAC+AGG - chr5.2:76604275-76604294 MS.gene017021:intron 70.0%


Chromosome Type Strat End Strand Name
chr5.2 gene 76604046 76604354 76604046 ID=MS.gene017021
chr5.2 mRNA 76604046 76604354 76604046 ID=MS.gene017021.t1;Parent=MS.gene017021
chr5.2 exon 76604336 76604354 76604336 ID=MS.gene017021.t1.exon1;Parent=MS.gene017021.t1
chr5.2 CDS 76604336 76604354 76604336 ID=cds.MS.gene017021.t1;Parent=MS.gene017021.t1
chr5.2 exon 76604046 76604239 76604046 ID=MS.gene017021.t1.exon2;Parent=MS.gene017021.t1
chr5.2 CDS 76604046 76604239 76604046 ID=cds.MS.gene017021.t1;Parent=MS.gene017021.t1
Gene Sequence

>MS.gene017021

ATGTCTGATGAATGCAAAGGTAAGGTGTTATAGTAATATAATATGTTTAAATTAAATGGTTTGTGGAATTTTAATTATAATTTGATGGTTGAATTAATCAATATTGTATGGTCAGGTAAGAGCTCATGGCCAGAGTTGGTTGGAGTGGAAGGAAAGGTAGCAGAAGCTACAATTGAGAGGGAGAATCCATTGGTGAATGCCATCATTGTGCCAGAAGGATCTTTTGTCACCGCCGACTTCCGCTGTGACAGGGTTAGGGTTTGGGTTGATAAAGATGGAATTGTCTATCAGGTTCCAGTAATTGGATAG
Protein sequence

>MS.gene017021.t1

MSDECKGKSSWPELVGVEGKVAEATIERENPLVNAIIVPEGSFVTADFRCDRVRVWVDKDGIVYQVPVIG