AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene40880


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene40880.t1 MTR_1g083350 98.810 168 2 0 1 168 1 168 2.66e-120 336
MS.gene40880.t1 MTR_1g083380 98.214 168 3 0 1 168 1 168 1.84e-119 334
MS.gene40880.t1 MTR_2g436620 85.714 168 23 1 1 168 1 167 6.07e-102 290
MS.gene40880.t1 MTR_1g083340 91.083 157 4 1 1 147 1 157 1.16e-97 279
MS.gene40880.t1 MTR_6g071090 80.745 161 30 1 1 161 1 160 1.85e-89 258
MS.gene40880.t1 MTR_2g436620 84.507 142 21 1 27 168 1 141 1.37e-83 243
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene40880.t1 AT3G16640 78.571 168 36 0 1 168 1 168 7.78e-96 275
MS.gene40880.t1 AT3G05540 79.882 169 32 2 1 168 1 168 5.06e-89 257

Find 42 sgRNAs with CRISPR-Local

Find 82 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTGATATTGTTGACACTTTC+AGG 0.110440 1.4:-67420374 MS.gene40880:CDS
AATTGTAGGTCCTTGAGTTT+AGG 0.253357 1.4:+67420210 None:intergenic
TCCATTCTCAATTTCCTTGC+AGG 0.264878 1.4:+67420640 None:intergenic
ATTGTAGGTCCTTGAGTTTA+GGG 0.271566 1.4:+67420211 None:intergenic
GTATACCAGGATCTTCTTAC+AGG 0.300413 1.4:-67421256 MS.gene40880:intron
TGTTGACACTTTCAGGCTTC+AGG 0.310211 1.4:-67420367 MS.gene40880:CDS
CTACTTTGCCTATGGCTTGA+AGG 0.378916 1.4:-67419802 MS.gene40880:CDS
AACAATATCAACCACTTTGA+CGG 0.381711 1.4:+67420386 None:intergenic
GATGAAATACATACAATTGT+AGG 0.387035 1.4:+67420196 None:intergenic
AATTGCTTCTTATCAAAAGC+TGG 0.428621 1.4:+67420339 None:intergenic
CCTTGTGTTTGCTTACTACA+AGG 0.455642 1.4:-67419850 MS.gene40880:CDS
GAATGGAATGTTGTGGGAAG+TGG 0.459626 1.4:-67420624 MS.gene40880:CDS
CCATTCTCAATTTCCTTGCA+GGG 0.465811 1.4:+67420641 None:intergenic
TAGGCAAAGTAGAGAAAAGT+TGG 0.474181 1.4:+67419813 None:intergenic
TCGTCTCCACCCTCTGCAGA+AGG 0.482179 1.4:+67420432 None:intergenic
TATTTGCAGTGGGTTGTTCA+AGG 0.483236 1.4:-67420483 MS.gene40880:intron
CCCTGCAAGGAAATTGAGAA+TGG 0.490398 1.4:-67420641 MS.gene40880:CDS
CTTGATTTCCTTCAAGCCAT+AGG 0.498561 1.4:+67419794 None:intergenic
GGAGCAGTGGATGTGAATAT+TGG 0.501116 1.4:-67420462 MS.gene40880:CDS
GGTGCTAACCCTTCTGCAGA+GGG 0.509467 1.4:-67420441 MS.gene40880:CDS
TGTAACCATGCTTGTATACC+AGG 0.532022 1.4:-67421269 None:intergenic
CTCTGACTCATTCCCCTGCA+AGG 0.534349 1.4:-67420654 MS.gene40880:CDS
GTGTTTGCTTACTACAAGGA+TGG 0.538874 1.4:-67419846 MS.gene40880:CDS
GGTCCTTGAGTTTAGGGAGA+AGG 0.545288 1.4:+67420217 None:intergenic
GTTCCTTCTCCCTAAACTCA+AGG 0.563294 1.4:-67420220 MS.gene40880:CDS
GGGGAGAGCATGCATGATGA+TGG 0.565967 1.4:-67419876 MS.gene40880:CDS
CATTCTCAATTTCCTTGCAG+GGG 0.578074 1.4:+67420642 None:intergenic
CGTCTCCACCCTCTGCAGAA+GGG 0.579433 1.4:+67420433 None:intergenic
ATTTACCTGTAAGAAGATCC+TGG 0.582754 1.4:+67421251 None:intergenic
GTTGTGGGAAGTGGAAGGAA+AGG 0.585239 1.4:-67420615 MS.gene40880:intron
AATTGAGAATGGAATGTTGT+GGG 0.593952 1.4:-67420630 MS.gene40880:CDS
TTCTGCAGAGGGTGGAGACG+AGG 0.598044 1.4:-67420430 MS.gene40880:CDS
GCTAACCCTTCTGCAGAGGG+TGG 0.604009 1.4:-67420438 MS.gene40880:CDS
GTAGAGAAAAGTTGGATCAG+TGG 0.605758 1.4:+67419821 None:intergenic
GAGGGTGGAGACGAGGATGA+CGG 0.612656 1.4:-67420423 MS.gene40880:CDS
TGGTGCTAACCCTTCTGCAG+AGG 0.618744 1.4:-67420442 MS.gene40880:CDS
AAGATCCTGGTATACAAGCA+TGG 0.621063 1.4:+67421264 None:intergenic
CCTTGTAGTAAGCAAACACA+AGG 0.635355 1.4:+67419850 None:intergenic
GTGGGTTGTTCAAGGAGCAG+TGG 0.636439 1.4:-67420475 MS.gene40880:CDS
GGAATGTTGTGGGAAGTGGA+AGG 0.687071 1.4:-67420620 MS.gene40880:CDS
TGATGATCAAGCCGTCAAAG+TGG 0.714042 1.4:-67420397 MS.gene40880:CDS
AAATTGAGAATGGAATGTTG+TGG 0.718062 1.4:-67420631 MS.gene40880:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AGTAAAGATTATTTATTTAT+GGG + chr1.4:67421121-67421140 None:intergenic 10.0%
!! CAGTAAAGATTATTTATTTA+TGG + chr1.4:67421122-67421141 None:intergenic 15.0%
!! CTAATTTATGAACATATATT+TGG + chr1.4:67420519-67420538 None:intergenic 15.0%
!!! AATTATTTAAAACTAAAGTG+AGG + chr1.4:67419976-67419995 None:intergenic 15.0%
!!! ATATTAGAGATTATTGTTTT+TGG - chr1.4:67420305-67420324 MS.gene40880:CDS 15.0%
!!! TTATCTTTCATCTTTTTATT+TGG - chr1.4:67420878-67420897 MS.gene40880:intron 15.0%
!! CTTAATCTAATACTTGATTA+TGG - chr1.4:67420250-67420269 MS.gene40880:CDS 20.0%
!! TAAGAGATAATCATGTTTAA+GGG + chr1.4:67420234-67420253 None:intergenic 20.0%
!! TAGAAAGAAACATTATAGAA+AGG + chr1.4:67420475-67420494 None:intergenic 20.0%
!! TTAAGAGATAATCATGTTTA+AGG + chr1.4:67420235-67420254 None:intergenic 20.0%
!!! ATAAAAACAGAGAAGTTTTA+AGG - chr1.4:67420076-67420095 MS.gene40880:intron 20.0%
!!! CTTTTTTGTGGATAAATAAA+GGG - chr1.4:67420917-67420936 MS.gene40880:intron 20.0%
!!! TAAAACTTCTCTGTTTTTAT+GGG + chr1.4:67420076-67420095 None:intergenic 20.0%
!!! TCTTTTTTGTGGATAAATAA+AGG - chr1.4:67420916-67420935 MS.gene40880:intron 20.0%
!!! TTAAAACTTCTCTGTTTTTA+TGG + chr1.4:67420077-67420096 None:intergenic 20.0%
! AAAAATCTCAAAGATGATGA+TGG + chr1.4:67419825-67419844 None:intergenic 25.0%
! ATTACACAACAATCAACTTT+AGG + chr1.4:67420542-67420561 None:intergenic 25.0%
! GAAATTCATTCACTAAATAC+AGG + chr1.4:67419917-67419936 None:intergenic 25.0%
! GATGAAATACATACAATTGT+AGG + chr1.4:67420857-67420876 None:intergenic 25.0%
! TTGTGACAGGATTAAATTTA+TGG - chr1.4:67420175-67420194 MS.gene40880:intron 25.0%
!! TCGTTTGTATTTCTTTTCAT+AGG - chr1.4:67419856-67419875 MS.gene40880:CDS 25.0%
!!! ATTAAGTTCTCTCTTTTTTG+TGG - chr1.4:67420905-67420924 MS.gene40880:intron 25.0%
AAATTGAGAATGGAATGTTG+TGG - chr1.4:67420419-67420438 MS.gene40880:CDS 30.0%
AACAATATCAACCACTTTGA+CGG + chr1.4:67420667-67420686 None:intergenic 30.0%
AATTGAGAATGGAATGTTGT+GGG - chr1.4:67420420-67420439 MS.gene40880:CDS 30.0%
AATTGCTTCTTATCAAAAGC+TGG + chr1.4:67420714-67420733 None:intergenic 30.0%
GTAATGTGATTATTTGCAGT+GGG - chr1.4:67420557-67420576 MS.gene40880:intron 30.0%
TGTAATGTGATTATTTGCAG+TGG - chr1.4:67420556-67420575 MS.gene40880:intron 30.0%
TTGATATTGTTGACACTTTC+AGG - chr1.4:67420676-67420695 MS.gene40880:intron 30.0%
! TTATGTTGTTTGTGTTCTGT+TGG - chr1.4:67420120-67420139 MS.gene40880:intron 30.0%
!! AATCAATGTTGCAGTTTTGT+TGG - chr1.4:67421153-67421172 MS.gene40880:intron 30.0%
!!! ATCAATGTTGCAGTTTTGTT+GGG - chr1.4:67421154-67421173 MS.gene40880:intron 30.0%
!!! TTATTGTTTTTGGTTGCTGA+TGG - chr1.4:67420315-67420334 MS.gene40880:CDS 30.0%
AATTGTAGGTCCTTGAGTTT+AGG + chr1.4:67420843-67420862 None:intergenic 35.0%
ATTGTAGGTCCTTGAGTTTA+GGG + chr1.4:67420842-67420861 None:intergenic 35.0%
ATTTACCTGTAAGAAGATCC+TGG + chr1.4:67419802-67419821 None:intergenic 35.0%
CTTTGCTGACGAATTTCTTT+AGG - chr1.4:67420361-67420380 MS.gene40880:CDS 35.0%
TAGGCAAAGTAGAGAAAAGT+TGG + chr1.4:67421240-67421259 None:intergenic 35.0%
! ACTTTTCTCTACTTTGCCTA+TGG - chr1.4:67421240-67421259 MS.gene40880:intron 35.0%
!! AAATGTTAACTTGTGCCCTT+GGG - chr1.4:67420940-67420959 MS.gene40880:intron 35.0%
!! TTGAACAACTCTTGCTTTTC+TGG + chr1.4:67420786-67420805 None:intergenic 35.0%
!!! TCAATGTTGCAGTTTTGTTG+GGG - chr1.4:67421155-67421174 MS.gene40880:intron 35.0%
CATTCTCAATTTCCTTGCAG+GGG + chr1.4:67420411-67420430 None:intergenic 40.0%
CCATTCTCAATTTCCTTGCA+GGG + chr1.4:67420412-67420431 None:intergenic 40.0%
CCTTGTAGTAAGCAAACACA+AGG + chr1.4:67421203-67421222 None:intergenic 40.0%
CCTTGTGTTTGCTTACTACA+AGG - chr1.4:67421200-67421219 MS.gene40880:intron 40.0%
CTTCTTAACTTATGCCCCAA+GGG + chr1.4:67420958-67420977 None:intergenic 40.0%
CTTGATTTCCTTCAAGCCAT+AGG + chr1.4:67421259-67421278 None:intergenic 40.0%
GTAGAGAAAAGTTGGATCAG+TGG + chr1.4:67421232-67421251 None:intergenic 40.0%
GTATACCAGGATCTTCTTAC+AGG - chr1.4:67419794-67419813 MS.gene40880:CDS 40.0%
GTGTTTGCTTACTACAAGGA+TGG - chr1.4:67421204-67421223 MS.gene40880:intron 40.0%
TCCATTCTCAATTTCCTTGC+AGG + chr1.4:67420413-67420432 None:intergenic 40.0%
TCTTCTTAACTTATGCCCCA+AGG + chr1.4:67420959-67420978 None:intergenic 40.0%
TGTTGTGTTTGTGTTGTGAC+AGG - chr1.4:67420162-67420181 MS.gene40880:intron 40.0%
!! AATGTTAACTTGTGCCCTTG+GGG - chr1.4:67420941-67420960 MS.gene40880:intron 40.0%
!! CATGTTAACTTGTGCCCTAA+GGG + chr1.4:67421097-67421116 None:intergenic 40.0%
!! CTCTTTAACTTGTGCCCTTA+GGG - chr1.4:67421080-67421099 MS.gene40880:intron 40.0%
!! GAAATGTTAACTTGTGCCCT+TGG - chr1.4:67420939-67420958 MS.gene40880:intron 40.0%
!! TATTTGCAGTGGGTTGTTCA+AGG - chr1.4:67420567-67420586 MS.gene40880:intron 40.0%
!! TCATGTTAACTTGTGCCCTA+AGG + chr1.4:67421098-67421117 None:intergenic 40.0%
!! TCTCTTTAACTTGTGCCCTT+AGG - chr1.4:67421079-67421098 MS.gene40880:intron 40.0%
CCCTGCAAGGAAATTGAGAA+TGG - chr1.4:67420409-67420428 MS.gene40880:CDS 45.0%
CTACTTTGCCTATGGCTTGA+AGG - chr1.4:67421248-67421267 MS.gene40880:intron 45.0%
GAATGGAATGTTGTGGGAAG+TGG - chr1.4:67420426-67420445 MS.gene40880:CDS 45.0%
GGAGCAGTGGATGTGAATAT+TGG - chr1.4:67420588-67420607 MS.gene40880:intron 45.0%
GTTCCTTCTCCCTAAACTCA+AGG - chr1.4:67420830-67420849 MS.gene40880:intron 45.0%
TGATGATCAAGCCGTCAAAG+TGG - chr1.4:67420653-67420672 MS.gene40880:CDS 45.0%
TGTTGACACTTTCAGGCTTC+AGG - chr1.4:67420683-67420702 MS.gene40880:intron 45.0%
GGAATGTTGTGGGAAGTGGA+AGG - chr1.4:67420430-67420449 MS.gene40880:CDS 50.0%
GGGAAGTGGAAGGAAAGGTT+AGG - chr1.4:67420440-67420459 MS.gene40880:CDS 50.0%
GGTCCTTGAGTTTAGGGAGA+AGG + chr1.4:67420836-67420855 None:intergenic 50.0%
GTTGTGGGAAGTGGAAGGAA+AGG - chr1.4:67420435-67420454 MS.gene40880:CDS 50.0%
CTCTGACTCATTCCCCTGCA+AGG - chr1.4:67420396-67420415 MS.gene40880:CDS 55.0%
GGTGCTAACCCTTCTGCAGA+GGG - chr1.4:67420609-67420628 MS.gene40880:intron 55.0%
! GGGGAGAGCATGCATGATGA+TGG - chr1.4:67421174-67421193 MS.gene40880:intron 55.0%
! GTGGGTTGTTCAAGGAGCAG+TGG - chr1.4:67420575-67420594 MS.gene40880:intron 55.0%
! TGGTGCTAACCCTTCTGCAG+AGG - chr1.4:67420608-67420627 MS.gene40880:intron 55.0%
CGTCTCCACCCTCTGCAGAA+GGG + chr1.4:67420620-67420639 None:intergenic 60.0%
GAGGGTGGAGACGAGGATGA+CGG - chr1.4:67420627-67420646 MS.gene40880:CDS 60.0%
GCTAACCCTTCTGCAGAGGG+TGG - chr1.4:67420612-67420631 MS.gene40880:intron 60.0%
TCGTCTCCACCCTCTGCAGA+AGG + chr1.4:67420621-67420640 None:intergenic 60.0%
TTCTGCAGAGGGTGGAGACG+AGG - chr1.4:67420620-67420639 MS.gene40880:CDS 60.0%


Chromosome Type Strat End Strand Name
chr1.4 gene 67419788 67421284 67419788 ID=MS.gene40880
chr1.4 mRNA 67419788 67421284 67419788 ID=MS.gene40880.t1;Parent=MS.gene40880
chr1.4 exon 67421257 67421284 67421257 ID=MS.gene40880.t1.exon1;Parent=MS.gene40880.t1
chr1.4 CDS 67421257 67421284 67421257 ID=cds.MS.gene40880.t1;Parent=MS.gene40880.t1
chr1.4 exon 67420616 67420689 67420616 ID=MS.gene40880.t1.exon2;Parent=MS.gene40880.t1
chr1.4 CDS 67420616 67420689 67420616 ID=cds.MS.gene40880.t1;Parent=MS.gene40880.t1
chr1.4 exon 67420210 67420496 67420210 ID=MS.gene40880.t1.exon3;Parent=MS.gene40880.t1
chr1.4 CDS 67420210 67420496 67420210 ID=cds.MS.gene40880.t1;Parent=MS.gene40880.t1
chr1.4 exon 67419788 67419905 67419788 ID=MS.gene40880.t1.exon4;Parent=MS.gene40880.t1
chr1.4 CDS 67419788 67419905 67419788 ID=cds.MS.gene40880.t1;Parent=MS.gene40880.t1
Gene Sequence

>MS.gene40880

ATGCTTGTATACCAGGATCTTCTTACAGGTAAATCCATCATCATCTTTGAGATTTTTTGCTTTAGTTTTCGTTTGTATTTCTTTTCATAGGATTTTGATATTGTGATGAATATTGAATACTTATTTCCTGTATTTAGTGAATGAATTTCTTGTTATGTTTTTATGCATATGTTGTTCATAATAAACCTCACTTTAGTTTTAAATAATTCTTCTTTATCTTGTTAGATAATTAATATTTTTCTAGCTGTAGAGTTTTTTTTTTTTTTTTTTTGTGATGTGTTTTGTCCCATAAAAACAGAGAAGTTTTAAGGTTTTCAAAAGAATATGAAATTTTATGTTGTTTGTGTTCTGTTGGTCTAATTTAAAGTAAAAGTTGTTGTGTTTGTGTTGTGACAGGATTAAATTTATGGTTTTATGACAAAGTGCTAAATTAATATTTTCAACCCTTAAACATGATTATCTCTTAATCTAATACTTGATTATGGATTTTAGTTTCTGAGATTGCTAACTGCTTCAAATATTAGAGATTATTGTTTTTGGTTGCTGATGGATTGAGTGAAATAATGTTTCTAACTTTGCTGACGAATTTCTTTAGGTGATGAGCTTCTCTCTGACTCATTCCCCTGCAAGGAAATTGAGAATGGAATGTTGTGGGAAGTGGAAGGAAAGGTTAGGAACAAATTTCCTTTCTATAATGTTTCTTTCTATATGCTTTATTTTTCATGTCACCAAATATATGTTCATAAATTAGCCTAAAGTTGATTGTTGTGTAATGTGATTATTTGCAGTGGGTTGTTCAAGGAGCAGTGGATGTGAATATTGGTGCTAACCCTTCTGCAGAGGGTGGAGACGAGGATGACGGTGTTGATGATCAAGCCGTCAAAGTGGTTGATATTGTTGACACTTTCAGGCTTCAGGAGCAACCAGCTTTTGATAAGAAGCAATTTGTTACTTATATGAAAAGATATATTAAGTTGCTGACATCTAAATTAGAGCCAGAAAAGCAAGAGTTGTTCAAGAAGCACATTGAAGCAGCAACTAAGTTCCTTCTCCCTAAACTCAAGGACCTACAATTGTATGTATTTCATCATTATCTTTCATCTTTTTATTTGGTTTTATTAAGTTCTCTCTTTTTTGTGGATAAATAAAGGGAAATGTTAACTTGTGCCCTTGGGGCATAAGTTAAGAAGACAAATATAGAAAGTTTTTCTTGAAACTTGTGTATTCAATGTCTAAAACGTTGCAAAAGTTATACTTTCAATGTAAAATTTATTTTTAATTTCTATTTTAATCTCTTTAACTTGTGCCCTTAGGGCACAAGTTAACATGACCCATAAATAAATAATCTTTACTGATTAAGTAATTAATCAATGTTGCAGTTTTGTTGGGGAGAGCATGCATGATGATGGAAGCCTTGTGTTTGCTTACTACAAGGATGGTGCCACTGATCCAACTTTTCTCTACTTTGCCTATGGCTTGAAGGAAATCAAGTGCTAA

Protein sequence

>MS.gene40880.t1

MLVYQDLLTGDELLSDSFPCKEIENGMLWEVEGKWVVQGAVDVNIGANPSAEGGDEDDGVDDQAVKVVDIVDTFRLQEQPAFDKKQFVTYMKRYIKLLTSKLEPEKQELFKKHIEAATKFLLPKLKDLQFFVGESMHDDGSLVFAYYKDGATDPTFLYFAYGLKEIKC