AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene77049

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene77049.t1 MTR_4g028930 93.462 260 12 3 17 275 127 382 2.46e-150 425
MS.gene77049.t1 MTR_7g072875 52.708 277 68 10 27 273 42 285 1.08e-72 224
MS.gene77049.t1 MTR_7g072630 52.878 278 66 11 27 273 104 347 1.38e-71 224
MS.gene77049.t1 MTR_5g075210 44.811 212 86 9 77 273 151 346 8.76e-42 147
MS.gene77049.t1 MTR_2g018030 60.294 68 27 0 208 275 278 345 1.07e-25 104
MS.gene77049.t1 MTR_8g087530 55.224 67 30 0 208 274 259 325 2.26e-21 92.0
MS.gene77049.t1 MTR_0907s0020 46.377 69 37 0 200 268 95 163 7.09e-16 74.3
MS.gene77049.t1 MTR_4g132740 47.761 67 35 0 205 271 79 145 4.75e-15 71.2
MS.gene77049.t1 MTR_8g103520 52.459 61 29 0 208 268 225 285 6.56e-15 73.6
MS.gene77049.t1 MTR_4g052040 49.180 61 31 0 208 268 100 160 2.27e-13 67.0
MS.gene77049.t1 MTR_7g105790 45.000 60 33 0 209 268 112 171 8.72e-13 65.9
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene77049.t1 AT2G30400 54.839 124 52 3 152 274 199 319 3.58e-31 118
MS.gene77049.t1 AT1G06920 54.206 107 43 1 165 271 207 307 3.18e-30 115
MS.gene77049.t1 AT5G01840 51.754 114 45 2 159 271 158 262 2.20e-27 107
MS.gene77049.t1 AT5G58360 50.000 114 50 2 160 273 184 290 9.35e-27 106
MS.gene77049.t1 AT4G18830 59.375 64 26 0 208 271 283 346 9.58e-20 87.8
MS.gene77049.t1 AT5G19650 53.125 64 30 0 208 271 155 218 1.17e-15 74.3
MS.gene77049.t1 AT3G52525 46.154 65 35 0 206 270 65 129 1.16e-14 70.5
MS.gene77049.t1 AT2G18500 46.032 63 34 0 209 271 228 290 2.69e-13 69.3
MS.gene77049.t1 AT4G04025 46.053 76 34 1 192 267 105 173 5.69e-13 66.2
MS.gene77049.t1 AT2G36026 50.000 56 28 0 213 268 92 147 1.41e-12 65.1

Find 43 sgRNAs with CRISPR-Local

Find 77 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ACACGGTCGGTCCTGAATTC+AGG 0.231482 4.3:-70783978 None:intergenic
TCAAGGTATTCAAGCAAATA+TGG 0.240278 4.3:+70784609 MS.gene77049:CDS
TGGTTTGATTTGACTGAAAC+AGG 0.278617 4.3:+70784629 MS.gene77049:CDS
TGATGAAACTGAACAATTCT+TGG 0.299759 4.3:-70784368 None:intergenic
CATAAGAGCATCAAAGGATT+TGG 0.303549 4.3:+70784529 MS.gene77049:CDS
AGTCCCCTGACCCTGAATTC+AGG 0.363541 4.3:+70783967 MS.gene77049:CDS
TGAACCATCGTTCGATGAAA+TGG 0.378307 4.3:+70784013 MS.gene77049:CDS
GTGTCATCGACGGTGACTTC+CGG 0.390752 4.3:+70784404 MS.gene77049:CDS
CTTGAGAGACTCTTGTTTGA+AGG 0.400641 4.3:-70784246 None:intergenic
GGAGAAGCTTCTCCGGTAAC+CGG 0.411867 4.3:-70784423 None:intergenic
AGCTTGTAAAACCAAGCATT+GGG 0.421130 4.3:-70783549 None:intergenic
CGACGGTGACTTCCGGTTAC+CGG 0.429785 4.3:+70784411 MS.gene77049:CDS
CAGATATGATTCCCAATGCT+TGG 0.444868 4.3:+70783538 MS.gene77049:CDS
AATGGTTCTGTAAATTCTCC+TGG 0.454172 4.3:+70784323 MS.gene77049:CDS
TAGCTTGTAAAACCAAGCAT+TGG 0.457451 4.3:-70783550 None:intergenic
TCGGTCCTGAATTCAGGGTC+AGG 0.466344 4.3:-70783972 None:intergenic
AGAAAAGATGATAAACTTGA+AGG 0.480676 4.3:+70784140 MS.gene77049:CDS
TTGAGAGACTCTTGTTTGAA+GGG 0.488524 4.3:-70784245 None:intergenic
GACTACCGGAGAAGCTTCTC+CGG 0.492235 4.3:-70784430 None:intergenic
AGAATTGTTCAGTTTCATCA+TGG 0.500576 4.3:+70784371 MS.gene77049:CDS
TTGTTCAGTTTCATCATGGC+CGG 0.517006 4.3:+70784375 MS.gene77049:CDS
GTTGCAAGAACAAGAAGAAG+TGG 0.529061 4.3:-70784045 None:intergenic
TTTATACGAAGTTTCACTCC+AGG 0.530998 4.3:-70784341 None:intergenic
CGGTCCTGAATTCAGGGTCA+GGG 0.533564 4.3:-70783971 None:intergenic
CACGGTCGGTCCTGAATTCA+GGG 0.533725 4.3:-70783977 None:intergenic
GAATAACATAAGAGCATCAA+AGG 0.542179 4.3:+70784523 MS.gene77049:CDS
GGTTACCGGAGAAGCTTCTC+CGG 0.543499 4.3:+70784425 MS.gene77049:CDS
TCATCGAACGATGGTTCAGT+TGG 0.543834 4.3:-70784008 None:intergenic
GTATCATGATCTTATTATCA+AGG 0.547052 4.3:+70784592 MS.gene77049:CDS
TGATTTGACTGAAACAGGGT+AGG 0.547431 4.3:+70784634 MS.gene77049:CDS
GAAAAGATGATAAACTTGAA+GGG 0.551953 4.3:+70784141 MS.gene77049:CDS
GATTTGACTGAAACAGGGTA+GGG 0.553104 4.3:+70784635 MS.gene77049:CDS
CTTCACTATTGCTAGACTAC+CGG 0.553123 4.3:-70784444 None:intergenic
GTCAATGGTGGAGATGATTG+TGG 0.584914 4.3:+70784499 MS.gene77049:CDS
GACTCTCTAAAATCCTTCTG+AGG 0.593112 4.3:-70784479 None:intergenic
GGTCCTGAATTCAGGGTCAG+GGG 0.604260 4.3:-70783970 None:intergenic
GATTCAGTTAAACTATCAAG+TGG 0.609478 4.3:-70783942 None:intergenic
CCGGAAAAGTGTGTCATCGA+CGG 0.614964 4.3:+70784394 MS.gene77049:CDS
GAAACCATTTCATCGAACGA+TGG 0.643541 4.3:-70784017 None:intergenic
AGTTGGTATCAGAACACGGT+CGG 0.669498 4.3:-70783991 None:intergenic
GGTTTGATTTGACTGAAACA+GGG 0.673887 4.3:+70784630 MS.gene77049:CDS
GAACGACGCTTGAATCAGTG+TGG 0.678886 4.3:+70783880 MS.gene77049:CDS
GTTCAGTTGGTATCAGAACA+CGG 0.691441 4.3:-70783995 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AATAACAAGAAGAAGAAAAA+TGG + chr4.3:70784305-70784324 MS.gene77049:CDS 20.0%
!!! ATTTTCTAGGATTATTACAT+TGG - chr4.3:70783692-70783711 None:intergenic 20.0%
!!! ATTTTTTGATGTTAATGTTG+TGG - chr4.3:70783805-70783824 None:intergenic 20.0%
!!! TTTTACAAGCTAAAAGAAAT+AGG + chr4.3:70783561-70783580 MS.gene77049:intron 20.0%
! AGAAAAGATGATAAACTTGA+AGG + chr4.3:70784140-70784159 MS.gene77049:CDS 25.0%
! GAAAAGATGATAAACTTGAA+GGG + chr4.3:70784141-70784160 MS.gene77049:CDS 25.0%
! GTATCATGATCTTATTATCA+AGG + chr4.3:70784592-70784611 MS.gene77049:CDS 25.0%
!! TCTTTTTCTTGTTCTGTTTT+TGG - chr4.3:70783778-70783797 None:intergenic 25.0%
!!! AAAAGGTTGTTTTTTCTTCT+TGG - chr4.3:70783619-70783638 None:intergenic 25.0%
!!! TTTGTGGTGTTTTTGTTTTT+GGG - chr4.3:70783749-70783768 None:intergenic 25.0%
!!! TTTTTGTTTTTGGGTTGTTT+TGG - chr4.3:70783740-70783759 None:intergenic 25.0%
ACAAAAGAGGTAACATGTTT+CGG - chr4.3:70783840-70783859 None:intergenic 30.0%
AGAATTGTTCAGTTTCATCA+TGG + chr4.3:70784371-70784390 MS.gene77049:CDS 30.0%
GATTCAGTTAAACTATCAAG+TGG - chr4.3:70783945-70783964 None:intergenic 30.0%
GTTGTTGAGGATAATGAAAA+AGG - chr4.3:70783636-70783655 None:intergenic 30.0%
TGATGAAACTGAACAATTCT+TGG - chr4.3:70784371-70784390 None:intergenic 30.0%
! CTAGGATTATTACATTGGTT+GGG - chr4.3:70783687-70783706 None:intergenic 30.0%
! GTGAAGTAGTAAGATTTTCT+AGG - chr4.3:70783705-70783724 None:intergenic 30.0%
! TCAAGGTATTCAAGCAAATA+TGG + chr4.3:70784609-70784628 MS.gene77049:CDS 30.0%
! TCTAGGATTATTACATTGGT+TGG - chr4.3:70783688-70783707 None:intergenic 30.0%
!! GAATAACATAAGAGCATCAA+AGG + chr4.3:70784523-70784542 MS.gene77049:CDS 30.0%
!!! ATGGTTGGTTTTGTAATGAT+AGG - chr4.3:70784209-70784228 None:intergenic 30.0%
!!! GTTTGTGGTGTTTTTGTTTT+TGG - chr4.3:70783750-70783769 None:intergenic 30.0%
!!! TTTCTTGTTCTGTTTTTGGA+TGG - chr4.3:70783774-70783793 None:intergenic 30.0%
AGCTTGTAAAACCAAGCATT+GGG - chr4.3:70783552-70783571 None:intergenic 35.0%
TTTATACGAAGTTTCACTCC+AGG - chr4.3:70784344-70784363 None:intergenic 35.0%
! AATGGTTCTGTAAATTCTCC+TGG + chr4.3:70784323-70784342 MS.gene77049:CDS 35.0%
! GAAGAAGAAGAGTTTTCATG+AGG - chr4.3:70783921-70783940 None:intergenic 35.0%
! GATTATTACATTGGTTGGGT+TGG - chr4.3:70783683-70783702 None:intergenic 35.0%
! GTCATCTTTTAATCCTCAGA+AGG + chr4.3:70784466-70784485 MS.gene77049:CDS 35.0%
! GTTGTTGTTGTTGTTGTTGT+TGG - chr4.3:70784078-70784097 None:intergenic 35.0%
! TAGCTTGTAAAACCAAGCAT+TGG - chr4.3:70783553-70783572 None:intergenic 35.0%
! TTGAGAGACTCTTGTTTGAA+GGG - chr4.3:70784248-70784267 None:intergenic 35.0%
!! CATAAGAGCATCAAAGGATT+TGG + chr4.3:70784529-70784548 MS.gene77049:CDS 35.0%
!! GAAGGATTTTAGAGAGTCAA+TGG + chr4.3:70784484-70784503 MS.gene77049:CDS 35.0%
!! GGTTTGATTTGACTGAAACA+GGG + chr4.3:70784630-70784649 MS.gene77049:CDS 35.0%
!! TGGTTTGATTTGACTGAAAC+AGG + chr4.3:70784629-70784648 MS.gene77049:CDS 35.0%
!! TTGTGCTCATTTTTCATGGT+TGG - chr4.3:70784224-70784243 None:intergenic 35.0%
!!! GGTTGTTTTTTCTTCTTGGA+AGG - chr4.3:70783615-70783634 None:intergenic 35.0%
!!! GTTGGTTTTGTAATGATAGG+AGG - chr4.3:70784206-70784225 None:intergenic 35.0%
CAGATATGATTCCCAATGCT+TGG + chr4.3:70783538-70783557 MS.gene77049:CDS 40.0%
CTTCACTATTGCTAGACTAC+CGG - chr4.3:70784447-70784466 None:intergenic 40.0%
GAAACCATTTCATCGAACGA+TGG - chr4.3:70784020-70784039 None:intergenic 40.0%
GGAATGTGTTGAAGTTGTTG+AGG - chr4.3:70783649-70783668 None:intergenic 40.0%
GTTGCAAGAACAAGAAGAAG+TGG - chr4.3:70784048-70784067 None:intergenic 40.0%
TGAACCATCGTTCGATGAAA+TGG + chr4.3:70784013-70784032 MS.gene77049:CDS 40.0%
TTGTTCAGTTTCATCATGGC+CGG + chr4.3:70784375-70784394 MS.gene77049:CDS 40.0%
! CTTGAGAGACTCTTGTTTGA+AGG - chr4.3:70784249-70784268 None:intergenic 40.0%
! GTTCAGTTGGTATCAGAACA+CGG - chr4.3:70783998-70784017 None:intergenic 40.0%
!! GACTCTCTAAAATCCTTCTG+AGG - chr4.3:70784482-70784501 None:intergenic 40.0%
!! GGATTTTAGAGAGTCAATGG+TGG + chr4.3:70784487-70784506 MS.gene77049:CDS 40.0%
!! GGGTTTGTGCTCATTTTTCA+TGG - chr4.3:70784228-70784247 None:intergenic 40.0%
!! TGGAAGGTGTTGTTGATGTT+TGG - chr4.3:70783599-70783618 None:intergenic 40.0%
!! TGTTACCTCTTTTGTTTCCG+CGG + chr4.3:70783845-70783864 MS.gene77049:intron 40.0%
!! TTACATTGGTTGGGTTGGTT+TGG - chr4.3:70783678-70783697 None:intergenic 40.0%
!!! CTGTTTTTGGATGGTGTTTG+TGG - chr4.3:70783765-70783784 None:intergenic 40.0%
TCATCGAACGATGGTTCAGT+TGG - chr4.3:70784011-70784030 None:intergenic 45.0%
! AGTTGGTATCAGAACACGGT+CGG - chr4.3:70783994-70784013 None:intergenic 45.0%
! GTCAATGGTGGAGATGATTG+TGG + chr4.3:70784499-70784518 MS.gene77049:CDS 45.0%
!! GTTACCTCTTTTGTTTCCGC+GGG + chr4.3:70783846-70783865 MS.gene77049:intron 45.0%
!!! GTTGGGTTGGTTTGGTTTTG+AGG - chr4.3:70783670-70783689 None:intergenic 45.0%
ACAACCCGCGGAAACAAAAG+AGG - chr4.3:70783853-70783872 None:intergenic 50.0%
GAACGACGCTTGAATCAGTG+TGG + chr4.3:70783880-70783899 MS.gene77049:CDS 50.0%
! CCGGAAAAGTGTGTCATCGA+CGG + chr4.3:70784394-70784413 MS.gene77049:CDS 50.0%
! CCGTCGATGACACACTTTTC+CGG - chr4.3:70784397-70784416 None:intergenic 50.0%
ACACGGTCGGTCCTGAATTC+AGG - chr4.3:70783981-70784000 None:intergenic 55.0%
AGTCCCCTGACCCTGAATTC+AGG + chr4.3:70783967-70783986 MS.gene77049:CDS 55.0%
CACGGTCGGTCCTGAATTCA+GGG - chr4.3:70783980-70783999 None:intergenic 55.0%
CGGTCCTGAATTCAGGGTCA+GGG - chr4.3:70783974-70783993 None:intergenic 55.0%
CGTTCGACAACTACAACCCG+CGG - chr4.3:70783865-70783884 None:intergenic 55.0%
GACTACCGGAGAAGCTTCTC+CGG - chr4.3:70784433-70784452 None:intergenic 55.0%
GGAGAAGCTTCTCCGGTAAC+CGG - chr4.3:70784426-70784445 None:intergenic 55.0%
GGTCCTGAATTCAGGGTCAG+GGG - chr4.3:70783973-70783992 None:intergenic 55.0%
GGTTACCGGAGAAGCTTCTC+CGG + chr4.3:70784425-70784444 MS.gene77049:CDS 55.0%
GTGTCATCGACGGTGACTTC+CGG + chr4.3:70784404-70784423 MS.gene77049:CDS 55.0%
TCGGTCCTGAATTCAGGGTC+AGG - chr4.3:70783975-70783994 None:intergenic 55.0%
CGACGGTGACTTCCGGTTAC+CGG + chr4.3:70784411-70784430 MS.gene77049:CDS 60.0%


Chromosome Type Strat End Strand Name
chr4.3 gene 70783513 70784655 70783513 ID=MS.gene77049
chr4.3 mRNA 70783513 70784655 70783513 ID=MS.gene77049.t1;Parent=MS.gene77049
chr4.3 exon 70783513 70783559 70783513 ID=MS.gene77049.t1.exon1;Parent=MS.gene77049.t1
chr4.3 CDS 70783513 70783559 70783513 ID=cds.MS.gene77049.t1;Parent=MS.gene77049.t1
chr4.3 exon 70783875 70784655 70783875 ID=MS.gene77049.t1.exon2;Parent=MS.gene77049.t1
chr4.3 CDS 70783875 70784655 70783875 ID=cds.MS.gene77049.t1;Parent=MS.gene77049.t1
Gene Sequence

>MS.gene77049

ATGAGGAATAACAAGTTTAAGCTATCAGATATGATTCCCAATGCTTGGTTTTACAAGCTAAAAGAAATAGGAAAAACAAAAAACCAAACATCAACAACACCTTCCAAGAAGAAAAAACAACCTTTTTCATTATCCTCAACAACTTCAACACATTCCTCAAAACCAAACCAACCCAACCAATGTAATAATCCTAGAAAATCTTACTACTTCACTAGAGAACTTAACCAAAACAACCCAAAAACAAAAACACCACAAACACCATCCAAAAACAGAACAAGAAAAAGAAGAACCACAACATTAACATCAAAAAATTCTTCTTCTTCTCCGAAACATGTTACCTCTTTTGTTTCCGCGGGTTGTAGTTGTCGAACGACGCTTGAATCAGTGTGGACAAAATCAGATTCTCCTCATGAAAACTCTTCTTCTTCTCCACTTGATAGTTTAACTGAATCAGAGTCCCCTGACCCTGAATTCAGGACCGACCGTGTTCTGATACCAACTGAACCATCGTTCGATGAAATGGTTTCATTAACCACTTCTTCTTGTTCTTGCAACAAAATCTCCAACAACAACAACAACAACAACAATATAGATATTGTTATTGATGTTGATAAAAATTCTCTAGCTAGAAAAGATGATAAACTTGAAGGGTATGATTATTCATATGATTCTTTTTCAAAGCTTGAACTTCCTCCTATCATTACAAAACCAACCATGAAAAATGAGCACAAACCCTTCAAACAAGAGTCTCTCAAGATTAAAATCATGAATGAACAACAACAGAAGAAGAAGAATAACAAGAAGAAGAAAAATGGTTCTGTAAATTCTCCTGGAGTGAAACTTCGTATAAAATCTCCAAGAATTGTTCAGTTTCATCATGGCCGGAAAAGTGTGTCATCGACGGTGACTTCCGGTTACCGGAGAAGCTTCTCCGGTAGTCTAGCAATAGTGAAGTCATCTTTTAATCCTCAGAAGGATTTTAGAGAGTCAATGGTGGAGATGATTGTGGAGAATAACATAAGAGCATCAAAGGATTTGGAAGATCTTCTTGCTTGTTATCTTTCTTTGAATTCAGATGAGTATCATGATCTTATTATCAAGGTATTCAAGCAAATATGGTTTGATTTGACTGAAACAGGGTAG
Protein sequence

>MS.gene77049.t1

MRNNKFKLSDMIPNACCRTTLESVWTKSDSPHENSSSSPLDSLTESESPDPEFRTDRVLIPTEPSFDEMVSLTTSSCSCNKISNNNNNNNNIDIVIDVDKNSLARKDDKLEGYDYSYDSFSKLELPPIITKPTMKNEHKPFKQESLKIKIMNEQQQKKKNNKKKKNGSVNSPGVKLRIKSPRIVQFHHGRKSVSSTVTSGYRRSFSGSLAIVKSSFNPQKDFRESMVEMIVENNIRASKDLEDLLACYLSLNSDEYHDLIIKVFKQIWFDLTETG