AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1373510


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1373510 MtrunA17_Chr4g0064971 96.525 259 6 2 1 259 1 256 0.0 516
Msa1373510 MtrunA17_Chr2g0304551 53.208 265 92 9 1 259 1 239 3.92e-83 248
Msa1373510 MtrunA17_Chr4g0003001 51.449 138 58 4 1 130 58 194 8.85e-37 130
Msa1373510 MtrunA17_Chr2g0333351 45.625 160 70 6 1 146 1 157 6.06e-33 119
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1373510 AT2G12462.1 33.929 280 133 13 1 259 1 249 9.91e-34 122
Msa1373510 AT1G15760.1 39.157 166 87 3 3 162 5 162 5.26e-31 114
Msa1373510 AT1G80520.1 51.923 104 43 2 1 98 1 103 4.59e-29 109

Find 48 sgRNAs with CRISPR-Local

Find 118 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ACTTCAATGCTTTATTATTT+TGG 0.098715 tig0019439:-27307 None:intergenic
TCACCTTTGGGTTTATTATA+AGG 0.198904 tig0019439:-27539 None:intergenic
TCAATAGCCCTACTTCTTAA+TGG 0.233145 tig0019439:-27392 None:intergenic
CCATCTAATGGTCCTGAATA+TGG 0.284057 tig0019439:-27260 None:intergenic
ATCAAAATCAAAATCACCTT+TGG 0.295369 tig0019439:-27552 None:intergenic
AATAAAGCATTGAAGTTATC+AGG 0.300318 tig0019439:+27314 Msa1373510:CDS
CATTCACTCATATATGATTA+TGG 0.310367 tig0019439:+26885 Msa1373510:CDS
GAGAATCTCTAGTCTGTGTT+TGG 0.350721 tig0019439:-26994 None:intergenic
TTCATCAATCTTCCATCAAT+TGG 0.355382 tig0019439:-27338 None:intergenic
ACAGAATTCCTTGTAATAGT+TGG 0.363635 tig0019439:-27485 None:intergenic
AGCAGAACAATGCCATATTC+AGG 0.374090 tig0019439:+27248 Msa1373510:CDS
TTCCAACTGAAGCTCATTGC+GGG 0.374523 tig0019439:-26919 None:intergenic
TCAAAATCAAAATCACCTTT+GGG 0.389288 tig0019439:-27551 None:intergenic
TCCAAGAGTATCTGGTCCTT+TGG 0.396596 tig0019439:+27433 Msa1373510:CDS
TCATGCATTCTTCCATCTAA+TGG 0.401833 tig0019439:-27272 None:intergenic
AAGTTATCAGGACCAATTGA+TGG 0.410093 tig0019439:+27326 Msa1373510:CDS
CCATATTCAGGACCATTAGA+TGG 0.411197 tig0019439:+27260 Msa1373510:CDS
ACCAAGAGTCCAAGAGTATC+TGG 0.415806 tig0019439:+27425 Msa1373510:CDS
ATAGAAGTCCATTAAGAAGT+AGG 0.426654 tig0019439:+27384 Msa1373510:CDS
ACCAGATACTCTTGGACTCT+TGG 0.427252 tig0019439:-27426 None:intergenic
ATTGTTCTGCTTCTATACAT+AGG 0.436227 tig0019439:-27236 None:intergenic
AAGAATGCATGAGCAGAAAA+TGG 0.442330 tig0019439:+27283 Msa1373510:CDS
TGGTTCTACACGAACCGAAT+TGG 0.445561 tig0019439:+27159 Msa1373510:CDS
TGTTGAAACTGATAGCCCTA+TGG 0.446699 tig0019439:+27505 Msa1373510:CDS
TTAAGAAGTAGGGCTATTGA+TGG 0.487712 tig0019439:+27395 Msa1373510:CDS
TCGTGTAGAACCACAGGTAA+AGG 0.487940 tig0019439:-27149 None:intergenic
CATAATCATATATGAGTGAA+TGG 0.492231 tig0019439:-26884 None:intergenic
CCATGCTTTGTAGAAACTCA+TGG 0.497469 tig0019439:-26959 None:intergenic
TTGATGATGAACATTCACTT+TGG 0.513853 tig0019439:+27570 Msa1373510:CDS
GTTGAAACTGATAGCCCTAT+GGG 0.514418 tig0019439:+27506 Msa1373510:CDS
CCATGAGTTTCTACAAAGCA+TGG 0.527981 tig0019439:+26959 Msa1373510:CDS
TAGAAGTCCATTAAGAAGTA+GGG 0.530916 tig0019439:+27385 Msa1373510:CDS
TCCAAAGGACCAGATACTCT+TGG 0.532457 tig0019439:-27434 None:intergenic
TTCCCGCAATGAGCTTCAGT+TGG 0.551524 tig0019439:+26917 Msa1373510:CDS
TTCGGTTCGTGTAGAACCAC+AGG 0.553276 tig0019439:-27155 None:intergenic
TAAGGACTACTATAACCCAT+AGG 0.553316 tig0019439:-27521 None:intergenic
CATGAGTTTCTACAAAGCAT+GGG 0.601787 tig0019439:+26960 Msa1373510:CDS
CTTCCAACTGAAGCTCATTG+CGG 0.606732 tig0019439:-26920 None:intergenic
ATTGATGAATGAGAGAATGA+TGG 0.606802 tig0019439:+27352 Msa1373510:CDS
AAGGACTACTATAACCCATA+GGG 0.607941 tig0019439:-27520 None:intergenic
TTAAGATCTTGAAAGAGTGT+AGG 0.613928 tig0019439:-27593 None:intergenic
TAACCATGAAAACCAGTCCA+TGG 0.615491 tig0019439:-26844 None:intergenic
AGTCCTTATAATAAACCCAA+AGG 0.617768 tig0019439:+27536 Msa1373510:CDS
ATGGAGAGGAGCATTGGTCA+AGG 0.622754 tig0019439:+27196 Msa1373510:CDS
GCTCATTGCGGGAAAAGATG+AGG 0.624567 tig0019439:-26908 None:intergenic
ACGAACCGAATTGGTACCAA+GGG 0.628752 tig0019439:+27168 Msa1373510:CDS
ATAGAAGTCCAACTATTACA+AGG 0.630633 tig0019439:+27477 Msa1373510:CDS
CACGAACCGAATTGGTACCA+AGG 0.659621 tig0019439:+27167 Msa1373510:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTTTTTTAGACACTTTTTGA+TGG - tig0019439:27081-27100 None:intergenic 20.0%
!!! ACTTCAATGCTTTATTATTT+TGG - tig0019439:27310-27329 None:intergenic 20.0%
!!! TTTTTTTAGACACTTTTTGA+TGG - tig0019439:27081-27100 None:intergenic 20.0%
!!! ACTTCAATGCTTTATTATTT+TGG - tig0019439:27310-27329 None:intergenic 20.0%
! CATAATCATATATGAGTGAA+TGG - tig0019439:26887-26906 None:intergenic 25.0%
! CATTCACTCATATATGATTA+TGG + tig0019439:26885-26904 Msa1373510:CDS 25.0%
!!! AATAAAGCATTGAAGTTATC+AGG + tig0019439:27314-27333 Msa1373510:CDS 25.0%
! TCAAAATCAAAATCACCTTT+GGG - tig0019439:27554-27573 None:intergenic 25.0%
! ATCAAAATCAAAATCACCTT+TGG - tig0019439:27555-27574 None:intergenic 25.0%
! CATAATCATATATGAGTGAA+TGG - tig0019439:26887-26906 None:intergenic 25.0%
! CATTCACTCATATATGATTA+TGG + tig0019439:26885-26904 Msa1373510:CDS 25.0%
!!! AATAAAGCATTGAAGTTATC+AGG + tig0019439:27314-27333 Msa1373510:CDS 25.0%
! TCAAAATCAAAATCACCTTT+GGG - tig0019439:27554-27573 None:intergenic 25.0%
! ATCAAAATCAAAATCACCTT+TGG - tig0019439:27555-27574 None:intergenic 25.0%
ATTGTTCTGCTTCTATACAT+AGG - tig0019439:27239-27258 None:intergenic 30.0%
TTCATCAATCTTCCATCAAT+TGG - tig0019439:27341-27360 None:intergenic 30.0%
ATTGATGAATGAGAGAATGA+TGG + tig0019439:27352-27371 Msa1373510:CDS 30.0%
ATAGAAGTCCATTAAGAAGT+AGG + tig0019439:27384-27403 Msa1373510:CDS 30.0%
TAGAAGTCCATTAAGAAGTA+GGG + tig0019439:27385-27404 Msa1373510:CDS 30.0%
!! AACATGATTTTAGCATCCAA+AGG - tig0019439:27452-27471 None:intergenic 30.0%
ATAGAAGTCCAACTATTACA+AGG + tig0019439:27477-27496 Msa1373510:CDS 30.0%
ACAGAATTCCTTGTAATAGT+TGG - tig0019439:27488-27507 None:intergenic 30.0%
AGTCCTTATAATAAACCCAA+AGG + tig0019439:27536-27555 Msa1373510:CDS 30.0%
! TCACCTTTGGGTTTATTATA+AGG - tig0019439:27542-27561 None:intergenic 30.0%
!! TTGATGATGAACATTCACTT+TGG + tig0019439:27570-27589 Msa1373510:CDS 30.0%
! TTAAGATCTTGAAAGAGTGT+AGG - tig0019439:27596-27615 None:intergenic 30.0%
ATTGTTCTGCTTCTATACAT+AGG - tig0019439:27239-27258 None:intergenic 30.0%
TTCATCAATCTTCCATCAAT+TGG - tig0019439:27341-27360 None:intergenic 30.0%
ATTGATGAATGAGAGAATGA+TGG + tig0019439:27352-27371 Msa1373510:CDS 30.0%
ATAGAAGTCCATTAAGAAGT+AGG + tig0019439:27384-27403 Msa1373510:CDS 30.0%
TAGAAGTCCATTAAGAAGTA+GGG + tig0019439:27385-27404 Msa1373510:CDS 30.0%
!! AACATGATTTTAGCATCCAA+AGG - tig0019439:27452-27471 None:intergenic 30.0%
ATAGAAGTCCAACTATTACA+AGG + tig0019439:27477-27496 Msa1373510:CDS 30.0%
ACAGAATTCCTTGTAATAGT+TGG - tig0019439:27488-27507 None:intergenic 30.0%
AGTCCTTATAATAAACCCAA+AGG + tig0019439:27536-27555 Msa1373510:CDS 30.0%
! TCACCTTTGGGTTTATTATA+AGG - tig0019439:27542-27561 None:intergenic 30.0%
!! TTGATGATGAACATTCACTT+TGG + tig0019439:27570-27589 Msa1373510:CDS 30.0%
! TTAAGATCTTGAAAGAGTGT+AGG - tig0019439:27596-27615 None:intergenic 30.0%
CATGAGTTTCTACAAAGCAT+GGG + tig0019439:26960-26979 Msa1373510:CDS 35.0%
!!! GAAAGGTTTTTTGGTCGTAA+TGG - tig0019439:27053-27072 None:intergenic 35.0%
TTACGACCAAAAAACCTTTC+TGG + tig0019439:27053-27072 Msa1373510:CDS 35.0%
!!! ATGGTACCAGAAAGGTTTTT+TGG - tig0019439:27062-27081 None:intergenic 35.0%
!! ACTTTTTGATGGTACCAGAA+AGG - tig0019439:27070-27089 None:intergenic 35.0%
TCATGCATTCTTCCATCTAA+TGG - tig0019439:27275-27294 None:intergenic 35.0%
AAGAATGCATGAGCAGAAAA+TGG + tig0019439:27283-27302 Msa1373510:CDS 35.0%
AAGTTATCAGGACCAATTGA+TGG + tig0019439:27326-27345 Msa1373510:CDS 35.0%
TCAATAGCCCTACTTCTTAA+TGG - tig0019439:27395-27414 None:intergenic 35.0%
TTAAGAAGTAGGGCTATTGA+TGG + tig0019439:27395-27414 Msa1373510:CDS 35.0%
AAGGACTACTATAACCCATA+GGG - tig0019439:27523-27542 None:intergenic 35.0%
TAAGGACTACTATAACCCAT+AGG - tig0019439:27524-27543 None:intergenic 35.0%
CATGAGTTTCTACAAAGCAT+GGG + tig0019439:26960-26979 Msa1373510:CDS 35.0%
!!! GAAAGGTTTTTTGGTCGTAA+TGG - tig0019439:27053-27072 None:intergenic 35.0%
TTACGACCAAAAAACCTTTC+TGG + tig0019439:27053-27072 Msa1373510:CDS 35.0%
!!! ATGGTACCAGAAAGGTTTTT+TGG - tig0019439:27062-27081 None:intergenic 35.0%
!! ACTTTTTGATGGTACCAGAA+AGG - tig0019439:27070-27089 None:intergenic 35.0%
TCATGCATTCTTCCATCTAA+TGG - tig0019439:27275-27294 None:intergenic 35.0%
AAGAATGCATGAGCAGAAAA+TGG + tig0019439:27283-27302 Msa1373510:CDS 35.0%
AAGTTATCAGGACCAATTGA+TGG + tig0019439:27326-27345 Msa1373510:CDS 35.0%
TCAATAGCCCTACTTCTTAA+TGG - tig0019439:27395-27414 None:intergenic 35.0%
TTAAGAAGTAGGGCTATTGA+TGG + tig0019439:27395-27414 Msa1373510:CDS 35.0%
AAGGACTACTATAACCCATA+GGG - tig0019439:27523-27542 None:intergenic 35.0%
TAAGGACTACTATAACCCAT+AGG - tig0019439:27524-27543 None:intergenic 35.0%
CCATGCTTTGTAGAAACTCA+TGG - tig0019439:26962-26981 None:intergenic 40.0%
CCATGAGTTTCTACAAAGCA+TGG + tig0019439:26959-26978 Msa1373510:CDS 40.0%
GAGAATCTCTAGTCTGTGTT+TGG - tig0019439:26997-27016 None:intergenic 40.0%
GAAAAACATGCCTTTACCTG+TGG + tig0019439:27139-27158 Msa1373510:CDS 40.0%
! TTTTGCCCTTGGTACCAATT+CGG - tig0019439:27176-27195 None:intergenic 40.0%
ATTGGTACCAAGGGCAAAAA+TGG + tig0019439:27177-27196 Msa1373510:CDS 40.0%
AGCAGAACAATGCCATATTC+AGG + tig0019439:27248-27267 Msa1373510:CDS 40.0%
CCATCTAATGGTCCTGAATA+TGG - tig0019439:27263-27282 None:intergenic 40.0%
CCATATTCAGGACCATTAGA+TGG + tig0019439:27260-27279 Msa1373510:CDS 40.0%
TGTTGAAACTGATAGCCCTA+TGG + tig0019439:27505-27524 Msa1373510:CDS 40.0%
GTTGAAACTGATAGCCCTAT+GGG + tig0019439:27506-27525 Msa1373510:CDS 40.0%
CCATGCTTTGTAGAAACTCA+TGG - tig0019439:26962-26981 None:intergenic 40.0%
CCATGAGTTTCTACAAAGCA+TGG + tig0019439:26959-26978 Msa1373510:CDS 40.0%
GAGAATCTCTAGTCTGTGTT+TGG - tig0019439:26997-27016 None:intergenic 40.0%
GAAAAACATGCCTTTACCTG+TGG + tig0019439:27139-27158 Msa1373510:CDS 40.0%
! TTTTGCCCTTGGTACCAATT+CGG - tig0019439:27176-27195 None:intergenic 40.0%
ATTGGTACCAAGGGCAAAAA+TGG + tig0019439:27177-27196 Msa1373510:CDS 40.0%
AGCAGAACAATGCCATATTC+AGG + tig0019439:27248-27267 Msa1373510:CDS 40.0%
CCATCTAATGGTCCTGAATA+TGG - tig0019439:27263-27282 None:intergenic 40.0%
CCATATTCAGGACCATTAGA+TGG + tig0019439:27260-27279 Msa1373510:CDS 40.0%
TGTTGAAACTGATAGCCCTA+TGG + tig0019439:27505-27524 Msa1373510:CDS 40.0%
GTTGAAACTGATAGCCCTAT+GGG + tig0019439:27506-27525 Msa1373510:CDS 40.0%
TTCCAACTGAAGCTCATTGC+GGG - tig0019439:26922-26941 None:intergenic 45.0%
CTTCCAACTGAAGCTCATTG+CGG - tig0019439:26923-26942 None:intergenic 45.0%
TCGTGTAGAACCACAGGTAA+AGG - tig0019439:27152-27171 None:intergenic 45.0%
! TGGTTCTACACGAACCGAAT+TGG + tig0019439:27159-27178 Msa1373510:CDS 45.0%
ACGAACCGAATTGGTACCAA+GGG + tig0019439:27168-27187 Msa1373510:CDS 45.0%
TACCAAGGGCAAAAATGGAG+AGG + tig0019439:27182-27201 Msa1373510:CDS 45.0%
! GCAAAAATGGAGAGGAGCAT+TGG + tig0019439:27190-27209 Msa1373510:CDS 45.0%
!! ACCAAGAGTCCAAGAGTATC+TGG + tig0019439:27425-27444 Msa1373510:CDS 45.0%
ACCAGATACTCTTGGACTCT+TGG - tig0019439:27429-27448 None:intergenic 45.0%
!! TCCAAGAGTATCTGGTCCTT+TGG + tig0019439:27433-27452 Msa1373510:CDS 45.0%
TCCAAAGGACCAGATACTCT+TGG - tig0019439:27437-27456 None:intergenic 45.0%
TTCCAACTGAAGCTCATTGC+GGG - tig0019439:26922-26941 None:intergenic 45.0%
CTTCCAACTGAAGCTCATTG+CGG - tig0019439:26923-26942 None:intergenic 45.0%
TCGTGTAGAACCACAGGTAA+AGG - tig0019439:27152-27171 None:intergenic 45.0%
! TGGTTCTACACGAACCGAAT+TGG + tig0019439:27159-27178 Msa1373510:CDS 45.0%
ACGAACCGAATTGGTACCAA+GGG + tig0019439:27168-27187 Msa1373510:CDS 45.0%
TACCAAGGGCAAAAATGGAG+AGG + tig0019439:27182-27201 Msa1373510:CDS 45.0%
! GCAAAAATGGAGAGGAGCAT+TGG + tig0019439:27190-27209 Msa1373510:CDS 45.0%
!! ACCAAGAGTCCAAGAGTATC+TGG + tig0019439:27425-27444 Msa1373510:CDS 45.0%
ACCAGATACTCTTGGACTCT+TGG - tig0019439:27429-27448 None:intergenic 45.0%
!! TCCAAGAGTATCTGGTCCTT+TGG + tig0019439:27433-27452 Msa1373510:CDS 45.0%
TCCAAAGGACCAGATACTCT+TGG - tig0019439:27437-27456 None:intergenic 45.0%
GCTCATTGCGGGAAAAGATG+AGG - tig0019439:26911-26930 None:intergenic 50.0%
TTCCCGCAATGAGCTTCAGT+TGG + tig0019439:26917-26936 Msa1373510:CDS 50.0%
! TTCGGTTCGTGTAGAACCAC+AGG - tig0019439:27158-27177 None:intergenic 50.0%
CACGAACCGAATTGGTACCA+AGG + tig0019439:27167-27186 Msa1373510:CDS 50.0%
!! CTCCTCTCCATTTTTGCCCT+TGG - tig0019439:27187-27206 None:intergenic 50.0%
!! ATGGAGAGGAGCATTGGTCA+AGG + tig0019439:27196-27215 Msa1373510:CDS 50.0%
GCTCATTGCGGGAAAAGATG+AGG - tig0019439:26911-26930 None:intergenic 50.0%
TTCCCGCAATGAGCTTCAGT+TGG + tig0019439:26917-26936 Msa1373510:CDS 50.0%
! TTCGGTTCGTGTAGAACCAC+AGG - tig0019439:27158-27177 None:intergenic 50.0%
CACGAACCGAATTGGTACCA+AGG + tig0019439:27167-27186 Msa1373510:CDS 50.0%
!! CTCCTCTCCATTTTTGCCCT+TGG - tig0019439:27187-27206 None:intergenic 50.0%
!! ATGGAGAGGAGCATTGGTCA+AGG + tig0019439:27196-27215 Msa1373510:CDS 50.0%
Chromosome Type Strat End Strand Name
tig0019439 gene 26846 27625 26846 ID=Msa1373510;Name=Msa1373510
tig0019439 mRNA 26846 27625 26846 ID=Msa1373510-mRNA-1;Parent=Msa1373510;Name=Msa1373510-mRNA-1;_AED=0.00;_eAED=0.00;_QI=0|-1|0|1|-1|1|1|0|259
tig0019439 exon 26846 27625 26846 ID=Msa1373510-mRNA-1:exon:3356;Parent=Msa1373510-mRNA-1
tig0019439 CDS 26846 27625 26846 ID=Msa1373510-mRNA-1:cds;Parent=Msa1373510-mRNA-1
Gene Sequence

>Msa1373510

ATGGACTGGTTTTCATGGTTATCAAAAACAACTCTTGACCATTCACTCATATATGATTATGGCCTCATCTTTTCCCGCAATGAGCTTCAGTTGGAAGATGCAACTTACTTCAACCATGAGTTTCTACAAAGCATGGGAATCTCAATAGCCAAACACAGACTAGAGATTCTCAAACTAGTCAAAAAAGAACAAGAACTTGATCAACCATTACGACCAAAAAACCTTTCTGGTACCATCAAAAAGTGTCTAAAAAAATGCATGAGCAAGTTTGTTTTTCGCGACGATAGTGTTAAGAAAAACATGCCTTTACCTGTGGTTCTACACGAACCGAATTGGTACCAAGGGCAAAAATGGAGAGGAGCATTGGTCAAGGAAGAGAAGCATCAGAAACCTATGTATAGAAGCAGAACAATGCCATATTCAGGACCATTAGATGGAAGAATGCATGAGCAGAAAATGGTCCAAAATAATAAAGCATTGAAGTTATCAGGACCAATTGATGGAAGATTGATGAATGAGAGAATGATGGTGTATACTAATAGAAGTCCATTAAGAAGTAGGGCTATTGATGGAAGATTCACCAAGAGTCCAAGAGTATCTGGTCCTTTGGATGCTAAAATCATGTTTGAGAATAGAAGTCCAACTATTACAAGGAATTCTGTTGAAACTGATAGCCCTATGGGTTATAGTAGTCCTTATAATAAACCCAAAGGTGATTTTGATTTTGATGATGAACATTCACTTTGGCCTACACTCTTTCAAGATCTTAATCCAACTTGA

Protein sequence

>Msa1373510

MDWFSWLSKTTLDHSLIYDYGLIFSRNELQLEDATYFNHEFLQSMGISIAKHRLEILKLVKKEQELDQPLRPKNLSGTIKKCLKKCMSKFVFRDDSVKKNMPLPVVLHEPNWYQGQKWRGALVKEEKHQKPMYRSRTMPYSGPLDGRMHEQKMVQNNKALKLSGPIDGRLMNERMMVYTNRSPLRSRAIDGRFTKSPRVSGPLDAKIMFENRSPTITRNSVETDSPMGYSSPYNKPKGDFDFDDEHSLWPTLFQDLNPT*