AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene001119

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene001119.t1 MTR_5g027020 93.557 357 22 1 1 356 1 357 0.0 696
MS.gene001119.t1 MTR_1g038390 50.649 77 33 2 220 291 4 80 2.06e-18 80.9
MS.gene001119.t1 MTR_3g073000 23.098 368 194 16 10 351 13 317 4.10e-13 70.1
MS.gene001119.t1 MTR_3g073000 23.098 368 194 16 10 351 13 317 4.59e-13 70.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene001119.t1 AT2G19640 44.103 390 166 7 8 353 11 392 1.63e-112 333
MS.gene001119.t1 AT2G19640 47.525 303 143 6 8 302 11 305 1.41e-95 288
MS.gene001119.t1 AT2G17900 23.810 336 210 15 10 336 18 316 6.56e-13 70.1

Find 65 sgRNAs with CRISPR-Local

Find 88 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTCAACCTCTCTCTTGAAAT+TGG 0.182162 5.2:+18016241 MS.gene001119:CDS
GTAAATTCCATAAGCCTTAA+TGG 0.186663 5.2:-18016849 None:intergenic
GGGATTCAGTGAGGATTATT+TGG 0.209184 5.2:-18016319 None:intergenic
GAAAGTAAAGTTTGAAGTTT+TGG 0.250619 5.2:-18016638 None:intergenic
CTGAAGCAGTTGTGACAATA+AGG 0.255076 5.2:-18016389 None:intergenic
CAAAGATCCATTAAGGCTTA+TGG 0.268080 5.2:+18016842 MS.gene001119:CDS
TGGATCTTTGAGGACCCTTT+TGG 0.292191 5.2:-18016829 None:intergenic
AGGATCTTGATGGATGATTA+TGG 0.293055 5.2:+18017058 MS.gene001119:CDS
CAAACTTTACTTTCACTTCA+TGG 0.305377 5.2:+18016647 MS.gene001119:CDS
TAATCAAATCTGCATGCATT+AGG 0.315519 5.2:-18016905 None:intergenic
TGAGATCTTGTGTTGCAATA+AGG 0.317003 5.2:-18016289 None:intergenic
TTCATGTGGGGTGGACAAAA+AGG 0.320238 5.2:-18016731 None:intergenic
GAAAGTTGACCCTGCTACTT+AGG 0.333316 5.2:+18017276 MS.gene001119:CDS
AAACTTAGCATTATCAACTA+TGG 0.347178 5.2:-18016690 None:intergenic
GGTGCAAGATTGAAGCAAAT+TGG 0.355945 5.2:+18017101 MS.gene001119:CDS
ATAAGGCCTCTACCTTTGTT+AGG 0.358422 5.2:-18016272 None:intergenic
GGGTCCTCAAAGATCCATTA+AGG 0.360632 5.2:+18016835 MS.gene001119:CDS
ATCTAAGTTTGTTTGTGATA+AGG 0.371788 5.2:+18017168 MS.gene001119:CDS
GGAGAATTGTGCAGGTACTA+TGG 0.393146 5.2:+18017189 MS.gene001119:CDS
ACTATGGAATCATGATCATT+AGG 0.397254 5.2:-18016674 None:intergenic
AATCAAATCTGCATGCATTA+GGG 0.408868 5.2:-18016904 None:intergenic
CCAAATAAGACCTAAGTAGC+AGG 0.442970 5.2:-18017286 None:intergenic
ATTGAAGCAAATTGGAATGA+TGG 0.446384 5.2:+18017109 MS.gene001119:CDS
AATGGAACCTTATACCCAAA+AGG 0.447342 5.2:+18016814 MS.gene001119:CDS
GTGAGAGGAATTGAGGGCAT+TGG 0.448917 5.2:-18016486 None:intergenic
AACAAGGAAAAGGATCTTGA+TGG 0.451958 5.2:+18017048 MS.gene001119:CDS
AGGATTATTCAACAAGGAAA+AGG 0.476736 5.2:+18017038 MS.gene001119:CDS
TCAATTCCTCTCACTCATCT+TGG 0.489766 5.2:+18016495 MS.gene001119:CDS
TAGCAGAATAGAGAAGAAGA+GGG 0.491920 5.2:-18016340 None:intergenic
AAGATGAGTGAGAGGAATTG+AGG 0.492387 5.2:-18016493 None:intergenic
AGATGAGTGAGAGGAATTGA+GGG 0.494037 5.2:-18016492 None:intergenic
TGCATGCAGATTTGATTATG+TGG 0.500019 5.2:+18016910 MS.gene001119:CDS
ATGGAACCTTATACCCAAAA+GGG 0.516328 5.2:+18016815 MS.gene001119:CDS
TGAAGCAGTTGTGACAATAA+GGG 0.517249 5.2:-18016388 None:intergenic
GTAGCAGAATAGAGAAGAAG+AGG 0.521798 5.2:-18016341 None:intergenic
GCTCCTCTGCCTCCAAAAGA+TGG 0.525196 5.2:+18017211 MS.gene001119:CDS
TAAGCCTTAATGGATCTTTG+AGG 0.528933 5.2:-18016839 None:intergenic
CATGGAAATGTTTGTGAAGG+TGG 0.530274 5.2:-18016419 None:intergenic
GAAGAAGAGGGGATTCAGTG+AGG 0.537045 5.2:-18016328 None:intergenic
TTGATTAAGGATGTTGCTGT+TGG 0.542851 5.2:+18016980 MS.gene001119:CDS
AGCAGAATAGAGAAGAAGAG+GGG 0.546586 5.2:-18016339 None:intergenic
AAAAGGTAGTTTGAGCAAGA+AGG 0.551661 5.2:-18016443 None:intergenic
AAATGTTTGTGAAGGTGGTA+AGG 0.557933 5.2:-18016414 None:intergenic
TTTCTGATAATGGTGAAGTG+GGG 0.567781 5.2:-18016547 None:intergenic
GCAACACAAGATCTCAAAGC+TGG 0.580231 5.2:+18016296 MS.gene001119:CDS
CACATACCTAACAAAGGTAG+AGG 0.580606 5.2:+18016266 MS.gene001119:CDS
GAGGGTGTATGAGAGAAAAG+AGG 0.582689 5.2:-18016365 None:intergenic
GAAGCAGTTGTGACAATAAG+GGG 0.584478 5.2:-18016387 None:intergenic
GTGCTCCAATTTCAAGAGAG+AGG 0.586066 5.2:-18016246 None:intergenic
TGTGATAAGGAGAATTGTGC+AGG 0.587133 5.2:+18017181 MS.gene001119:CDS
TAGTTTGAGCAAGAAGGACA+TGG 0.592796 5.2:-18016437 None:intergenic
AGATTTGATTATGTGGAAAG+TGG 0.595188 5.2:+18016917 MS.gene001119:CDS
TATGTGGAAAGTGGTGAACC+TGG 0.596809 5.2:+18016926 MS.gene001119:CDS
TCAATATTATGTTCATCACC+AGG 0.599920 5.2:-18016944 None:intergenic
CAAATAAGACCTAAGTAGCA+GGG 0.606280 5.2:-18017285 None:intergenic
ACATGACCAAGATGAGTGAG+AGG 0.606296 5.2:-18016501 None:intergenic
AGGAATTGAGGGCATTGGAG+AGG 0.625591 5.2:-18016481 None:intergenic
GCTTGAACTTGAAGTTCACA+AGG 0.648973 5.2:-18016572 None:intergenic
CAGTTGTGACAATAAGGGGA+GGG 0.650828 5.2:-18016383 None:intergenic
GCAGTTGTGACAATAAGGGG+AGG 0.655954 5.2:-18016384 None:intergenic
GGACATGGAAATGTTTGTGA+AGG 0.669839 5.2:-18016422 None:intergenic
TTGGAGCACATACCTAACAA+AGG 0.675712 5.2:+18016260 MS.gene001119:CDS
TTAGATAAGAAAATCACATG+TGG 0.682821 5.2:-18017151 None:intergenic
ATGCATTAGGGATACAACCA+TGG 0.710306 5.2:-18016892 None:intergenic
TTAATAAGGATTATTCAACA+AGG 0.719519 5.2:+18017032 MS.gene001119:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ATAATATTGATATTGTTTTT+AGG + chr5.2:18016957-18016976 MS.gene001119:CDS 10.0%
!! TTAATAAGGATTATTCAACA+AGG + chr5.2:18017032-18017051 MS.gene001119:CDS 20.0%
!!! AAGCTATTTTAGGATTAATA+AGG + chr5.2:18017018-18017037 MS.gene001119:CDS 20.0%
!!! AGATTTGTATAAGCTATTTT+AGG + chr5.2:18017008-18017027 MS.gene001119:CDS 20.0%
!!! ATTAAACTCTTTTTGCTTAA+TGG + chr5.2:18016796-18016815 MS.gene001119:CDS 20.0%
!!! TATTGTTTTTAGGTTGATTA+AGG + chr5.2:18016967-18016986 MS.gene001119:CDS 20.0%
! AAACTTAGCATTATCAACTA+TGG - chr5.2:18016693-18016712 None:intergenic 25.0%
! TTAGATAAGAAAATCACATG+TGG - chr5.2:18017154-18017173 None:intergenic 25.0%
!! ATCTAAGTTTGTTTGTGATA+AGG + chr5.2:18017168-18017187 MS.gene001119:CDS 25.0%
!! GGTTAAAAAAAGTAGCTTTT+TGG - chr5.2:18016874-18016893 None:intergenic 25.0%
!! TTAGATTTTTCACCATCTTT+TGG - chr5.2:18017226-18017245 None:intergenic 25.0%
!!! AAAGCTACTTTTTTTAACCA+TGG + chr5.2:18016875-18016894 MS.gene001119:CDS 25.0%
!!! GAAAGTAAAGTTTGAAGTTT+TGG - chr5.2:18016641-18016660 None:intergenic 25.0%
AATCAAATCTGCATGCATTA+GGG - chr5.2:18016907-18016926 None:intergenic 30.0%
ACTATGGAATCATGATCATT+AGG - chr5.2:18016677-18016696 None:intergenic 30.0%
AGATTTGATTATGTGGAAAG+TGG + chr5.2:18016917-18016936 MS.gene001119:CDS 30.0%
AGGATTATTCAACAAGGAAA+AGG + chr5.2:18017038-18017057 MS.gene001119:CDS 30.0%
ATTGAAGCAAATTGGAATGA+TGG + chr5.2:18017109-18017128 MS.gene001119:CDS 30.0%
CAAACTTTACTTTCACTTCA+TGG + chr5.2:18016647-18016666 MS.gene001119:CDS 30.0%
GTAAATTCCATAAGCCTTAA+TGG - chr5.2:18016852-18016871 None:intergenic 30.0%
TAATCAAATCTGCATGCATT+AGG - chr5.2:18016908-18016927 None:intergenic 30.0%
TCAATATTATGTTCATCACC+AGG - chr5.2:18016947-18016966 None:intergenic 30.0%
TTCAGCTGAAAAATTCATGT+GGG - chr5.2:18016747-18016766 None:intergenic 30.0%
! TCACAAGGTTTTTCTGATAA+TGG - chr5.2:18016560-18016579 None:intergenic 30.0%
!! AGTAAAGTTTGAAGTTTTGG+AGG - chr5.2:18016638-18016657 None:intergenic 30.0%
!!! GTAAAGTTTGAAGTTTTGGA+GGG - chr5.2:18016637-18016656 None:intergenic 30.0%
!!! TAAAGTTTGAAGTTTTGGAG+GGG - chr5.2:18016636-18016655 None:intergenic 30.0%
!!! TTTTCTGATAATGGTGAAGT+GGG - chr5.2:18016551-18016570 None:intergenic 30.0%
!!! TTTTTCTGATAATGGTGAAG+TGG - chr5.2:18016552-18016571 None:intergenic 30.0%
AAAAGGTAGTTTGAGCAAGA+AGG - chr5.2:18016446-18016465 None:intergenic 35.0%
AAATGTTTGTGAAGGTGGTA+AGG - chr5.2:18016417-18016436 None:intergenic 35.0%
AACAAGGAAAAGGATCTTGA+TGG + chr5.2:18017048-18017067 MS.gene001119:CDS 35.0%
AATGGAACCTTATACCCAAA+AGG + chr5.2:18016814-18016833 MS.gene001119:CDS 35.0%
ATGGAACCTTATACCCAAAA+GGG + chr5.2:18016815-18016834 MS.gene001119:CDS 35.0%
CAAAGATCCATTAAGGCTTA+TGG + chr5.2:18016842-18016861 MS.gene001119:CDS 35.0%
GTTCAGCTGAAAAATTCATG+TGG - chr5.2:18016748-18016767 None:intergenic 35.0%
TAGCAGAATAGAGAAGAAGA+GGG - chr5.2:18016343-18016362 None:intergenic 35.0%
TCAGCTGAAAAATTCATGTG+GGG - chr5.2:18016746-18016765 None:intergenic 35.0%
TGAAGCAGTTGTGACAATAA+GGG - chr5.2:18016391-18016410 None:intergenic 35.0%
TGAGATCTTGTGTTGCAATA+AGG - chr5.2:18016292-18016311 None:intergenic 35.0%
TGCATGCAGATTTGATTATG+TGG + chr5.2:18016910-18016929 MS.gene001119:CDS 35.0%
TTCAACCTCTCTCTTGAAAT+TGG + chr5.2:18016241-18016260 MS.gene001119:CDS 35.0%
TTGATTAAGGATGTTGCTGT+TGG + chr5.2:18016980-18016999 MS.gene001119:CDS 35.0%
! AGGATCTTGATGGATGATTA+TGG + chr5.2:18017058-18017077 MS.gene001119:CDS 35.0%
! GATTTTTCACCATCTTTTGG+AGG - chr5.2:18017223-18017242 None:intergenic 35.0%
! GTTCTTGAGTGTAACTTTTG+TGG + chr5.2:18017247-18017266 MS.gene001119:CDS 35.0%
! GTTTTGCTTGTGAATGTGAT+AGG + chr5.2:18017080-18017099 MS.gene001119:CDS 35.0%
! TAAGCCTTAATGGATCTTTG+AGG - chr5.2:18016842-18016861 None:intergenic 35.0%
!! TTTCTGATAATGGTGAAGTG+GGG - chr5.2:18016550-18016569 None:intergenic 35.0%
AAGATGAGTGAGAGGAATTG+AGG - chr5.2:18016496-18016515 None:intergenic 40.0%
AGATGAGTGAGAGGAATTGA+GGG - chr5.2:18016495-18016514 None:intergenic 40.0%
AGCAGAATAGAGAAGAAGAG+GGG - chr5.2:18016342-18016361 None:intergenic 40.0%
ATAAGGCCTCTACCTTTGTT+AGG - chr5.2:18016275-18016294 None:intergenic 40.0%
ATGCATTAGGGATACAACCA+TGG - chr5.2:18016895-18016914 None:intergenic 40.0%
CACATACCTAACAAAGGTAG+AGG + chr5.2:18016266-18016285 MS.gene001119:CDS 40.0%
CATGGAAATGTTTGTGAAGG+TGG - chr5.2:18016422-18016441 None:intergenic 40.0%
CTGAAGCAGTTGTGACAATA+AGG - chr5.2:18016392-18016411 None:intergenic 40.0%
GAAGCAGTTGTGACAATAAG+GGG - chr5.2:18016390-18016409 None:intergenic 40.0%
GCTTGAACTTGAAGTTCACA+AGG - chr5.2:18016575-18016594 None:intergenic 40.0%
GGACATGGAAATGTTTGTGA+AGG - chr5.2:18016425-18016444 None:intergenic 40.0%
GGGATTCAGTGAGGATTATT+TGG - chr5.2:18016322-18016341 None:intergenic 40.0%
GGTGCAAGATTGAAGCAAAT+TGG + chr5.2:18017101-18017120 MS.gene001119:CDS 40.0%
GTAGCAGAATAGAGAAGAAG+AGG - chr5.2:18016344-18016363 None:intergenic 40.0%
TAGTTTGAGCAAGAAGGACA+TGG - chr5.2:18016440-18016459 None:intergenic 40.0%
TCAATTCCTCTCACTCATCT+TGG + chr5.2:18016495-18016514 MS.gene001119:CDS 40.0%
TGTGATAAGGAGAATTGTGC+AGG + chr5.2:18017181-18017200 MS.gene001119:CDS 40.0%
TTGGAGCACATACCTAACAA+AGG + chr5.2:18016260-18016279 MS.gene001119:CDS 40.0%
ACATGACCAAGATGAGTGAG+AGG - chr5.2:18016504-18016523 None:intergenic 45.0%
CAGTTGTGACAATAAGGGGA+GGG - chr5.2:18016386-18016405 None:intergenic 45.0%
GCAACACAAGATCTCAAAGC+TGG + chr5.2:18016296-18016315 MS.gene001119:CDS 45.0%
GCTGAAAAATTCATGTGGGG+TGG - chr5.2:18016743-18016762 None:intergenic 45.0%
GGAGAATTGTGCAGGTACTA+TGG + chr5.2:18017189-18017208 MS.gene001119:CDS 45.0%
GGGTCCTCAAAGATCCATTA+AGG + chr5.2:18016835-18016854 MS.gene001119:CDS 45.0%
GTGCTCCAATTTCAAGAGAG+AGG - chr5.2:18016249-18016268 None:intergenic 45.0%
TATGTGGAAAGTGGTGAACC+TGG + chr5.2:18016926-18016945 MS.gene001119:CDS 45.0%
TTCATGTGGGGTGGACAAAA+AGG - chr5.2:18016734-18016753 None:intergenic 45.0%
! GAGGGTGTATGAGAGAAAAG+AGG - chr5.2:18016368-18016387 None:intergenic 45.0%
!! GGATCTTTGAGGACCCTTTT+GGG - chr5.2:18016831-18016850 None:intergenic 45.0%
!! TGAGGACCCTTTTGGGTATA+AGG - chr5.2:18016824-18016843 None:intergenic 45.0%
!! TGGATCTTTGAGGACCCTTT+TGG - chr5.2:18016832-18016851 None:intergenic 45.0%
!!! GGCATTTTTGGCTGCAGAAA+AGG - chr5.2:18016463-18016482 None:intergenic 45.0%
GAAGAAGAGGGGATTCAGTG+AGG - chr5.2:18016331-18016350 None:intergenic 50.0%
GCAGTTGTGACAATAAGGGG+AGG - chr5.2:18016387-18016406 None:intergenic 50.0%
! GTGAGAGGAATTGAGGGCAT+TGG - chr5.2:18016489-18016508 None:intergenic 50.0%
!! AGGAATTGAGGGCATTGGAG+AGG - chr5.2:18016484-18016503 None:intergenic 50.0%
!! TCACCATCTTTTGGAGGCAG+AGG - chr5.2:18017217-18017236 None:intergenic 50.0%
!!! GGGCATTGGAGAGGCATTTT+TGG - chr5.2:18016475-18016494 None:intergenic 50.0%
GCTCCTCTGCCTCCAAAAGA+TGG + chr5.2:18017211-18017230 MS.gene001119:CDS 55.0%


Chromosome Type Strat End Strand Name
chr5.2 gene 18016227 18017297 18016227 ID=MS.gene001119
chr5.2 mRNA 18016227 18017297 18016227 ID=MS.gene001119.t1;Parent=MS.gene001119
chr5.2 exon 18016227 18017297 18016227 ID=MS.gene001119.t1.exon1;Parent=MS.gene001119.t1
chr5.2 CDS 18016227 18017297 18016227 ID=cds.MS.gene001119.t1;Parent=MS.gene001119.t1
Gene Sequence

>MS.gene001119

ATGGCTGCTCAAACTTCAACCTCTCTCTTGAAATTGGAGCACATACCTAACAAAGGTAGAGGCCTTATTGCAACACAAGATCTCAAAGCTGGCCAAATAATCCTCACTGAATCCCCTCTTCTTCTCTATTCTGCTACACCTCTTTTCTCTCATACACCCTCCCCTTATTGTCACAACTGCTTCAGAACCTTACCACCTTCACAAACATTTCCATGTCCTTCTTGCTCAAACTACCTTTTCTGCAGCCAAAAATGCCTCTCCAATGCCCTCAATTCCTCTCACTCATCTTGGTCATGTCAAACACTCTCTCATCTTCAAAACCCCACTTCACCATTATCAGAAAAACCTTGTGAACTTCAAGTTCAAGCTCGTTTGATTGTTGCTGCTTACAATCTTGCTATTCACACCCCTCCAAAACTTCAAACTTTACTTTCACTTCATGGTAGTCCTAATGATCATGATTCCATAGTTGATAATGCTAAGTTTATTCATGCTCTTATCTCACCTTTTTGTCCACCCCACATGAATTTTTCAGCTGAACTAGCTGCTAAAGTCATTGCTAAAGAAAGATTAAACTCTTTTTGCTTAATGGAACCTTATACCCAAAAGGGTCCTCAAAGATCCATTAAGGCTTATGGAATTTACCAAAAAGCTACTTTTTTTAACCATGGTTGTATCCCTAATGCATGCAGATTTGATTATGTGGAAAGTGGTGAACCTGGTGATGAACATAATATTGATATTGTTTTTAGGTTGATTAAGGATGTTGCTGTTGGAAGTGAGATTTGTATAAGCTATTTTAGGATTAATAAGGATTATTCAACAAGGAAAAGGATCTTGATGGATGATTATGGTTTTGCTTGTGAATGTGATAGGTGCAAGATTGAAGCAAATTGGAATGATGGAGAAGACAACAGTGATCTGCCACATGTGATTTTCTTATCTAAGTTTGTTTGTGATAAGGAGAATTGTGCAGGTACTATGGCTCCTCTGCCTCCAAAAGATGGTGAAAAATCTAATGTTCTTGAGTGTAACTTTTGTGGTAATTTGAAAGTTGACCCTGCTACTTAG
Protein sequence

>MS.gene001119.t1

MAAQTSTSLLKLEHIPNKGRGLIATQDLKAGQIILTESPLLLYSATPLFSHTPSPYCHNCFRTLPPSQTFPCPSCSNYLFCSQKCLSNALNSSHSSWSCQTLSHLQNPTSPLSEKPCELQVQARLIVAAYNLAIHTPPKLQTLLSLHGSPNDHDSIVDNAKFIHALISPFCPPHMNFSAELAAKVIAKERLNSFCLMEPYTQKGPQRSIKAYGIYQKATFFNHGCIPNACRFDYVESGEPGDEHNIDIVFRLIKDVAVGSEICISYFRINKDYSTRKRILMDDYGFACECDRCKIEANWNDGEDNSDLPHVIFLSKFVCDKENCAGTMAPLPPKDGEKSNVLECNFCGNLKVDPAT