AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene76980

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene76980.t1 MTR_2g015010 85.714 63 9 0 13 75 72 134 1.79e-31 115
MS.gene76980.t1 MTR_8g040300 77.273 44 10 0 106 149 113 156 2.87e-17 76.6
MS.gene76980.t1 MTR_8g035890 70.455 44 13 0 106 149 119 162 6.40e-15 70.5
MS.gene76980.t1 MTR_3g110405 47.368 57 28 1 106 160 140 196 7.15e-11 59.3
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene76980.t1 AT2G36230 68.254 63 19 1 13 75 66 127 2.05e-21 88.6
MS.gene76980.t1 AT2G45490 61.364 44 17 0 106 149 125 168 5.62e-12 62.4
MS.gene76980.t1 AT2G45490 61.364 44 17 0 106 149 125 168 7.67e-12 62.0
MS.gene76980.t1 AT2G25880 47.368 57 28 1 106 160 189 245 5.12e-11 60.1
MS.gene76980.t1 AT2G25880 47.368 57 28 1 106 160 128 184 5.64e-11 59.7
MS.gene76980.t1 AT2G25880 47.368 57 28 1 106 160 141 197 5.83e-11 59.7
MS.gene76980.t1 AT4G32830 47.368 57 28 1 106 160 134 190 9.13e-11 59.3

Find 28 sgRNAs with CRISPR-Local

Find 86 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTCAAACAAGATGGACTTAA+AGG 0.177160 6.3:-62090959 MS.gene76980:CDS
TCAGGCTCAAAATTGGTAAT+TGG 0.210433 6.3:+62091010 None:intergenic
TGCACAACTTACTTTGTTGC+AGG 0.290633 6.3:-62090728 MS.gene76980:intron
ATACAGATACAGATACTTAT+TGG 0.297550 6.3:-62089626 MS.gene76980:intron
AGATTTATCAGGCTCAAAAT+TGG 0.342018 6.3:+62091003 None:intergenic
TACTCAGCTGCAGATTTATC+AGG 0.375812 6.3:+62090992 None:intergenic
GCGCAAGAAGCAATACATTT+CGG 0.391492 6.3:-62090800 MS.gene76980:CDS
AACATTGCAAGACAGTTGTT+TGG 0.395025 6.3:-62089569 MS.gene76980:CDS
GAAGCATTGCATGCTTATCC+TGG 0.477302 6.3:-62090884 MS.gene76980:CDS
AAAGATTTGAAAGAGGATGA+TGG 0.480092 6.3:-62091040 MS.gene76980:intron
TACCTTGTGAATATCGATGC+AGG 0.487164 6.3:+62091209 None:intergenic
TACTTATTGGCGAGCTGAAG+TGG 0.491124 6.3:-62089613 MS.gene76980:CDS
GGTGGTCATGTTATCATGCT+TGG 0.505881 6.3:-62090938 MS.gene76980:CDS
AACCCTTAAAGATTTGAAAG+AGG 0.519640 6.3:-62091047 MS.gene76980:intron
AAGATTTGAAAGAGGATGAT+GGG 0.525706 6.3:-62091039 MS.gene76980:CDS
ACCTTGTGAATATCGATGCA+GGG 0.538181 6.3:+62091210 None:intergenic
AGAGAAGCATCTTTACTCAA+AGG 0.547387 6.3:+62090908 None:intergenic
AAATTTGTTGCTTGATCACG+AGG 0.555828 6.3:-62089807 MS.gene76980:intron
CATTTCGGAGCTAGAACACA+AGG 0.586933 6.3:-62090785 MS.gene76980:CDS
TGTGAATAACATGGTTCTCG+TGG 0.625512 6.3:+62089846 None:intergenic
CCCCTGCATCGATATTCACA+AGG 0.632190 6.3:-62091211 MS.gene76980:intron
TGTAATCAAACTAAAATACC+AGG 0.633384 6.3:+62090866 None:intergenic
AAACAAGATGGACTTAAAGG+TGG 0.633622 6.3:-62090956 MS.gene76980:CDS
TGATATCTCTGTGAATAACA+TGG 0.634938 6.3:+62089837 None:intergenic
CCTTGTGAATATCGATGCAG+GGG 0.636281 6.3:+62091211 None:intergenic
AAGTTGTGCAGAAAGTGTAG+TGG 0.665732 6.3:+62090741 None:intergenic
TGTGAATATCGATGCAGGGG+CGG 0.677623 6.3:+62091214 None:intergenic
AATATGTCAATGCTTCCGTG+AGG 0.756689 6.3:+62089870 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAAAACAATTATTTCATCTA+TGG + chr6.3:62091139-62091158 None:intergenic 15.0%
!! AAAACAATTATTTCATCTAT+GGG + chr6.3:62091138-62091157 None:intergenic 15.0%
!! AAACTTACAAAAATCAATAT+AGG + chr6.3:62090606-62090625 None:intergenic 15.0%
!! CATATTACTAAAATAAAACA+CGG + chr6.3:62090119-62090138 None:intergenic 15.0%
!! AAATTATAAGTAGCATAGAA+TGG + chr6.3:62090818-62090837 None:intergenic 20.0%
!! AAGGTATATCTAAGAAATAT+TGG + chr6.3:62090366-62090385 None:intergenic 20.0%
!! ATACACATATTTCAAACTAA+AGG - chr6.3:62090441-62090460 MS.gene76980:intron 20.0%
!! GAACAGAAAAGTAAAAAAAA+TGG + chr6.3:62089954-62089973 None:intergenic 20.0%
!!! AGAAGTTAATATTGATTGAA+AGG + chr6.3:62089613-62089632 None:intergenic 20.0%
!!! GAAGTTAATATTGATTGAAA+GGG + chr6.3:62089612-62089631 None:intergenic 20.0%
! ACAAAAATCAATATAGGACA+TGG + chr6.3:62090600-62090619 None:intergenic 25.0%
! ATACAAAGAATTGCTACAAA+AGG + chr6.3:62090849-62090868 None:intergenic 25.0%
! ATACAGATACAGATACTTAT+TGG - chr6.3:62091168-62091187 MS.gene76980:intron 25.0%
! ATCCTCTTTCAAATCTTTAA+GGG + chr6.3:62089752-62089771 None:intergenic 25.0%
! TAATGACATGCTATGAAATA+TGG - chr6.3:62090727-62090746 MS.gene76980:intron 25.0%
! TGTAATCAAACTAAAATACC+AGG + chr6.3:62089931-62089950 None:intergenic 25.0%
!! AATTTTACATGTGGGTTTTT+AGG - chr6.3:62089658-62089677 MS.gene76980:intron 25.0%
!! ATTTTACATGTGGGTTTTTA+GGG - chr6.3:62089659-62089678 MS.gene76980:intron 25.0%
!!! TTTCCACATTGATAATGTTT+TGG - chr6.3:62090247-62090266 MS.gene76980:intron 25.0%
AAAGATTTGAAAGAGGATGA+TGG - chr6.3:62089754-62089773 MS.gene76980:intron 30.0%
AACATACATCGTGAAAAACA+TGG + chr6.3:62090787-62090806 None:intergenic 30.0%
AACCCTTAAAGATTTGAAAG+AGG - chr6.3:62089747-62089766 MS.gene76980:intron 30.0%
AAGATTTGAAAGAGGATGAT+GGG - chr6.3:62089755-62089774 MS.gene76980:intron 30.0%
AGATTTATCAGGCTCAAAAT+TGG + chr6.3:62089794-62089813 None:intergenic 30.0%
ATTATTTCATCTATGGGCAA+TGG + chr6.3:62091132-62091151 None:intergenic 30.0%
CACAAAATATCACATGTGTT+TGG + chr6.3:62090478-62090497 None:intergenic 30.0%
CATCCTCTTTCAAATCTTTA+AGG + chr6.3:62089753-62089772 None:intergenic 30.0%
GATACTTTACGACACATATA+TGG + chr6.3:62090633-62090652 None:intergenic 30.0%
GGAAAGTGAAACAAATTGTT+GGG - chr6.3:62089722-62089741 MS.gene76980:intron 30.0%
GTTCCAAAACATTATCAATG+TGG + chr6.3:62090253-62090272 None:intergenic 30.0%
TAAGCCTTCAATTGATATTG+TGG - chr6.3:62090159-62090178 MS.gene76980:intron 30.0%
TAAGTATCTGTATCTGTATG+AGG + chr6.3:62091167-62091186 None:intergenic 30.0%
TAGTCGAAGAGATGTTAAAA+CGG + chr6.3:62091075-62091094 None:intergenic 30.0%
TCTGTATCATACTATCTATC+TGG - chr6.3:62090651-62090670 MS.gene76980:intron 30.0%
TGATATCTCTGTGAATAACA+TGG + chr6.3:62090960-62090979 None:intergenic 30.0%
TTAACTTCAACTCACTATTC+TGG + chr6.3:62090279-62090298 None:intergenic 30.0%
! AAGGTACGAATTTTACATGT+GGG - chr6.3:62089650-62089669 MS.gene76980:intron 30.0%
! TGAGTTGAAGTTAACATTGA+AGG - chr6.3:62090285-62090304 MS.gene76980:intron 30.0%
! TGATCAAGCAACAAATTTTC+AGG + chr6.3:62090985-62091004 None:intergenic 30.0%
! TGGTGTGTTTTGTAAAATTG+CGG - chr6.3:62090179-62090198 MS.gene76980:intron 30.0%
! TTAGTACATTTTAAGCCTCA+CGG - chr6.3:62090909-62090928 MS.gene76980:CDS 30.0%
! TTCAAACAAGATGGACTTAA+AGG - chr6.3:62089835-62089854 MS.gene76980:CDS 30.0%
!! AAAGGTACGAATTTTACATG+TGG - chr6.3:62089649-62089668 MS.gene76980:intron 30.0%
!!! GCAATGAAATTTTAAGACGT+GGG - chr6.3:62089681-62089700 MS.gene76980:intron 30.0%
AACATTGCAAGACAGTTGTT+TGG - chr6.3:62091225-62091244 MS.gene76980:CDS 35.0%
ACTATCTATCTGGACTTCTT+TGG - chr6.3:62090661-62090680 MS.gene76980:intron 35.0%
CACACCACAATATCAATTGA+AGG + chr6.3:62090166-62090185 None:intergenic 35.0%
CTTGCCAATTCATGTCAAAA+AGG - chr6.3:62089631-62089650 MS.gene76980:intron 35.0%
GATGAGATCATCAGCATAAT+TGG + chr6.3:62091051-62091070 None:intergenic 35.0%
GGGAAAGTGAAACAAATTGT+TGG - chr6.3:62089721-62089740 MS.gene76980:intron 35.0%
TGCATGGAAGGTTATCTTTA+AGG - chr6.3:62090315-62090334 MS.gene76980:intron 35.0%
! AAACAAGATGGACTTAAAGG+TGG - chr6.3:62089838-62089857 MS.gene76980:CDS 35.0%
! CGTACCTTTTTGACATGAAT+TGG + chr6.3:62089638-62089657 None:intergenic 35.0%
! GCTACTCTTTTCAAACAAGA+TGG - chr6.3:62089826-62089845 MS.gene76980:CDS 35.0%
! TCAGGCTCAAAATTGGTAAT+TGG + chr6.3:62089787-62089806 None:intergenic 35.0%
! TGTGTTTTGTAAAATTGCGG+TGG - chr6.3:62090182-62090201 MS.gene76980:intron 35.0%
! TTTTCTGTTCATGCTTATCC+TGG - chr6.3:62089964-62089983 MS.gene76980:intron 35.0%
!! AAATTTGTTGCTTGATCACG+AGG - chr6.3:62090987-62091006 MS.gene76980:CDS 35.0%
!! AGAGAAGCATCTTTACTCAA+AGG + chr6.3:62089889-62089908 None:intergenic 35.0%
!! TGGGTCATTGTGTTTTTGTA+GGG - chr6.3:62089700-62089719 MS.gene76980:intron 35.0%
!!! GGCAATGAAATTTTAAGACG+TGG - chr6.3:62089680-62089699 MS.gene76980:intron 35.0%
AATATGTCAATGCTTCCGTG+AGG + chr6.3:62090927-62090946 None:intergenic 40.0%
ACAACTTACTTTGTTGCAGG+TGG - chr6.3:62090069-62090088 MS.gene76980:intron 40.0%
ACCTTGTGAATATCGATGCA+GGG + chr6.3:62089587-62089606 None:intergenic 40.0%
ACTCAAGACACGATTGTCAT+AGG - chr6.3:62090554-62090573 MS.gene76980:intron 40.0%
CAACTTACTTTGTTGCAGGT+GGG - chr6.3:62090070-62090089 MS.gene76980:intron 40.0%
GAGTCAGAAATACGTATCGA+AGG + chr6.3:62090385-62090404 None:intergenic 40.0%
GCGCAAGAAGCAATACATTT+CGG - chr6.3:62089994-62090013 MS.gene76980:intron 40.0%
TACCTTGTGAATATCGATGC+AGG + chr6.3:62089588-62089607 None:intergenic 40.0%
TACTCAGCTGCAGATTTATC+AGG + chr6.3:62089805-62089824 None:intergenic 40.0%
TGCACAACTTACTTTGTTGC+AGG - chr6.3:62090066-62090085 MS.gene76980:intron 40.0%
TGTGAATAACATGGTTCTCG+TGG + chr6.3:62090951-62090970 None:intergenic 40.0%
! AAGTTGTGCAGAAAGTGTAG+TGG + chr6.3:62090056-62090075 None:intergenic 40.0%
!! GGGTCATTGTGTTTTTGTAG+GGG - chr6.3:62089701-62089720 MS.gene76980:intron 40.0%
!! GTGGGTCATTGTGTTTTTGT+AGG - chr6.3:62089699-62089718 MS.gene76980:intron 40.0%
AAGTAGCTTTCATGTCAGCG+TGG + chr6.3:62090212-62090231 None:intergenic 45.0%
CATTGAAGGCTGTAGTTGCA+TGG - chr6.3:62090299-62090318 MS.gene76980:intron 45.0%
CATTTCGGAGCTAGAACACA+AGG - chr6.3:62090009-62090028 MS.gene76980:intron 45.0%
CCTTGTGAATATCGATGCAG+GGG + chr6.3:62089586-62089605 None:intergenic 45.0%
GGTGGTCATGTTATCATGCT+TGG - chr6.3:62089856-62089875 MS.gene76980:CDS 45.0%
TACTTATTGGCGAGCTGAAG+TGG - chr6.3:62091181-62091200 MS.gene76980:intron 45.0%
!! GAAGCATTGCATGCTTATCC+TGG - chr6.3:62089910-62089929 MS.gene76980:intron 45.0%
GAAGGCTGTAGTTGCATGGA+AGG - chr6.3:62090303-62090322 MS.gene76980:intron 50.0%
GCTTCTTGCGCTCAAATACC+AGG + chr6.3:62089985-62090004 None:intergenic 50.0%
TGTGAATATCGATGCAGGGG+CGG + chr6.3:62089583-62089602 None:intergenic 50.0%
! CCCCTGCATCGATATTCACA+AGG - chr6.3:62089583-62089602 MS.gene76980:CDS 50.0%


Chromosome Type Strat End Strand Name
chr6.3 gene 62089565 62091251 62089565 ID=MS.gene76980
chr6.3 mRNA 62089565 62091251 62089565 ID=MS.gene76980.t1;Parent=MS.gene76980
chr6.3 exon 62091212 62091251 62091212 ID=MS.gene76980.t1.exon1;Parent=MS.gene76980.t1
chr6.3 CDS 62091212 62091251 62091212 ID=cds.MS.gene76980.t1;Parent=MS.gene76980.t1
chr6.3 exon 62090877 62091058 62090877 ID=MS.gene76980.t1.exon2;Parent=MS.gene76980.t1
chr6.3 CDS 62090877 62091058 62090877 ID=cds.MS.gene76980.t1;Parent=MS.gene76980.t1
chr6.3 exon 62090729 62090821 62090729 ID=MS.gene76980.t1.exon3;Parent=MS.gene76980.t1
chr6.3 CDS 62090729 62090821 62090729 ID=cds.MS.gene76980.t1;Parent=MS.gene76980.t1
chr6.3 exon 62089808 62089903 62089808 ID=MS.gene76980.t1.exon4;Parent=MS.gene76980.t1
chr6.3 CDS 62089808 62089903 62089808 ID=cds.MS.gene76980.t1;Parent=MS.gene76980.t1
chr6.3 exon 62089565 62089642 62089565 ID=MS.gene76980.t1.exon5;Parent=MS.gene76980.t1
chr6.3 CDS 62089565 62089642 62089565 ID=cds.MS.gene76980.t1;Parent=MS.gene76980.t1
Gene Sequence

>MS.gene76980

ATGCTCTATTCAATTCCGCCCCTGCATCGATATTCACAAGGTAACCCTTTCAATCAATATTAACTTCTTGCCAATTCATGTCAAAAAGGTACGAATTTTACATGTGGGTTTTTAGGGCAATGAAATTTTAAGACGTGGGTCATTGTGTTTTTGTAGGGGAAAGTGAAACAAATTGTTGGGTCAACCCTTAAAGATTTGAAAGAGGATGATGGGTCAGATCCAATTACCAATTTTGAGCCTGATAAATCTGCAGCTGAGTATGCTACTCTTTTCAAACAAGATGGACTTAAAGGTGGTCATGTTATCATGCTTGGTACTGATCCTTTGAGTAAAGATGCTTCTCTTGAAGCATTGCATGCTTATCCTGGTATTTTAGTTTGATTACACCATTTTTTTTACTTTTCTGTTCATGCTTATCCTGGTATTTGAGCGCAAGAAGCAATACATTTCGGAGCTAGAACACAAGGTTCAGACTCTGCAGACTGAAGCCACTACACTTTCTGCACAACTTACTTTGTTGCAGGTGGGAACATTTATTTAAGTTTGTGAAACCGTGTTTTATTTTAGTAATATGATCTTAGTTTCTTTTTTTACTAAGCCTTCAATTGATATTGTGGTGTGTTTTGTAAAATTGCGGTGGAAATCCACGCTGACATGAAAGCTACTTATTGTAGCTTCTTTGTTTCCACATTGATAATGTTTTGGAACTAACCAGAATAGTGAGTTGAAGTTAACATTGAAGGCTGTAGTTGCATGGAAGGTTATCTTTAAGGAACAACTTGAAAAGTACAAATTTCACCAATATTTCTTAGATATACCTTCGATACGTATTTCTGACTCGCGACACATTTGTCATCTAGATACGATACATCTTTGATACACATATTTCAAACTAAAGGCATATTTCTAACCAAACACATGTGATATTTTGTGATTTGTACACAAAAAGCATTCAGTATTTGTTTTAATATCTTCGATACGTATTTCTGACTCAAGACACGATTGTCATAGGTTTTTAGTAAATGTATCTTGCCATGTCCTATATTGATTTTTGTAAGTTTCTCACCATATATGTGTCGTAAAGTATCTGTATCATACTATCTATCTGGACTTCTTTGGAAGTATGATATGTATGTGATCATTTTAGCAGTTGAGCTAATTGTAATGACATGCTATGAAATATGGATTATAGAGAAAGTGAAAATTTGATTTGAAACTACCATGTTTTTCACGATGTATGTTATATTCTACCATTCTATGCTACTTATAATTTTACTCTTTCCTTTTGTAGCAATTCTTTGTATTATATTGAATCTTACTTAGTTTATTTCAACTTTGAAAATGTTAGTACATTTTAAGCCTCACGGAAGCATTGACATATTGCCACGAGAACCATGTTATTCACAGAGATATCAAGCCTGAAAATTTGTTGCTTGATCACGAGGTATCTTTCTATTATTTTACTTATATTTGAACTGCTCTTCCAATTATGCTGATGATCTCATCGCCGTTTTAACATCTCTTCGACTACTAAATTTTGTTTTCTTTTTGATAGTGTTTCGATCCATTGCCCATAGATGAAATAATTGTTTTTAGTTGCCTCATACAGATACAGATACTTATTGGCGAGCTGAAGTGGAAGCTCTATGAGAGAAGACGAAACATTGCAAGACAGTTGTTTGGAGCT
Protein sequence

>MS.gene76980.t1

MLYSIPPLHRYSQDLKEDDGSDPITNFEPDKSAAEYATLFKQDGLKGGHVIMLGTDPLSKDASLEALHAYPGILRKKQYISELEHKVQTLQTEATTLSAQLTLLQYILSLTEALTYCHENHVIHRDIKPENLLLDHEIQILIGELKWKLYERRRNIARQLFGA