AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene90956


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene90956.t1 MTR_4g074140 80.569 211 24 4 23 231 4 199 2.90e-102 296
MS.gene90956.t1 MTR_4g074140 80.861 209 23 4 25 231 1 194 8.16e-102 295
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 52 sgRNAs with CRISPR-Local

Find 88 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AACTTTGTTGTGTTTCTGTC+TGG 0.261804 4.2:-34559493 None:intergenic
GTGGCCGGAAATTGCCAATT+TGG 0.274884 4.2:-34560744 None:intergenic
TGAGCCAAATTGGCAATTTC+CGG 0.286882 4.2:+34560740 MS.gene90956:CDS
TCAATGACGCTGACGCTAAC+TGG 0.319388 4.2:-34560012 None:intergenic
GTCATTGATGGCATCGCTTA+TGG 0.330311 4.2:+34560027 MS.gene90956:CDS
GCATCATCGACCTTCGGAAT+TGG 0.354610 4.2:-34560066 None:intergenic
CATTGCCGGAGTCACTTTCA+TGG 0.363002 4.2:-34560092 None:intergenic
TAATGAAAATAAGAAGAAAA+AGG 0.372353 4.2:+34560284 MS.gene90956:CDS
GTAGACAGTGTGAGCCAAAT+TGG 0.380599 4.2:+34560730 MS.gene90956:CDS
AAAGAAACGCGGAAATTTAG+AGG 0.388630 4.2:+34560344 MS.gene90956:CDS
TTTGATGGCAATTGCAGAAC+AGG 0.393940 4.2:+34560446 MS.gene90956:CDS
TTTAGACCAACGGAATGAAA+TGG 0.394245 4.2:+34560248 MS.gene90956:CDS
TCTATAGAAAATGAAGCTAT+TGG 0.404032 4.2:+34560132 MS.gene90956:CDS
AGAACCACTTGTACATGAAC+GGG 0.407641 4.2:+34559524 MS.gene90956:CDS
TAGTGCAAAAGGTGAGGTTA+AGG 0.416681 4.2:+34560215 MS.gene90956:CDS
AGTGTCTAGCGACGATGATA+TGG 0.425121 4.2:+34560407 MS.gene90956:CDS
ACTTTGTTGTGTTTCTGTCT+GGG 0.437039 4.2:-34559492 None:intergenic
ATTAGCTTCAACAACATTGC+CGG 0.440034 4.2:-34560106 None:intergenic
GTTAGCGTCAGCGTCATTGA+TGG 0.440543 4.2:+34560015 MS.gene90956:CDS
GGAATGAATAACTGTGTTGA+GGG 0.446298 4.2:+34559955 MS.gene90956:intron
CATCACCCATTTCATTCCGT+TGG 0.460429 4.2:-34560254 None:intergenic
GTTGACGGTTGATGATTTGA+TGG 0.465634 4.2:+34560431 MS.gene90956:CDS
GTTCCTGCTTCAGCTGTGGC+CGG 0.472137 4.2:-34560759 None:intergenic
AGTGCAAAAGGTGAGGTTAA+GGG 0.475605 4.2:+34560216 MS.gene90956:CDS
TGGCTTGCATCATCGACCTT+CGG 0.485290 4.2:-34560072 None:intergenic
AAGTCGAATTCTAGTGCAAA+AGG 0.494931 4.2:+34560204 MS.gene90956:CDS
AGTTACCATCATGGATGAAA+AGG 0.495277 4.2:+34559989 MS.gene90956:CDS
TTAGACCAACGGAATGAAAT+GGG 0.495671 4.2:+34560249 MS.gene90956:CDS
AGGCGATCAAATCGAAGGAT+GGG 0.513205 4.2:+34560304 MS.gene90956:CDS
AGACAGAAACACAACAAAGT+TGG 0.524143 4.2:+34559495 MS.gene90956:CDS
CGACGATGATATGGAGTTGA+CGG 0.527405 4.2:+34560416 MS.gene90956:CDS
CGTTGTTCCTGCTTCAGCTG+TGG 0.533603 4.2:-34560763 None:intergenic
TAGAACCACTTGTACATGAA+CGG 0.536560 4.2:+34559523 MS.gene90956:CDS
CGTTTCTTTATAGAACGTCT+AGG 0.537766 4.2:-34560330 None:intergenic
TTTCCGGCCACAGCTGAAGC+AGG 0.538346 4.2:+34560756 MS.gene90956:CDS
GCAGTATGTCAAAGATTATG+AGG 0.550398 4.2:+34560683 MS.gene90956:intron
GCAAGAAGGAAACGATAAAG+AGG 0.562260 4.2:+34560181 MS.gene90956:CDS
GGAATTGGCATCATGCATGA+TGG 0.562904 4.2:-34560051 None:intergenic
AGGAATGAATAACTGTGTTG+AGG 0.565426 4.2:+34559954 MS.gene90956:intron
TTCACCCGTTCATGTACAAG+TGG 0.569191 4.2:-34559528 None:intergenic
AAGGCGATCAAATCGAAGGA+TGG 0.570967 4.2:+34560303 MS.gene90956:CDS
TTGTACATGAACGGGTGAAG+AGG 0.584728 4.2:+34559532 MS.gene90956:CDS
GGCGATCAAATCGAAGGATG+GGG 0.592288 4.2:+34560305 MS.gene90956:CDS
GAAGAAAATTGATTGCAAGA+AGG 0.594859 4.2:+34560167 MS.gene90956:CDS
GAAAACGCCAGTTACCATCA+TGG 0.601249 4.2:+34559980 MS.gene90956:CDS
GCAAGCCATGAAAGTGACTC+CGG 0.612685 4.2:+34560087 MS.gene90956:CDS
ATGCATGATGCCAATTCCGA+AGG 0.620795 4.2:+34560056 MS.gene90956:CDS
AATTTAGAGGATCTTAGCCA+TGG 0.622615 4.2:+34560357 MS.gene90956:CDS
GAATTCTAGTGCAAAAGGTG+AGG 0.665140 4.2:+34560209 MS.gene90956:CDS
ATACATCATCACTACCACCA+TGG 0.727291 4.2:-34560374 None:intergenic
TTAGAGGATCTTAGCCATGG+TGG 0.730179 4.2:+34560360 MS.gene90956:CDS
AGACGTTCTATAAAGAAACG+CGG 0.745605 4.2:+34560333 MS.gene90956:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TAATGAAAATAAGAAGAAAA+AGG + chr4.2:34560284-34560303 MS.gene90956:CDS 15.0%
!!! TTTTTAAAGAATTGGAAATT+TGG - chr4.2:34559832-34559851 None:intergenic 15.0%
!! ATTTAATTGGGGTTAAAATT+AGG - chr4.2:34559792-34559811 None:intergenic 20.0%
!! ATTTGATTGATGTTATCAAT+AGG + chr4.2:34559934-34559953 MS.gene90956:intron 20.0%
!! GAATTTGAATATGAATGATA+GGG - chr4.2:34559635-34559654 None:intergenic 20.0%
!! TGAATTTGAATATGAATGAT+AGG - chr4.2:34559636-34559655 None:intergenic 20.0%
!! TTTAATTGGGGTTAAAATTA+GGG - chr4.2:34559791-34559810 None:intergenic 20.0%
!!! AATAGTTTAACGGATTTAAT+TGG - chr4.2:34559805-34559824 None:intergenic 20.0%
!!! ATAGTTTAACGGATTTAATT+GGG - chr4.2:34559804-34559823 None:intergenic 20.0%
!!! ATTTGGAATGAATAGTTTAA+CGG - chr4.2:34559815-34559834 None:intergenic 20.0%
! AGATTGAGAAAATGGAAATT+TGG - chr4.2:34559709-34559728 None:intergenic 25.0%
! GAAAAACAAATTTAGACCAA+CGG + chr4.2:34560238-34560257 MS.gene90956:CDS 25.0%
! GATTCATACCTAGAATTATT+GGG - chr4.2:34559687-34559706 None:intergenic 25.0%
! TCTATAGAAAATGAAGCTAT+TGG + chr4.2:34560132-34560151 MS.gene90956:CDS 25.0%
!!! TAGTTTAACGGATTTAATTG+GGG - chr4.2:34559803-34559822 None:intergenic 25.0%
AAAATTGTTCAAGCGGTTAT+AGG - chr4.2:34560652-34560671 None:intergenic 30.0%
AAATTAGGGTTTAAGAGAAG+AGG - chr4.2:34559777-34559796 None:intergenic 30.0%
AAATTGTTCAAGCGGTTATA+GGG - chr4.2:34560651-34560670 None:intergenic 30.0%
AATTAGGGTTTAAGAGAAGA+GGG - chr4.2:34559776-34559795 None:intergenic 30.0%
ATACGACAAAATTGTTCAAG+CGG - chr4.2:34560659-34560678 None:intergenic 30.0%
GAAGAAAATTGATTGCAAGA+AGG + chr4.2:34560167-34560186 MS.gene90956:CDS 30.0%
GCATAAAGAGATTGAGAAAA+TGG - chr4.2:34559717-34559736 None:intergenic 30.0%
GGATTCATACCTAGAATTAT+TGG - chr4.2:34559688-34559707 None:intergenic 30.0%
TTAAGAGAAGAGGGTTAAAT+TGG - chr4.2:34559767-34559786 None:intergenic 30.0%
! GCAATCAATTTTCTTCACAT+TGG - chr4.2:34560163-34560182 None:intergenic 30.0%
AAACAATGTAAAAGCTACCG+TGG - chr4.2:34560509-34560528 None:intergenic 35.0%
AAAGAAACGCGGAAATTTAG+AGG + chr4.2:34560344-34560363 MS.gene90956:CDS 35.0%
AAGTCGAATTCTAGTGCAAA+AGG + chr4.2:34560204-34560223 MS.gene90956:CDS 35.0%
AATATTGCTTCCCAAGACAA+TGG + chr4.2:34560599-34560618 MS.gene90956:intron 35.0%
AATTTAGAGGATCTTAGCCA+TGG + chr4.2:34560357-34560376 MS.gene90956:CDS 35.0%
AGACAGAAACACAACAAAGT+TGG + chr4.2:34559495-34559514 MS.gene90956:CDS 35.0%
AGACGTTCTATAAAGAAACG+CGG + chr4.2:34560333-34560352 MS.gene90956:CDS 35.0%
AGGAATGAATAACTGTGTTG+AGG + chr4.2:34559954-34559973 MS.gene90956:intron 35.0%
AGTTAAGTTACACTCTCAAG+TGG - chr4.2:34559911-34559930 None:intergenic 35.0%
AGTTACCATCATGGATGAAA+AGG + chr4.2:34559989-34560008 MS.gene90956:CDS 35.0%
ATCACATCAACCATTGTCTT+GGG - chr4.2:34560612-34560631 None:intergenic 35.0%
CGTTTCTTTATAGAACGTCT+AGG - chr4.2:34560333-34560352 None:intergenic 35.0%
GAATTGCACCCAATAATTCT+AGG + chr4.2:34559676-34559695 MS.gene90956:intron 35.0%
GCAGTATGTCAAAGATTATG+AGG + chr4.2:34560683-34560702 MS.gene90956:intron 35.0%
GGAATGAATAACTGTGTTGA+GGG + chr4.2:34559955-34559974 MS.gene90956:intron 35.0%
TAGAACCACTTGTACATGAA+CGG + chr4.2:34559523-34559542 MS.gene90956:CDS 35.0%
TTAGACCAACGGAATGAAAT+GGG + chr4.2:34560249-34560268 MS.gene90956:CDS 35.0%
TTTAGACCAACGGAATGAAA+TGG + chr4.2:34560248-34560267 MS.gene90956:CDS 35.0%
! AACTTTGTTGTGTTTCTGTC+TGG - chr4.2:34559496-34559515 None:intergenic 35.0%
! ACTTTGTTGTGTTTCTGTCT+GGG - chr4.2:34559495-34559514 None:intergenic 35.0%
! ATTAGCTTCAACAACATTGC+CGG - chr4.2:34560109-34560128 None:intergenic 35.0%
! TTTTCATCCATGATGGTAAC+TGG - chr4.2:34559990-34560009 None:intergenic 35.0%
AGAACCACTTGTACATGAAC+GGG + chr4.2:34559524-34559543 MS.gene90956:CDS 40.0%
AGTGCAAAAGGTGAGGTTAA+GGG + chr4.2:34560216-34560235 MS.gene90956:CDS 40.0%
ATACATCATCACTACCACCA+TGG - chr4.2:34560377-34560396 None:intergenic 40.0%
ATAGGGAGTTTCAGATCAGA+AGG - chr4.2:34559618-34559637 None:intergenic 40.0%
CATCACATCAACCATTGTCT+TGG - chr4.2:34560613-34560632 None:intergenic 40.0%
GAAAAAGGCGATCAAATCGA+AGG + chr4.2:34560299-34560318 MS.gene90956:CDS 40.0%
GAATTCTAGTGCAAAAGGTG+AGG + chr4.2:34560209-34560228 MS.gene90956:CDS 40.0%
GCAAGAAGGAAACGATAAAG+AGG + chr4.2:34560181-34560200 MS.gene90956:CDS 40.0%
GCTGATAATTCAAGCATCCA+CGG + chr4.2:34560489-34560508 MS.gene90956:intron 40.0%
TAGGGAGTTTCAGATCAGAA+GGG - chr4.2:34559617-34559636 None:intergenic 40.0%
TAGTGCAAAAGGTGAGGTTA+AGG + chr4.2:34560215-34560234 MS.gene90956:CDS 40.0%
TGAGCCAAATTGGCAATTTC+CGG + chr4.2:34560740-34560759 MS.gene90956:CDS 40.0%
! CAAGACAATGGTTGATGTGA+TGG + chr4.2:34560611-34560630 MS.gene90956:intron 40.0%
! TTTGATGGCAATTGCAGAAC+AGG + chr4.2:34560446-34560465 MS.gene90956:CDS 40.0%
!! GTTGACGGTTGATGATTTGA+TGG + chr4.2:34560431-34560450 MS.gene90956:CDS 40.0%
AAGGCGATCAAATCGAAGGA+TGG + chr4.2:34560303-34560322 MS.gene90956:CDS 45.0%
AGGCGATCAAATCGAAGGAT+GGG + chr4.2:34560304-34560323 MS.gene90956:CDS 45.0%
AGTGTCTAGCGACGATGATA+TGG + chr4.2:34560407-34560426 MS.gene90956:CDS 45.0%
ATGCATGATGCCAATTCCGA+AGG + chr4.2:34560056-34560075 MS.gene90956:CDS 45.0%
CATCACCCATTTCATTCCGT+TGG - chr4.2:34560257-34560276 None:intergenic 45.0%
CGACGATGATATGGAGTTGA+CGG + chr4.2:34560416-34560435 MS.gene90956:CDS 45.0%
GAAAACGCCAGTTACCATCA+TGG + chr4.2:34559980-34559999 MS.gene90956:CDS 45.0%
GGAATTGGCATCATGCATGA+TGG - chr4.2:34560054-34560073 None:intergenic 45.0%
GTAGACAGTGTGAGCCAAAT+TGG + chr4.2:34560730-34560749 MS.gene90956:CDS 45.0%
TTAGAGGATCTTAGCCATGG+TGG + chr4.2:34560360-34560379 MS.gene90956:CDS 45.0%
TTCACCCGTTCATGTACAAG+TGG - chr4.2:34559531-34559550 None:intergenic 45.0%
TTGTACATGAACGGGTGAAG+AGG + chr4.2:34559532-34559551 MS.gene90956:CDS 45.0%
! GTCATTGATGGCATCGCTTA+TGG + chr4.2:34560027-34560046 MS.gene90956:CDS 45.0%
!!! ACTGGCCTTTTCATCCATGA+TGG - chr4.2:34559997-34560016 None:intergenic 45.0%
!!! TTTTTTAATTTTTAAAGAAT+TGG - chr4.2:34559840-34559859 None:intergenic 5.0%
GCAAGCCATGAAAGTGACTC+CGG + chr4.2:34560087-34560106 MS.gene90956:CDS 50.0%
GCATCATCGACCTTCGGAAT+TGG - chr4.2:34560069-34560088 None:intergenic 50.0%
GGCGATCAAATCGAAGGATG+GGG + chr4.2:34560305-34560324 MS.gene90956:CDS 50.0%
GTGGCCGGAAATTGCCAATT+TGG - chr4.2:34560747-34560766 None:intergenic 50.0%
GTTAGCGTCAGCGTCATTGA+TGG + chr4.2:34560015-34560034 MS.gene90956:CDS 50.0%
TCAATGACGCTGACGCTAAC+TGG - chr4.2:34560015-34560034 None:intergenic 50.0%
! CATTGCCGGAGTCACTTTCA+TGG - chr4.2:34560095-34560114 None:intergenic 50.0%
! TGGCTTGCATCATCGACCTT+CGG - chr4.2:34560075-34560094 None:intergenic 50.0%
CGTTGTTCCTGCTTCAGCTG+TGG - chr4.2:34560766-34560785 None:intergenic 55.0%
GTTCCTGCTTCAGCTGTGGC+CGG - chr4.2:34560762-34560781 None:intergenic 60.0%
TTTCCGGCCACAGCTGAAGC+AGG + chr4.2:34560756-34560775 MS.gene90956:CDS 60.0%


Chromosome Type Strat End Strand Name
chr4.2 gene 34559489 34560798 34559489 ID=MS.gene90956
chr4.2 mRNA 34559489 34560798 34559489 ID=MS.gene90956.t1;Parent=MS.gene90956
chr4.2 exon 34559489 34559558 34559489 ID=MS.gene90956.t1.exon1;Parent=MS.gene90956.t1
chr4.2 CDS 34559489 34559558 34559489 ID=cds.MS.gene90956.t1;Parent=MS.gene90956.t1
chr4.2 exon 34559956 34560467 34559956 ID=MS.gene90956.t1.exon2;Parent=MS.gene90956.t1
chr4.2 CDS 34559956 34560467 34559956 ID=cds.MS.gene90956.t1;Parent=MS.gene90956.t1
chr4.2 exon 34560687 34560798 34560687 ID=MS.gene90956.t1.exon3;Parent=MS.gene90956.t1
chr4.2 CDS 34560687 34560798 34560687 ID=cds.MS.gene90956.t1;Parent=MS.gene90956.t1
Gene Sequence

>MS.gene90956

ATGCCCAGACAGAAACACAACAAAGTTGGTTTTTTAGAACCACTTGTACATGAACGGGTGAAGAGGATAAGTTAGTCATTTTAACTCTTATAAATTCAATTTGAATTTCAATTAACACTTCTTTTCCCTTCTGATCTGAAACTCCCTATCATTCATATTCAAATTCAACACTGAATTAGCGTGTGTCGAATTGCACCCAATAATTCTAGGTATGAATCCAAATTTCCATTTTCTCAATCTCTTTATGCTAATTTAGAATTCGCTTTCTCTTTTCACCAATTTAACCCTCTTCTCTTAAACCCTAATTTTAACCCCAATTAAATCCGTTAAACTATTCATTCCAAATTTCCAATTCTTTAAAAATTAAAAAATCACTTTGTTATGTAATTGAAAAGTTATTGTTATATTTTTTTTTTGTTCCACTTGAGAGTGTAACTTAACTTTAATTTGATTGATGTTATCAATAGGAATGAATAACTGTGTTGAGGGAAGAAAACGCCAGTTACCATCATGGATGAAAAGGCCAGTTAGCGTCAGCGTCATTGATGGCATCGCTTATGGTCCATCATGCATGATGCCAATTCCGAAGGTCGATGATGCAAGCCATGAAAGTGACTCCGGCAATGTTGTTGAAGCTAATCACTCTATAGAAAATGAAGCTATTGGTGCAGCCAATGTGAAGAAAATTGATTGCAAGAAGGAAACGATAAAGAGGAAGTCGAATTCTAGTGCAAAAGGTGAGGTTAAGGGAAAAACAAATTTAGACCAACGGAATGAAATGGGTGATGATGATGCTAATGAAAATAAGAAGAAAAAGGCGATCAAATCGAAGGATGGGGCTCCTAGACGTTCTATAAAGAAACGCGGAAATTTAGAGGATCTTAGCCATGGTGGTAGTGATGATGTATGTCTAGTTCAAGTGTCTAGCGACGATGATATGGAGTTGACGGTTGATGATTTGATGGCAATTGCAGAACAGGTAATTTTCTTTTTCTGATAAGCTGATAATTCAAGCATCCACGGTAGCTTTTACATTGTTTGAGTAAGCTGAATTGAAATGTCTGTCACTATAGCATTTCTTTGTATCATCATATGATCTATTGAATTTATAATATTGCTTCCCAAGACAATGGTTGATGTGATGGAGATTTTAATTTCGCCCTATAACCGCTTGAACAATTTTGTCGTATGTGTGCAGTATGTCAAAGATTATGAGGAGAAAGAGCTGCAAGAAACGTCAAGTAGACAGTGTGAGCCAAATTGGCAATTTCCGGCCACAGCTGAAGCAGGAACAACGCTTGATTCCTTTC

Protein sequence

>MS.gene90956.t1

MPRQKHNKVGFLEPLVHERVKRIRMNNCVEGRKRQLPSWMKRPVSVSVIDGIAYGPSCMMPIPKVDDASHESDSGNVVEANHSIENEAIGAANVKKIDCKKETIKRKSNSSAKGEVKGKTNLDQRNEMGDDDANENKKKKAIKSKDGAPRRSIKKRGNLEDLSHGGSDDVCLVQVSSDDDMELTVDDLMAIAEQYVKDYEEKELQETSSRQCEPNWQFPATAEAGTTLDSF