AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene98895

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene98895.t1 MTR_2g043530 97.297 37 1 0 52 88 153 189 2.39e-17 77.0
MS.gene98895.t1 MTR_2g043530 79.104 67 13 1 1 67 1 66 1.30e-16 74.7
MS.gene98895.t1 MTR_2g043530 97.297 37 1 0 52 88 153 189 2.68e-17 76.6
MS.gene98895.t1 MTR_2g043530 79.104 67 13 1 1 67 1 66 1.52e-16 74.7
MS.gene98895.t1 MTR_4g124880 83.784 37 6 0 52 88 10 46 2.58e-14 67.8
MS.gene98895.t1 MTR_4g124880 83.784 37 6 0 52 88 156 192 2.86e-14 68.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene98895.t1 AT1G74960 67.500 40 13 0 52 91 206 245 6.55e-12 61.2
MS.gene98895.t1 AT1G74960 67.500 40 13 0 52 91 206 245 6.55e-12 61.2
MS.gene98895.t1 AT1G74960 67.500 40 13 0 52 91 206 245 6.55e-12 61.2

Find 28 sgRNAs with CRISPR-Local

Find 105 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GATTGGGAGAAGAGAGATTA+AGG 0.255347 6.2:-38881318 None:intergenic
CAGCAACAAGGTGTCGGTTT+GGG 0.261752 6.2:+38882976 MS.gene98895:CDS
AAGTGTGAAATTACCAGAAC+GGG 0.377735 6.2:-38881347 None:intergenic
CCCAATCGAATGCCCCGTTC+TGG 0.390260 6.2:+38881334 MS.gene98895:CDS
TACCTGCATTCCGCCCATTC+CGG 0.392453 6.2:-38882111 None:intergenic
GCAGCAACAAGGTGTCGGTT+TGG 0.418108 6.2:+38882975 MS.gene98895:CDS
ACCAGAACGGGGCATTCGAT+TGG 0.437348 6.2:-38881335 None:intergenic
ATCGTTCTCGTCGTCGCAGC+AGG 0.443712 6.2:+38881287 MS.gene98895:CDS
CCAGAACGGGGCATTCGATT+GGG 0.459160 6.2:-38881334 None:intergenic
CTCCGGAATGGGCGGAATGC+AGG 0.470231 6.2:+38882109 MS.gene98895:CDS
TGCAGTGGTGTTTCTCTCAG+AGG 0.524537 6.2:+38882935 MS.gene98895:intron
AGCAACAAGGTGTCGGTTTG+GGG 0.536057 6.2:+38882977 MS.gene98895:CDS
CATGAGTTACGCCACATCAA+AGG 0.563445 6.2:-38883031 None:intergenic
TGGAATTACTGAAGAAGTAA+TGG 0.572336 6.2:+38882049 MS.gene98895:CDS
TTTCCTCTCCTCTCTGCACG+TGG 0.572661 6.2:+38881212 MS.gene98895:CDS
TTGATTGGCTCCGGAATGGG+CGG 0.583042 6.2:+38882101 MS.gene98895:CDS
GAGACTAAATTGCAGCAACA+AGG 0.585339 6.2:+38882964 MS.gene98895:CDS
GAGTTAGATAAAACAAAATG+TGG 0.592751 6.2:+38882074 MS.gene98895:CDS
AAAGTGTGAAATTACCAGAA+CGG 0.595522 6.2:-38881348 None:intergenic
GCATTGTCTCTGCCATCGTA+TGG 0.604310 6.2:+38883005 MS.gene98895:CDS
TGGGAGAAGAGAGATTAAGG+TGG 0.610292 6.2:-38881315 None:intergenic
AAATTGCAGCAACAAGGTGT+CGG 0.617045 6.2:+38882970 MS.gene98895:CDS
AGTAATTCCAGCATTGACCA+AGG 0.637726 6.2:-38882036 None:intergenic
TCGTATGGTAGCCTTTGATG+TGG 0.645854 6.2:+38883020 MS.gene98895:CDS
AAGCCACGTGCAGAGAGGAG+AGG 0.663817 6.2:-38881215 None:intergenic
CATCAAAGGCTACCATACGA+TGG 0.709186 6.2:-38883017 None:intergenic
GTAACAAGCCACGTGCAGAG+AGG 0.721156 6.2:-38881220 None:intergenic
AGTGTGAAATTACCAGAACG+GGG 0.769634 6.2:-38881346 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AATAATTCATTACATATTAT+TGG - chr6.2:38881700-38881719 None:intergenic 10.0%
!! AGATATTTAAAAAATAAAAC+AGG + chr6.2:38882462-38882481 MS.gene98895:intron 10.0%
!! AAATATCTCTAAATTAAGTA+AGG - chr6.2:38882450-38882469 None:intergenic 15.0%
!! TAATATCAAAAAACTACAAA+AGG - chr6.2:38881889-38881908 None:intergenic 15.0%
!!! CATCATGATATTTTTTTTTT+TGG - chr6.2:38881506-38881525 None:intergenic 15.0%
!! ATATATTAAGTAACAGTTAC+TGG - chr6.2:38882330-38882349 None:intergenic 20.0%
!! GTTGTTTATAATTGACTATT+TGG + chr6.2:38882820-38882839 MS.gene98895:intron 20.0%
! AAAACATTTGCATAAGAAAC+AGG - chr6.2:38882916-38882935 None:intergenic 25.0%
! AATCTAAAAATTCAAGAGAG+TGG - chr6.2:38882138-38882157 None:intergenic 25.0%
! ATATAAAGTAAACTGCTGAA+TGG - chr6.2:38882195-38882214 None:intergenic 25.0%
! GAGTTAGATAAAACAAAATG+TGG + chr6.2:38882074-38882093 MS.gene98895:CDS 25.0%
! GCATAATAACATTTGTTTGT+AGG + chr6.2:38882224-38882243 MS.gene98895:intron 25.0%
! TATAAAGTAAACTGCTGAAT+GGG - chr6.2:38882194-38882213 None:intergenic 25.0%
!! TGAGAAGTTTTCATTATAGT+GGG - chr6.2:38882644-38882663 None:intergenic 25.0%
!! TGTTACTTAATATATTACCC+TGG + chr6.2:38882335-38882354 MS.gene98895:intron 25.0%
AAAGTGTGAAATTACCAGAA+CGG - chr6.2:38881351-38881370 None:intergenic 30.0%
ATCAAATCTTTCTCAACTGA+TGG + chr6.2:38881942-38881961 MS.gene98895:intron 30.0%
CATGTCTCGAGATAAAATTT+GGG + chr6.2:38882882-38882901 MS.gene98895:intron 30.0%
CTAACTGTAGTACAAACTAA+AGG - chr6.2:38882608-38882627 None:intergenic 30.0%
GAAATCTAACTAGTATGCTA+TGG + chr6.2:38882570-38882589 MS.gene98895:intron 30.0%
GAAGAAATATTGTTTGTCGT+TGG - chr6.2:38881845-38881864 None:intergenic 30.0%
TCGATCTGAACTATAAGATA+AGG - chr6.2:38882706-38882725 None:intergenic 30.0%
TGGAATTACTGAAGAAGTAA+TGG + chr6.2:38882049-38882068 MS.gene98895:CDS 30.0%
! AACTGTAAGTTGAGGTTTAT+TGG + chr6.2:38882797-38882816 MS.gene98895:intron 30.0%
! ACTGTAAGTTGAGGTTTATT+GGG + chr6.2:38882798-38882817 MS.gene98895:intron 30.0%
! GTGAGAAGTTTTCATTATAG+TGG - chr6.2:38882645-38882664 None:intergenic 30.0%
! TGACTATTTGGTACATCTTT+TGG + chr6.2:38882832-38882851 MS.gene98895:intron 30.0%
!!! ACAAAATGTGGTGTTTTGAT+TGG + chr6.2:38882086-38882105 MS.gene98895:CDS 30.0%
AAGTGTGAAATTACCAGAAC+GGG - chr6.2:38881350-38881369 None:intergenic 35.0%
AATCTACTTGATGCTGTTAG+TGG + chr6.2:38881782-38881801 MS.gene98895:intron 35.0%
ACAAAGCTGATACAGAAACA+AGG - chr6.2:38881580-38881599 None:intergenic 35.0%
AGTTTGTACTACAGTTAGTG+TGG + chr6.2:38882610-38882629 MS.gene98895:intron 35.0%
ATCTACTTGATGCTGTTAGT+GGG + chr6.2:38881783-38881802 MS.gene98895:intron 35.0%
GCACGAATATGAATGAACTT+CGG - chr6.2:38881867-38881886 None:intergenic 35.0%
GCATGTCTCGAGATAAAATT+TGG + chr6.2:38882881-38882900 MS.gene98895:intron 35.0%
TAAGTATTCTCTGTTTCCAG+AGG + chr6.2:38881907-38881926 MS.gene98895:intron 35.0%
TATATATAACTTCTGCCCCT+AGG - chr6.2:38882276-38882295 None:intergenic 35.0%
TGTCCAAACTTGGAATCAAA+GGG + chr6.2:38882403-38882422 MS.gene98895:intron 35.0%
TGTTAGTAATAAGCCTCCTA+GGG + chr6.2:38882257-38882276 MS.gene98895:intron 35.0%
TTGTTAGTAATAAGCCTCCT+AGG + chr6.2:38882256-38882275 MS.gene98895:intron 35.0%
! ACCAAAGTTTTCAAAGAGGA+TGG + chr6.2:38881974-38881993 MS.gene98895:intron 35.0%
! CATGTTCTAAACACGAAAAC+AGG - chr6.2:38882862-38882881 None:intergenic 35.0%
! CTTATGCAAATGTTTTGCAG+TGG + chr6.2:38882920-38882939 MS.gene98895:intron 35.0%
! TAGCACCAAAGTTTTCAAAG+AGG + chr6.2:38881970-38881989 MS.gene98895:intron 35.0%
! TCCATCCTCTTTGAAAACTT+TGG - chr6.2:38881978-38881997 None:intergenic 35.0%
! TGTTGATGAACTGTAAGTTG+AGG + chr6.2:38882789-38882808 MS.gene98895:intron 35.0%
AAAAAAGCCTTGGTCAATGC+TGG + chr6.2:38882029-38882048 MS.gene98895:CDS 40.0%
AAATTGCAGCAACAAGGTGT+CGG + chr6.2:38882970-38882989 MS.gene98895:CDS 40.0%
AAATTGTGATGCAGGTGAAG+AGG + chr6.2:38882731-38882750 MS.gene98895:intron 40.0%
ACGCCTTTGATCAGAGATAT+CGG + chr6.2:38881750-38881769 MS.gene98895:intron 40.0%
AGTGGGATAAGCGAGATTAA+TGG + chr6.2:38881800-38881819 MS.gene98895:intron 40.0%
AGTGTGAAATTACCAGAACG+GGG - chr6.2:38881349-38881368 None:intergenic 40.0%
ATCAAAGGGCAAAGTCATCA+TGG + chr6.2:38882417-38882436 MS.gene98895:intron 40.0%
GAGACTAAATTGCAGCAACA+AGG + chr6.2:38882964-38882983 MS.gene98895:CDS 40.0%
GATTGGGAGAAGAGAGATTA+AGG - chr6.2:38881321-38881340 None:intergenic 40.0%
GTGTCCAAACTTGGAATCAA+AGG + chr6.2:38882402-38882421 MS.gene98895:intron 40.0%
GTTAGTAATAAGCCTCCTAG+GGG + chr6.2:38882258-38882277 MS.gene98895:intron 40.0%
TTGCCCTTTGATTCCAAGTT+TGG - chr6.2:38882409-38882428 None:intergenic 40.0%
! AGGTTGAAGTGGAAGTTTTG+AGG + chr6.2:38882751-38882770 MS.gene98895:intron 40.0%
! GTAGTAACTTGTGTTGTGTC+CGG + chr6.2:38881725-38881744 MS.gene98895:intron 40.0%
!! AGTAATTCCAGCATTGACCA+AGG - chr6.2:38882039-38882058 None:intergenic 40.0%
ACCGTAAGGGAAAGAAAGTG+TGG - chr6.2:38882370-38882389 None:intergenic 45.0%
ATATAACTTCTGCCCCTAGG+AGG - chr6.2:38882273-38882292 None:intergenic 45.0%
ATGTTGTATCTGCTGACAGC+TGG + chr6.2:38882005-38882024 MS.gene98895:intron 45.0%
CATCAAAGGCTACCATACGA+TGG - chr6.2:38883020-38883039 None:intergenic 45.0%
CCCACACTTTCTTTCCCTTA+CGG + chr6.2:38882366-38882385 MS.gene98895:intron 45.0%
CGATAGCGAAATTGTGATGC+AGG + chr6.2:38882723-38882742 MS.gene98895:intron 45.0%
GACAGCTGGAAAAAAAGCCT+TGG + chr6.2:38882019-38882038 MS.gene98895:intron 45.0%
TCGTATGGTAGCCTTTGATG+TGG + chr6.2:38883020-38883039 MS.gene98895:CDS 45.0%
TCTGTTTCCAGAGGATTGCT+GGG + chr6.2:38881916-38881935 MS.gene98895:intron 45.0%
TGGGAGAAGAGAGATTAAGG+TGG - chr6.2:38881318-38881337 None:intergenic 45.0%
! CCGTAAGGGAAAGAAAGTGT+GGG - chr6.2:38882369-38882388 None:intergenic 45.0%
! GCACCGATATCTCTGATCAA+AGG - chr6.2:38881756-38881775 None:intergenic 45.0%
!!! GTTTTGATTGGCTCCGGAAT+GGG + chr6.2:38882098-38882117 MS.gene98895:CDS 45.0%
!!! TGTGGTGTTTTGATTGGCTC+CGG + chr6.2:38882092-38882111 MS.gene98895:CDS 45.0%
!!! TGTTTTGATTGGCTCCGGAA+TGG + chr6.2:38882097-38882116 MS.gene98895:CDS 45.0%
CGATGTTGGGTGTCCAAACT+TGG + chr6.2:38882393-38882412 MS.gene98895:intron 50.0%
CTCTGTTTCCAGAGGATTGC+TGG + chr6.2:38881915-38881934 MS.gene98895:intron 50.0%
CTGTTTCCAGAGGATTGCTG+GGG + chr6.2:38881917-38881936 MS.gene98895:intron 50.0%
GCATTGTCTCTGCCATCGTA+TGG + chr6.2:38883005-38883024 MS.gene98895:CDS 50.0%
TGCAGGTGAAGAGGTTGAAG+TGG + chr6.2:38882740-38882759 MS.gene98895:intron 50.0%
TGCAGTGGTGTTTCTCTCAG+AGG + chr6.2:38882935-38882954 MS.gene98895:intron 50.0%
! AGGGAAAGAAAGTGTGGGCA+AGG - chr6.2:38882364-38882383 None:intergenic 50.0%
! GGGAAAGAAAGTGTGGGCAA+GGG - chr6.2:38882363-38882382 None:intergenic 50.0%
! TCTCTGATCAAAGGCGTGTC+CGG - chr6.2:38881747-38881766 None:intergenic 50.0%
!! AGCAACAAGGTGTCGGTTTG+GGG + chr6.2:38882977-38882996 MS.gene98895:CDS 50.0%
!! CAGCAACAAGGTGTCGGTTT+GGG + chr6.2:38882976-38882995 MS.gene98895:CDS 50.0%
AAAGTGTGGGCAAGGGAACC+AGG - chr6.2:38882356-38882375 None:intergenic 55.0%
AAGTGTGGGCAAGGGAACCA+GGG - chr6.2:38882355-38882374 None:intergenic 55.0%
ACCCAACATCGACGACCGTA+AGG - chr6.2:38882384-38882403 None:intergenic 55.0%
CCCAACATCGACGACCGTAA+GGG - chr6.2:38882383-38882402 None:intergenic 55.0%
CCCTTACGGTCGTCGATGTT+GGG + chr6.2:38882380-38882399 MS.gene98895:intron 55.0%
GTAACAAGCCACGTGCAGAG+AGG - chr6.2:38881223-38881242 None:intergenic 55.0%
TACCTGCATTCCGCCCATTC+CGG - chr6.2:38882114-38882133 None:intergenic 55.0%
TCCCTTACGGTCGTCGATGT+TGG + chr6.2:38882379-38882398 MS.gene98895:intron 55.0%
TGATCTCCCCAGCAATCCTC+TGG - chr6.2:38881926-38881945 None:intergenic 55.0%
TTTCCTCTCCTCTCTGCACG+TGG + chr6.2:38881212-38881231 MS.gene98895:CDS 55.0%
! ACCAGAACGGGGCATTCGAT+TGG - chr6.2:38881338-38881357 None:intergenic 55.0%
! CCAGAACGGGGCATTCGATT+GGG - chr6.2:38881337-38881356 None:intergenic 55.0%
! TTGATTGGCTCCGGAATGGG+CGG + chr6.2:38882101-38882120 MS.gene98895:CDS 55.0%
!! GCAGCAACAAGGTGTCGGTT+TGG + chr6.2:38882975-38882994 MS.gene98895:CDS 55.0%
AAGCCACGTGCAGAGAGGAG+AGG - chr6.2:38881218-38881237 None:intergenic 60.0%
ATCGTTCTCGTCGTCGCAGC+AGG + chr6.2:38881287-38881306 MS.gene98895:CDS 60.0%
CCCAATCGAATGCCCCGTTC+TGG + chr6.2:38881334-38881353 MS.gene98895:CDS 60.0%
CTCCGGAATGGGCGGAATGC+AGG + chr6.2:38882109-38882128 MS.gene98895:CDS 65.0%


Chromosome Type Strat End Strand Name
chr6.2 gene 38881199 38883047 38881199 ID=MS.gene98895
chr6.2 mRNA 38881199 38883047 38881199 ID=MS.gene98895.t1;Parent=MS.gene98895
chr6.2 exon 38881199 38881355 38881199 ID=MS.gene98895.t1.exon1;Parent=MS.gene98895.t1
chr6.2 CDS 38881199 38881355 38881199 ID=cds.MS.gene98895.t1;Parent=MS.gene98895.t1
chr6.2 exon 38882024 38882130 38882024 ID=MS.gene98895.t1.exon2;Parent=MS.gene98895.t1
chr6.2 CDS 38882024 38882130 38882024 ID=cds.MS.gene98895.t1;Parent=MS.gene98895.t1
chr6.2 exon 38882940 38883047 38882940 ID=MS.gene98895.t1.exon3;Parent=MS.gene98895.t1
chr6.2 CDS 38882940 38883047 38882940 ID=cds.MS.gene98895.t1;Parent=MS.gene98895.t1
Gene Sequence

>MS.gene98895

ATGGCTTCTTCACTTTCCTCTCCTCTCTGCACGTGGCTTGTTACTGCTTGCATGTCAGTCACGTGTGACTCTCACTCTTCTCAATCTCATCGTTCTCGTCGTCGCAGCAGGAGCAACCACCTTAATCTCTCTTCTCCCAATCGAATGCCCCGTTCTGGTAATTTCACACTTTTTTTAATATTATTAATTGCTCAATTTTCATTTCATTTTATTATTTTAAGTTTATTCGTTAATTCTGATGTTTATTATTTTTTTTCTTATTTGTAGTTTATAATTAATTTTTATATCATGATGAATTTAGTAACCAAAAAAAAAAATATCATGATGAATTTTATGTTAGTTATTTTGAAACAATAAGCATTTGATTTTAGTTTTTTTCCTTGTTTCTGTATCAGCTTTGTTTATTCATTTTTGCAAATGTAAATATGCTTGTTGTTTTAATTTATTAATTAATTTGCTTATATCTATATATGAAGCGCAGACAATGACACGTCGACACCAATAATATGTAATGAATTATTTGAATGTAGTAACTTGTGTTGTGTCCGGACACGCCTTTGATCAGAGATATCGGTGCTATAATAATCTACTTGATGCTGTTAGTGGGATAAGCGAGATTAATGGTTTTGATTGTGCACAATATCCAACGACAAACAATATTTCTTCCGAAGTTCATTCATATTCGTGCCTTTTGTAGTTTTTTGATATTAAGTATTCTCTGTTTCCAGAGGATTGCTGGGGAGATCAAATCTTTCTCAACTGATGGCTTTGTAGCACCAAAGTTTTCAAAGAGGATGGATAAATTTATGTTGTATCTGCTGACAGCTGGAAAAAAAGCCTTGGTCAATGCTGGAATTACTGAAGAAGTAATGGATGAGTTAGATAAAACAAAATGTGGTGTTTTGATTGGCTCCGGAATGGGCGGAATGCAGGTAACCACTCTCTTGAATTTTTAGATTATGCTTTAGCACATTGAGAGAAGAGACAGTTGTCCCATTCAGCAGTTTACTTTATATTTAGACGAAGCATAATAACATTTGTTTGTAGGAAGATGTTATTGTTAGTAATAAGCCTCCTAGGGGCAGAAGTTATATATACTAGTAAATTGTTTACTTAATATATTATAAACCAGTAACTGTTACTTAATATATTACCCTGGTTCCCTTGCCCACACTTTCTTTCCCTTACGGTCGTCGATGTTGGGTGTCCAAACTTGGAATCAAAGGGCAAAGTCATCATGGTTCTCTGCCTTACTTAATTTAGAGATATTTAAAAAATAAAACAGGATGCACTATAGTTTTTCTCGTATATTATAACTGTTTATATTCATATATGTGAACAAATCTCATTATAGTTCAATCAATTTAGTTAGAAATCTAACTAGTATGCTATGGTGTTTGTACTCGCCTTTAGTTTGTACTACAGTTAGTGTGGAAGTGAATCCCACTATAATGAAAACTTCTCACTTACATAAATATAAACATATATAATATACAAGTATGATCCTTATCTTATAGTTCAGATCGATAGCGAAATTGTGATGCAGGTGAAGAGGTTGAAGTGGAAGTTTTGAGGAAATCTTACTATACTTGTTGATGAACTGTAAGTTGAGGTTTATTGGGTTGTTTATAATTGACTATTTGGTACATCTTTTGGAAATCCTGTTTTCGTGTTTAGAACATGCATGTCTCGAGATAAAATTTGGGATGCTCAACCTGTTTCTTATGCAAATGTTTTGCAGTGGTGTTTCTCTCAGAGGTTTTTTGAGACTAAATTGCAGCAACAAGGTGTCGGTTTGGGGCTGTTGCATTGTCTCTGCCATCGTATGGTAGCCTTTGATGTGGCGTAA
Protein sequence

>MS.gene98895.t1

MASSLSSPLCTWLVTACMSVTCDSHSSQSHRSRRRSRSNHLNLSSPNRMPRSAGKKALVNAGITEEVMDELDKTKCGVLIGSGMGGMQWCFSQRFFETKLQQQGVGLGLLHCLCHRMVAFDVA