AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene84390


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene84390.t1 MTR_7g067000 96.109 257 10 0 1 257 1 257 1.06e-178 491
MS.gene84390.t1 MTR_4g015010 59.127 252 90 6 1 239 14 265 7.96e-89 265
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene84390.t1 AT3G09050 60.938 192 73 2 49 240 56 245 1.53e-77 235

Find 36 sgRNAs with CRISPR-Local

Find 53 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTCATTGTTGGTCTTTCTTA+TGG 0.167344 7.3:-37857657 None:intergenic
TCTGCATACTTAACCCAATT+TGG 0.242948 7.3:+37857071 MS.gene84390:CDS
AATGTTTACCTCTTCTTCAT+TGG 0.306206 7.3:+37857497 MS.gene84390:CDS
TAAAGGCTGGTAGCGGAATC+AGG 0.365890 7.3:+37857471 MS.gene84390:CDS
CTTGATGTTGTTCAGTTTGA+AGG 0.387068 7.3:-37856868 None:intergenic
TTGCGTCGCCTTCGACTGAT+TGG 0.388513 7.3:+37857549 MS.gene84390:CDS
AGCGGAGTTTGAAGTTCAAA+TGG 0.433795 7.3:+37857337 MS.gene84390:CDS
AACGCCGAGTTTGAAAAGAT+TGG 0.435378 7.3:+37857104 MS.gene84390:CDS
TGTGCCTCTGCAAGTCCAAT+GGG 0.448799 7.3:+37856937 MS.gene84390:CDS
CAGTTTGAAGGAAGGATGTA+GGG 0.450731 7.3:-37856856 None:intergenic
TCCGCTACCAGCCTTTAGTC+TGG 0.451103 7.3:-37857465 None:intergenic
TCAGTTTGAAGGAAGGATGT+AGG 0.456859 7.3:-37856857 None:intergenic
TTGTGCCTCTGCAAGTCCAA+TGG 0.464033 7.3:+37856936 MS.gene84390:CDS
ATTCCTCGAATTCTAGCATC+TGG 0.480236 7.3:-37857268 None:intergenic
TTTGAAGTTCAAATGGAAAA+CGG 0.485912 7.3:+37857344 MS.gene84390:CDS
CTTTAAGAACCTCAGAAAGA+AGG 0.494681 7.3:+37857385 MS.gene84390:CDS
TCTCATCTAGATATTCTGTA+AGG 0.518089 7.3:-37857046 None:intergenic
AAACTACTGTAAAGGTCAGC+AGG 0.526715 7.3:-37857520 None:intergenic
ATCTGCAGAAATTAACAGAC+AGG 0.528683 7.3:+37857289 MS.gene84390:CDS
AGCTTGAGAATCAGACCCAT+TGG 0.534125 7.3:-37856952 None:intergenic
GAGCCAGATGCTAGAATTCG+AGG 0.536260 7.3:+37857265 MS.gene84390:CDS
CAACAGGTACCTTCTTTCTG+AGG 0.538228 7.3:-37857394 None:intergenic
AATAGAATAAACTACTGTAA+AGG 0.541708 7.3:-37857528 None:intergenic
TAAAGATGTCACCAGACTAA+AGG 0.542082 7.3:+37857454 MS.gene84390:CDS
GATTCTCAAGCTCCTCAACC+AGG 0.562806 7.3:+37856963 MS.gene84390:CDS
AGAGCGTGAAAACGAATTAG+CGG 0.567801 7.3:+37857319 MS.gene84390:CDS
ATGGAAAACGGCAGAAACGA+AGG 0.568917 7.3:+37857356 MS.gene84390:CDS
ACCAGACTAAAGGCTGGTAG+CGG 0.574115 7.3:+37857464 MS.gene84390:CDS
TCAGCAGGCCAATGAAGAAG+AGG 0.579281 7.3:-37857505 None:intergenic
TAAAGCAAAAGCCAAAGAAG+AGG 0.598747 7.3:+37857421 MS.gene84390:CDS
GATGTCACCAGACTAAAGGC+TGG 0.604550 7.3:+37857458 MS.gene84390:CDS
TTAACAGATAACAGCAAACA+TGG 0.611396 7.3:+37857241 MS.gene84390:intron
ATGTTGTTCAGTTTGAAGGA+AGG 0.625091 7.3:-37856864 None:intergenic
TGGAAAACGGCAGAAACGAA+GGG 0.629953 7.3:+37857357 MS.gene84390:CDS
CAGACCCATTGGACTTGCAG+AGG 0.674115 7.3:-37856941 None:intergenic
CATCTAGATATTCTGTAAGG+CGG 0.677478 7.3:-37857043 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTTTTTATTTACATTTTACA+TGG - chr7.3:37857197-37857216 None:intergenic 10.0%
!! AAATACAAAGTGAATATAAG+AGG - chr7.3:37857223-37857242 None:intergenic 20.0%
!! AATAGAATAAACTACTGTAA+AGG - chr7.3:37857531-37857550 None:intergenic 20.0%
!! TTTGAAGTTCAAATGGAAAA+CGG + chr7.3:37857344-37857363 MS.gene84390:CDS 25.0%
!!! TTTGTTTTCTTCTTCATTGT+TGG - chr7.3:37857672-37857691 None:intergenic 25.0%
AATGTTTACCTCTTCTTCAT+TGG + chr7.3:37857497-37857516 MS.gene84390:CDS 30.0%
TCTCATCTAGATATTCTGTA+AGG - chr7.3:37857049-37857068 None:intergenic 30.0%
TTAACAGATAACAGCAAACA+TGG + chr7.3:37857241-37857260 MS.gene84390:intron 30.0%
! TTCTCCAATCTTTTCAAACT+CGG - chr7.3:37857111-37857130 None:intergenic 30.0%
!! TTCATTGTTGGTCTTTCTTA+TGG - chr7.3:37857660-37857679 None:intergenic 30.0%
!!! AATTTTTTCTGCCTCTTCTT+TGG - chr7.3:37857435-37857454 None:intergenic 30.0%
!!! GTTGACTTTTTCACCAAATT+GGG - chr7.3:37857087-37857106 None:intergenic 30.0%
!!! TCTTGTTTTTTTGTATCTCC+TGG - chr7.3:37856984-37857003 None:intergenic 30.0%
ATCTGCAGAAATTAACAGAC+AGG + chr7.3:37857289-37857308 MS.gene84390:CDS 35.0%
ATGTTGTTCAGTTTGAAGGA+AGG - chr7.3:37856867-37856886 None:intergenic 35.0%
CATCTAGATATTCTGTAAGG+CGG - chr7.3:37857046-37857065 None:intergenic 35.0%
CTTGATGTTGTTCAGTTTGA+AGG - chr7.3:37856871-37856890 None:intergenic 35.0%
TAAAGATGTCACCAGACTAA+AGG + chr7.3:37857454-37857473 MS.gene84390:CDS 35.0%
TAAAGCAAAAGCCAAAGAAG+AGG + chr7.3:37857421-37857440 MS.gene84390:CDS 35.0%
TCTGCATACTTAACCCAATT+TGG + chr7.3:37857071-37857090 MS.gene84390:CDS 35.0%
! CTTTAAGAACCTCAGAAAGA+AGG + chr7.3:37857385-37857404 MS.gene84390:CDS 35.0%
! GCTTTTGCTTTATCAACAAC+AGG - chr7.3:37857413-37857432 None:intergenic 35.0%
! TGGAGAAAAGTTGCAGTTTT+TGG + chr7.3:37857569-37857588 MS.gene84390:CDS 35.0%
! TGTTGTAAAGTCTTTTGCAG+TGG - chr7.3:37856902-37856921 None:intergenic 35.0%
!!! AGTTTTTGGAGCAATTCTTG+TGG + chr7.3:37857583-37857602 MS.gene84390:CDS 35.0%
!!! CGTTGACTTTTTCACCAAAT+TGG - chr7.3:37857088-37857107 None:intergenic 35.0%
!!! TTTTTTGTATCTCCTGGTTG+AGG - chr7.3:37856978-37856997 None:intergenic 35.0%
AAACTACTGTAAAGGTCAGC+AGG - chr7.3:37857523-37857542 None:intergenic 40.0%
AACGCCGAGTTTGAAAAGAT+TGG + chr7.3:37857104-37857123 MS.gene84390:CDS 40.0%
AGAGCGTGAAAACGAATTAG+CGG + chr7.3:37857319-37857338 MS.gene84390:CDS 40.0%
ATTCCTCGAATTCTAGCATC+TGG - chr7.3:37857271-37857290 None:intergenic 40.0%
CAGTTTGAAGGAAGGATGTA+GGG - chr7.3:37856859-37856878 None:intergenic 40.0%
TCAGTTTGAAGGAAGGATGT+AGG - chr7.3:37856860-37856879 None:intergenic 40.0%
! ACTTTTCTCCAATCAGTCGA+AGG - chr7.3:37857560-37857579 None:intergenic 40.0%
! AGCGGAGTTTGAAGTTCAAA+TGG + chr7.3:37857337-37857356 MS.gene84390:CDS 40.0%
! TTACATGGTTAGCTCGAAAG+TGG - chr7.3:37857182-37857201 None:intergenic 40.0%
!!! GACTTTTCGAGTTTGTAGCA+TGG - chr7.3:37857024-37857043 None:intergenic 40.0%
AAGTGGAAGCAAGCATACTC+TGG - chr7.3:37857165-37857184 None:intergenic 45.0%
AGCTTGAGAATCAGACCCAT+TGG - chr7.3:37856955-37856974 None:intergenic 45.0%
ATGGAAAACGGCAGAAACGA+AGG + chr7.3:37857356-37857375 MS.gene84390:CDS 45.0%
CAACAGGTACCTTCTTTCTG+AGG - chr7.3:37857397-37857416 None:intergenic 45.0%
TGGAAAACGGCAGAAACGAA+GGG + chr7.3:37857357-37857376 MS.gene84390:CDS 45.0%
ACCAGACTAAAGGCTGGTAG+CGG + chr7.3:37857464-37857483 MS.gene84390:CDS 50.0%
GAGCCAGATGCTAGAATTCG+AGG + chr7.3:37857265-37857284 MS.gene84390:CDS 50.0%
GATGTCACCAGACTAAAGGC+TGG + chr7.3:37857458-37857477 MS.gene84390:CDS 50.0%
GATTCTCAAGCTCCTCAACC+AGG + chr7.3:37856963-37856982 MS.gene84390:CDS 50.0%
TCAGCAGGCCAATGAAGAAG+AGG - chr7.3:37857508-37857527 None:intergenic 50.0%
TGTGCCTCTGCAAGTCCAAT+GGG + chr7.3:37856937-37856956 MS.gene84390:CDS 50.0%
TTGTGCCTCTGCAAGTCCAA+TGG + chr7.3:37856936-37856955 MS.gene84390:CDS 50.0%
!! TAAAGGCTGGTAGCGGAATC+AGG + chr7.3:37857471-37857490 MS.gene84390:CDS 50.0%
CAGACCCATTGGACTTGCAG+AGG - chr7.3:37856944-37856963 None:intergenic 55.0%
TCCGCTACCAGCCTTTAGTC+TGG - chr7.3:37857468-37857487 None:intergenic 55.0%
TTGCGTCGCCTTCGACTGAT+TGG + chr7.3:37857549-37857568 MS.gene84390:CDS 55.0%


Chromosome Type Strat End Strand Name
chr7.3 gene 37856840 37857694 37856840 ID=MS.gene84390
chr7.3 mRNA 37856840 37857694 37856840 ID=MS.gene84390.t1;Parent=MS.gene84390
chr7.3 exon 37856840 37857166 37856840 ID=MS.gene84390.t1.exon1;Parent=MS.gene84390.t1
chr7.3 CDS 37856840 37857166 37856840 ID=cds.MS.gene84390.t1;Parent=MS.gene84390.t1
chr7.3 exon 37857248 37857694 37857248 ID=MS.gene84390.t1.exon2;Parent=MS.gene84390.t1
chr7.3 CDS 37857248 37857694 37857248 ID=cds.MS.gene84390.t1;Parent=MS.gene84390.t1
Gene Sequence

>MS.gene84390

ATGATTGCTCTCAAATCCCTACATCCTTCCTTCAAACTGAACAACATCAAGTGTAATATCCACTGCAAAAGACTTTACAACACAAGAAGTTATACTTTGTGCCTCTGCAAGTCCAATGGGTCTGATTCTCAAGCTCCTCAACCAGGAGATACAAAAAAACAAGAACTGCTAGCACAGATTGCCATGCTACAAACTCGAAAAGTCCGCCTTACAGAATATCTAGATGAGAGATCTGCATACTTAACCCAATTTGGTGAAAAAGTCAACGCCGAGTTTGAAAAGATTGGAGAAGATGCACTCAAAGAATTAGATGAAGCTAGTGCCAGAGTATGCTTGCTTCCACTTTCGAGCTAACCATGTAAAATGTAAATAAAAAACGACCTCTTATATTCACTTTGTATTTAACAGATAACAGCAAACATGGAGAGCCAGATGCTAGAATTCGAGGAATCTGCAGAAATTAACAGACAGGAGATTCAAGAGCGTGAAAACGAATTAGCGGAGTTTGAAGTTCAAATGGAAAACGGCAGAAACGAAGGGCTATTCTTTAAGAACCTCAGAAAGAAGGTACCTGTTGTTGATAAAGCAAAAGCCAAAGAAGAGGCAGAAAAAATTAAAGATGTCACCAGACTAAAGGCTGGTAGCGGAATCAGGAAAAATGTTTACCTCTTCTTCATTGGCCTGCTGACCTTTACAGTAGTTTATTCTATTGCGTCGCCTTCGACTGATTGGAGAAAAGTTGCAGTTTTTGGAGCAATTCTTGTGGCTTTGACTTCTCAGTTCGTCTATGAACAAAACATGTCAGCAGACACTAGAACCATAAGAAAGACCAACAATGAAGAAGAAAACAAATGA

Protein sequence

>MS.gene84390.t1

MIALKSLHPSFKLNNIKCNIHCKRLYNTRSYTLCLCKSNGSDSQAPQPGDTKKQELLAQIAMLQTRKVRLTEYLDERSAYLTQFGEKVNAEFEKIGEDALKELDEASARITANMESQMLEFEESAEINRQEIQERENELAEFEVQMENGRNEGLFFKNLRKKVPVVDKAKAKEEAEKIKDVTRLKAGSGIRKNVYLFFIGLLTFTVVYSIASPSTDWRKVAVFGAILVALTSQFVYEQNMSADTRTIRKTNNEEENK