AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene054983


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene054983.t1 MTR_7g067000 96.109 257 10 0 1 257 1 257 1.06e-178 491
MS.gene054983.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.gene054983.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 7.4:+36525361 None:intergenic
TCTGCATACTTAACCCAATT+TGG 0.242948 7.4:-36525947 MS.gene054983:CDS
AATGTTTACCTCTTCTTCAT+TGG 0.306206 7.4:-36525521 MS.gene054983:CDS
TAAAGGCTGGTAGCGGAATC+AGG 0.365890 7.4:-36525547 MS.gene054983:CDS
CTTGATGTTGTTCAGTTTGA+AGG 0.387068 7.4:+36526150 None:intergenic
TTGCGTCGCCTTCGACTGAT+TGG 0.388513 7.4:-36525469 MS.gene054983:CDS
AGCGGAGTTTGAAGTTCAAA+TGG 0.433795 7.4:-36525681 MS.gene054983:CDS
AACGCCGAGTTTGAAAAGAT+TGG 0.435378 7.4:-36525914 MS.gene054983:CDS
TGTGCCTCTGCAAGTCCAAT+GGG 0.448799 7.4:-36526081 MS.gene054983:CDS
CAGTTTGAAGGAAGGATGTA+GGG 0.450731 7.4:+36526162 None:intergenic
TCCGCTACCAGCCTTTAGTC+TGG 0.451103 7.4:+36525553 None:intergenic
TCAGTTTGAAGGAAGGATGT+AGG 0.456859 7.4:+36526161 None:intergenic
TTGTGCCTCTGCAAGTCCAA+TGG 0.464033 7.4:-36526082 MS.gene054983:CDS
ATTCCTCGAATTCTAGCATC+TGG 0.480236 7.4:+36525750 None:intergenic
TTTGAAGTTCAAATGGAAAA+CGG 0.485912 7.4:-36525674 MS.gene054983:CDS
CTTTAAGAACCTCAGAAAGA+AGG 0.494681 7.4:-36525633 MS.gene054983:CDS
TCTCATCTAGATATTCTGTA+AGG 0.518089 7.4:+36525972 None:intergenic
AAACTACTGTAAAGGTCAGC+AGG 0.526715 7.4:+36525498 None:intergenic
ATCTGCAGAAATTAACAGAC+AGG 0.528683 7.4:-36525729 MS.gene054983:CDS
AGCTTGAGAATCAGACCCAT+TGG 0.534125 7.4:+36526066 None:intergenic
GAGCCAGATGCTAGAATTCG+AGG 0.536260 7.4:-36525753 MS.gene054983:CDS
CAACAGGTACCTTCTTTCTG+AGG 0.538228 7.4:+36525624 None:intergenic
AATAGAATAAACTACTGTAA+AGG 0.541708 7.4:+36525490 None:intergenic
TAAAGATGTCACCAGACTAA+AGG 0.542082 7.4:-36525564 MS.gene054983:CDS
GATTCTCAAGCTCCTCAACC+AGG 0.562806 7.4:-36526055 MS.gene054983:CDS
AGAGCGTGAAAACGAATTAG+CGG 0.567801 7.4:-36525699 MS.gene054983:CDS
ATGGAAAACGGCAGAAACGA+AGG 0.568917 7.4:-36525662 MS.gene054983:CDS
ACCAGACTAAAGGCTGGTAG+CGG 0.574115 7.4:-36525554 MS.gene054983:CDS
TCAGCAGGCCAATGAAGAAG+AGG 0.579281 7.4:+36525513 None:intergenic
TAAAGCAAAAGCCAAAGAAG+AGG 0.598747 7.4:-36525597 MS.gene054983:CDS
GATGTCACCAGACTAAAGGC+TGG 0.604550 7.4:-36525560 MS.gene054983:CDS
TTAACAGATAACAGCAAACA+TGG 0.611396 7.4:-36525777 MS.gene054983:intron
ATGTTGTTCAGTTTGAAGGA+AGG 0.625091 7.4:+36526154 None:intergenic
TGGAAAACGGCAGAAACGAA+GGG 0.629953 7.4:-36525661 MS.gene054983:CDS
CAGACCCATTGGACTTGCAG+AGG 0.674115 7.4:+36526077 None:intergenic
CATCTAGATATTCTGTAAGG+CGG 0.677478 7.4:+36525975 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTTTTTATTTACATTTTACA+TGG + chr7.4:36525703-36525722 None:intergenic 10.0%
!! AAATACAAAGTGAATATAAG+AGG + chr7.4:36525729-36525748 None:intergenic 20.0%
!! AATAGAATAAACTACTGTAA+AGG + chr7.4:36526037-36526056 None:intergenic 20.0%
!! TTTGAAGTTCAAATGGAAAA+CGG - chr7.4:36525850-36525869 MS.gene054983:intron 25.0%
!!! TTTGTTTTCTTCTTCATTGT+TGG + chr7.4:36526178-36526197 None:intergenic 25.0%
AATGTTTACCTCTTCTTCAT+TGG - chr7.4:36526003-36526022 MS.gene054983:CDS 30.0%
TCTCATCTAGATATTCTGTA+AGG + chr7.4:36525555-36525574 None:intergenic 30.0%
TTAACAGATAACAGCAAACA+TGG - chr7.4:36525747-36525766 MS.gene054983:CDS 30.0%
! TTCTCCAATCTTTTCAAACT+CGG + chr7.4:36525617-36525636 None:intergenic 30.0%
!! TTCATTGTTGGTCTTTCTTA+TGG + chr7.4:36526166-36526185 None:intergenic 30.0%
!!! AATTTTTTCTGCCTCTTCTT+TGG + chr7.4:36525941-36525960 None:intergenic 30.0%
!!! GTTGACTTTTTCACCAAATT+GGG + chr7.4:36525593-36525612 None:intergenic 30.0%
!!! TCTTGTTTTTTTGTATCTCC+TGG + chr7.4:36525490-36525509 None:intergenic 30.0%
ATCTGCAGAAATTAACAGAC+AGG - chr7.4:36525795-36525814 MS.gene054983:intron 35.0%
ATGTTGTTCAGTTTGAAGGA+AGG + chr7.4:36525373-36525392 None:intergenic 35.0%
CATCTAGATATTCTGTAAGG+CGG + chr7.4:36525552-36525571 None:intergenic 35.0%
CTTGATGTTGTTCAGTTTGA+AGG + chr7.4:36525377-36525396 None:intergenic 35.0%
TAAAGATGTCACCAGACTAA+AGG - chr7.4:36525960-36525979 MS.gene054983:CDS 35.0%
TAAAGCAAAAGCCAAAGAAG+AGG - chr7.4:36525927-36525946 MS.gene054983:CDS 35.0%
TCTGCATACTTAACCCAATT+TGG - chr7.4:36525577-36525596 MS.gene054983:CDS 35.0%
! CTTTAAGAACCTCAGAAAGA+AGG - chr7.4:36525891-36525910 MS.gene054983:CDS 35.0%
! GCTTTTGCTTTATCAACAAC+AGG + chr7.4:36525919-36525938 None:intergenic 35.0%
! TGGAGAAAAGTTGCAGTTTT+TGG - chr7.4:36526075-36526094 MS.gene054983:CDS 35.0%
! TGTTGTAAAGTCTTTTGCAG+TGG + chr7.4:36525408-36525427 None:intergenic 35.0%
!!! AGTTTTTGGAGCAATTCTTG+TGG - chr7.4:36526089-36526108 MS.gene054983:CDS 35.0%
!!! CGTTGACTTTTTCACCAAAT+TGG + chr7.4:36525594-36525613 None:intergenic 35.0%
!!! TTTTTTGTATCTCCTGGTTG+AGG + chr7.4:36525484-36525503 None:intergenic 35.0%
AAACTACTGTAAAGGTCAGC+AGG + chr7.4:36526029-36526048 None:intergenic 40.0%
AACGCCGAGTTTGAAAAGAT+TGG - chr7.4:36525610-36525629 MS.gene054983:CDS 40.0%
AGAGCGTGAAAACGAATTAG+CGG - chr7.4:36525825-36525844 MS.gene054983:intron 40.0%
ATTCCTCGAATTCTAGCATC+TGG + chr7.4:36525777-36525796 None:intergenic 40.0%
CAGTTTGAAGGAAGGATGTA+GGG + chr7.4:36525365-36525384 None:intergenic 40.0%
TCAGTTTGAAGGAAGGATGT+AGG + chr7.4:36525366-36525385 None:intergenic 40.0%
! ACTTTTCTCCAATCAGTCGA+AGG + chr7.4:36526066-36526085 None:intergenic 40.0%
! AGCGGAGTTTGAAGTTCAAA+TGG - chr7.4:36525843-36525862 MS.gene054983:intron 40.0%
! TTACATGGTTAGCTCGAAAG+TGG + chr7.4:36525688-36525707 None:intergenic 40.0%
!!! GACTTTTCGAGTTTGTAGCA+TGG + chr7.4:36525530-36525549 None:intergenic 40.0%
AAGTGGAAGCAAGCATACTC+TGG + chr7.4:36525671-36525690 None:intergenic 45.0%
AGCTTGAGAATCAGACCCAT+TGG + chr7.4:36525461-36525480 None:intergenic 45.0%
ATGGAAAACGGCAGAAACGA+AGG - chr7.4:36525862-36525881 MS.gene054983:intron 45.0%
CAACAGGTACCTTCTTTCTG+AGG + chr7.4:36525903-36525922 None:intergenic 45.0%
TGGAAAACGGCAGAAACGAA+GGG - chr7.4:36525863-36525882 MS.gene054983:intron 45.0%
ACCAGACTAAAGGCTGGTAG+CGG - chr7.4:36525970-36525989 MS.gene054983:CDS 50.0%
GAGCCAGATGCTAGAATTCG+AGG - chr7.4:36525771-36525790 MS.gene054983:CDS 50.0%
GATGTCACCAGACTAAAGGC+TGG - chr7.4:36525964-36525983 MS.gene054983:CDS 50.0%
GATTCTCAAGCTCCTCAACC+AGG - chr7.4:36525469-36525488 MS.gene054983:CDS 50.0%
TCAGCAGGCCAATGAAGAAG+AGG + chr7.4:36526014-36526033 None:intergenic 50.0%
TGTGCCTCTGCAAGTCCAAT+GGG - chr7.4:36525443-36525462 MS.gene054983:CDS 50.0%
TTGTGCCTCTGCAAGTCCAA+TGG - chr7.4:36525442-36525461 MS.gene054983:CDS 50.0%
!! TAAAGGCTGGTAGCGGAATC+AGG - chr7.4:36525977-36525996 MS.gene054983:CDS 50.0%
CAGACCCATTGGACTTGCAG+AGG + chr7.4:36525450-36525469 None:intergenic 55.0%
TCCGCTACCAGCCTTTAGTC+TGG + chr7.4:36525974-36525993 None:intergenic 55.0%
TTGCGTCGCCTTCGACTGAT+TGG - chr7.4:36526055-36526074 MS.gene054983:CDS 55.0%


Chromosome Type Strat End Strand Name
chr7.4 gene 36525346 36526200 36525346 ID=MS.gene054983
chr7.4 mRNA 36525346 36526200 36525346 ID=MS.gene054983.t1;Parent=MS.gene054983
chr7.4 exon 36525874 36526200 36525874 ID=MS.gene054983.t1.exon1;Parent=MS.gene054983.t1
chr7.4 CDS 36525874 36526200 36525874 ID=cds.MS.gene054983.t1;Parent=MS.gene054983.t1
chr7.4 exon 36525346 36525792 36525346 ID=MS.gene054983.t1.exon2;Parent=MS.gene054983.t1
chr7.4 CDS 36525346 36525792 36525346 ID=cds.MS.gene054983.t1;Parent=MS.gene054983.t1
Gene Sequence

>MS.gene054983

ATGATTGCTCTCAAATCCCTACATCCTTCCTTCAAACTGAACAACATCAAGTGTAATATCCACTGCAAAAGACTTTACAACACAAGAAGTTATACTTTGTGCCTCTGCAAGTCCAATGGGTCTGATTCTCAAGCTCCTCAACCAGGAGATACAAAAAAACAAGAACTGCTAGCACAGATTGCCATGCTACAAACTCGAAAAGTCCGCCTTACAGAATATCTAGATGAGAGATCTGCATACTTAACCCAATTTGGTGAAAAAGTCAACGCCGAGTTTGAAAAGATTGGAGAAGATGCACTCAAAGAATTAGATGAAGCTAGTGCCAGAGTATGCTTGCTTCCACTTTCGAGCTAACCATGTAAAATGTAAATAAAAAACGACCTCTTATATTCACTTTGTATTTAACAGATAACAGCAAACATGGAGAGCCAGATGCTAGAATTCGAGGAATCTGCAGAAATTAACAGACAGGAGATTCAAGAGCGTGAAAACGAATTAGCGGAGTTTGAAGTTCAAATGGAAAACGGCAGAAACGAAGGGCTATTCTTTAAGAACCTCAGAAAGAAGGTACCTGTTGTTGATAAAGCAAAAGCCAAAGAAGAGGCAGAAAAAATTAAAGATGTCACCAGACTAAAGGCTGGTAGCGGAATCAGGAAAAATGTTTACCTCTTCTTCATTGGCCTGCTGACCTTTACAGTAGTTTATTCTATTGCGTCGCCTTCGACTGATTGGAGAAAAGTTGCAGTTTTTGGAGCAATTCTTGTGGCTTTGACTTCTCAGTTCGTCTATGAACAAAACATGTCAGCAGACACTAGAACCATAAGAAAGACCAACAATGAAGAAGAAAACAAATGA

Protein sequence

>MS.gene054983.t1

MIALKSLHPSFKLNNIKCNIHCKRLYNTRSYTLCLCKSNGSDSQAPQPGDTKKQELLAQIAMLQTRKVRLTEYLDERSAYLTQFGEKVNAEFEKIGEDALKELDEASARITANMESQMLEFEESAEINRQEIQERENELAEFEVQMENGRNEGLFFKNLRKKVPVVDKAKAKEEAEKIKDVTRLKAGSGIRKNVYLFFIGLLTFTVVYSIASPSTDWRKVAVFGAILVALTSQFVYEQNMSADTRTIRKTNNEEENK