AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene03179

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene03179.t1 MTR_3g088515 66.525 236 19 2 2 177 13 248 5.85e-97 281
MS.gene03179.t1 MTR_1g046200 49.321 221 60 3 5 176 2 219 1.11e-58 186
MS.gene03179.t1 MTR_1g046340 80.180 111 22 0 1 111 1 111 1.46e-58 186
MS.gene03179.t1 MTR_1g046340 88.095 42 3 1 137 176 189 230 1.57e-18 81.6
MS.gene03179.t1 MTR_1g046320 71.560 109 31 0 1 109 1 109 2.24e-47 157
MS.gene03179.t1 MTR_1g046320 76.744 43 8 1 136 176 187 229 1.35e-15 73.6
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 28 sgRNAs with CRISPR-Local

Find 59 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATTTCATCATCTTCAAGTTT+TGG 0.269280 3.3:+73979854 None:intergenic
GCATAGAAGTATGGATTTCC+TGG 0.326303 3.3:+73979809 None:intergenic
CAGAGAAGAAAATTCATTAG+AGG 0.353395 3.3:-73980378 MS.gene03179:CDS
ATGAGCTTCACAAAAGCAAT+TGG 0.382357 3.3:+73980521 None:intergenic
CGCGTCAAAGCACATTCAAT+TGG 0.401347 3.3:-73980437 MS.gene03179:CDS
ACATTACAGACCCAACGAAT+TGG 0.430909 3.3:-73979783 MS.gene03179:CDS
GATTGTGGTTTAGGGAGCAT+TGG 0.466163 3.3:-73979893 MS.gene03179:intron
AAGAACTAAACCAATTCGTT+GGG 0.487807 3.3:+73979773 None:intergenic
ATGAAAGCAGAAAAGAAGAA+AGG 0.488071 3.3:-73980065 MS.gene03179:intron
AAAGAACTAAACCAATTCGT+TGG 0.488811 3.3:+73979772 None:intergenic
CTCTTCCTCTATGATCCCTT+AGG 0.492258 3.3:+73980465 None:intergenic
TCTCATAATGCTTCTCTATG+AGG 0.504327 3.3:+73980736 None:intergenic
GGGATCATAGAGGAAGAGAT+TGG 0.510517 3.3:-73980460 MS.gene03179:CDS
AAGCACATTCAATTGGTGGC+AGG 0.516729 3.3:-73980430 MS.gene03179:CDS
AAGAAGAAAGGAGTTGACAA+GGG 0.522584 3.3:-73980053 MS.gene03179:CDS
AGAGAAGCATTATGAGAGAA+TGG 0.527328 3.3:-73980730 MS.gene03179:intron
GTTGAAATGTATATTCAGCC+AGG 0.532204 3.3:-73979827 MS.gene03179:CDS
AAAGAAGAAAGGAGTTGACA+AGG 0.542225 3.3:-73980054 MS.gene03179:CDS
TGAGCTTCACAAAAGCAATT+GGG 0.545679 3.3:+73980522 None:intergenic
GTCAAAGCACATTCAATTGG+TGG 0.546694 3.3:-73980434 MS.gene03179:CDS
TTTCAATATGTGTGAAAACA+AGG 0.554136 3.3:+73980345 None:intergenic
GAGGAACACCTTGGCAGTGT+TGG 0.557953 3.3:+73980776 None:intergenic
AGCTCATGCTTTCGAAACAA+AGG 0.561664 3.3:-73980505 MS.gene03179:CDS
GGAAGACTTTGAAGAAGTTG+AGG 0.564880 3.3:+73980757 None:intergenic
GCTCATGCTTTCGAAACAAA+GGG 0.566004 3.3:-73980504 MS.gene03179:CDS
GAAGAAGTTGAGGAACACCT+TGG 0.598409 3.3:+73980767 None:intergenic
TTTATCCTAAGGGATCATAG+AGG 0.616153 3.3:-73980470 MS.gene03179:CDS
AATTATGACCAACACTGCCA+AGG 0.625272 3.3:-73980784 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ATCAGTTTTTTTTTTTTTTT+TGG + chr3.3:73979957-73979976 None:intergenic 10.0%
!! AACTTAATAATAATAATCGG+AGG + chr3.3:73979879-73979898 None:intergenic 20.0%
!!! ATTGCAATATTTTATCCTAA+GGG - chr3.3:73980078-73980097 MS.gene03179:intron 20.0%
!!! TATTGCAATATTTTATCCTA+AGG - chr3.3:73980077-73980096 MS.gene03179:intron 20.0%
! ATCAATGTGTAAAAAGACAA+AGG - chr3.3:73980270-73980289 MS.gene03179:intron 25.0%
! ATTTACCTAATGATTGATTG+TGG - chr3.3:73980650-73980669 MS.gene03179:intron 25.0%
! GGAAAATAATAATATGTTGG+AGG - chr3.3:73980306-73980325 MS.gene03179:CDS 25.0%
! GGAGGAAAATAATAATATGT+TGG - chr3.3:73980303-73980322 MS.gene03179:CDS 25.0%
! TAATGATTGATTGTGGTTTA+GGG - chr3.3:73980657-73980676 MS.gene03179:intron 25.0%
! TTTCAATATGTGTGAAAACA+AGG + chr3.3:73980216-73980235 None:intergenic 25.0%
!! TAATGTTTTGCATAGAAGTA+TGG + chr3.3:73980761-73980780 None:intergenic 25.0%
!!! ATTTCATCATCTTCAAGTTT+TGG + chr3.3:73980707-73980726 None:intergenic 25.0%
ATGAAAGCAGAAAAGAAGAA+AGG - chr3.3:73980493-73980512 MS.gene03179:CDS 30.0%
CAAAAACATACATGCTTTGA+AGG + chr3.3:73980566-73980585 None:intergenic 30.0%
CAGAGAAGAAAATTCATTAG+AGG - chr3.3:73980180-73980199 MS.gene03179:intron 30.0%
CTAAACCACAATCAATCATT+AGG + chr3.3:73980658-73980677 None:intergenic 30.0%
CTAATGATTGATTGTGGTTT+AGG - chr3.3:73980656-73980675 MS.gene03179:intron 30.0%
GTGTAAAAAGACAAAGGTAA+TGG - chr3.3:73980276-73980295 MS.gene03179:intron 30.0%
TAATAATATGTTGGAGGATG+AGG - chr3.3:73980312-73980331 MS.gene03179:CDS 30.0%
! AGATCAATGTTACTTAAGAG+TGG + chr3.3:73979984-73980003 None:intergenic 30.0%
AAAGAAGAAAGGAGTTGACA+AGG - chr3.3:73980504-73980523 MS.gene03179:CDS 35.0%
AAGAAGAAAGGAGTTGACAA+GGG - chr3.3:73980505-73980524 MS.gene03179:CDS 35.0%
ATGAGCTTCACAAAAGCAAT+TGG + chr3.3:73980040-73980059 None:intergenic 35.0%
GTTGAAATGTATATTCAGCC+AGG - chr3.3:73980731-73980750 MS.gene03179:CDS 35.0%
TCTCATAATGCTTCTCTATG+AGG + chr3.3:73979825-73979844 None:intergenic 35.0%
TGAGCTTCACAAAAGCAATT+GGG + chr3.3:73980039-73980058 None:intergenic 35.0%
TTTATCCTAAGGGATCATAG+AGG - chr3.3:73980088-73980107 MS.gene03179:intron 35.0%
!! AAAGACAAAGGTAATGGATG+AGG - chr3.3:73980282-73980301 MS.gene03179:intron 35.0%
!! AGAGAAGCATTATGAGAGAA+TGG - chr3.3:73979828-73979847 MS.gene03179:CDS 35.0%
!!! GGCTTTATTTTGATGATGGT+TGG - chr3.3:73980149-73980168 MS.gene03179:intron 35.0%
AATGGTAGAGGAAGAAGAAG+AGG - chr3.3:73980387-73980406 MS.gene03179:CDS 40.0%
ACATTACAGACCCAACGAAT+TGG - chr3.3:73980775-73980794 MS.gene03179:CDS 40.0%
AGCTCATGCTTTCGAAACAA+AGG - chr3.3:73980053-73980072 MS.gene03179:CDS 40.0%
GAAGAAGATGAAGATGGTGA+TGG - chr3.3:73980409-73980428 MS.gene03179:CDS 40.0%
GAAGAGGAAGAAGATGAAGA+TGG - chr3.3:73980403-73980422 MS.gene03179:CDS 40.0%
GCTCATGCTTTCGAAACAAA+GGG - chr3.3:73980054-73980073 MS.gene03179:CDS 40.0%
GTCAAAGCACATTCAATTGG+TGG - chr3.3:73980124-73980143 MS.gene03179:intron 40.0%
! GCATAGAAGTATGGATTTCC+TGG + chr3.3:73980752-73980771 None:intergenic 40.0%
! GGAAGACTTTGAAGAAGTTG+AGG + chr3.3:73979804-73979823 None:intergenic 40.0%
! TGATGATGAAGACGATGATG+AGG - chr3.3:73980432-73980451 MS.gene03179:CDS 40.0%
!!! GGCAGGCTTTATTTTGATGA+TGG - chr3.3:73980145-73980164 MS.gene03179:intron 40.0%
CGACGGTTATACAATGGTAG+AGG - chr3.3:73980375-73980394 MS.gene03179:CDS 45.0%
CGCGTCAAAGCACATTCAAT+TGG - chr3.3:73980121-73980140 MS.gene03179:intron 45.0%
CTCTTCCTCTATGATCCCTT+AGG + chr3.3:73980096-73980115 None:intergenic 45.0%
GAAGAAGTTGAGGAACACCT+TGG + chr3.3:73979794-73979813 None:intergenic 45.0%
GGGATCATAGAGGAAGAGAT+TGG - chr3.3:73980098-73980117 MS.gene03179:intron 45.0%
TATGTTGGAGGATGAGGAAG+AGG - chr3.3:73980318-73980337 MS.gene03179:CDS 45.0%
TGAAGACGATGATGAGGATG+AGG - chr3.3:73980438-73980457 MS.gene03179:CDS 45.0%
TGACGACGACGGTTATACAA+TGG - chr3.3:73980369-73980388 MS.gene03179:CDS 45.0%
! AAGCACATTCAATTGGTGGC+AGG - chr3.3:73980128-73980147 MS.gene03179:intron 45.0%
! GAAGAGGAAGGTGATGATGA+TGG - chr3.3:73980334-73980353 MS.gene03179:CDS 45.0%
! GATTGTGGTTTAGGGAGCAT+TGG - chr3.3:73980665-73980684 MS.gene03179:intron 45.0%
!! GACAAAGGTAATGGATGAGG+AGG - chr3.3:73980285-73980304 MS.gene03179:intron 45.0%
!! AAAAACTTAATAATAATAAT+CGG + chr3.3:73979882-73979901 None:intergenic 5.0%
CGATGATGAGGATGAGGATG+AGG - chr3.3:73980444-73980463 MS.gene03179:CDS 50.0%
TTGGAGGATGAGGAAGAGGA+AGG - chr3.3:73980322-73980341 MS.gene03179:CDS 50.0%
! GGAGATGATGATGACGACGA+CGG - chr3.3:73980358-73980377 MS.gene03179:CDS 50.0%
!! GAGGAAGGTGATGATGATGG+TGG - chr3.3:73980337-73980356 MS.gene03179:CDS 50.0%
GAGGAACACCTTGGCAGTGT+TGG + chr3.3:73979785-73979804 None:intergenic 55.0%


Chromosome Type Strat End Strand Name
chr3.3 gene 73979778 73980802 73979778 ID=MS.gene03179
chr3.3 mRNA 73979778 73980802 73979778 ID=MS.gene03179.t1;Parent=MS.gene03179
chr3.3 exon 73980731 73980802 73980731 ID=MS.gene03179.t1.exon1;Parent=MS.gene03179.t1
chr3.3 CDS 73980731 73980802 73980731 ID=cds.MS.gene03179.t1;Parent=MS.gene03179.t1
chr3.3 exon 73980289 73980549 73980289 ID=MS.gene03179.t1.exon2;Parent=MS.gene03179.t1
chr3.3 CDS 73980289 73980549 73980289 ID=cds.MS.gene03179.t1;Parent=MS.gene03179.t1
chr3.3 exon 73980002 73980077 73980002 ID=MS.gene03179.t1.exon3;Parent=MS.gene03179.t1
chr3.3 CDS 73980002 73980077 73980002 ID=cds.MS.gene03179.t1;Parent=MS.gene03179.t1
chr3.3 exon 73979778 73979902 73979778 ID=MS.gene03179.t1.exon4;Parent=MS.gene03179.t1
chr3.3 CDS 73979778 73979902 73979778 ID=cds.MS.gene03179.t1;Parent=MS.gene03179.t1
Gene Sequence

>MS.gene03179

ATGACCAACACTGCCAAGGTGTTCCTCAACTTCTTCAAAGTCTTCCTCATAGAGAAGCATTATGAGAGAATGGTATTTTCTTATTCTTTATCATGCTTCCTCCGATTATTATTATTAAGTTTTTTTGCATAATATGTGATGTAAGTAGTCATTAACTACATGATACATATTTCATACCAAAAAAAAAAAAAAAACTGATATATCCACTCTTAAGTAACATTGATCTTCATCTTTTTTCTAAAATCTATTGCAGCTTATCCCAATTGCTTTTGTGAAGCTCATGCTTTCGAAACAAAGGGTATTGCAATATTTTATCCTAAGGGATCATAGAGGAAGAGATTGGCGCGTCAAAGCACATTCAATTGGTGGCAGGCTTTATTTTGATGATGGTTGGAAACTATTCAGAGAAGAAAATTCATTAGAGGACAGTGACTTCCTTGTTTTCACACATATTGAAAACAATGTATTCAAGTTCAAAATTCTTGAACTATCATCAATGTGTAAAAAGACAAAGGTAATGGATGAGGAGGAAAATAATAATATGTTGGAGGATGAGGAAGAGGAAGGTGATGATGATGGTGGAGATGATGATGACGACGACGGTTATACAATGGTAGAGGAAGAAGAAGAGGAAGAAGATGAAGATGGTGATGGTGATGATGAAGACGATGATGAGGATGAGGATGAGGATGCTGATGATGATGTGCATATAATAATGAAAGCAGAAAAGAAGAAAGGAGTTGACAAGGGAATCAGTAGAAGCTGTGAACATCAACATTGTAGAACCTTCAAAGCATGTATGTTTTTGACATCGTACTGAAGAAGAAAATACTATTTTGTTTTTTCAGTTGTATATTTATTTGAGATTCAACATTTACCTAATGATTGATTGTGGTTTAGGGAGCATTGGAAGCAGCTCTGCAGCTCCAAAACTTGAAGATGATGAAATTGATGTTGAAATGTATATTCAGCCAGGAAATCCATACTTCTATGCAAAACATTACAGACCCAACGAATTGGTTTAG
Protein sequence

>MS.gene03179.t1

MTNTAKVFLNFFKVFLIEKHYERMLIPIAFVKLMLSKQRVLQYFILRDHRGRDWRVKAHSIGGRLYFDDGWKLFREENSLEDSDFLVFTHIENNVFKFKILELSSMCKKTKKRRKELTRESVEAVNINIVEPSKHVWSIGSSSAAPKLEDDEIDVEMYIQPGNPYFYAKHYRPNELV