AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene055580


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene055580.t1 MTR_1g082950 97.758 223 5 0 1 223 40 262 9.37e-162 447
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene055580.t1 AT1G55000 63.761 218 76 2 7 221 2 219 1.19e-97 283
MS.gene055580.t1 AT1G55000 63.761 218 76 2 7 221 2 219 1.19e-97 283
MS.gene055580.t1 AT1G55000 63.761 218 76 2 7 221 2 219 1.19e-97 283

Find 52 sgRNAs with CRISPR-Local

Find 99 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ACCCGATTTCTAGAAGCTTC+TGG 0.301921 1.2:-60005591 MS.gene055580:CDS
CTCCAGAAGCTTCTAGAAAT+CGG 0.322000 1.2:+60005589 None:intergenic
AACTTGCATGCTTCTCTTCA+AGG 0.333288 1.2:+60004441 None:intergenic
CGAGTTGCGTCTGCCGAGTC+TGG 0.340636 1.2:-60005690 MS.gene055580:CDS
GAAGGTTCTGGAAGATGATT+TGG 0.344754 1.2:+60005734 None:intergenic
AGAATATCGGGATTACTAAT+AGG 0.352325 1.2:+60004610 None:intergenic
GATCGGGGATGGGAAGGTTC+TGG 0.355186 1.2:+60005722 None:intergenic
CTCAGAAGAAACCAACAAAA+AGG 0.366398 1.2:-60004473 MS.gene055580:CDS
CGCCGTTAAGTACTCCGTTC+AGG 0.393861 1.2:-60005500 MS.gene055580:intron
AAGAACTTGCTTTATTGAGC+TGG 0.414503 1.2:-60004581 MS.gene055580:CDS
CTTAGCACCGTGGAAATTGA+AGG 0.424552 1.2:-60005626 MS.gene055580:CDS
CAACTCGCACGTGCGAGATC+GGG 0.428494 1.2:+60005706 None:intergenic
TCCAGAAGCTTCTAGAAATC+GGG 0.438818 1.2:+60005590 None:intergenic
CCGCGGACCTTCAGTGGGGC+AGG 0.445516 1.2:-60004348 MS.gene055580:CDS
GCAACTCGCACGTGCGAGAT+CGG 0.461154 1.2:+60005705 None:intergenic
AGAAGTTGCAGTGTTGTATC+CGG 0.473663 1.2:-60004542 MS.gene055580:CDS
GACCTGAACGGAGTACTTAA+CGG 0.475918 1.2:+60005498 None:intergenic
GATTTGGAGGGTGTCGGTGG+AGG 0.478995 1.2:+60005750 None:intergenic
AACAACATGATGAGCGATCA+TGG 0.498173 1.2:-60004661 MS.gene055580:CDS
CCACGGTGCTAAGAAAGCTC+TGG 0.499969 1.2:+60005636 None:intergenic
CGCACGTGCGAGATCGGGGA+TGG 0.503094 1.2:+60005711 None:intergenic
CTACTTGCCTGCCCCACTGA+AGG 0.503713 1.2:+60004341 None:intergenic
TACTACTGGTCTGTTTCAAA+CGG 0.508801 1.2:-60004400 MS.gene055580:CDS
TGGAAATTGAAGGACGTAGT+TGG 0.509813 1.2:-60005616 MS.gene055580:CDS
TTTATGTCAGGTACATCATC+CGG 0.516672 1.2:+60004523 None:intergenic
CTTCAGTGGGGCAGGCAAGT+AGG 0.518848 1.2:-60004340 MS.gene055580:CDS
GATGATTTGGAGGGTGTCGG+TGG 0.523454 1.2:+60005747 None:intergenic
GTGCGAGATCGGGGATGGGA+AGG 0.529104 1.2:+60005716 None:intergenic
GCGGAGAAATGAGAATTCAT+TGG 0.531909 1.2:+60005778 None:intergenic
GTGAAACTGCTCAATACTAC+TGG 0.532559 1.2:-60004414 MS.gene055580:CDS
GGTTCTGGAAGATGATTTGG+AGG 0.546672 1.2:+60005737 None:intergenic
ACATAGCTACTCTTTATGTC+AGG 0.547238 1.2:+60004511 None:intergenic
GCACGTGCGAGATCGGGGAT+GGG 0.550351 1.2:+60005712 None:intergenic
GCGATCATGGTATATACTCA+AGG 0.575308 1.2:-60004648 MS.gene055580:CDS
AACTCGCACGTGCGAGATCG+GGG 0.575733 1.2:+60005707 None:intergenic
GAAGATGATTTGGAGGGTGT+CGG 0.579288 1.2:+60005744 None:intergenic
ATGGTATATACTCAAGGGAA+AGG 0.586472 1.2:-60004642 MS.gene055580:CDS
ACTACGTCCTTCAATTTCCA+CGG 0.587526 1.2:+60005619 None:intergenic
GGTGTCGGTGGAGGAAAGTG+CGG 0.588317 1.2:+60005759 None:intergenic
GGTTACCATCTCCCTTTGTG+AGG 0.590197 1.2:+60005657 None:intergenic
GGTAGCCTCACAAAGGGAGA+TGG 0.593006 1.2:-60005662 MS.gene055580:CDS
CGTCTGCCGAGTCTGGAACT+CGG 0.602052 1.2:-60005683 MS.gene055580:CDS
CGATCATGGTATATACTCAA+GGG 0.604160 1.2:-60004647 MS.gene055580:CDS
GAACTCGGTAGCCTCACAAA+GGG 0.613154 1.2:-60005668 MS.gene055580:CDS
ATCTCGCATCGTATTGTGCG+TGG 0.618881 1.2:-60005541 MS.gene055580:CDS
CCTGCCCCACTGAAGGTCCG+CGG 0.625706 1.2:+60004348 None:intergenic
GGAACTCGGTAGCCTCACAA+AGG 0.631909 1.2:-60005669 MS.gene055580:CDS
TAAACCCAAACGGACCTGAA+CGG 0.641440 1.2:+60005486 None:intergenic
AGGCTACCGAGTTCCAGACT+CGG 0.651299 1.2:+60005677 None:intergenic
GTTCTGGAAGATGATTTGGA+GGG 0.706445 1.2:+60005738 None:intergenic
AATTCAGCAAGAGCAGCACG+AGG 0.707212 1.2:+60004373 None:intergenic
CCAGAGCTTTCTTAGCACCG+TGG 0.711370 1.2:-60005636 MS.gene055580:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! CTAGTTTATAAATTCTTAAT+AGG + chr1.2:60005280-60005299 None:intergenic 15.0%
!!! TTAAAATGTTTTTAATTTCG+TGG - chr1.2:60005151-60005170 MS.gene055580:intron 15.0%
!!! TTTAATACTTTTGATAAAGT+TGG - chr1.2:60005373-60005392 MS.gene055580:intron 15.0%
!! AAATGATGACAATGAAATTA+TGG - chr1.2:60004716-60004735 MS.gene055580:intron 20.0%
!! TTCAATGTAATTATATGTGT+TGG - chr1.2:60004946-60004965 MS.gene055580:intron 20.0%
!!! AGTTCTTTTAACAAGAATAT+CGG + chr1.2:60005511-60005530 None:intergenic 20.0%
!!! TACTGTGATCAAATATTTTA+GGG - chr1.2:60005120-60005139 MS.gene055580:intron 20.0%
!!! TGATTTTCTCAAATTATTAG+CGG + chr1.2:60004921-60004940 None:intergenic 20.0%
! AACAAAGTAATAAACCCAAA+CGG + chr1.2:60004632-60004651 None:intergenic 25.0%
! AGTATTAAACAGAAAAAACC+AGG + chr1.2:60005362-60005381 None:intergenic 25.0%
!! CTACTGTGATCAAATATTTT+AGG - chr1.2:60005119-60005138 MS.gene055580:intron 25.0%
!! GTTCTTTTAACAAGAATATC+GGG + chr1.2:60005510-60005529 None:intergenic 25.0%
!!! AAATTTTTTGATGTTTCGAC+AGG - chr1.2:60005401-60005420 MS.gene055580:intron 25.0%
AGAATATCGGGATTACTAAT+AGG + chr1.2:60005498-60005517 None:intergenic 30.0%
TGAATTATGAAGCATGAAAC+CGG - chr1.2:60004856-60004875 MS.gene055580:intron 30.0%
AAACCTGATATTGCAGTGAT+AGG + chr1.2:60005187-60005206 None:intergenic 35.0%
AACCTGATATTGCAGTGATA+GGG + chr1.2:60005186-60005205 None:intergenic 35.0%
ACATAGCTACTCTTTATGTC+AGG + chr1.2:60005597-60005616 None:intergenic 35.0%
ATGGTATATACTCAAGGGAA+AGG - chr1.2:60005463-60005482 MS.gene055580:intron 35.0%
ATTGCAGTGATAGGGAAATT+TGG + chr1.2:60005178-60005197 None:intergenic 35.0%
CATAGATTGCATCAAACAGT+AGG - chr1.2:60005033-60005052 MS.gene055580:intron 35.0%
CGATCATGGTATATACTCAA+GGG - chr1.2:60005458-60005477 MS.gene055580:intron 35.0%
CTAAATTGATCGTTCCTTGT+TGG - chr1.2:60005096-60005115 MS.gene055580:intron 35.0%
CTCAGAAGAAACCAACAAAA+AGG - chr1.2:60005632-60005651 MS.gene055580:CDS 35.0%
TCTCAAATTATTAGCGGTGT+TGG + chr1.2:60004915-60004934 None:intergenic 35.0%
TTTATGTCAGGTACATCATC+CGG + chr1.2:60005585-60005604 None:intergenic 35.0%
! AAGAACTTGCTTTATTGAGC+TGG - chr1.2:60005524-60005543 MS.gene055580:CDS 35.0%
! TACTACTGGTCTGTTTCAAA+CGG - chr1.2:60005705-60005724 MS.gene055580:CDS 35.0%
! TATTTTCATTGTTCTGTGCC+TGG - chr1.2:60005341-60005360 MS.gene055580:intron 35.0%
! TCACTGCAATATCAGGTTTT+AGG - chr1.2:60005188-60005207 MS.gene055580:intron 35.0%
!!! CTTTTTGTTGGTTTCTTCTG+AGG + chr1.2:60005634-60005653 None:intergenic 35.0%
AACAACATGATGAGCGATCA+TGG - chr1.2:60005444-60005463 MS.gene055580:intron 40.0%
AACTTGCATGCTTCTCTTCA+AGG + chr1.2:60005667-60005686 None:intergenic 40.0%
ACTACGTCCTTCAATTTCCA+CGG + chr1.2:60004489-60004508 None:intergenic 40.0%
AGAAGTTGCAGTGTTGTATC+CGG - chr1.2:60005563-60005582 MS.gene055580:CDS 40.0%
GCGATCATGGTATATACTCA+AGG - chr1.2:60005457-60005476 MS.gene055580:intron 40.0%
GGTTTCTGTGCTTTATAGTC+AGG - chr1.2:60005072-60005091 MS.gene055580:intron 40.0%
GTGAAACTGCTCAATACTAC+TGG - chr1.2:60005691-60005710 MS.gene055580:CDS 40.0%
TGGAAATTGAAGGACGTAGT+TGG - chr1.2:60004489-60004508 MS.gene055580:CDS 40.0%
TTCCCTATCACTGCAATATC+AGG - chr1.2:60005181-60005200 MS.gene055580:intron 40.0%
TTTGATCACAGTAGCCAACA+AGG + chr1.2:60005113-60005132 None:intergenic 40.0%
TTTGATGTTTCGACAGGTGA+TGG - chr1.2:60005407-60005426 MS.gene055580:intron 40.0%
! CTCCAGAAGCTTCTAGAAAT+CGG + chr1.2:60004519-60004538 None:intergenic 40.0%
! GGAATCAAGCACCTTTTTGT+TGG + chr1.2:60005646-60005665 None:intergenic 40.0%
! TCCAGAAGCTTCTAGAAATC+GGG + chr1.2:60004518-60004537 None:intergenic 40.0%
!! GAAGGTTCTGGAAGATGATT+TGG + chr1.2:60004374-60004393 None:intergenic 40.0%
!! GCACAGAAACCTCTAAGATT+AGG + chr1.2:60005063-60005082 None:intergenic 40.0%
!! GTTCTGGAAGATGATTTGGA+GGG + chr1.2:60004370-60004389 None:intergenic 40.0%
ACCGAGACACTACACTGATA+CGG - chr1.2:60004809-60004828 MS.gene055580:intron 45.0%
CTTAGCACCGTGGAAATTGA+AGG - chr1.2:60004479-60004498 MS.gene055580:CDS 45.0%
GTAGGCATGCCTAATCTTAG+AGG - chr1.2:60005051-60005070 MS.gene055580:intron 45.0%
TAAACCCAAACGGACCTGAA+CGG + chr1.2:60004622-60004641 None:intergenic 45.0%
TCCGTATCAGTGTAGTGTCT+CGG + chr1.2:60004813-60004832 None:intergenic 45.0%
! ACCCGATTTCTAGAAGCTTC+TGG - chr1.2:60004514-60004533 MS.gene055580:CDS 45.0%
! GAAGATGATTTGGAGGGTGT+CGG + chr1.2:60004364-60004383 None:intergenic 45.0%
! GACCTGAACGGAGTACTTAA+CGG + chr1.2:60004610-60004629 None:intergenic 45.0%
! TGCTCTTGCTGAATTTTCCG+CGG - chr1.2:60005740-60005759 MS.gene055580:CDS 45.0%
!! GGTTCTGGAAGATGATTTGG+AGG + chr1.2:60004371-60004390 None:intergenic 45.0%
AATTCAGCAAGAGCAGCACG+AGG + chr1.2:60005735-60005754 None:intergenic 50.0%
ACACGACACATGTCTGACAC+CGG - chr1.2:60004980-60004999 MS.gene055580:intron 50.0%
ATCTCGCATCGTATTGTGCG+TGG - chr1.2:60004564-60004583 MS.gene055580:CDS 50.0%
GAACTCGGTAGCCTCACAAA+GGG - chr1.2:60004437-60004456 MS.gene055580:CDS 50.0%
GACATGAACCGGACATGTCA+AGG - chr1.2:60004878-60004897 MS.gene055580:intron 50.0%
GCATGAAACCGGACATGAAC+CGG - chr1.2:60004867-60004886 MS.gene055580:intron 50.0%
GGTTACCATCTCCCTTTGTG+AGG + chr1.2:60004451-60004470 None:intergenic 50.0%
GTCAGTGTCCTTGACATGTC+CGG + chr1.2:60004889-60004908 None:intergenic 50.0%
TACTCCGTTCAGGTCCGTTT+GGG - chr1.2:60004615-60004634 MS.gene055580:CDS 50.0%
TGACATGTCCGGTTCATGTC+CGG + chr1.2:60004878-60004897 None:intergenic 50.0%
! AATTTTCCGCGGACCTTCAG+TGG - chr1.2:60005751-60005770 MS.gene055580:CDS 50.0%
! ATTTTCCGCGGACCTTCAGT+GGG - chr1.2:60005752-60005771 MS.gene055580:CDS 50.0%
ACCACGACACTCCTCGCATT+AGG + chr1.2:60005012-60005031 None:intergenic 55.0%
AGGCTACCGAGTTCCAGACT+CGG + chr1.2:60004431-60004450 None:intergenic 55.0%
CACGACACATGTCTGACACC+GGG - chr1.2:60004981-60005000 MS.gene055580:intron 55.0%
CCAGAGCTTTCTTAGCACCG+TGG - chr1.2:60004469-60004488 MS.gene055580:CDS 55.0%
CGCCGTTAAGTACTCCGTTC+AGG - chr1.2:60004605-60004624 MS.gene055580:CDS 55.0%
GGAACTCGGTAGCCTCACAA+AGG - chr1.2:60004436-60004455 MS.gene055580:CDS 55.0%
GGTAGCCTCACAAAGGGAGA+TGG - chr1.2:60004443-60004462 MS.gene055580:CDS 55.0%
GTACTCCGTTCAGGTCCGTT+TGG - chr1.2:60004614-60004633 MS.gene055580:CDS 55.0%
TCCTCGCATTAGGCAAGTCC+CGG + chr1.2:60005002-60005021 None:intergenic 55.0%
! CCACGGTGCTAAGAAAGCTC+TGG + chr1.2:60004472-60004491 None:intergenic 55.0%
! TTTTCCGCGGACCTTCAGTG+GGG - chr1.2:60005753-60005772 MS.gene055580:CDS 55.0%
!! GATGATTTGGAGGGTGTCGG+TGG + chr1.2:60004361-60004380 None:intergenic 55.0%
AACTCGCACGTGCGAGATCG+GGG + chr1.2:60004401-60004420 None:intergenic 60.0%
ACCGGGACTTGCCTAATGCG+AGG - chr1.2:60004998-60005017 MS.gene055580:intron 60.0%
CAACTCGCACGTGCGAGATC+GGG + chr1.2:60004402-60004421 None:intergenic 60.0%
CTACTTGCCTGCCCCACTGA+AGG + chr1.2:60005767-60005786 None:intergenic 60.0%
CTTCAGTGGGGCAGGCAAGT+AGG - chr1.2:60005765-60005784 MS.gene055580:CDS 60.0%
GATCGGGGATGGGAAGGTTC+TGG + chr1.2:60004386-60004405 None:intergenic 60.0%
GCAACTCGCACGTGCGAGAT+CGG + chr1.2:60004403-60004422 None:intergenic 60.0%
! CGTCTGCCGAGTCTGGAACT+CGG - chr1.2:60004422-60004441 MS.gene055580:CDS 60.0%
!! GATTTGGAGGGTGTCGGTGG+AGG + chr1.2:60004358-60004377 None:intergenic 60.0%
!! GCCTAATGCGAGGAGTGTCG+TGG - chr1.2:60005008-60005027 MS.gene055580:intron 60.0%
!! GGTGTCGGTGGAGGAAAGTG+CGG + chr1.2:60004349-60004368 None:intergenic 60.0%
CGAGTTGCGTCTGCCGAGTC+TGG - chr1.2:60004415-60004434 MS.gene055580:CDS 65.0%
GCACGTGCGAGATCGGGGAT+GGG + chr1.2:60004396-60004415 None:intergenic 65.0%
GTGCGAGATCGGGGATGGGA+AGG + chr1.2:60004392-60004411 None:intergenic 65.0%
CCTGCCCCACTGAAGGTCCG+CGG + chr1.2:60005760-60005779 None:intergenic 70.0%
CGCACGTGCGAGATCGGGGA+TGG + chr1.2:60004397-60004416 None:intergenic 70.0%
CCGCGGACCTTCAGTGGGGC+AGG - chr1.2:60005757-60005776 MS.gene055580:CDS 75.0%


Chromosome Type Strat End Strand Name
chr1.2 gene 60004330 60005797 60004330 ID=MS.gene055580
chr1.2 mRNA 60004330 60005797 60004330 ID=MS.gene055580.t1;Parent=MS.gene055580
chr1.2 exon 60005501 60005797 60005501 ID=MS.gene055580.t1.exon1;Parent=MS.gene055580.t1
chr1.2 CDS 60005501 60005797 60005501 ID=cds.MS.gene055580.t1;Parent=MS.gene055580.t1
chr1.2 exon 60004330 60004704 60004330 ID=MS.gene055580.t1.exon2;Parent=MS.gene055580.t1
chr1.2 CDS 60004330 60004704 60004330 ID=cds.MS.gene055580.t1;Parent=MS.gene055580.t1
Gene Sequence

>MS.gene055580

ATGAATTCTCATTTCTCCGCACTTTCCTCCACCGACACCCTCCAAATCATCTTCCAGAACCTTCCCATCCCCGATCTCGCACGTGCGAGTTGCGTCTGCCGAGTCTGGAACTCGGTAGCCTCACAAAGGGAGATGGTAACCAGAGCTTTCTTAGCACCGTGGAAATTGAAGGACGTAGTTGGAAACCCGATTTCTAGAAGCTTCTGGAGAGATAATTCACTTGCTAAATTCGCAATCTCGCATCGTATTGTGCGTGGTGATAGTGTTGCTAGTCTCGCCGTTAAGTACTCCGTTCAGGTCCGTTTGGGTTTATTACTTTGTTTCAGAAATTGAAATGCATAATTTGTTGTTGTTGTTGATAATACACTATGCGCTTGTGCTTTTGAAAATGATGACAATGAAATTATGGAATCATCTCTCTCTGAAATTCAAGATTATGTTTGAATATAGTTCATATGAGATAATTTTATGTATAAAGCACCGAGACACTACACTGATACGGATACATCGTGATAATTTGAGAAAATGAATTATGAAGCATGAAACCGGACATGAACCGGACATGTCAAGGACACTGACACACCAACACCGCTAATAATTTGAGAAAATCACATAATTCAATGTAATTATATGTGTTGGTGTCGTGTCAGACACGACACATGTCTGACACCGGGACTTGCCTAATGCGAGGAGTGTCGTGGTTCATAGATTGCATCAAACAGTAGGCATGCCTAATCTTAGAGGTTTCTGTGCTTTATAGTCAGGTCTAAATTGATCGTTCCTTGTTGGCTACTGTGATCAAATATTTTAGGGATATCATTTTAAAATGTTTTTAATTTCGTGGACCAAATTTCCCTATCACTGCAATATCAGGTTTTAGGATTAAAATTTTGATTAGCTCAAATCAAATTGTTAACATCTACTTGTTGTGTATAATTTAGCATTTTCCTATTAAGAATTTATAAACTAGTTGATCTTTTTCTGACTATTTTTACTGTAAGCACTAAGCTATATTTTCATTGTTCTGTGCCTGGTTTTTTCTGTTTAATACTTTTGATAAAGTTGGATGATAAATTTTTTGATGTTTCGACAGGTGATGGACATAAAACGATTGAACAACATGATGAGCGATCATGGTATATACTCAAGGGAAAGGTTATTAATTCCTATTAGTAATCCCGATATTCTTGTTAAAAGAACTTGCTTTATTGAGCTGGATGTTAATGCGAAACGAGAAGTTGCAGTGTTGTATCCGGATGATGTACCTGACATAAAGAGTAGCTATGTATCAAACAGAATATCCTCAGAAGAAACCAACAAAAAGGTGCTTGATTCCTTGAAGAGAAGCATGCAAGTTGATAGTGAAACTGCTCAATACTACTGGTCTGTTTCAAACGGTGATCCTCGTGCTGCTCTTGCTGAATTTTCCGCGGACCTTCAGTGGGGCAGGCAAGTAGGTCACTCCTAG

Protein sequence

>MS.gene055580.t1

MNSHFSALSSTDTLQIIFQNLPIPDLARASCVCRVWNSVASQREMVTRAFLAPWKLKDVVGNPISRSFWRDNSLAKFAISHRIVRGDSVASLAVKYSVQVMDIKRLNNMMSDHGIYSRERLLIPISNPDILVKRTCFIELDVNAKREVAVLYPDDVPDIKSSYVSNRISSEETNKKVLDSLKRSMQVDSETAQYYWSVSNGDPRAALAEFSADLQWGRQVGHS