AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene48808

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene48808.t1 MTR_4g029130 93.182 88 6 0 1 88 1 88 9.07e-55 169
MS.gene48808.t1 MTR_4g029130 92.105 38 3 0 88 125 153 190 1.40e-18 77.4
MS.gene48808.t1 MTR_7g072540 64.045 89 27 2 1 86 1 87 3.36e-31 110
MS.gene48808.t1 MTR_5g083970 59.259 81 26 2 11 85 15 94 6.08e-23 89.4
MS.gene48808.t1 MTR_3g072360 52.439 82 32 1 11 85 19 100 2.45e-13 63.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 25 sgRNAs with CRISPR-Local

Find 44 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTGTTGCAGTTCCATTTGTT+TGG 0.199775 4.4:-73715488 MS.gene48808:CDS
GTCTTTAGAGAATGTATGTT+TGG 0.305846 4.4:+73715446 None:intergenic
TGTTGCAGTTCCATTTGTTT+GGG 0.310743 4.4:-73715487 MS.gene48808:CDS
AATGTATGTTTGGGAGTTCC+AGG 0.349044 4.4:+73715456 None:intergenic
CCAACTTCTACTTTGTGCTT+TGG 0.382263 4.4:-73715114 MS.gene48808:CDS
TCTAAAAGATGGGTGACAAT+TGG 0.418920 4.4:+73715515 None:intergenic
CACGCCTCTTGTAGTTACTT+TGG 0.419541 4.4:+73715058 None:intergenic
GATAAGAAGGTGGAGGTGTA+AGG 0.431589 4.4:+73715412 None:intergenic
TCTTTAGAGAATGTATGTTT+GGG 0.435030 4.4:+73715447 None:intergenic
GCAACAGAAACTCTAAAAGA+TGG 0.459895 4.4:+73715504 None:intergenic
GTAACTACAAGAGGCGTGTA+AGG 0.469845 4.4:-73715053 MS.gene48808:CDS
ATAAGAAGGTGGAGGTGTAA+GGG 0.477682 4.4:+73715413 None:intergenic
GGTTGAGATTCCCAAACAAA+TGG 0.489006 4.4:+73715477 None:intergenic
TTTCAGCAGATTACTTTCAA+AGG 0.492999 4.4:-73715544 MS.gene48808:CDS
TAAGAAGGTGGAGGTGTAAG+GGG 0.511212 4.4:+73715414 None:intergenic
CCAAAGCACAAAGTAGAAGT+TGG 0.519370 4.4:+73715114 None:intergenic
TTCAGGGGTGAAAATGAAGA+TGG 0.539909 4.4:-73715147 MS.gene48808:intron
CAACAGAAACTCTAAAAGAT+GGG 0.546913 4.4:+73715505 None:intergenic
TTTGTTTGGGAATCTCAACC+TGG 0.562667 4.4:-73715474 MS.gene48808:CDS
CGTTCGATCAGCTCGAACAG+TGG 0.567340 4.4:-73715084 MS.gene48808:CDS
GCATTGTTGAAATGATAAGA+AGG 0.591984 4.4:+73715399 None:intergenic
GAAGGTGGAGGTGTAAGGGG+AGG 0.592725 4.4:+73715417 None:intergenic
GCTTCCAAAGTAACTACAAG+AGG 0.633252 4.4:-73715062 MS.gene48808:CDS
TTGTTGAAATGATAAGAAGG+TGG 0.647192 4.4:+73715402 None:intergenic
TTGAAATGATAAGAAGGTGG+AGG 0.647831 4.4:+73715405 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTTTTTCTCATTCTTTTTGT+TGG + chr4.4:73715276-73715295 None:intergenic 20.0%
! AGAAGAAAATTCTTAAGCTT+TGG - chr4.4:73715467-73715486 MS.gene48808:CDS 25.0%
! AGATTCTTCCAAAATTATCT+CGG - chr4.4:73715427-73715446 MS.gene48808:CDS 25.0%
! TGTTTCAAAAACTAAACTTC+AGG - chr4.4:73715327-73715346 MS.gene48808:intron 25.0%
!! AAAATCTTCCAAGTATCTTT+TGG - chr4.4:73715301-73715320 MS.gene48808:intron 25.0%
!! TCTTTAGAGAATGTATGTTT+GGG + chr4.4:73715206-73715225 None:intergenic 25.0%
!!! ATTTTGGAAGAATCTATTGA+TGG + chr4.4:73715422-73715441 None:intergenic 25.0%
AAACAATGCCAAAAGATACT+TGG + chr4.4:73715312-73715331 None:intergenic 30.0%
ATTCTTCCAAAATTATCTCG+GGG - chr4.4:73715429-73715448 MS.gene48808:CDS 30.0%
GATTCTTCCAAAATTATCTC+GGG - chr4.4:73715428-73715447 MS.gene48808:CDS 30.0%
GCATTGTTGAAATGATAAGA+AGG + chr4.4:73715254-73715273 None:intergenic 30.0%
TTCAAAAACTAAACTTCAGG+AGG - chr4.4:73715330-73715349 MS.gene48808:intron 30.0%
TTGTTGAAATGATAAGAAGG+TGG + chr4.4:73715251-73715270 None:intergenic 30.0%
TTTCAGCAGATTACTTTCAA+AGG - chr4.4:73715106-73715125 MS.gene48808:CDS 30.0%
! CAACAGAAACTCTAAAAGAT+GGG + chr4.4:73715148-73715167 None:intergenic 30.0%
! GAATTTTCTTCTACTAACCT+TGG + chr4.4:73715459-73715478 None:intergenic 30.0%
! GTCTTTAGAGAATGTATGTT+TGG + chr4.4:73715207-73715226 None:intergenic 30.0%
!!! TGGATCTTCTTTTGATTTCA+GGG - chr4.4:73715487-73715506 MS.gene48808:CDS 30.0%
!!! TTGGATCTTCTTTTGATTTC+AGG - chr4.4:73715486-73715505 MS.gene48808:CDS 30.0%
TCTAAAAGATGGGTGACAAT+TGG + chr4.4:73715138-73715157 None:intergenic 35.0%
TGTTGCAGTTCCATTTGTTT+GGG - chr4.4:73715163-73715182 MS.gene48808:intron 35.0%
TTGAAATGATAAGAAGGTGG+AGG + chr4.4:73715248-73715267 None:intergenic 35.0%
! ATTGATGGCAATGAAAACGA+AGG + chr4.4:73715407-73715426 None:intergenic 35.0%
! GCAACAGAAACTCTAAAAGA+TGG + chr4.4:73715149-73715168 None:intergenic 35.0%
! TTGATGGCAATGAAAACGAA+GGG + chr4.4:73715406-73715425 None:intergenic 35.0%
!!! GGATCTTCTTTTGATTTCAG+GGG - chr4.4:73715488-73715507 MS.gene48808:CDS 35.0%
AATGTATGTTTGGGAGTTCC+AGG + chr4.4:73715197-73715216 None:intergenic 40.0%
CCAAAGCACAAAGTAGAAGT+TGG + chr4.4:73715539-73715558 None:intergenic 40.0%
CCAACTTCTACTTTGTGCTT+TGG - chr4.4:73715536-73715555 MS.gene48808:CDS 40.0%
CGATGACAAAGAAGATGATG+AGG + chr4.4:73715378-73715397 None:intergenic 40.0%
CTGTTGCAGTTCCATTTGTT+TGG - chr4.4:73715162-73715181 MS.gene48808:intron 40.0%
GCTTCCAAAGTAACTACAAG+AGG - chr4.4:73715588-73715607 MS.gene48808:CDS 40.0%
GGTTGAGATTCCCAAACAAA+TGG + chr4.4:73715176-73715195 None:intergenic 40.0%
TTCAGGGGTGAAAATGAAGA+TGG - chr4.4:73715503-73715522 MS.gene48808:CDS 40.0%
TTTGTTTGGGAATCTCAACC+TGG - chr4.4:73715176-73715195 MS.gene48808:intron 40.0%
! ATAAGAAGGTGGAGGTGTAA+GGG + chr4.4:73715240-73715259 None:intergenic 40.0%
CACGCCTCTTGTAGTTACTT+TGG + chr4.4:73715595-73715614 None:intergenic 45.0%
! GATAAGAAGGTGGAGGTGTA+AGG + chr4.4:73715241-73715260 None:intergenic 45.0%
! GTAACTACAAGAGGCGTGTA+AGG - chr4.4:73715597-73715616 MS.gene48808:CDS 45.0%
! TAAGAAGGTGGAGGTGTAAG+GGG + chr4.4:73715239-73715258 None:intergenic 45.0%
AATTATCTCGGGGACGACCA+AGG - chr4.4:73715439-73715458 MS.gene48808:CDS 50.0%
! GGTCGTCCCCGAGATAATTT+TGG + chr4.4:73715438-73715457 None:intergenic 50.0%
CGTTCGATCAGCTCGAACAG+TGG - chr4.4:73715566-73715585 MS.gene48808:CDS 55.0%
! GAAGGTGGAGGTGTAAGGGG+AGG + chr4.4:73715236-73715255 None:intergenic 60.0%


Chromosome Type Strat End Strand Name
chr4.4 gene 73715050 73715622 73715050 ID=MS.gene48808
chr4.4 mRNA 73715050 73715622 73715050 ID=MS.gene48808.t1;Parent=MS.gene48808
chr4.4 exon 73715360 73715622 73715360 ID=MS.gene48808.t1.exon1;Parent=MS.gene48808.t1
chr4.4 CDS 73715360 73715622 73715360 ID=cds.MS.gene48808.t1;Parent=MS.gene48808.t1
chr4.4 exon 73715050 73715164 73715050 ID=MS.gene48808.t1.exon2;Parent=MS.gene48808.t1
chr4.4 CDS 73715050 73715164 73715050 ID=cds.MS.gene48808.t1;Parent=MS.gene48808.t1
Gene Sequence

>MS.gene48808

ATGTTCAATTCAACATGTGAGAAGAGTGTTCTTCAAATCAAACAAGATGACAAGTTTTTCAGCAGATTACTTTCAAAGGAAAATTCCAATTGTCACCCATCTTTTAGAGTTTCTGTTGCAGTTCCATTTGTTTGGGAATCTCAACCTGGAACTCCCAAACATACATTCTCTAAAGACATTATTCCTCCCCTTACACCTCCACCTTCTTATCATTTCAACAATGCCAACAAAAAGAATGAGAAAAAACACTCAAAATCTTCCAAGTATCTTTTGGCATTGTTTCAAAAACTAAACTTCAGGAGGAACAATCAGTCGTCGTCTTCATCCTCATCATCTTCTTTGTCATCGTCATACCCTTCGTTTTCATTGCCATCAATAGATTCTTCCAAAATTATCTCGGGGACGACCAAGGTTAGTAGAAGAAAATTCTTAAGCTTTGGATCTTCTTTTGATTTCAGGGGTGAAAATGAAGATGGTAATGATTCACCAACTTCTACTTTGTGCTTTGGAATTCATCGTTCGATCAGCTCGAACAGTGGCTTCCAAAGTAACTACAAGAGGCGTGTAAGGTAA
Protein sequence

>MS.gene48808.t1

MFNSTCEKSVLQIKQDDKFFSRLLSKENSNCHPSFRVSVAVPFVWESQPGTPKHTFSKDIIPPLTPPPSYHFNNANKKNEKKHSKSSKGENEDGNDSPTSTLCFGIHRSISSNSGFQSNYKRRVR