AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene57242

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene57242.t1 MTR_1g016200 56.122 98 33 3 13 100 7 104 8.82e-24 88.2
MS.gene57242.t1 MTR_1g016170 62.500 48 15 1 56 100 187 234 4.53e-13 64.3
MS.gene57242.t1 MTR_7g112330 42.373 59 34 0 56 114 22 80 2.54e-11 57.0
MS.gene57242.t1 MTR_4g121110 48.276 58 25 2 54 111 28 80 4.99e-11 56.6
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene57242.t1 AT5G49300 44.928 69 32 2 56 120 36 102 9.36e-12 58.5
MS.gene57242.t1 AT5G56860 46.154 65 31 1 25 89 203 263 1.03e-11 60.8
MS.gene57242.t1 AT4G26150 71.875 32 9 0 56 87 199 230 5.41e-11 58.5

Find 27 sgRNAs with CRISPR-Local

Find 40 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTCTTCTTTGTGGCTGGAAC+TGG 0.239072 1.4:-6118289 None:intergenic
AGTATTCGCCATTGCCCTTT+TGG 0.253039 1.4:-6118400 None:intergenic
ATGAGTATCAAGACCCTTAT+CGG 0.303482 1.4:-6118695 None:intergenic
ATACAAACACTACTCCTCTT+TGG 0.387924 1.4:+6118452 MS.gene57242:CDS
GGAAGAGGCAAAAGCCGATA+AGG 0.448770 1.4:+6118681 MS.gene57242:CDS
CAATCGAAACAAACCCTAGT+TGG 0.460017 1.4:-6118427 None:intergenic
TCTTGATACTCATAAGGAAA+AGG 0.465163 1.4:+6118705 MS.gene57242:CDS
TTGCCTCTTCCCTTCTTCGT+CGG 0.477939 1.4:-6118669 None:intergenic
CTTGATACTCATAAGGAAAA+GGG 0.489428 1.4:+6118706 MS.gene57242:CDS
TAAGGGTCTTGATACTCATA+AGG 0.492473 1.4:+6118699 MS.gene57242:CDS
ACCGAATACGAATACCCAAA+AGG 0.493067 1.4:+6118385 MS.gene57242:CDS
CCGAATACGAATACCCAAAA+GGG 0.528839 1.4:+6118386 MS.gene57242:CDS
GAAGAGGCAAAAGCCGATAA+GGG 0.529120 1.4:+6118682 MS.gene57242:CDS
ATGTGGACTCCGACGAAGAA+GGG 0.540307 1.4:+6118660 MS.gene57242:CDS
CTTTGGAGGAGTGATCCTAC+AGG 0.546346 1.4:+6118469 MS.gene57242:CDS
GGCGAATACTATATCCAACT+AGG 0.572160 1.4:+6118413 MS.gene57242:CDS
CATGTGGACTCCGACGAAGA+AGG 0.573346 1.4:+6118659 MS.gene57242:CDS
GAGTGATCCTACAGGTTCCA+AGG 0.583772 1.4:+6118477 MS.gene57242:CDS
ACTCCGACGAAGAAGGGAAG+AGG 0.589069 1.4:+6118666 MS.gene57242:CDS
CAAACACTACTCCTCTTTGG+AGG 0.592172 1.4:+6118455 MS.gene57242:CDS
GCGAATACTATATCCAACTA+GGG 0.606852 1.4:+6118414 MS.gene57242:CDS
CAGTCGTTGTGCAATGCATG+TGG 0.610062 1.4:+6118643 MS.gene57242:intron
ACGAATACCCAAAAGGGCAA+TGG 0.610371 1.4:+6118392 MS.gene57242:CDS
ACTCATAAGGAAAAGGGCAA+TGG 0.616678 1.4:+6118712 MS.gene57242:CDS
TGGCGAACGCTCATCATCTG+AGG 0.618644 1.4:+6118732 MS.gene57242:CDS
CTAATTACCTTGGAACCTGT+AGG 0.643620 1.4:-6118484 None:intergenic
GTAGGATCACTCCTCCAAAG+AGG 0.666474 1.4:-6118466 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTAATCAATATGTATAAGTA+TGG - chr1.4:6118576-6118595 None:intergenic 15.0%
!!! AAATTTGATAGTAAATAAGT+TGG - chr1.4:6118525-6118544 None:intergenic 15.0%
!!! AATTTGATAGTAAATAAGTT+GGG - chr1.4:6118524-6118543 None:intergenic 15.0%
!!! AGCAATTTTTATTTTCTTTT+TGG - chr1.4:6118365-6118384 None:intergenic 15.0%
!! ATAGTTAACAAGAAATATGT+TGG + chr1.4:6118618-6118637 MS.gene57242:intron 20.0%
!!! TTACTATCAAATTTCACTTT+TGG + chr1.4:6118531-6118550 MS.gene57242:intron 20.0%
!!! AGTAGTTTTTTTCTTCTTTG+TGG - chr1.4:6118302-6118321 None:intergenic 25.0%
CTTGATACTCATAAGGAAAA+GGG + chr1.4:6118706-6118725 MS.gene57242:CDS 30.0%
TCTTGATACTCATAAGGAAA+AGG + chr1.4:6118705-6118724 MS.gene57242:CDS 30.0%
ATACAAACACTACTCCTCTT+TGG + chr1.4:6118452-6118471 MS.gene57242:CDS 35.0%
ATGAGTATCAAGACCCTTAT+CGG - chr1.4:6118698-6118717 None:intergenic 35.0%
GAGAGATGAACTAATTACCT+TGG - chr1.4:6118497-6118516 None:intergenic 35.0%
GCGAATACTATATCCAACTA+GGG + chr1.4:6118414-6118433 MS.gene57242:CDS 35.0%
TAAGGGTCTTGATACTCATA+AGG + chr1.4:6118699-6118718 MS.gene57242:CDS 35.0%
! AGCAGGTGATTTCTTCTTTT+TGG - chr1.4:6118335-6118354 None:intergenic 35.0%
!!! GTTTTTTTCTTCTTTGTGGC+TGG - chr1.4:6118298-6118317 None:intergenic 35.0%
ACCGAATACGAATACCCAAA+AGG + chr1.4:6118385-6118404 MS.gene57242:CDS 40.0%
ACTCATAAGGAAAAGGGCAA+TGG + chr1.4:6118712-6118731 MS.gene57242:CDS 40.0%
CAATCGAAACAAACCCTAGT+TGG - chr1.4:6118430-6118449 None:intergenic 40.0%
CCGAATACGAATACCCAAAA+GGG + chr1.4:6118386-6118405 MS.gene57242:CDS 40.0%
CTAATTACCTTGGAACCTGT+AGG - chr1.4:6118487-6118506 None:intergenic 40.0%
GGCGAATACTATATCCAACT+AGG + chr1.4:6118413-6118432 MS.gene57242:CDS 40.0%
!! CCCTTTTGGGTATTCGTATT+CGG - chr1.4:6118389-6118408 None:intergenic 40.0%
ACGAATACCCAAAAGGGCAA+TGG + chr1.4:6118392-6118411 MS.gene57242:CDS 45.0%
CAAACACTACTCCTCTTTGG+AGG + chr1.4:6118455-6118474 MS.gene57242:CDS 45.0%
GAAGAGGCAAAAGCCGATAA+GGG + chr1.4:6118682-6118701 MS.gene57242:CDS 45.0%
TTCTTCTTTGTGGCTGGAAC+TGG - chr1.4:6118292-6118311 None:intergenic 45.0%
! AGTATTCGCCATTGCCCTTT+TGG - chr1.4:6118403-6118422 None:intergenic 45.0%
! GTATTCGCCATTGCCCTTTT+GGG - chr1.4:6118402-6118421 None:intergenic 45.0%
!! TTCTTTTTGGCAGCACTAGC+AGG - chr1.4:6118322-6118341 None:intergenic 45.0%
ATGTGGACTCCGACGAAGAA+GGG + chr1.4:6118660-6118679 MS.gene57242:CDS 50.0%
CAGTCGTTGTGCAATGCATG+TGG + chr1.4:6118643-6118662 MS.gene57242:intron 50.0%
GAGTGATCCTACAGGTTCCA+AGG + chr1.4:6118477-6118496 MS.gene57242:CDS 50.0%
GGAAGAGGCAAAAGCCGATA+AGG + chr1.4:6118681-6118700 MS.gene57242:CDS 50.0%
GTAGGATCACTCCTCCAAAG+AGG - chr1.4:6118469-6118488 None:intergenic 50.0%
TTGCCTCTTCCCTTCTTCGT+CGG - chr1.4:6118672-6118691 None:intergenic 50.0%
! CTTTGGAGGAGTGATCCTAC+AGG + chr1.4:6118469-6118488 MS.gene57242:CDS 50.0%
ACTCCGACGAAGAAGGGAAG+AGG + chr1.4:6118666-6118685 MS.gene57242:CDS 55.0%
CATGTGGACTCCGACGAAGA+AGG + chr1.4:6118659-6118678 MS.gene57242:CDS 55.0%
TGGCGAACGCTCATCATCTG+AGG + chr1.4:6118732-6118751 MS.gene57242:CDS 55.0%


Chromosome Type Strat End Strand Name
chr1.4 gene 6118268 6118783 6118268 ID=MS.gene57242
chr1.4 mRNA 6118268 6118783 6118268 ID=MS.gene57242.t1;Parent=MS.gene57242
chr1.4 exon 6118268 6118498 6118268 ID=MS.gene57242.t1.exon1;Parent=MS.gene57242.t1
chr1.4 CDS 6118268 6118498 6118268 ID=cds.MS.gene57242.t1;Parent=MS.gene57242.t1
chr1.4 exon 6118646 6118783 6118646 ID=MS.gene57242.t1.exon2;Parent=MS.gene57242.t1
chr1.4 CDS 6118646 6118783 6118646 ID=cds.MS.gene57242.t1;Parent=MS.gene57242.t1
Gene Sequence

>MS.gene57242

ATGAGAGTAAGTAACGATGATCCAGTTCCAGCCACAAAGAAGAAAAAAACTACTGCTAGTGCTGCCAAAAAGAAGAAATCACCTGCTAGTGCTGCCAAAAAGAAAATAAAAATTGCTACCGAATACGAATACCCAAAAGGGCAATGGCGAATACTATATCCAACTAGGGTTTGTTTCGATTGCAATACAAACACTACTCCTCTTTGGAGGAGTGATCCTACAGGTTCCAAGGTAATTAGTTCATCTCTCTTCTCCCAACTTATTTACTATCAAATTTCACTTTTGGTTCATGCAAAAGTGTTATTCCATACTTATACATATTGATTAATAATTTGAGTATCTAGTTATATATAGTTAACAAGAAATATGTTGGTGCAGTCGTTGTGCAATGCATGTGGACTCCGACGAAGAAGGGAAGAGGCAAAAGCCGATAAGGGTCTTGATACTCATAAGGAAAAGGGCAATGGCGAACGCTCATCATCTGAGGATGTGAAGAATGTTTTAATGTTCATCTGA
Protein sequence

>MS.gene57242.t1

MRVSNDDPVPATKKKKTTASAAKKKKSPASAAKKKIKIATEYEYPKGQWRILYPTRVCFDCNTNTTPLWRSDPTGSKSLCNACGLRRRREEAKADKGLDTHKEKGNGERSSSEDVKNVLMFI