AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1150870


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1150870 MtrunA17_Chr7g0240471 92.708 96 5 1 1 94 1 96 2.32e-59 178
Msa1150870 MtrunA17_Chr7g0240451 83.333 96 14 1 1 94 1 96 2.71e-53 162
Msa1150870 MtrunA17_Chr7g0240441 65.574 61 5 1 34 94 29 73 3.58e-18 73.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1150870 AT3G53980.2 62.319 69 25 1 26 94 26 93 1.39e-25 92.8
Msa1150870 AT3G53980.1 62.319 69 25 1 26 94 26 93 1.39e-25 92.8
Msa1150870 AT5G05960.1 52.273 88 37 2 7 94 13 95 3.51e-25 92.0
Msa1150870 AT2G37870.1 40.000 85 47 3 11 92 9 92 4.92e-11 55.8

Find 26 sgRNAs with CRISPR-Local

Find 104 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTGATGAAAACAAACATAAA+TGG 0.241413 7_4:-34705703 Msa1150870:CDS
AGCTTAAATGCTTCCATATC+TGG 0.280630 7_4:+34706321 None:intergenic
CAACAACCTCAACTCTTTCA+AGG 0.388840 7_4:+34705723 None:intergenic
GTGAAGATGCTGTGCCTAGT+TGG 0.440569 7_4:-34706411 Msa1150870:CDS
AAGGGGTACCACACCAGATA+TGG 0.445913 7_4:-34706334 Msa1150870:CDS
TGATGAAAACAAACATAAAT+GGG 0.460009 7_4:-34705702 Msa1150870:CDS
TCAAACGTTGCTAAAATGTC+TGG 0.462464 7_4:-34706186 Msa1150870:CDS
GATGCTGTTAGCTACTAGTA+TGG 0.463264 7_4:-34705670 Msa1150870:three_prime_UTR
GGATAGTAACAGCAATTTGA+GGG 0.472152 7_4:+34706157 None:intergenic
CAAGATCCTCACATGTTTAG+CGG 0.498681 7_4:+34705421 None:intergenic
GGGATAGTAACAGCAATTTG+AGG 0.508534 7_4:+34706156 None:intergenic
GTTGAAAGTGCAGGTGAATG+TGG 0.515102 7_4:-34706357 Msa1150870:intron
AATAAAACATGCTCTTTCAG+TGG 0.535975 7_4:-34705561 Msa1150870:three_prime_UTR
TCTTGTGCTGCACTTGCACA+AGG 0.541464 7_4:+34706294 None:intergenic
AAAGTGCAGGTGAATGTGGA+AGG 0.549386 7_4:-34706353 Msa1150870:intron
ATCTTTATCAACTATTGTAA+CGG 0.556242 7_4:+34705479 None:intergenic
TAACTTTGTTGTTTATAGTG+TGG 0.565157 7_4:-34705620 Msa1150870:three_prime_UTR
ACTCTTCCTTGAAAGAGTTG+AGG 0.566469 7_4:-34705729 Msa1150870:CDS
AAAACTGCACAAAGACAACT+TGG 0.590774 7_4:+34706213 None:intergenic
TGTGCTCAGACTAAGAAACT+TGG 0.591888 7_4:-34706243 Msa1150870:CDS
CAAGAACTACAAAACCAACT+AGG 0.604153 7_4:+34706397 None:intergenic
AAATGCTTCCATATCTGGTG+TGG 0.609029 7_4:+34706326 None:intergenic
CGAATTCCGCTAAACATGTG+AGG 0.618333 7_4:-34705427 Msa1150870:three_prime_UTR
AATACAACACAACTAAGTTG+TGG 0.625133 7_4:+34705644 None:intergenic
AGTGCAGGTGAATGTGGAAG+GGG 0.630405 7_4:-34706351 Msa1150870:intron
AAGTGCAGGTGAATGTGGAA+GGG 0.641454 7_4:-34706352 Msa1150870:intron

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATGTAACATTAATTATTGAT+AGG - chr7_4:34705847-34705866 Msa1150870:intron 15.0%
!! ATGTAACATTAATTATTGAT+AGG - chr7_4:34705847-34705866 Msa1150870:intron 15.0%
!! AATGAGATTATAGATAGTTA+AGG - chr7_4:34705873-34705892 Msa1150870:intron 20.0%
!! ATGAGATTATAGATAGTTAA+GGG - chr7_4:34705874-34705893 Msa1150870:intron 20.0%
!!! TTGTTAAAATCTTCCTTTTA+TGG - chr7_4:34705947-34705966 Msa1150870:intron 20.0%
!!! TATGATTTTAGTTCCATAAA+AGG + chr7_4:34705963-34705982 None:intergenic 20.0%
!!! CTATTTGTTAATTTTCTTGA+TGG - chr7_4:34706044-34706063 Msa1150870:intron 20.0%
!! TTGATGAAAACAAACATAAA+TGG - chr7_4:34706139-34706158 Msa1150870:intron 20.0%
!! TGATGAAAACAAACATAAAT+GGG - chr7_4:34706140-34706159 Msa1150870:intron 20.0%
!! ATCTTTATCAACTATTGTAA+CGG + chr7_4:34706366-34706385 None:intergenic 20.0%
!! AATGAGATTATAGATAGTTA+AGG - chr7_4:34705873-34705892 Msa1150870:intron 20.0%
!! ATGAGATTATAGATAGTTAA+GGG - chr7_4:34705874-34705893 Msa1150870:intron 20.0%
!!! TTGTTAAAATCTTCCTTTTA+TGG - chr7_4:34705947-34705966 Msa1150870:intron 20.0%
!!! TATGATTTTAGTTCCATAAA+AGG + chr7_4:34705963-34705982 None:intergenic 20.0%
!!! CTATTTGTTAATTTTCTTGA+TGG - chr7_4:34706044-34706063 Msa1150870:intron 20.0%
!! TTGATGAAAACAAACATAAA+TGG - chr7_4:34706139-34706158 Msa1150870:intron 20.0%
!! TGATGAAAACAAACATAAAT+GGG - chr7_4:34706140-34706159 Msa1150870:intron 20.0%
!! ATCTTTATCAACTATTGTAA+CGG + chr7_4:34706366-34706385 None:intergenic 20.0%
!!! TAGATAGTTAAGGGTATTAT+AGG - chr7_4:34705883-34705902 Msa1150870:intron 25.0%
!!! TAACTTTGTTGTTTATAGTG+TGG - chr7_4:34706222-34706241 Msa1150870:CDS 25.0%
!!! ATCGACTAAAAAGTTTTAGT+AGG + chr7_4:34706320-34706339 None:intergenic 25.0%
!!! TAGATAGTTAAGGGTATTAT+AGG - chr7_4:34705883-34705902 Msa1150870:intron 25.0%
!!! TAACTTTGTTGTTTATAGTG+TGG - chr7_4:34706222-34706241 Msa1150870:CDS 25.0%
!!! ATCGACTAAAAAGTTTTAGT+AGG + chr7_4:34706320-34706339 None:intergenic 25.0%
! TACCGTTTCACATTTTTCTT+GGG + chr7_4:34705992-34706011 None:intergenic 30.0%
AATACAACACAACTAAGTTG+TGG + chr7_4:34706201-34706220 None:intergenic 30.0%
!! AGAGCATGTTTTATTCATGA+GGG + chr7_4:34706276-34706295 None:intergenic 30.0%
!! AAGAGCATGTTTTATTCATG+AGG + chr7_4:34706277-34706296 None:intergenic 30.0%
AATAAAACATGCTCTTTCAG+TGG - chr7_4:34706281-34706300 Msa1150870:CDS 30.0%
! TACCGTTTCACATTTTTCTT+GGG + chr7_4:34705992-34706011 None:intergenic 30.0%
AATACAACACAACTAAGTTG+TGG + chr7_4:34706201-34706220 None:intergenic 30.0%
!! AGAGCATGTTTTATTCATGA+GGG + chr7_4:34706276-34706295 None:intergenic 30.0%
!! AAGAGCATGTTTTATTCATG+AGG + chr7_4:34706277-34706296 None:intergenic 30.0%
AATAAAACATGCTCTTTCAG+TGG - chr7_4:34706281-34706300 Msa1150870:CDS 30.0%
CAAGAACTACAAAACCAACT+AGG + chr7_4:34705448-34705467 None:intergenic 35.0%
! GTTTTGTAGTTCTTGTTGCA+GGG - chr7_4:34705453-34705472 Msa1150870:three_prime_UTR 35.0%
! ATTCATAGAGTTGAAAGTGC+AGG - chr7_4:34705476-34705495 Msa1150870:three_prime_UTR 35.0%
AGCTTAAATGCTTCCATATC+TGG + chr7_4:34705524-34705543 None:intergenic 35.0%
AAAACTGCACAAAGACAACT+TGG + chr7_4:34705632-34705651 None:intergenic 35.0%
TCAAACGTTGCTAAAATGTC+TGG - chr7_4:34705656-34705675 Msa1150870:three_prime_UTR 35.0%
GGATAGTAACAGCAATTTGA+GGG + chr7_4:34705688-34705707 None:intergenic 35.0%
TAAGTAACTAACAAGTCCCT+CGG - chr7_4:34705757-34705776 Msa1150870:intron 35.0%
GACAACTTAAAAGAAACCGA+GGG + chr7_4:34705776-34705795 None:intergenic 35.0%
TGCCCAAGAAAAATGTGAAA+CGG - chr7_4:34705987-34706006 Msa1150870:intron 35.0%
! GTACCGTTTCACATTTTTCT+TGG + chr7_4:34705993-34706012 None:intergenic 35.0%
CAAGAACTACAAAACCAACT+AGG + chr7_4:34705448-34705467 None:intergenic 35.0%
! GTTTTGTAGTTCTTGTTGCA+GGG - chr7_4:34705453-34705472 Msa1150870:three_prime_UTR 35.0%
! ATTCATAGAGTTGAAAGTGC+AGG - chr7_4:34705476-34705495 Msa1150870:three_prime_UTR 35.0%
AGCTTAAATGCTTCCATATC+TGG + chr7_4:34705524-34705543 None:intergenic 35.0%
AAAACTGCACAAAGACAACT+TGG + chr7_4:34705632-34705651 None:intergenic 35.0%
TCAAACGTTGCTAAAATGTC+TGG - chr7_4:34705656-34705675 Msa1150870:three_prime_UTR 35.0%
GGATAGTAACAGCAATTTGA+GGG + chr7_4:34705688-34705707 None:intergenic 35.0%
TAAGTAACTAACAAGTCCCT+CGG - chr7_4:34705757-34705776 Msa1150870:intron 35.0%
GACAACTTAAAAGAAACCGA+GGG + chr7_4:34705776-34705795 None:intergenic 35.0%
TGCCCAAGAAAAATGTGAAA+CGG - chr7_4:34705987-34706006 Msa1150870:intron 35.0%
! GTACCGTTTCACATTTTTCT+TGG + chr7_4:34705993-34706012 None:intergenic 35.0%
!! GGTTTTGTAGTTCTTGTTGC+AGG - chr7_4:34705452-34705471 Msa1150870:three_prime_UTR 40.0%
AAATGCTTCCATATCTGGTG+TGG + chr7_4:34705519-34705538 None:intergenic 40.0%
TGTGCTCAGACTAAGAAACT+TGG - chr7_4:34705599-34705618 Msa1150870:three_prime_UTR 40.0%
GGGATAGTAACAGCAATTTG+AGG + chr7_4:34705689-34705708 None:intergenic 40.0%
TAGCAAAGTTGCAGCGTTTA+GGG + chr7_4:34705709-34705728 None:intergenic 40.0%
TTAGCAAAGTTGCAGCGTTT+AGG + chr7_4:34705710-34705729 None:intergenic 40.0%
CGACAACTTAAAAGAAACCG+AGG + chr7_4:34705777-34705796 None:intergenic 40.0%
ACTCTTCCTTGAAAGAGTTG+AGG - chr7_4:34706113-34706132 Msa1150870:intron 40.0%
CAACAACCTCAACTCTTTCA+AGG + chr7_4:34706122-34706141 None:intergenic 40.0%
GATGCTGTTAGCTACTAGTA+TGG - chr7_4:34706172-34706191 Msa1150870:CDS 40.0%
CAAGATCCTCACATGTTTAG+CGG + chr7_4:34706424-34706443 None:intergenic 40.0%
!! GGTTTTGTAGTTCTTGTTGC+AGG - chr7_4:34705452-34705471 Msa1150870:three_prime_UTR 40.0%
AAATGCTTCCATATCTGGTG+TGG + chr7_4:34705519-34705538 None:intergenic 40.0%
TGTGCTCAGACTAAGAAACT+TGG - chr7_4:34705599-34705618 Msa1150870:three_prime_UTR 40.0%
GGGATAGTAACAGCAATTTG+AGG + chr7_4:34705689-34705708 None:intergenic 40.0%
TAGCAAAGTTGCAGCGTTTA+GGG + chr7_4:34705709-34705728 None:intergenic 40.0%
TTAGCAAAGTTGCAGCGTTT+AGG + chr7_4:34705710-34705729 None:intergenic 40.0%
CGACAACTTAAAAGAAACCG+AGG + chr7_4:34705777-34705796 None:intergenic 40.0%
ACTCTTCCTTGAAAGAGTTG+AGG - chr7_4:34706113-34706132 Msa1150870:intron 40.0%
CAACAACCTCAACTCTTTCA+AGG + chr7_4:34706122-34706141 None:intergenic 40.0%
GATGCTGTTAGCTACTAGTA+TGG - chr7_4:34706172-34706191 Msa1150870:CDS 40.0%
CAAGATCCTCACATGTTTAG+CGG + chr7_4:34706424-34706443 None:intergenic 40.0%
! GTTGAAAGTGCAGGTGAATG+TGG - chr7_4:34705485-34705504 Msa1150870:three_prime_UTR 45.0%
AAAGTGCAGGTGAATGTGGA+AGG - chr7_4:34705489-34705508 Msa1150870:three_prime_UTR 45.0%
AAGTGCAGGTGAATGTGGAA+GGG - chr7_4:34705490-34705509 Msa1150870:three_prime_UTR 45.0%
AACTTTGCTAATCGCCCCAT+TGG - chr7_4:34705719-34705738 Msa1150870:CDS 45.0%
GTCCGCACTTATAACCAATG+GGG + chr7_4:34705736-34705755 None:intergenic 45.0%
CGTCCGCACTTATAACCAAT+GGG + chr7_4:34705737-34705756 None:intergenic 45.0%
ACGTCCGCACTTATAACCAA+TGG + chr7_4:34705738-34705757 None:intergenic 45.0%
CGAATTCCGCTAAACATGTG+AGG - chr7_4:34706415-34706434 Msa1150870:CDS 45.0%
! GTTGAAAGTGCAGGTGAATG+TGG - chr7_4:34705485-34705504 Msa1150870:three_prime_UTR 45.0%
AAAGTGCAGGTGAATGTGGA+AGG - chr7_4:34705489-34705508 Msa1150870:three_prime_UTR 45.0%
AAGTGCAGGTGAATGTGGAA+GGG - chr7_4:34705490-34705509 Msa1150870:three_prime_UTR 45.0%
AACTTTGCTAATCGCCCCAT+TGG - chr7_4:34705719-34705738 Msa1150870:CDS 45.0%
GTCCGCACTTATAACCAATG+GGG + chr7_4:34705736-34705755 None:intergenic 45.0%
CGTCCGCACTTATAACCAAT+GGG + chr7_4:34705737-34705756 None:intergenic 45.0%
ACGTCCGCACTTATAACCAA+TGG + chr7_4:34705738-34705757 None:intergenic 45.0%
CGAATTCCGCTAAACATGTG+AGG - chr7_4:34706415-34706434 Msa1150870:CDS 45.0%
GTGAAGATGCTGTGCCTAGT+TGG - chr7_4:34705431-34705450 Msa1150870:three_prime_UTR 50.0%
AGTGCAGGTGAATGTGGAAG+GGG - chr7_4:34705491-34705510 Msa1150870:three_prime_UTR 50.0%
!! AAGGGGTACCACACCAGATA+TGG - chr7_4:34705508-34705527 Msa1150870:three_prime_UTR 50.0%
TCTTGTGCTGCACTTGCACA+AGG + chr7_4:34705551-34705570 None:intergenic 50.0%
! CGCCCCATTGGTTATAAGTG+CGG - chr7_4:34705731-34705750 Msa1150870:CDS 50.0%
GTGAAGATGCTGTGCCTAGT+TGG - chr7_4:34705431-34705450 Msa1150870:three_prime_UTR 50.0%
AGTGCAGGTGAATGTGGAAG+GGG - chr7_4:34705491-34705510 Msa1150870:three_prime_UTR 50.0%
!! AAGGGGTACCACACCAGATA+TGG - chr7_4:34705508-34705527 Msa1150870:three_prime_UTR 50.0%
TCTTGTGCTGCACTTGCACA+AGG + chr7_4:34705551-34705570 None:intergenic 50.0%
! CGCCCCATTGGTTATAAGTG+CGG - chr7_4:34705731-34705750 Msa1150870:CDS 50.0%
Chromosome Type Strat End Strand Name
chr7_4 gene 34705419 34706445 34705419 ID=Msa1150870;Name=Msa1150870
chr7_4 mRNA 34705419 34706445 34705419 ID=Msa1150870-mRNA-1;Parent=Msa1150870;Name=Msa1150870-mRNA-1;_AED=0.28;_eAED=0.28;_QI=0|0|0.33|1|0|0.33|3|272|112
chr7_4 exon 34705419 34705756 34705419 ID=Msa1150870-mRNA-1:exon:8246;Parent=Msa1150870-mRNA-1
chr7_4 exon 34706167 34706366 34706167 ID=Msa1150870-mRNA-1:exon:8245;Parent=Msa1150870-mRNA-1
chr7_4 exon 34706373 34706445 34706373 ID=Msa1150870-mRNA-1:exon:8244;Parent=Msa1150870-mRNA-1
chr7_4 CDS 34706373 34706445 34706373 ID=Msa1150870-mRNA-1:cds;Parent=Msa1150870-mRNA-1
chr7_4 CDS 34706167 34706366 34706167 ID=Msa1150870-mRNA-1:cds;Parent=Msa1150870-mRNA-1
chr7_4 CDS 34705691 34705756 34705691 ID=Msa1150870-mRNA-1:cds;Parent=Msa1150870-mRNA-1
chr7_4 three_prime_UTR 34705419 34705690 34705419 ID=Msa1150870-mRNA-1:three_prime_utr;Parent=Msa1150870-mRNA-1
Gene Sequence

>Msa1150870

ATGGAGGGTCTTGTGAAGATGCTGTGCCTAGTTGGTTTTGTAGTTCTTGTTGCAGGGATTCATAGAGTTGAAAGTGAATGTGGAAGGGGTACCACACCAGATATGGAAGCATTTAAGCTAGCTCCTTGTGCAAGTGCAGCACAAGATGAAAATGCTAGTGTCTCACAAAGTTGTTGTGCTCAGACTAAGAAACTTGGTCAGAATCCAAGTTGTCTTTGTGCAGTTTTGCTCTCAAACGTTGCTAAAATGTCTGGTGTTAACCCTCAAATTGCTCTTACACTCTTCCTTGAAAGAGTTGAGGTTGTTGATGAAAACAAACATAAATGGGATATGCATTGA

Protein sequence

>Msa1150870

MEGLVKMLCLVGFVVLVAGIHRVESECGRGTTPDMEAFKLAPCASAAQDENASVSQSCCAQTKKLGQNPSCLCAVLLSNVAKMSGVNPQIALTLFLERVEVVDENKHKWDMH*