AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene004963

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene004963.t1 MTR_1g077700 55.376 186 21 4 1 124 1 186 2.43e-45 145
MS.gene004963.t1 MTR_1g077730 89.474 76 6 2 1 75 1 75 7.55e-40 132
MS.gene004963.t1 MTR_1g077730 65.854 82 11 1 43 124 130 194 3.00e-30 107
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 49 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AATGAATGTCTCTTTGGATT+TGG 0.240224 1.4:+63663175 MS.gene004963:CDS
AAAGAAAATGAATGTCTCTT+TGG 0.284507 1.4:+63663169 MS.gene004963:CDS
CATGAACAACAACTCTCTTT+AGG 0.379285 1.4:+63662654 MS.gene004963:CDS
CTCGATGAGGTTGCCTCCAC+CGG 0.381070 1.4:-63663101 None:intergenic
GGTTCTTCATCTTCTTCGTC+TGG 0.390134 1.4:-63663140 None:intergenic
CTTTGATCTGCTTAAGCTGC+AGG 0.428529 1.4:-63663209 None:intergenic
GAATAAGCAATGATGGAGAA+AGG 0.431980 1.4:-63662702 None:intergenic
TTCACTTCATTTCAATCACT+TGG 0.434926 1.4:+63662798 MS.gene004963:CDS
TCGTCTGGTTTCAAAGCCAT+TGG 0.468001 1.4:-63663125 None:intergenic
GTGCATGGTGGAAGGTCATA+TGG 0.468572 1.4:-63663079 None:intergenic
TTCACATCTGGCCAGGCACT+TGG 0.470440 1.4:+63663053 MS.gene004963:intron
TGTAGAAGAATAAGCAATGA+TGG 0.477070 1.4:-63662709 None:intergenic
TATTCTTCTACAAGAGAAGA+AGG 0.493297 1.4:+63662720 MS.gene004963:CDS
AATAAGCAATGATGGAGAAA+GGG 0.498901 1.4:-63662701 None:intergenic
CTTCCACCATGCACCGGTGG+AGG 0.506143 1.4:+63663088 MS.gene004963:CDS
ACTTCATTTCAATCACTTGG+AGG 0.515461 1.4:+63662801 MS.gene004963:CDS
GAAGCCTAGAGATGATTGTC+AGG 0.519135 1.4:+63662842 MS.gene004963:CDS
GCAATGATGGAGAAAGGGAT+AGG 0.524368 1.4:-63662696 None:intergenic
ACATCTGGCCAGGCACTTGG+TGG 0.529943 1.4:+63663056 MS.gene004963:intron
CTCCACCGGTGCATGGTGGA+AGG 0.537215 1.4:-63663087 None:intergenic
TGAACCTGACAATCATCTCT+AGG 0.556365 1.4:-63662846 None:intergenic
AGGTTGCCTCCACCGGTGCA+TGG 0.568155 1.4:-63663094 None:intergenic
TATGACCTTCCACCATGCAC+CGG 0.585865 1.4:+63663082 MS.gene004963:CDS
CAAAGCCATTGGTCTCGATG+AGG 0.605389 1.4:-63663114 None:intergenic
GGCAACCTCATCGAGACCAA+TGG 0.607582 1.4:+63663109 MS.gene004963:CDS
GACCTTCCACCATGCACCGG+TGG 0.615351 1.4:+63663085 MS.gene004963:CDS
GATCTGCTTAAGCTGCAGGA+AGG 0.638172 1.4:-63663205 None:intergenic
TTGCCTCCACCGGTGCATGG+TGG 0.647313 1.4:-63663091 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATTGATACTATTCAATTTAA+GGG - chr1.4:63662907-63662926 None:intergenic 15.0%
!! CATTGATACTATTCAATTTA+AGG - chr1.4:63662908-63662927 None:intergenic 20.0%
!! CTTAAATTGAATAGTATCAA+TGG + chr1.4:63662906-63662925 MS.gene004963:intron 20.0%
! AAAGAAAATGAATGTCTCTT+TGG + chr1.4:63663169-63663188 MS.gene004963:CDS 25.0%
! ATTGAATAGTATCAATGGTA+TGG + chr1.4:63662911-63662930 MS.gene004963:intron 25.0%
! TTGAATAGTATCAATGGTAT+GGG + chr1.4:63662912-63662931 MS.gene004963:intron 25.0%
AACAACAAAACCAAGGTTTA+TGG + chr1.4:63663008-63663027 MS.gene004963:intron 30.0%
AATGAATGTCTCTTTGGATT+TGG + chr1.4:63663175-63663194 MS.gene004963:CDS 30.0%
ACAACAAAACCAAGGTTTAT+GGG + chr1.4:63663009-63663028 MS.gene004963:intron 30.0%
TATTCTTCTACAAGAGAAGA+AGG + chr1.4:63662720-63662739 MS.gene004963:CDS 30.0%
TGTAGAAGAATAAGCAATGA+TGG - chr1.4:63662712-63662731 None:intergenic 30.0%
TTCACTTCATTTCAATCACT+TGG + chr1.4:63662798-63662817 MS.gene004963:CDS 30.0%
! AATAAGCAATGATGGAGAAA+GGG - chr1.4:63662704-63662723 None:intergenic 30.0%
! ACATTCATTTTCTTTGTAGG+TGG - chr1.4:63663164-63663183 None:intergenic 30.0%
! GAGACATTCATTTTCTTTGT+AGG - chr1.4:63663167-63663186 None:intergenic 30.0%
! TGTGAATTTAGAACCACAAA+TGG - chr1.4:63663039-63663058 None:intergenic 30.0%
ACTTCATTTCAATCACTTGG+AGG + chr1.4:63662801-63662820 MS.gene004963:CDS 35.0%
CAACAACAACAACAAAACCA+AGG + chr1.4:63663001-63663020 MS.gene004963:intron 35.0%
CATGAACAACAACTCTCTTT+AGG + chr1.4:63662654-63662673 MS.gene004963:CDS 35.0%
! GAATAAGCAATGATGGAGAA+AGG - chr1.4:63662705-63662724 None:intergenic 35.0%
! GCTTCTTGTGAACTTTTCTA+TGG - chr1.4:63662827-63662846 None:intergenic 35.0%
! GTTATTGTTGTTGTTGGTAG+TGG - chr1.4:63662976-63662995 None:intergenic 35.0%
!! TGTGGTTCTAAATTCACATC+TGG + chr1.4:63663041-63663060 MS.gene004963:intron 35.0%
!!! CTTGGTTTTGTTGTTGTTGT+TGG - chr1.4:63663003-63663022 None:intergenic 35.0%
TGAACCTGACAATCATCTCT+AGG - chr1.4:63662849-63662868 None:intergenic 40.0%
TTCTAAATTCACATCTGGCC+AGG + chr1.4:63663046-63663065 MS.gene004963:intron 40.0%
!! ATTGTTGTTGTTGGTAGTGG+TGG - chr1.4:63662973-63662992 None:intergenic 40.0%
!! GGTGGTGTTATTGTTGTTGT+TGG - chr1.4:63662982-63663001 None:intergenic 40.0%
!!! GGTTTTGTTGTTGTTGTTGG+TGG - chr1.4:63663000-63663019 None:intergenic 40.0%
AATGGTGCACCCATAAACCT+TGG - chr1.4:63663021-63663040 None:intergenic 45.0%
GAAGCCTAGAGATGATTGTC+AGG + chr1.4:63662842-63662861 MS.gene004963:CDS 45.0%
GGTTCTTCATCTTCTTCGTC+TGG - chr1.4:63663143-63663162 None:intergenic 45.0%
GTTTATGGGTGCACCATTTG+TGG + chr1.4:63663023-63663042 MS.gene004963:intron 45.0%
! GCAATGATGGAGAAAGGGAT+AGG - chr1.4:63662699-63662718 None:intergenic 45.0%
! TCGTCTGGTTTCAAAGCCAT+TGG - chr1.4:63663128-63663147 None:intergenic 45.0%
TATGACCTTCCACCATGCAC+CGG + chr1.4:63663082-63663101 MS.gene004963:CDS 50.0%
! CAAAGCCATTGGTCTCGATG+AGG - chr1.4:63663117-63663136 None:intergenic 50.0%
! GTGCATGGTGGAAGGTCATA+TGG - chr1.4:63663082-63663101 None:intergenic 50.0%
!! GTTGTTGTTGGTAGTGGTGG+TGG - chr1.4:63662970-63662989 None:intergenic 50.0%
GGCAACCTCATCGAGACCAA+TGG + chr1.4:63663109-63663128 MS.gene004963:CDS 55.0%
TCATATGGCCACCAAGTGCC+TGG - chr1.4:63663067-63663086 None:intergenic 55.0%
TTCACATCTGGCCAGGCACT+TGG + chr1.4:63663053-63663072 MS.gene004963:intron 55.0%
ACATCTGGCCAGGCACTTGG+TGG + chr1.4:63663056-63663075 MS.gene004963:intron 60.0%
CTCGATGAGGTTGCCTCCAC+CGG - chr1.4:63663104-63663123 None:intergenic 60.0%
AGGTTGCCTCCACCGGTGCA+TGG - chr1.4:63663097-63663116 None:intergenic 65.0%
GACCTTCCACCATGCACCGG+TGG + chr1.4:63663085-63663104 MS.gene004963:CDS 65.0%
TTGCCTCCACCGGTGCATGG+TGG - chr1.4:63663094-63663113 None:intergenic 65.0%
! CTCCACCGGTGCATGGTGGA+AGG - chr1.4:63663090-63663109 None:intergenic 65.0%
! CTTCCACCATGCACCGGTGG+AGG + chr1.4:63663088-63663107 MS.gene004963:CDS 65.0%


Chromosome Type Strat End Strand Name
chr1.4 gene 63662642 63663220 63662642 ID=MS.gene004963
chr1.4 mRNA 63662642 63663220 63662642 ID=MS.gene004963.t1;Parent=MS.gene004963
chr1.4 exon 63662642 63662863 63662642 ID=MS.gene004963.t1.exon1;Parent=MS.gene004963.t1
chr1.4 CDS 63662642 63662863 63662642 ID=cds.MS.gene004963.t1;Parent=MS.gene004963.t1
chr1.4 exon 63663068 63663220 63663068 ID=MS.gene004963.t1.exon2;Parent=MS.gene004963.t1
chr1.4 CDS 63663068 63663220 63663068 ID=cds.MS.gene004963.t1;Parent=MS.gene004963.t1
Gene Sequence

>MS.gene004963

ATGGAAGCATCTCATGAACAACAACTCTCTTTAGGCTCTATAGAACAACAATCTCCTATCCCTTTCTCCATCATTGCTTATTCTTCTACAAGAGAAGAAGGAACAAGAGAAAGTGCACGTTACAATGTGTATGCATGCAAAACATGCAAGAAAACTTTCACTTCATTTCAATCACTTGGAGGCCATAGAAAAGTTCACAAGAAGCCTAGAGATGATTGTCAGGTTCAAGAGTTTCAATTCAAAATCAATAATAAATCAATTTCCCTTAAATTGAATAGTATCAATGGTATGGGAAATATATATGCTAGTAGCAACAACAACAACACCACCACCACTACCAACAACAACAATAACACCACCAACAACAACAACAAAACCAAGGTTTATGGGTGCACCATTTGTGGTTCTAAATTCACATCTGGCCAGGCACTTGGTGGCCATATGACCTTCCACCATGCACCGGTGGAGGCAACCTCATCGAGACCAATGGCTTTGAAACCAGACGAAGAAGATGAAGAACCACCTACAAAGAAAATGAATGTCTCTTTGGATTTGGATCTCAACCTTCCTGCAGCTTAA
Protein sequence

>MS.gene004963.t1

MEASHEQQLSLGSIEQQSPIPFSIIAYSSTREEGTRESARYNVYACKTCKKTFTSFQSLGGHRKVHKKPRDDCQALGGHMTFHHAPVEATSSRPMALKPDEEDEEPPTKKMNVSLDLDLNLPAA