AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene69003

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene69003.t1 MTR_6g088270 52.980 151 14 4 5 98 845 995 9.80e-35 125
MS.gene69003.t1 MTR_6g088270 39.333 150 34 3 6 98 605 754 2.32e-24 95.9
MS.gene69003.t1 MTR_6g088240 66.667 96 21 1 3 98 52 136 1.06e-32 112
MS.gene69003.t1 MTR_6g087300 54.918 122 27 2 5 98 205 326 1.04e-29 108
MS.gene69003.t1 MTR_2g039780 74.545 55 12 2 46 98 104 158 2.97e-19 78.6
MS.gene69003.t1 MTR_6g027070 39.370 127 39 3 10 98 13 139 1.42e-18 75.5
MS.gene69003.t1 MTR_2g039790 96.875 32 1 0 5 36 16 47 7.49e-14 63.2
MS.gene69003.t1 MTR_6g081090 90.625 32 3 0 5 36 6 37 2.13e-12 58.9
MS.gene69003.t1 MTR_6g488290 90.625 32 3 0 5 36 39 70 1.22e-11 58.2
MS.gene69003.t1 MTR_0428s0020 90.625 32 3 0 5 36 39 70 1.32e-11 58.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene69003.t1 AT4G29060 46.309 149 23 4 7 98 754 902 1.38e-26 102
MS.gene69003.t1 AT4G29060 41.781 146 28 3 10 98 519 664 4.22e-24 95.1
MS.gene69003.t1 AT4G29060 44.138 145 20 3 10 98 519 658 4.84e-25 97.8

Find 17 sgRNAs with CRISPR-Local

Find 42 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTCCTTCGTCACAATAGTTT+TGG 0.223500 6.2:-86966877 None:intergenic
GGTAGTGGTCTCGGCCTCTT+TGG 0.356320 6.2:+86966554 MS.gene69003:CDS
AGAAACCGGTGCAGGGATGA+TGG 0.468491 6.2:+86966593 MS.gene69003:CDS
CAGACTTTGTTCACAGGAGT+TGG 0.468902 6.2:+86966791 MS.gene69003:intron
GAAATCAACGGTAGTGGTCT+CGG 0.470731 6.2:+86966545 MS.gene69003:CDS
CTACGAGAAGAAACCGGTGC+AGG 0.539828 6.2:+86966585 MS.gene69003:CDS
TTGCAGGAAATCAACGGTAG+TGG 0.544055 6.2:+86966539 MS.gene69003:intron
AAGCAACTACGAGAAGAAAC+CGG 0.544505 6.2:+86966579 MS.gene69003:CDS
TCGTAGTTGCTTAACCAAAG+AGG 0.558812 6.2:-86966568 None:intergenic
ACAGTCCATCATCCCTGCAC+CGG 0.573161 6.2:-86966598 None:intergenic
GAGAGAAAATTATCGAGGGA+AGG 0.574527 6.2:+86966952 MS.gene69003:CDS
GTCAAACAGACTTTGTTCAC+AGG 0.577694 6.2:+86966785 MS.gene69003:intron
AACAAGAGAGAAAATTATCG+AGG 0.594552 6.2:+86966947 MS.gene69003:CDS
TCCCAAAACTATTGTGACGA+AGG 0.601393 6.2:+86966875 MS.gene69003:CDS
TACGAGAAGAAACCGGTGCA+GGG 0.620957 6.2:+86966586 MS.gene69003:CDS
ACAAGAGAGAAAATTATCGA+GGG 0.629594 6.2:+86966948 MS.gene69003:CDS
AAAAGAACTTGAGATGCAGA+GGG 0.654942 6.2:+86966899 MS.gene69003:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAGAAAAATTGAGAAAAAAA+TGG + chr6.2:86966478-86966497 MS.gene69003:intron 15.0%
!!! ATTGTTTAATTTTTTATTGC+AGG + chr6.2:86966523-86966542 MS.gene69003:intron 15.0%
!! TTTTTATTGCAGGAAATCAA+CGG + chr6.2:86966533-86966552 MS.gene69003:intron 25.0%
!!! AATTTTCTCTCTTGTTTTCT+CGG - chr6.2:86966943-86966962 None:intergenic 25.0%
!!! TTTTCAAGATCACTTTGTTT+CGG - chr6.2:86966637-86966656 None:intergenic 25.0%
AACAAGAGAGAAAATTATCG+AGG + chr6.2:86966947-86966966 MS.gene69003:CDS 30.0%
ACAAGAGAGAAAATTATCGA+GGG + chr6.2:86966948-86966967 MS.gene69003:CDS 30.0%
GAAACAAAGTGATCTTGAAA+AGG + chr6.2:86966636-86966655 MS.gene69003:intron 30.0%
!!! ATTTTCTCTCTTGTTTTCTC+GGG - chr6.2:86966942-86966961 None:intergenic 30.0%
AAAAAGAACTTGAGATGCAG+AGG + chr6.2:86966898-86966917 MS.gene69003:CDS 35.0%
AAAAGAACTTGAGATGCAGA+GGG + chr6.2:86966899-86966918 MS.gene69003:CDS 35.0%
ACAAGCATACCTCAGAAAAA+AGG + chr6.2:86966660-86966679 MS.gene69003:intron 35.0%
CAAGCATACCTCAGAAAAAA+GGG + chr6.2:86966661-86966680 MS.gene69003:intron 35.0%
! TCCTTCGTCACAATAGTTTT+GGG - chr6.2:86966879-86966898 None:intergenic 35.0%
! TTCCTTCGTCACAATAGTTT+TGG - chr6.2:86966880-86966899 None:intergenic 35.0%
AAGCAACTACGAGAAGAAAC+CGG + chr6.2:86966579-86966598 MS.gene69003:CDS 40.0%
AATGTCTACATGTCGACATG+TGG - chr6.2:86966390-86966409 None:intergenic 40.0%
ACATGTCGACATGTAGACAT+TGG + chr6.2:86966389-86966408 MS.gene69003:intron 40.0%
GAGAGAAAATTATCGAGGGA+AGG + chr6.2:86966952-86966971 MS.gene69003:CDS 40.0%
GTCAAACAGACTTTGTTCAC+AGG + chr6.2:86966785-86966804 MS.gene69003:intron 40.0%
TACATTCACGATTCACGCAT+TGG + chr6.2:86966742-86966761 MS.gene69003:intron 40.0%
TCATCTGCTGACAAGAAATC+CGG + chr6.2:86966688-86966707 MS.gene69003:intron 40.0%
TCCCAAAACTATTGTGACGA+AGG + chr6.2:86966875-86966894 MS.gene69003:CDS 40.0%
TCGTAGTTGCTTAACCAAAG+AGG - chr6.2:86966571-86966590 None:intergenic 40.0%
! ACAACTAACCGTGTTTCTGT+CGG - chr6.2:86966356-86966375 None:intergenic 40.0%
!!! ATGACAGACCCTTTTTTCTG+AGG - chr6.2:86966672-86966691 None:intergenic 40.0%
ACAACTAACACCTACGCATG+TGG - chr6.2:86966448-86966467 None:intergenic 45.0%
CAGACTTTGTTCACAGGAGT+TGG + chr6.2:86966791-86966810 MS.gene69003:intron 45.0%
CGAAAACACCGACAGAAACA+CGG + chr6.2:86966345-86966364 MS.gene69003:intron 45.0%
CTAGCAGCTGAAGGAAGAAT+CGG + chr6.2:86966715-86966734 MS.gene69003:intron 45.0%
CTGAACATAACCACATGCGT+AGG + chr6.2:86966435-86966454 MS.gene69003:intron 45.0%
TTGCAGGAAATCAACGGTAG+TGG + chr6.2:86966539-86966558 MS.gene69003:intron 45.0%
! GAAATCAACGGTAGTGGTCT+CGG + chr6.2:86966545-86966564 MS.gene69003:CDS 45.0%
! TTTTCTCGGGTTTGGAAGCA+AGG - chr6.2:86966929-86966948 None:intergenic 45.0%
!!! CTCTCTTGTTTTCTCGGGTT+TGG - chr6.2:86966937-86966956 None:intergenic 45.0%
TACGAGAAGAAACCGGTGCA+GGG + chr6.2:86966586-86966605 MS.gene69003:CDS 50.0%
!! TCCTTCAGCTGCTAGTCTTC+CGG - chr6.2:86966710-86966729 None:intergenic 50.0%
ACAGTCCATCATCCCTGCAC+CGG - chr6.2:86966601-86966620 None:intergenic 55.0%
AGAAACCGGTGCAGGGATGA+TGG + chr6.2:86966593-86966612 MS.gene69003:CDS 55.0%
CTACGAGAAGAAACCGGTGC+AGG + chr6.2:86966585-86966604 MS.gene69003:CDS 55.0%
TCCGGAAGACTAGCAGCTGA+AGG + chr6.2:86966706-86966725 MS.gene69003:intron 55.0%
! GGTAGTGGTCTCGGCCTCTT+TGG + chr6.2:86966554-86966573 MS.gene69003:CDS 60.0%


Chromosome Type Strat End Strand Name
chr6.2 gene 86966319 86966980 86966319 ID=MS.gene69003
chr6.2 mRNA 86966319 86966980 86966319 ID=MS.gene69003.t1;Parent=MS.gene69003
chr6.2 exon 86966319 86966329 86966319 ID=MS.gene69003.t1.exon1;Parent=MS.gene69003.t1
chr6.2 CDS 86966319 86966329 86966319 ID=cds.MS.gene69003.t1;Parent=MS.gene69003.t1
chr6.2 exon 86966545 86966643 86966545 ID=MS.gene69003.t1.exon2;Parent=MS.gene69003.t1
chr6.2 CDS 86966545 86966643 86966545 ID=cds.MS.gene69003.t1;Parent=MS.gene69003.t1
chr6.2 exon 86966794 86966980 86966794 ID=MS.gene69003.t1.exon3;Parent=MS.gene69003.t1
chr6.2 CDS 86966794 86966980 86966794 ID=cds.MS.gene69003.t1;Parent=MS.gene69003.t1
Gene Sequence

>MS.gene69003

ATGAATGACATGTAAGCATCAGTCTACGAAAACACCGACAGAAACACGGTTAGTTGTAAGATCAACAACCACATGTCGACATGTAGACATTGGTAATAATTTTAGAAAATGCAAAACTGAACATAACCACATGCGTAGGTGTTAGTTGTACTTATACACAAGAAAAATTGAGAAAAAAATGGATGTCTTTGATGCAAATATTAAATTGTTTAATTTTTTATTGCAGGAAATCAACGGTAGTGGTCTCGGCCTCTTTGGTTAAGCAACTACGAGAAGAAACCGGTGCAGGGATGATGGACTGTAAGAAAGCTCTTGCCGAAACAAAGTGATCTTGAAAAGGCACAAGCATACCTCAGAAAAAAGGGTCTGTCATCTGCTGACAAGAAATCCGGAAGACTAGCAGCTGAAGGAAGAATCGGTACATACATTCACGATTCACGCATTGGTATTCTAATTGAAGTGAACTGTCAAACAGACTTTGTTCACAGGAGTTGGTTGATGATCTTGCATTGCAAGTAGCTGCTTGTTCAGTTCAGTTTGTTTCTATTGAAGATATTCCCAAAACTATTGTGACGAAGGAAAAAGAACTTGAGATGCAGAGGGAAGACCTTGCTTCCAAACCCGAGAAAACAAGAGAGAAAATTATCGAGGGAAGGATCTGA
Protein sequence

>MS.gene69003.t1

MNDMKSTVVVSASLVKQLREETGAGMMDCKKALAETKLCSQELVDDLALQVAACSVQFVSIEDIPKTIVTKEKELEMQREDLASKPEKTREKIIEGRI