AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar ZhongmuNo.1 / MsG0380014639.01


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0380014639.01.T02 MTR_3g061480 89.011 91 8 2 1 90 1 90 1.41e-49 154
MsG0380014639.01.T01 MTR_3g061480 89.011 91 8 2 5 94 1 90 1.33e-49 154
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 16 sgRNAs with CRISPR-Local

Find 19 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AAGCTCTTTGAGGGCTTCTT+TGG 0.197880 3:+57606397 None:intergenic
AGGGCTTCTTTGGCCTTCTC+TGG 0.212908 3:+57606407 None:intergenic
CTGCATAGTTCATGCATTAA+AGG 0.282045 3:-57606456 MsG0380014639.01.T01:CDS
GTTCCAACACCCTTGAGTTT+TGG 0.308749 3:+57606332 None:intergenic
TTATTACATAATAATGATAA+AGG 0.418724 3:-57606530 MsG0380014639.01.T01:CDS
TTTCTGGTCAAGCTCTTTGA+GGG 0.426726 3:+57606388 None:intergenic
GGGCTTCTTTGGCCTTCTCT+GGG 0.431800 3:+57606408 None:intergenic
AGTGGTTGCTTGATGCTAAG+AGG 0.489873 3:+57606584 None:intergenic
AGTGATGCAAATAATAATAG+TGG 0.491359 3:+57606566 None:intergenic
TCTCCAAAACTCAAGGGTGT+TGG 0.528353 3:-57606335 MsG0380014639.01.T01:CDS
AGTTTCCTCTCCAAAACTCA+AGG 0.554422 3:-57606342 MsG0380014639.01.T01:CDS
TCATTATTATGTAATAATGA+CGG 0.562748 3:+57606536 None:intergenic
ATAAAGGCATATTCAAAGAG+AGG 0.608157 3:-57606514 MsG0380014639.01.T01:CDS
GTTTCCTCTCCAAAACTCAA+GGG 0.622427 3:-57606341 MsG0380014639.01.T01:CDS
ATATGAGATAGACCCAGAGA+AGG 0.653858 3:-57606420 MsG0380014639.01.T01:CDS
AAGGCATATTCAAAGAGAGG+AGG 0.658459 3:-57606511 MsG0380014639.01.T01:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTATTACATAATAATGATAA+AGG - Chr3:57606391-57606410 MsG0380014639.01.T01:CDS 10.0%
!! TCATTATTATGTAATAATGA+CGG + Chr3:57606388-57606407 None:intergenic 15.0%
! AGTGATGCAAATAATAATAG+TGG + Chr3:57606358-57606377 None:intergenic 25.0%
!! TAGAGATAGATTGAATTTTC+TGG + Chr3:57606552-57606571 None:intergenic 25.0%
! ATAAAGGCATATTCAAAGAG+AGG - Chr3:57606407-57606426 MsG0380014639.01.T01:CDS 30.0%
CTGCATAGTTCATGCATTAA+AGG - Chr3:57606465-57606484 MsG0380014639.01.T01:CDS 35.0%
AAGGCATATTCAAAGAGAGG+AGG - Chr3:57606410-57606429 MsG0380014639.01.T01:CDS 40.0%
AGTTTCCTCTCCAAAACTCA+AGG - Chr3:57606579-57606598 MsG0380014639.01.T01:CDS 40.0%
ATATGAGATAGACCCAGAGA+AGG - Chr3:57606501-57606520 MsG0380014639.01.T01:CDS 40.0%
GTTTCCTCTCCAAAACTCAA+GGG - Chr3:57606580-57606599 MsG0380014639.01.T01:CDS 40.0%
! TTTCTGGTCAAGCTCTTTGA+GGG + Chr3:57606536-57606555 None:intergenic 40.0%
!! TTTTCTGGTCAAGCTCTTTG+AGG + Chr3:57606537-57606556 None:intergenic 40.0%
AGTGGTTGCTTGATGCTAAG+AGG + Chr3:57606340-57606359 None:intergenic 45.0%
! AAGCTCTTTGAGGGCTTCTT+TGG + Chr3:57606527-57606546 None:intergenic 45.0%
! GTTCCAACACCCTTGAGTTT+TGG + Chr3:57606592-57606611 None:intergenic 45.0%
! TCTCCAAAACTCAAGGGTGT+TGG - Chr3:57606586-57606605 MsG0380014639.01.T01:CDS 45.0%
!!! AACACCCTTGAGTTTTGGAG+AGG + Chr3:57606587-57606606 None:intergenic 45.0%
! AGGGCTTCTTTGGCCTTCTC+TGG + Chr3:57606517-57606536 None:intergenic 55.0%
! GGGCTTCTTTGGCCTTCTCT+GGG + Chr3:57606516-57606535 None:intergenic 55.0%
Chromosome Type Strat End Strand Name
Chr3 gene 57606319 57606624 57606319 ID=MsG0380014639.01;Name=MsG0380014639.01
Chr3 mRNA 57606319 57606624 57606319 ID=MsG0380014639.01.T01;Parent=MsG0380014639.01;Name=MsG0380014639.01.T01;_AED=0.50;_eAED=0.54;_QI=0|-1|0|1|-1|0|1|0|101
Chr3 exon 57606319 57606624 57606319 ID=MsG0380014639.01.T01:exon:11139;Parent=MsG0380014639.01.T01
Chr3 CDS 57606319 57606624 57606319 ID=MsG0380014639.01.T01:cds;Parent=MsG0380014639.01.T01
Chr3 mRNA 57606319 57606612 57606319 ID=MsG0380014639.01.T02;Parent=MsG0380014639.01;Name=MsG0380014639.01.T02;_AED=0.50;_eAED=0.54;_QI=0|-1|0|1|-1|0|1|0|97
Chr3 exon 57606319 57606612 57606319 ID=MsG0380014639.01.T02:exon:11140;Parent=MsG0380014639.01.T02
Chr3 CDS 57606319 57606612 57606319 ID=MsG0380014639.01.T02:cds;Parent=MsG0380014639.01.T02
Gene Sequence

>MsG0380014639.01.T02

ATGAAACCTCTTAGCATCAAGCAACCACTATTATTATTTGCATCACTTTCTAAACCGTCATTATTACATAATAATGATAAAGGCATATTCAAAGAGAGGAGGCACATAAAATATTCTTCTTCATTTAATTCATGCTGCATAGTTCATGCATTAAAGGAAGATTCAAAGCAATATGAGATAGACCCAGAGAAGGCCAAAGAAGCCCTCAAAGAGCTTGACCAGAAAATTCAATCTATCTCTACTAGAGAAGTTTCCTCTCCAAAACTCAAGGGTGTTGGAACAAAATGTGTTTAA

>MsG0380014639.01.T01

ATGTTATTCTCTATGAAACCTCTTAGCATCAAGCAACCACTATTATTATTTGCATCACTTTCTAAACCGTCATTATTACATAATAATGATAAAGGCATATTCAAAGAGAGGAGGCACATAAAATATTCTTCTTCATTTAATTCATGCTGCATAGTTCATGCATTAAAGGAAGATTCAAAGCAATATGAGATAGACCCAGAGAAGGCCAAAGAAGCCCTCAAAGAGCTTGACCAGAAAATTCAATCTATCTCTACTAGAGAAGTTTCCTCTCCAAAACTCAAGGGTGTTGGAACAAAATGTGTTTAA

Protein sequence

>MsG0380014639.01.T02

MKPLSIKQPLLLFASLSKPSLLHNNDKGIFKERRHIKYSSSFNSCCIVHALKEDSKQYEIDPEKAKEALKELDQKIQSISTREVSSPKLKGVGTKCV*

>MsG0380014639.01.T01

MLFSMKPLSIKQPLLLFASLSKPSLLHNNDKGIFKERRHIKYSSSFNSCCIVHALKEDSKQYEIDPEKAKEALKELDQKIQSISTREVSSPKLKGVGTKCV*