AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0831710


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0831710 MtrunA17_Chr5g0394361 97.143 210 5 1 1 210 1 209 9.60e-150 414
Msa0831710 MtrunA17_Chr1g0205591 89.888 89 9 0 122 210 1 89 3.30e-55 170
Msa0831710 MtrunA17_Chr1g0205601 49.533 107 29 3 1 100 1 89 1.10e-19 80.1
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0831710 AT1G03130.1 73.684 209 49 3 3 210 1 204 2.56e-105 302
Msa0831710 AT4G02770.1 72.770 213 48 4 3 210 1 208 7.72e-102 293

Find 60 sgRNAs with CRISPR-Local

Find 63 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CCAATTGAAGTTAAGTTTAC+TGG 0.207430 5_4:+4726605 Msa0831710:CDS
AAGGAGTTGGTCAGAATTTC+AGG 0.217942 5_4:+4726561 Msa0831710:CDS
AAAGAACAGTGTTTGGCTTT+AGG 0.250321 5_4:+4726416 Msa0831710:CDS
GATGGTTGTTTCCATGGTTT+AGG 0.251347 5_4:-4726065 None:intergenic
CCAGTAAACTTAACTTCAAT+TGG 0.254455 5_4:-4726605 None:intergenic
TGGCTTTAGGAAATAGATTA+AGG 0.256198 5_4:+4726429 Msa0831710:CDS
AACACACCTTCACCAATCTT+TGG 0.314938 5_4:+4726245 Msa0831710:CDS
GTTAGGACCTTCTCTCATTA+TGG 0.318870 5_4:-4726375 None:intergenic
CGACCAGGGTTAACCTTCTC+AGG 0.322720 5_4:-4726536 None:intergenic
AAATATTGAACCTCACCATT+AGG 0.330180 5_4:-4726491 None:intergenic
ATGGTTGTTTCCATGGTTTA+GGG 0.335226 5_4:-4726064 None:intergenic
GGTCAGAATTTCAGGTCTAT+TGG 0.346075 5_4:+4726569 Msa0831710:CDS
CTTGCTAACTTAAGAAGGTT+AGG 0.358826 5_4:-4726392 None:intergenic
TGTTCTTGTTGTGAACTTGA+TGG 0.369555 5_4:-4726114 None:intergenic
AAGATTGGTGAAGGTGTGTT+TGG 0.388416 5_4:-4726242 None:intergenic
AATATTGAACCTCACCATTA+GGG 0.389009 5_4:-4726490 None:intergenic
AGCAAGGAAAGAACAGTGTT+TGG 0.399243 5_4:+4726409 Msa0831710:CDS
GAGATGAAGGATAAAGTTGA+TGG 0.402382 5_4:-4726083 None:intergenic
CTTTCCTTGCTAACTTAAGA+AGG 0.421239 5_4:-4726397 None:intergenic
GGTGTGTTTGGGTCTAGTTC+AGG 0.421350 5_4:-4726230 None:intergenic
CAGTAAACTTAACTTCAATT+GGG 0.432988 5_4:-4726604 None:intergenic
AAAGTTGATGGTTGTTTCCA+TGG 0.433796 5_4:-4726071 None:intergenic
GTTCTTGTTGTGAACTTGAT+GGG 0.443234 5_4:-4726113 None:intergenic
ATCTCAAAGATTTGTTCCTT+AGG 0.450732 5_4:-4726335 None:intergenic
GATGGGTTTGAGAGAGATGA+AGG 0.471436 5_4:-4726096 None:intergenic
TCAGGGTACACACCATCCTT+AGG 0.473133 5_4:-4726518 None:intergenic
CAAATCTTTGAGATGCCAAC+TGG 0.474824 5_4:+4726344 Msa0831710:CDS
GTGAAACCAACTGGTGCAGC+AGG 0.478227 5_4:-4726203 None:intergenic
AGATTGGTGAAGGTGTGTTT+GGG 0.480790 5_4:-4726241 None:intergenic
GTCAACCCTTACACATCAAA+AGG 0.481319 5_4:-4726635 None:intergenic
CCAATCTTTGGAGGAAGCAC+TGG 0.483310 5_4:+4726257 Msa0831710:CDS
CACTGGTGGTTTGTTACGTA+AGG 0.494140 5_4:+4726274 Msa0831710:CDS
CCAGTGCTTCCTCCAAAGAT+TGG 0.498438 5_4:-4726257 None:intergenic
TCAGGTGGAGTGAAACCAAC+TGG 0.512231 5_4:-4726212 None:intergenic
TGACCAACTCCTTCACGACC+AGG 0.519461 5_4:-4726551 None:intergenic
GGTTCAATATTTGCATCCTA+AGG 0.527977 5_4:+4726502 Msa0831710:CDS
CTAACCTTCTTAAGTTAGCA+AGG 0.531725 5_4:+4726393 Msa0831710:CDS
GAGAGGTGGAGTGAAGAGAG+AGG 0.532656 5_4:-4726036 None:intergenic
ACACCTTCACCAATCTTTGG+AGG 0.538603 5_4:+4726248 Msa0831710:CDS
GAAGCTCCTGCTGCACCAGT+TGG 0.541120 5_4:+4726197 Msa0831710:CDS
ATCTTTGGAGGAAGCACTGG+TGG 0.547257 5_4:+4726260 Msa0831710:CDS
GTGTTTGGGTCTAGTTCAGG+TGG 0.547713 5_4:-4726227 None:intergenic
CAATATTTGCATCCTAAGGA+TGG 0.551649 5_4:+4726506 Msa0831710:CDS
GGTTTAGGGCTTGAGAGAGG+TGG 0.569137 5_4:-4726050 None:intergenic
AAGGTTAACCCTGGTCGTGA+AGG 0.571068 5_4:+4726542 Msa0831710:CDS
CATGGTTTAGGGCTTGAGAG+AGG 0.581991 5_4:-4726053 None:intergenic
CTCTCTCAAGCCCTAAACCA+TGG 0.587901 5_4:+4726054 Msa0831710:CDS
GATCACATGGGAGTCACCTA+AGG 0.589857 5_4:+4726319 Msa0831710:CDS
GGATGGTGTGTACCCTGAGA+AGG 0.597067 5_4:+4726523 Msa0831710:CDS
AAGAATTCTATGTGATCACA+TGG 0.598132 5_4:+4726306 Msa0831710:CDS
AACCCTGGTCGTGAAGGAGT+TGG 0.600436 5_4:+4726548 Msa0831710:CDS
CTTCCTCCAAAGATTGGTGA+AGG 0.600903 5_4:-4726251 None:intergenic
ATTATGGCTGCACCACCAGT+TGG 0.609110 5_4:-4726359 None:intergenic
GACCAACTCCTTCACGACCA+GGG 0.644619 5_4:-4726550 None:intergenic
GGTGCAGCCATAATGAGAGA+AGG 0.648728 5_4:+4726368 Msa0831710:CDS
TACCCTGAGAAGGTTAACCC+TGG 0.651425 5_4:+4726533 Msa0831710:CDS
ATTCATCAACAACATGGCAA+TGG 0.658103 5_4:+4726004 None:intergenic
GACCAGGGTTAACCTTCTCA+GGG 0.658939 5_4:-4726535 None:intergenic
ATCTTTGAGATGCCAACTGG+TGG 0.674480 5_4:+4726347 Msa0831710:CDS
AGAATTCTATGTGATCACAT+GGG 0.727784 5_4:+4726307 Msa0831710:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AGATTAAGTATCAGTTTTAC+AGG + chr5_4:4726462-4726481 Msa0831710:CDS 25.0%
!! GATTAAGTATCAGTTTTACA+GGG + chr5_4:4726463-4726482 Msa0831710:CDS 25.0%
! CAGTAAACTTAACTTCAATT+GGG - chr5_4:4726607-4726626 None:intergenic 25.0%
AAGAATTCTATGTGATCACA+TGG + chr5_4:4726306-4726325 Msa0831710:CDS 30.0%
AGAATTCTATGTGATCACAT+GGG + chr5_4:4726307-4726326 Msa0831710:CDS 30.0%
! ATCTCAAAGATTTGTTCCTT+AGG - chr5_4:4726338-4726357 None:intergenic 30.0%
!! TGGCTTTAGGAAATAGATTA+AGG + chr5_4:4726429-4726448 Msa0831710:CDS 30.0%
AATATTGAACCTCACCATTA+GGG - chr5_4:4726493-4726512 None:intergenic 30.0%
AAATATTGAACCTCACCATT+AGG - chr5_4:4726494-4726513 None:intergenic 30.0%
CCAGTAAACTTAACTTCAAT+TGG - chr5_4:4726608-4726627 None:intergenic 30.0%
CCAATTGAAGTTAAGTTTAC+TGG + chr5_4:4726605-4726624 Msa0831710:CDS 30.0%
! ATGGTTGTTTCCATGGTTTA+GGG - chr5_4:4726067-4726086 None:intergenic 35.0%
!! AAAGTTGATGGTTGTTTCCA+TGG - chr5_4:4726074-4726093 None:intergenic 35.0%
GAGATGAAGGATAAAGTTGA+TGG - chr5_4:4726086-4726105 None:intergenic 35.0%
! GTTCTTGTTGTGAACTTGAT+GGG - chr5_4:4726116-4726135 None:intergenic 35.0%
! TGTTCTTGTTGTGAACTTGA+TGG - chr5_4:4726117-4726136 None:intergenic 35.0%
CTTGCTAACTTAAGAAGGTT+AGG - chr5_4:4726395-4726414 None:intergenic 35.0%
CTAACCTTCTTAAGTTAGCA+AGG + chr5_4:4726393-4726412 Msa0831710:CDS 35.0%
CTTTCCTTGCTAACTTAAGA+AGG - chr5_4:4726400-4726419 None:intergenic 35.0%
!! AAAGAACAGTGTTTGGCTTT+AGG + chr5_4:4726416-4726435 Msa0831710:CDS 35.0%
! TTTTACAGGGTTTTCCCTAA+TGG + chr5_4:4726476-4726495 Msa0831710:CDS 35.0%
GGTTCAATATTTGCATCCTA+AGG + chr5_4:4726502-4726521 Msa0831710:CDS 35.0%
CAATATTTGCATCCTAAGGA+TGG + chr5_4:4726506-4726525 Msa0831710:CDS 35.0%
! GATGGTTGTTTCCATGGTTT+AGG - chr5_4:4726068-4726087 None:intergenic 40.0%
! GCTTCTTCTTTTGTTGCAAC+TGG - chr5_4:4726182-4726201 None:intergenic 40.0%
! AGATTGGTGAAGGTGTGTTT+GGG - chr5_4:4726244-4726263 None:intergenic 40.0%
! AAGATTGGTGAAGGTGTGTT+TGG - chr5_4:4726245-4726264 None:intergenic 40.0%
AACACACCTTCACCAATCTT+TGG + chr5_4:4726245-4726264 Msa0831710:CDS 40.0%
!! CAAATCTTTGAGATGCCAAC+TGG + chr5_4:4726344-4726363 Msa0831710:CDS 40.0%
GTTAGGACCTTCTCTCATTA+TGG - chr5_4:4726378-4726397 None:intergenic 40.0%
AGCAAGGAAAGAACAGTGTT+TGG + chr5_4:4726409-4726428 Msa0831710:CDS 40.0%
! AAGGAGTTGGTCAGAATTTC+AGG + chr5_4:4726561-4726580 Msa0831710:CDS 40.0%
! GGTCAGAATTTCAGGTCTAT+TGG + chr5_4:4726569-4726588 Msa0831710:CDS 40.0%
! GATGGGTTTGAGAGAGATGA+AGG - chr5_4:4726099-4726118 None:intergenic 45.0%
ACACCTTCACCAATCTTTGG+AGG + chr5_4:4726248-4726267 Msa0831710:CDS 45.0%
CTTCCTCCAAAGATTGGTGA+AGG - chr5_4:4726254-4726273 None:intergenic 45.0%
!! CACTGGTGGTTTGTTACGTA+AGG + chr5_4:4726274-4726293 Msa0831710:CDS 45.0%
!! ATCTTTGAGATGCCAACTGG+TGG + chr5_4:4726347-4726366 Msa0831710:CDS 45.0%
! CATGGTTTAGGGCTTGAGAG+AGG - chr5_4:4726056-4726075 None:intergenic 50.0%
CTCTCTCAAGCCCTAAACCA+TGG + chr5_4:4726054-4726073 Msa0831710:CDS 50.0%
TCAGGTGGAGTGAAACCAAC+TGG - chr5_4:4726215-4726234 None:intergenic 50.0%
! GTGTTTGGGTCTAGTTCAGG+TGG - chr5_4:4726230-4726249 None:intergenic 50.0%
! GGTGTGTTTGGGTCTAGTTC+AGG - chr5_4:4726233-4726252 None:intergenic 50.0%
CCAGTGCTTCCTCCAAAGAT+TGG - chr5_4:4726260-4726279 None:intergenic 50.0%
! CCAATCTTTGGAGGAAGCAC+TGG + chr5_4:4726257-4726276 Msa0831710:CDS 50.0%
!! ATCTTTGGAGGAAGCACTGG+TGG + chr5_4:4726260-4726279 Msa0831710:CDS 50.0%
GATCACATGGGAGTCACCTA+AGG + chr5_4:4726319-4726338 Msa0831710:CDS 50.0%
ATTATGGCTGCACCACCAGT+TGG - chr5_4:4726362-4726381 None:intergenic 50.0%
GGTGCAGCCATAATGAGAGA+AGG + chr5_4:4726368-4726387 Msa0831710:CDS 50.0%
! CAGGGTTTTCCCTAATGGTG+AGG + chr5_4:4726481-4726500 Msa0831710:CDS 50.0%
TCAGGGTACACACCATCCTT+AGG - chr5_4:4726521-4726540 None:intergenic 50.0%
TACCCTGAGAAGGTTAACCC+TGG + chr5_4:4726533-4726552 Msa0831710:CDS 50.0%
GACCAGGGTTAACCTTCTCA+GGG - chr5_4:4726538-4726557 None:intergenic 50.0%
AAGGTTAACCCTGGTCGTGA+AGG + chr5_4:4726542-4726561 Msa0831710:CDS 50.0%
GAGAGGTGGAGTGAAGAGAG+AGG - chr5_4:4726039-4726058 None:intergenic 55.0%
! GGTTTAGGGCTTGAGAGAGG+TGG - chr5_4:4726053-4726072 None:intergenic 55.0%
GTGAAACCAACTGGTGCAGC+AGG - chr5_4:4726206-4726225 None:intergenic 55.0%
GGATGGTGTGTACCCTGAGA+AGG + chr5_4:4726523-4726542 Msa0831710:CDS 55.0%
CGACCAGGGTTAACCTTCTC+AGG - chr5_4:4726539-4726558 None:intergenic 55.0%
AACCCTGGTCGTGAAGGAGT+TGG + chr5_4:4726548-4726567 Msa0831710:CDS 55.0%
GACCAACTCCTTCACGACCA+GGG - chr5_4:4726553-4726572 None:intergenic 55.0%
TGACCAACTCCTTCACGACC+AGG - chr5_4:4726554-4726573 None:intergenic 55.0%
GAAGCTCCTGCTGCACCAGT+TGG + chr5_4:4726197-4726216 Msa0831710:CDS 60.0%
Chromosome Type Strat End Strand Name
chr5_4 gene 4726017 4726649 4726017 ID=Msa0831710;Name=Msa0831710
chr5_4 mRNA 4726017 4726649 4726017 ID=Msa0831710-mRNA-1;Parent=Msa0831710;Name=Msa0831710-mRNA-1;_AED=0.00;_eAED=0.01;_QI=0|-1|0|1|-1|1|1|0|210
chr5_4 exon 4726017 4726649 4726017 ID=Msa0831710-mRNA-1:exon:1943;Parent=Msa0831710-mRNA-1
chr5_4 CDS 4726017 4726649 4726017 ID=Msa0831710-mRNA-1:cds;Parent=Msa0831710-mRNA-1
Gene Sequence

>Msa0831710

ATGGCAATGGCAACTCAAGCCTCTCTCTTCACTCCACCTCTCTCAAGCCCTAAACCATGGAAACAACCATCAACTTTATCCTTCATCTCTCTCAAACCCATCAAGTTCACAACAAGAACAACAAAAATCTCAGCTGCAGATGACAAAACAGAAGCAGCAGCACCAGTTGCAACAAAAGAAGAAGCTCCTGCTGCACCAGTTGGTTTCACTCCACCTGAACTAGACCCAAACACACCTTCACCAATCTTTGGAGGAAGCACTGGTGGTTTGTTACGTAAGGCACAAGTTGAAGAATTCTATGTGATCACATGGGAGTCACCTAAGGAACAAATCTTTGAGATGCCAACTGGTGGTGCAGCCATAATGAGAGAAGGTCCTAACCTTCTTAAGTTAGCAAGGAAAGAACAGTGTTTGGCTTTAGGAAATAGATTAAGGTCTAAGTACAAGATTAAGTATCAGTTTTACAGGGTTTTCCCTAATGGTGAGGTTCAATATTTGCATCCTAAGGATGGTGTGTACCCTGAGAAGGTTAACCCTGGTCGTGAAGGAGTTGGTCAGAATTTCAGGTCTATTGGAAAGAATGTTAGCCCAATTGAAGTTAAGTTTACTGGTAAGCAACCTTTTGATGTGTAA

Protein sequence

>Msa0831710

MAMATQASLFTPPLSSPKPWKQPSTLSFISLKPIKFTTRTTKISAADDKTEAAAPVATKEEAPAAPVGFTPPELDPNTPSPIFGGSTGGLLRKAQVEEFYVITWESPKEQIFEMPTGGAAIMREGPNLLKLARKEQCLALGNRLRSKYKIKYQFYRVFPNGEVQYLHPKDGVYPEKVNPGREGVGQNFRSIGKNVSPIEVKFTGKQPFDV*