AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0749080


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0749080 MtrunA17_Chr5g0399261 85.461 282 21 4 1 282 5 266 1.76e-168 467
Msa0749080 MtrunA17_Chr4g0056091 41.925 322 122 12 1 279 1 300 4.07e-57 186
Msa0749080 MtrunA17_Chr7g0231181 32.764 351 151 12 1 280 1 337 2.63e-37 135
Msa0749080 MtrunA17_Chr4g0012691 28.701 331 132 11 1 259 2 300 1.81e-23 98.6
Msa0749080 MtrunA17_Chr3g0079061 28.125 288 154 12 6 264 8 271 2.58e-14 71.2
Msa0749080 MtrunA17_Chr4g0018761 26.394 269 143 12 6 260 9 236 2.61e-14 71.2
Msa0749080 MtrunA17_Chr3g0079131 24.828 290 159 11 3 260 5 267 1.01e-12 67.0
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0749080 AT3G60580.1 29.321 324 137 11 1 280 1 276 2.92e-25 102
Msa0749080 AT1G02030.1 28.443 334 107 16 2 282 3 257 4.41e-22 93.2
Msa0749080 AT4G16610.1 35.052 194 93 5 3 191 4 169 7.97e-22 90.9
Msa0749080 AT2G45120.1 30.877 285 151 8 1 259 1 265 3.57e-20 89.0

Find 42 sgRNAs with CRISPR-Local

Find 110 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTTGTACTACTACTGTTTGT+TGG 0.284162 5_2:-2442909 None:intergenic
GTTATAGCAGCTTCTTCTTC+AGG 0.287165 5_2:-2443204 None:intergenic
AGAAGATGAAAATGAGAGTA+TGG 0.289041 5_2:-2442869 None:intergenic
GTGAGATTGTGTTTGTGGTT+GGG 0.304906 5_2:-2442827 None:intergenic
TTTGGTTCTTATCAAGCATT+AGG 0.305236 5_2:+2443453 Msa0749080:CDS
TGATGCTATCAAGAGATAAA+TGG 0.312199 5_2:+2443232 Msa0749080:CDS
TGAGATTGTGTTTGTGGTTG+GGG 0.323538 5_2:-2442826 None:intergenic
AAAAGTGAAGTAACAGGTTC+TGG 0.326984 5_2:-2443171 None:intergenic
GGTGAGATTGTGTTTGTGGT+TGG 0.402930 5_2:-2442828 None:intergenic
TGTTGTTGAGAAAGAAAACT+TGG 0.417388 5_2:-2443004 None:intergenic
GTGTGGTGAGATTGTGTTTG+TGG 0.419011 5_2:-2442832 None:intergenic
ATGAAAAGAGTCCAATGTAT+AGG 0.422671 5_2:+2442941 Msa0749080:CDS
TCTTCTTCCAAGATGGATAG+AGG 0.427918 5_2:-2443494 None:intergenic
AATCTCACCTCTATCCATCT+TGG 0.444489 5_2:+2443487 Msa0749080:CDS
TTCATCAATGGTAAAGCATT+GGG 0.449808 5_2:+2442754 Msa0749080:CDS
TTATAGCAGCTTCTTCTTCA+GGG 0.455323 5_2:-2443203 None:intergenic
ATTATAAATGTGACAAATGT+GGG 0.460652 5_2:+2443301 Msa0749080:CDS
GAAGAAGAACAAGAAGTTTG+TGG 0.463316 5_2:+2443276 Msa0749080:CDS
AAGAAGAACAAGAAGTTTGT+GGG 0.463576 5_2:+2443277 Msa0749080:CDS
ATTCATCAATGGTAAAGCAT+TGG 0.467655 5_2:+2442753 Msa0749080:CDS
TGCTCAAGAACATTCATCAA+TGG 0.467969 5_2:+2442742 Msa0749080:CDS
TGGAAGAGGAAGAGGGAGGG+TGG 0.478080 5_2:-2442800 None:intergenic
GAGAGTATGGTAGAAGAAGT+AGG 0.483653 5_2:-2442856 None:intergenic
CTTTAGAAGTTCACAAGCAA+TGG 0.490495 5_2:+2443332 Msa0749080:CDS
GGTTTGGAAGAGGAAGAGGG+AGG 0.491265 5_2:-2442804 None:intergenic
TTGAGTTGGGTTCTTTGACT+CGG 0.515544 5_2:-2443058 None:intergenic
AAGTTGAAAAGTGAAGTAAC+AGG 0.534456 5_2:-2443177 None:intergenic
GTTGTTGAGAAAGAAAACTT+GGG 0.543214 5_2:-2443003 None:intergenic
GGATCATCTTCTTATGATGA+AGG 0.547481 5_2:-2443555 None:intergenic
TGGTAGAAGAAGTAGGAGTG+TGG 0.559870 5_2:-2442849 None:intergenic
AATTATAAATGTGACAAATG+TGG 0.560495 5_2:+2443300 Msa0749080:CDS
GTTTGGAAGAGGAAGAGGGA+GGG 0.560895 5_2:-2442803 None:intergenic
AGCATTGGGTGGACACATGA+AGG 0.563543 5_2:+2442768 Msa0749080:CDS
GAGATTGTGTTTGTGGTTGG+GGG 0.564499 5_2:-2442825 None:intergenic
TATAGCAGCTTCTTCTTCAG+GGG 0.571162 5_2:-2443202 None:intergenic
CCTTAGGACAAAACACACAT+TGG 0.573593 5_2:-2443428 None:intergenic
ATCTCTTGATAGCATCATGA+GGG 0.581541 5_2:-2443226 None:intergenic
GGTTCTTATCAAGCATTAGG+TGG 0.596035 5_2:+2443456 Msa0749080:CDS
ATCAATGGTAAAGCATTGGG+TGG 0.611558 5_2:+2442757 Msa0749080:CDS
TATCTCTTGATAGCATCATG+AGG 0.628708 5_2:-2443227 None:intergenic
GTAGTTAGTGCCAAATGGAG+AGG 0.644078 5_2:+2442704 None:intergenic
TCATCTTCTTATGATGAAGG+TGG 0.658652 5_2:-2443552 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! GAAAGTTTGAAACTTTTTTT+GGG - chr5_2:2442979-2442998 None:intergenic 20.0%
!!! TGAAAGTTTGAAACTTTTTT+TGG - chr5_2:2442980-2442999 None:intergenic 20.0%
!! AATTATAAATGTGACAAATG+TGG + chr5_2:2443300-2443319 Msa0749080:CDS 20.0%
!! ATTATAAATGTGACAAATGT+GGG + chr5_2:2443301-2443320 Msa0749080:CDS 20.0%
!!! ATTGGAATATTTTATGATCA+CGG - chr5_2:2443413-2443432 None:intergenic 20.0%
!!! GAAAGTTTGAAACTTTTTTT+GGG - chr5_2:2442979-2442998 None:intergenic 20.0%
!!! TGAAAGTTTGAAACTTTTTT+TGG - chr5_2:2442980-2442999 None:intergenic 20.0%
!! AATTATAAATGTGACAAATG+TGG + chr5_2:2443300-2443319 Msa0749080:CDS 20.0%
!! ATTATAAATGTGACAAATGT+GGG + chr5_2:2443301-2443320 Msa0749080:CDS 20.0%
!!! ATTGGAATATTTTATGATCA+CGG - chr5_2:2443413-2443432 None:intergenic 20.0%
ATTCATCAATGGTAAAGCAT+TGG + chr5_2:2442753-2442772 Msa0749080:CDS 30.0%
! TTCATCAATGGTAAAGCATT+GGG + chr5_2:2442754-2442773 Msa0749080:CDS 30.0%
AGAAGATGAAAATGAGAGTA+TGG - chr5_2:2442872-2442891 None:intergenic 30.0%
TTTGTACTACTACTGTTTGT+TGG - chr5_2:2442912-2442931 None:intergenic 30.0%
ATGAAAAGAGTCCAATGTAT+AGG + chr5_2:2442941-2442960 Msa0749080:CDS 30.0%
! TTTTCTCTCAACCTATACAT+TGG - chr5_2:2442955-2442974 None:intergenic 30.0%
GTTGTTGAGAAAGAAAACTT+GGG - chr5_2:2443006-2443025 None:intergenic 30.0%
TGTTGTTGAGAAAGAAAACT+TGG - chr5_2:2443007-2443026 None:intergenic 30.0%
!!! TGAGTTTTCGTTTTTGAGTT+GGG - chr5_2:2443074-2443093 None:intergenic 30.0%
!! TTGTTCTGAATTTTGGACAA+AGG - chr5_2:2443097-2443116 None:intergenic 30.0%
!! GCTTCTTTTGTTCTGAATTT+TGG - chr5_2:2443104-2443123 None:intergenic 30.0%
AAGTTGAAAAGTGAAGTAAC+AGG - chr5_2:2443180-2443199 None:intergenic 30.0%
TGATGCTATCAAGAGATAAA+TGG + chr5_2:2443232-2443251 Msa0749080:CDS 30.0%
AAGAAGAACAAGAAGTTTGT+GGG + chr5_2:2443277-2443296 Msa0749080:CDS 30.0%
TGATAAGAACCAAAAACCTT+AGG - chr5_2:2443447-2443466 None:intergenic 30.0%
!! TTTGGTTCTTATCAAGCATT+AGG + chr5_2:2443453-2443472 Msa0749080:CDS 30.0%
ATTCATCAATGGTAAAGCAT+TGG + chr5_2:2442753-2442772 Msa0749080:CDS 30.0%
! TTCATCAATGGTAAAGCATT+GGG + chr5_2:2442754-2442773 Msa0749080:CDS 30.0%
AGAAGATGAAAATGAGAGTA+TGG - chr5_2:2442872-2442891 None:intergenic 30.0%
TTTGTACTACTACTGTTTGT+TGG - chr5_2:2442912-2442931 None:intergenic 30.0%
ATGAAAAGAGTCCAATGTAT+AGG + chr5_2:2442941-2442960 Msa0749080:CDS 30.0%
! TTTTCTCTCAACCTATACAT+TGG - chr5_2:2442955-2442974 None:intergenic 30.0%
GTTGTTGAGAAAGAAAACTT+GGG - chr5_2:2443006-2443025 None:intergenic 30.0%
TGTTGTTGAGAAAGAAAACT+TGG - chr5_2:2443007-2443026 None:intergenic 30.0%
!!! TGAGTTTTCGTTTTTGAGTT+GGG - chr5_2:2443074-2443093 None:intergenic 30.0%
!! TTGTTCTGAATTTTGGACAA+AGG - chr5_2:2443097-2443116 None:intergenic 30.0%
!! GCTTCTTTTGTTCTGAATTT+TGG - chr5_2:2443104-2443123 None:intergenic 30.0%
AAGTTGAAAAGTGAAGTAAC+AGG - chr5_2:2443180-2443199 None:intergenic 30.0%
TGATGCTATCAAGAGATAAA+TGG + chr5_2:2443232-2443251 Msa0749080:CDS 30.0%
AAGAAGAACAAGAAGTTTGT+GGG + chr5_2:2443277-2443296 Msa0749080:CDS 30.0%
TGATAAGAACCAAAAACCTT+AGG - chr5_2:2443447-2443466 None:intergenic 30.0%
!! TTTGGTTCTTATCAAGCATT+AGG + chr5_2:2443453-2443472 Msa0749080:CDS 30.0%
TGCTCAAGAACATTCATCAA+TGG + chr5_2:2442742-2442761 Msa0749080:CDS 35.0%
!!! GTGAGTTTTCGTTTTTGAGT+TGG - chr5_2:2443075-2443094 None:intergenic 35.0%
AAAAGTGAAGTAACAGGTTC+TGG - chr5_2:2443174-2443193 None:intergenic 35.0%
TTATAGCAGCTTCTTCTTCA+GGG - chr5_2:2443206-2443225 None:intergenic 35.0%
! ATCTCTTGATAGCATCATGA+GGG - chr5_2:2443229-2443248 None:intergenic 35.0%
! TATCTCTTGATAGCATCATG+AGG - chr5_2:2443230-2443249 None:intergenic 35.0%
GAAGAAGAACAAGAAGTTTG+TGG + chr5_2:2443276-2443295 Msa0749080:CDS 35.0%
! CTTTAGAAGTTCACAAGCAA+TGG + chr5_2:2443332-2443351 Msa0749080:CDS 35.0%
! GTGTTTTGTCCTAAGGTTTT+TGG + chr5_2:2443435-2443454 Msa0749080:CDS 35.0%
TTCTTCTTCTTCTTCCAAGA+TGG - chr5_2:2443504-2443523 None:intergenic 35.0%
TGCTCAAGAACATTCATCAA+TGG + chr5_2:2442742-2442761 Msa0749080:CDS 35.0%
!!! GTGAGTTTTCGTTTTTGAGT+TGG - chr5_2:2443075-2443094 None:intergenic 35.0%
AAAAGTGAAGTAACAGGTTC+TGG - chr5_2:2443174-2443193 None:intergenic 35.0%
TTATAGCAGCTTCTTCTTCA+GGG - chr5_2:2443206-2443225 None:intergenic 35.0%
! ATCTCTTGATAGCATCATGA+GGG - chr5_2:2443229-2443248 None:intergenic 35.0%
! TATCTCTTGATAGCATCATG+AGG - chr5_2:2443230-2443249 None:intergenic 35.0%
GAAGAAGAACAAGAAGTTTG+TGG + chr5_2:2443276-2443295 Msa0749080:CDS 35.0%
! CTTTAGAAGTTCACAAGCAA+TGG + chr5_2:2443332-2443351 Msa0749080:CDS 35.0%
! GTGTTTTGTCCTAAGGTTTT+TGG + chr5_2:2443435-2443454 Msa0749080:CDS 35.0%
TTCTTCTTCTTCTTCCAAGA+TGG - chr5_2:2443504-2443523 None:intergenic 35.0%
!! ATCAATGGTAAAGCATTGGG+TGG + chr5_2:2442757-2442776 Msa0749080:CDS 40.0%
TGAGATTGTGTTTGTGGTTG+GGG - chr5_2:2442829-2442848 None:intergenic 40.0%
GTGAGATTGTGTTTGTGGTT+GGG - chr5_2:2442830-2442849 None:intergenic 40.0%
! GAGAGTATGGTAGAAGAAGT+AGG - chr5_2:2442859-2442878 None:intergenic 40.0%
!! TTGAGTTGGGTTCTTTGACT+CGG - chr5_2:2443061-2443080 None:intergenic 40.0%
TATAGCAGCTTCTTCTTCAG+GGG - chr5_2:2443205-2443224 None:intergenic 40.0%
GTTATAGCAGCTTCTTCTTC+AGG - chr5_2:2443207-2443226 None:intergenic 40.0%
CCTTAGGACAAAACACACAT+TGG - chr5_2:2443431-2443450 None:intergenic 40.0%
! CCAATGTGTGTTTTGTCCTA+AGG + chr5_2:2443428-2443447 Msa0749080:CDS 40.0%
GGTTCTTATCAAGCATTAGG+TGG + chr5_2:2443456-2443475 Msa0749080:CDS 40.0%
AATCTCACCTCTATCCATCT+TGG + chr5_2:2443487-2443506 Msa0749080:CDS 40.0%
TCTTCTTCCAAGATGGATAG+AGG - chr5_2:2443497-2443516 None:intergenic 40.0%
!! ATCAATGGTAAAGCATTGGG+TGG + chr5_2:2442757-2442776 Msa0749080:CDS 40.0%
TGAGATTGTGTTTGTGGTTG+GGG - chr5_2:2442829-2442848 None:intergenic 40.0%
GTGAGATTGTGTTTGTGGTT+GGG - chr5_2:2442830-2442849 None:intergenic 40.0%
! GAGAGTATGGTAGAAGAAGT+AGG - chr5_2:2442859-2442878 None:intergenic 40.0%
!! TTGAGTTGGGTTCTTTGACT+CGG - chr5_2:2443061-2443080 None:intergenic 40.0%
TATAGCAGCTTCTTCTTCAG+GGG - chr5_2:2443205-2443224 None:intergenic 40.0%
GTTATAGCAGCTTCTTCTTC+AGG - chr5_2:2443207-2443226 None:intergenic 40.0%
CCTTAGGACAAAACACACAT+TGG - chr5_2:2443431-2443450 None:intergenic 40.0%
! CCAATGTGTGTTTTGTCCTA+AGG + chr5_2:2443428-2443447 Msa0749080:CDS 40.0%
GGTTCTTATCAAGCATTAGG+TGG + chr5_2:2443456-2443475 Msa0749080:CDS 40.0%
AATCTCACCTCTATCCATCT+TGG + chr5_2:2443487-2443506 Msa0749080:CDS 40.0%
TCTTCTTCCAAGATGGATAG+AGG - chr5_2:2443497-2443516 None:intergenic 40.0%
GAGATTGTGTTTGTGGTTGG+GGG - chr5_2:2442828-2442847 None:intergenic 45.0%
GGTGAGATTGTGTTTGTGGT+TGG - chr5_2:2442831-2442850 None:intergenic 45.0%
GTGTGGTGAGATTGTGTTTG+TGG - chr5_2:2442835-2442854 None:intergenic 45.0%
TGGTAGAAGAAGTAGGAGTG+TGG - chr5_2:2442852-2442871 None:intergenic 45.0%
GAGATTGTGTTTGTGGTTGG+GGG - chr5_2:2442828-2442847 None:intergenic 45.0%
GGTGAGATTGTGTTTGTGGT+TGG - chr5_2:2442831-2442850 None:intergenic 45.0%
GTGTGGTGAGATTGTGTTTG+TGG - chr5_2:2442835-2442854 None:intergenic 45.0%
TGGTAGAAGAAGTAGGAGTG+TGG - chr5_2:2442852-2442871 None:intergenic 45.0%
! AGCATTGGGTGGACACATGA+AGG + chr5_2:2442768-2442787 Msa0749080:CDS 50.0%
GTTTGGAAGAGGAAGAGGGA+GGG - chr5_2:2442806-2442825 None:intergenic 50.0%
TGTGTTTGTGGTTGGGGGTT+TGG - chr5_2:2442823-2442842 None:intergenic 50.0%
! AGCATTGGGTGGACACATGA+AGG + chr5_2:2442768-2442787 Msa0749080:CDS 50.0%
GTTTGGAAGAGGAAGAGGGA+GGG - chr5_2:2442806-2442825 None:intergenic 50.0%
TGTGTTTGTGGTTGGGGGTT+TGG - chr5_2:2442823-2442842 None:intergenic 50.0%
GGTTTGGAAGAGGAAGAGGG+AGG - chr5_2:2442807-2442826 None:intergenic 55.0%
GGGGGTTTGGAAGAGGAAGA+GGG - chr5_2:2442810-2442829 None:intergenic 55.0%
TGGGGGTTTGGAAGAGGAAG+AGG - chr5_2:2442811-2442830 None:intergenic 55.0%
TGTGGTTGGGGGTTTGGAAG+AGG - chr5_2:2442817-2442836 None:intergenic 55.0%
GGTTTGGAAGAGGAAGAGGG+AGG - chr5_2:2442807-2442826 None:intergenic 55.0%
GGGGGTTTGGAAGAGGAAGA+GGG - chr5_2:2442810-2442829 None:intergenic 55.0%
TGGGGGTTTGGAAGAGGAAG+AGG - chr5_2:2442811-2442830 None:intergenic 55.0%
TGTGGTTGGGGGTTTGGAAG+AGG - chr5_2:2442817-2442836 None:intergenic 55.0%
TGGAAGAGGAAGAGGGAGGG+TGG - chr5_2:2442803-2442822 None:intergenic 60.0%
TGGAAGAGGAAGAGGGAGGG+TGG - chr5_2:2442803-2442822 None:intergenic 60.0%
Chromosome Type Strat End Strand Name
chr5_2 gene 2442718 2443566 2442718 ID=Msa0749080;Name=Msa0749080
chr5_2 mRNA 2442718 2443566 2442718 ID=Msa0749080-mRNA-1;Parent=Msa0749080;Name=Msa0749080-mRNA-1;_AED=0.00;_eAED=0.01;_QI=0|-1|0|1|-1|1|1|0|282
chr5_2 exon 2442718 2443566 2442718 ID=Msa0749080-mRNA-1:exon:711;Parent=Msa0749080-mRNA-1
chr5_2 CDS 2442718 2443566 2442718 ID=Msa0749080-mRNA-1:cds;Parent=Msa0749080-mRNA-1
Gene Sequence

>Msa0749080

ATGGAGAGGTACAAATGCAAGCTTTGCTCAAGAACATTCATCAATGGTAAAGCATTGGGTGGACACATGAAGGCTCATTTTGCCACCCTCCCTCTTCCTCTTCCAAACCCCCAACCACAAACACAATCTCACCACACTCCTACTTCTTCTACCATACTCTCATTTTCATCTTCTTCTGAAAATGAACAAGACCAACAAACAGTAGTAGTACAAAGAGACTCAAATGAAAAGAGTCCAATGTATAGGTTGAGAGAAAATCCCAAAAAAAGTTTCAAACTTTCAGATCCCAAGTTTTCTTTCTCAACAACAGAGACTATTGTTCATGACAGAGAGAGTGAAACCGAGTCAAAGAACCCAACTCAAAAACGAAAACTCACCTTTGTCCAAAATTCAGAACAAAAGAAGCTTAAACAAAGTTTGAAAGATTCACATTCACAACTAACAGAAACTGAACCAGAACCTGTTACTTCACTTTTCAACTTTTCCCCTGAAGAAGAAGCTGCTATAACCCTCATGATGCTATCAAGAGATAAATGGAAGATCAATGTTGCTGTCAAAGAAGAAGAACAAGAAGTTTGTGGGAATTATAAATGTGACAAATGTGGGAATAATAACTTTAGAAGTTCACAAGCAATGGAAAGTCACAAAAGTATTTGTCTTCAAAATGAAACAAATCTTGCTTCAACAAGTAGCCGTGATCATAAAATATTCCAATGTGTGTTTTGTCCTAAGGTTTTTGGTTCTTATCAAGCATTAGGTGGTCACAAAAAATCTCACCTCTATCCATCTTGGAAGAAGAAGAAGAAGAAGCTATGTTTTTTCGATCTCAACTTGCCACCTTCATCATAA

Protein sequence

>Msa0749080

MERYKCKLCSRTFINGKALGGHMKAHFATLPLPLPNPQPQTQSHHTPTSSTILSFSSSSENEQDQQTVVVQRDSNEKSPMYRLRENPKKSFKLSDPKFSFSTTETIVHDRESETESKNPTQKRKLTFVQNSEQKKLKQSLKDSHSQLTETEPEPVTSLFNFSPEEEAAITLMMLSRDKWKINVAVKEEEQEVCGNYKCDKCGNNNFRSSQAMESHKSICLQNETNLASTSSRDHKIFQCVFCPKVFGSYQALGGHKKSHLYPSWKKKKKKLCFFDLNLPPSS*