AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1453610

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1453610 MtrunA17_Chr7g0244951 98.507 67 1 0 18 84 559 625 8.93e-44 149
Msa1453610 MtrunA17_Chr8g0334591 61.429 70 21 2 18 84 559 625 1.65e-22 89.4
Msa1453610 MtrunA17_Chr5g0393731 48.485 66 31 1 17 82 561 623 1.92e-16 72.4
Msa1453610 MtrunA17_Chr1g0207291 54.386 57 26 0 22 78 572 628 2.57e-16 72.0
Msa1453610 MtrunA17_Chr2g0296671 65.714 35 12 0 40 74 578 612 4.55e-11 57.0
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1453610 AT2G14740.2 51.613 62 27 1 22 83 568 626 4.50e-17 74.3
Msa1453610 AT2G14740.1 51.613 62 27 1 22 83 568 626 4.50e-17 74.3
Msa1453610 AT2G14720.1 56.364 55 23 1 22 76 568 621 1.54e-16 72.8
Msa1453610 AT2G14720.2 56.364 55 23 1 22 76 568 621 1.54e-16 72.8
Msa1453610 AT3G52850.1 49.315 73 31 2 15 84 554 623 6.82e-16 71.2
Msa1453610 AT2G30290.1 64.444 45 16 0 27 71 571 615 3.21e-15 69.3
Msa1453610 AT2G30290.2 64.444 45 16 0 27 71 571 615 3.22e-15 69.3
Msa1453610 AT1G30900.1 50.000 54 26 1 30 82 569 622 2.53e-12 60.8

Find 26 sgRNAs with CRISPR-Local

Find 106 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GTGATGGTCGTTACCCTTTC+TGG 0.105774 tig0034810:+963 Msa1453610:CDS
CTTCTTCAGTAGTGAGTATT+TGG 0.126902 tig0034810:+928 Msa1453610:CDS
GTCCTTTATCACTCCTAATT+TGG 0.157985 tig0034810:+1666 Msa1453610:three_prime_UTR
CACTGAGATACGTGCAATTA+TGG 0.263270 tig0034810:+1387 Msa1453610:CDS
TGCTGGTTCTTTGTTTCTTT+AGG 0.301653 tig0034810:+1542 Msa1453610:three_prime_UTR
GCAACTTGAGAAGCCAAATT+AGG 0.327426 tig0034810:-1679 None:intergenic
TTATTCTGTGCAGAGATATA+TGG 0.332728 tig0034810:+1363 Msa1453610:intron
ATATCATGATGAACTTGATT+AGG 0.359207 tig0034810:-1454 None:intergenic
TGATGAACTTGATTAGGATT+AGG 0.367926 tig0034810:-1448 None:intergenic
AGCCAAATTAGGAGTGATAA+AGG 0.408701 tig0034810:-1668 None:intergenic
TTAGGATTAGGAACAATAAG+AGG 0.470855 tig0034810:-1436 None:intergenic
ATTTGGTATATTATAAATGC+AGG 0.495780 tig0034810:+897 Msa1453610:CDS
AATAAGAGGTTGATTATCCA+AGG 0.521981 tig0034810:-1422 None:intergenic
GCACTATATTCTGTTCAAGC+GGG 0.527587 tig0034810:+1700 Msa1453610:three_prime_UTR
AAAATGCATATCCTCCAGAA+AGG 0.538733 tig0034810:-977 None:intergenic
TATGGCTCAATACATGCCCT+TGG 0.543355 tig0034810:+1405 Msa1453610:CDS
AAATGCATATCCTCCAGAAA+GGG 0.551290 tig0034810:-976 None:intergenic
TTGGATGATTATCCTTGTGA+TGG 0.555886 tig0034810:+947 Msa1453610:CDS
TTAAAGCAGAACAAAGATGC+TGG 0.561915 tig0034810:+1525 Msa1453610:three_prime_UTR
TGCACTATATTCTGTTCAAG+CGG 0.566801 tig0034810:+1699 Msa1453610:three_prime_UTR
ATGGTCGTTACCCTTTCTGG+AGG 0.623695 tig0034810:+966 Msa1453610:CDS
ATAAGAGGTTGATTATCCAA+GGG 0.659505 tig0034810:-1421 None:intergenic
TGTAAATCTCAACAATGTGG+TGG 0.667968 tig0034810:+1576 Msa1453610:three_prime_UTR
ACATTGTTGAGATTTACAAG+AGG 0.673620 tig0034810:-1571 None:intergenic
AAAGGGTAACGACCATCACA+AGG 0.679891 tig0034810:-959 None:intergenic
TCTTGTAAATCTCAACAATG+TGG 0.690711 tig0034810:+1573 Msa1453610:three_prime_UTR

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TATTCAAATTTTCACTCATT+TGG + tig0034810:880-899 Msa1453610:CDS 20.0%
!! ATTTGGTATATTATAAATGC+AGG + tig0034810:897-916 Msa1453610:CDS 20.0%
!!! AAGAATAGTTGAGAATATTT+TGG + tig0034810:1090-1109 Msa1453610:intron 20.0%
!!! TTAAGAACTCTGTTTTATAT+GGG + tig0034810:1212-1231 Msa1453610:intron 20.0%
!! AAAAAATCAGTAGGAAAATA+AGG - tig0034810:1611-1630 None:intergenic 20.0%
!!! TATTCAAATTTTCACTCATT+TGG + tig0034810:880-899 Msa1453610:CDS 20.0%
!! ATTTGGTATATTATAAATGC+AGG + tig0034810:897-916 Msa1453610:CDS 20.0%
!!! AAGAATAGTTGAGAATATTT+TGG + tig0034810:1090-1109 Msa1453610:intron 20.0%
!!! TTAAGAACTCTGTTTTATAT+GGG + tig0034810:1212-1231 Msa1453610:intron 20.0%
!! AAAAAATCAGTAGGAAAATA+AGG - tig0034810:1611-1630 None:intergenic 20.0%
! AGTTCTTAAGTTTAAACCTT+GGG - tig0034810:1201-1220 None:intergenic 25.0%
!! CTTAAGAACTCTGTTTTATA+TGG + tig0034810:1211-1230 Msa1453610:intron 25.0%
! ATAAACAAACAATTTCAGGA+GGG - tig0034810:1347-1366 None:intergenic 25.0%
! AATAAACAAACAATTTCAGG+AGG - tig0034810:1348-1367 None:intergenic 25.0%
! CAGAATAAACAAACAATTTC+AGG - tig0034810:1351-1370 None:intergenic 25.0%
! ATATCATGATGAACTTGATT+AGG - tig0034810:1457-1476 None:intergenic 25.0%
! AGTTCTTAAGTTTAAACCTT+GGG - tig0034810:1201-1220 None:intergenic 25.0%
!! CTTAAGAACTCTGTTTTATA+TGG + tig0034810:1211-1230 Msa1453610:intron 25.0%
! ATAAACAAACAATTTCAGGA+GGG - tig0034810:1347-1366 None:intergenic 25.0%
! AATAAACAAACAATTTCAGG+AGG - tig0034810:1348-1367 None:intergenic 25.0%
! CAGAATAAACAAACAATTTC+AGG - tig0034810:1351-1370 None:intergenic 25.0%
! ATATCATGATGAACTTGATT+AGG - tig0034810:1457-1476 None:intergenic 25.0%
! ATTTTACAAGTACAGAATCC+AGG + tig0034810:995-1014 Msa1453610:CDS 30.0%
GAGTTCTTAAGTTTAAACCT+TGG - tig0034810:1202-1221 None:intergenic 30.0%
TTATTCTGTGCAGAGATATA+TGG + tig0034810:1363-1382 Msa1453610:intron 30.0%
! ATAAGAGGTTGATTATCCAA+GGG - tig0034810:1424-1443 None:intergenic 30.0%
! AATAAGAGGTTGATTATCCA+AGG - tig0034810:1425-1444 None:intergenic 30.0%
TTAGGATTAGGAACAATAAG+AGG - tig0034810:1439-1458 None:intergenic 30.0%
TGATGAACTTGATTAGGATT+AGG - tig0034810:1451-1470 None:intergenic 30.0%
!! GTCTTGTTAATCTTTTTCTG+AGG + tig0034810:1484-1503 Msa1453610:three_prime_UTR 30.0%
ACATTGTTGAGATTTACAAG+AGG - tig0034810:1574-1593 None:intergenic 30.0%
TCTTGTAAATCTCAACAATG+TGG + tig0034810:1573-1592 Msa1453610:three_prime_UTR 30.0%
ACGTCAAAGAAAAAATCAGT+AGG - tig0034810:1620-1639 None:intergenic 30.0%
! ATTTTACAAGTACAGAATCC+AGG + tig0034810:995-1014 Msa1453610:CDS 30.0%
GAGTTCTTAAGTTTAAACCT+TGG - tig0034810:1202-1221 None:intergenic 30.0%
TTATTCTGTGCAGAGATATA+TGG + tig0034810:1363-1382 Msa1453610:intron 30.0%
! ATAAGAGGTTGATTATCCAA+GGG - tig0034810:1424-1443 None:intergenic 30.0%
! AATAAGAGGTTGATTATCCA+AGG - tig0034810:1425-1444 None:intergenic 30.0%
TTAGGATTAGGAACAATAAG+AGG - tig0034810:1439-1458 None:intergenic 30.0%
TGATGAACTTGATTAGGATT+AGG - tig0034810:1451-1470 None:intergenic 30.0%
!! GTCTTGTTAATCTTTTTCTG+AGG + tig0034810:1484-1503 Msa1453610:three_prime_UTR 30.0%
ACATTGTTGAGATTTACAAG+AGG - tig0034810:1574-1593 None:intergenic 30.0%
TCTTGTAAATCTCAACAATG+TGG + tig0034810:1573-1592 Msa1453610:three_prime_UTR 30.0%
ACGTCAAAGAAAAAATCAGT+AGG - tig0034810:1620-1639 None:intergenic 30.0%
CTTCTTCAGTAGTGAGTATT+TGG + tig0034810:928-947 Msa1453610:CDS 35.0%
TTGGATGATTATCCTTGTGA+TGG + tig0034810:947-966 Msa1453610:CDS 35.0%
AAATGCATATCCTCCAGAAA+GGG - tig0034810:979-998 None:intergenic 35.0%
AAAATGCATATCCTCCAGAA+AGG - tig0034810:980-999 None:intergenic 35.0%
AATCCAGGTATGATTATTGC+AGG + tig0034810:1010-1029 Msa1453610:intron 35.0%
TATTCTTCGCTTTCTCAATG+TGG - tig0034810:1077-1096 None:intergenic 35.0%
! GAAGCAGCATAAAACTTTTC+AGG - tig0034810:1175-1194 None:intergenic 35.0%
!! CTATTCAACTCAAGAGTGTT+TGG - tig0034810:1253-1272 None:intergenic 35.0%
CAGTAAATATGTAATGTCGG+TGG - tig0034810:1324-1343 None:intergenic 35.0%
GGGCAGTAAATATGTAATGT+CGG - tig0034810:1327-1346 None:intergenic 35.0%
TTAAAGCAGAACAAAGATGC+TGG + tig0034810:1525-1544 Msa1453610:three_prime_UTR 35.0%
!! TGCTGGTTCTTTGTTTCTTT+AGG + tig0034810:1542-1561 Msa1453610:three_prime_UTR 35.0%
TGTAAATCTCAACAATGTGG+TGG + tig0034810:1576-1595 Msa1453610:three_prime_UTR 35.0%
GTCCTTTATCACTCCTAATT+TGG + tig0034810:1666-1685 Msa1453610:three_prime_UTR 35.0%
AGCCAAATTAGGAGTGATAA+AGG - tig0034810:1671-1690 None:intergenic 35.0%
CTTCTTCAGTAGTGAGTATT+TGG + tig0034810:928-947 Msa1453610:CDS 35.0%
TTGGATGATTATCCTTGTGA+TGG + tig0034810:947-966 Msa1453610:CDS 35.0%
AAATGCATATCCTCCAGAAA+GGG - tig0034810:979-998 None:intergenic 35.0%
AAAATGCATATCCTCCAGAA+AGG - tig0034810:980-999 None:intergenic 35.0%
AATCCAGGTATGATTATTGC+AGG + tig0034810:1010-1029 Msa1453610:intron 35.0%
TATTCTTCGCTTTCTCAATG+TGG - tig0034810:1077-1096 None:intergenic 35.0%
! GAAGCAGCATAAAACTTTTC+AGG - tig0034810:1175-1194 None:intergenic 35.0%
!! CTATTCAACTCAAGAGTGTT+TGG - tig0034810:1253-1272 None:intergenic 35.0%
CAGTAAATATGTAATGTCGG+TGG - tig0034810:1324-1343 None:intergenic 35.0%
GGGCAGTAAATATGTAATGT+CGG - tig0034810:1327-1346 None:intergenic 35.0%
TTAAAGCAGAACAAAGATGC+TGG + tig0034810:1525-1544 Msa1453610:three_prime_UTR 35.0%
!! TGCTGGTTCTTTGTTTCTTT+AGG + tig0034810:1542-1561 Msa1453610:three_prime_UTR 35.0%
TGTAAATCTCAACAATGTGG+TGG + tig0034810:1576-1595 Msa1453610:three_prime_UTR 35.0%
GTCCTTTATCACTCCTAATT+TGG + tig0034810:1666-1685 Msa1453610:three_prime_UTR 35.0%
AGCCAAATTAGGAGTGATAA+AGG - tig0034810:1671-1690 None:intergenic 35.0%
AAGCCTGCAATAATCATACC+TGG - tig0034810:1016-1035 None:intergenic 40.0%
! TTTATGCTGCTTCATTCCCA+AGG + tig0034810:1182-1201 Msa1453610:intron 40.0%
!! TCAACTCAAGAGTGTTTGGA+TGG - tig0034810:1249-1268 None:intergenic 40.0%
CACTGAGATACGTGCAATTA+TGG + tig0034810:1387-1406 Msa1453610:CDS 40.0%
GCAACTTGAGAAGCCAAATT+AGG - tig0034810:1682-1701 None:intergenic 40.0%
AAGCCTGCAATAATCATACC+TGG - tig0034810:1016-1035 None:intergenic 40.0%
! TTTATGCTGCTTCATTCCCA+AGG + tig0034810:1182-1201 Msa1453610:intron 40.0%
!! TCAACTCAAGAGTGTTTGGA+TGG - tig0034810:1249-1268 None:intergenic 40.0%
CACTGAGATACGTGCAATTA+TGG + tig0034810:1387-1406 Msa1453610:CDS 40.0%
GCAACTTGAGAAGCCAAATT+AGG - tig0034810:1682-1701 None:intergenic 40.0%
AAAGGGTAACGACCATCACA+AGG - tig0034810:962-981 None:intergenic 45.0%
TCGCTTTCTCAATGTGGCAT+TGG - tig0034810:1071-1090 None:intergenic 45.0%
TATGGCTCAATACATGCCCT+TGG + tig0034810:1405-1424 Msa1453610:CDS 45.0%
AAAGGGTAACGACCATCACA+AGG - tig0034810:962-981 None:intergenic 45.0%
TCGCTTTCTCAATGTGGCAT+TGG - tig0034810:1071-1090 None:intergenic 45.0%
TATGGCTCAATACATGCCCT+TGG + tig0034810:1405-1424 Msa1453610:CDS 45.0%
GTGATGGTCGTTACCCTTTC+TGG + tig0034810:963-982 Msa1453610:CDS 50.0%
ATGGTCGTTACCCTTTCTGG+AGG + tig0034810:966-985 Msa1453610:CDS 50.0%
! TGTGATCCTACCTGACTCGA+GGG - tig0034810:1135-1154 None:intergenic 50.0%
! ATGTGATCCTACCTGACTCG+AGG - tig0034810:1136-1155 None:intergenic 50.0%
GTCAGGTAGGATCACATGAG+CGG + tig0034810:1139-1158 Msa1453610:intron 50.0%
GTGATGGTCGTTACCCTTTC+TGG + tig0034810:963-982 Msa1453610:CDS 50.0%
ATGGTCGTTACCCTTTCTGG+AGG + tig0034810:966-985 Msa1453610:CDS 50.0%
! TGTGATCCTACCTGACTCGA+GGG - tig0034810:1135-1154 None:intergenic 50.0%
! ATGTGATCCTACCTGACTCG+AGG - tig0034810:1136-1155 None:intergenic 50.0%
GTCAGGTAGGATCACATGAG+CGG + tig0034810:1139-1158 Msa1453610:intron 50.0%
! TCCTACCTGACTCGAGGGTT+CGG - tig0034810:1130-1149 None:intergenic 55.0%
! TCCTACCTGACTCGAGGGTT+CGG - tig0034810:1130-1149 None:intergenic 55.0%
AGTGTCCGAACCCTCGAGTC+AGG + tig0034810:1122-1141 Msa1453610:intron 60.0%
TCCGAACCCTCGAGTCAGGT+AGG + tig0034810:1126-1145 Msa1453610:intron 60.0%
AGTGTCCGAACCCTCGAGTC+AGG + tig0034810:1122-1141 Msa1453610:intron 60.0%
TCCGAACCCTCGAGTCAGGT+AGG + tig0034810:1126-1145 Msa1453610:intron 60.0%
Chromosome Type Strat End Strand Name
tig0034810 gene 853 1719 853 ID=Msa1453610;Name=Msa1453610
tig0034810 mRNA 853 1719 853 ID=Msa1453610-mRNA-1;Parent=Msa1453610;Name=Msa1453610-mRNA-1;_AED=0.00;_eAED=0.00;_QI=14|1|1|1|1|1|2|239|84
tig0034810 exon 853 1016 853 ID=Msa1453610-mRNA-1:exon:19226;Parent=Msa1453610-mRNA-1
tig0034810 exon 1376 1719 1376 ID=Msa1453610-mRNA-1:exon:19227;Parent=Msa1453610-mRNA-1
tig0034810 five_prime_UTR 853 866 853 ID=Msa1453610-mRNA-1:five_prime_utr;Parent=Msa1453610-mRNA-1
tig0034810 CDS 867 1016 867 ID=Msa1453610-mRNA-1:cds;Parent=Msa1453610-mRNA-1
tig0034810 CDS 1376 1480 1376 ID=Msa1453610-mRNA-1:cds;Parent=Msa1453610-mRNA-1
tig0034810 three_prime_UTR 1481 1719 1481 ID=Msa1453610-mRNA-1:three_prime_utr;Parent=Msa1453610-mRNA-1
Gene Sequence

>Msa1453610

ATGAAGAATAATTTATTCAAATTTTCACTCATTTGGTATATTATAAATGCAGGTAAATATACTTCTTCAGTAGTGAGTATTTGGATGATTATCCTTGTGATGGTCGTTACCCTTTCTGGAGGATATGCATTTTACAAGTACAGAATCCAGAGATATATGGACACTGAGATACGTGCAATTATGGCTCAATACATGCCCTTGGATAATCAACCTCTTATTGTTCCTAATCCTAATCAAGTTCATCATGATATCTAG
Protein sequence

>Msa1453610

MKNNLFKFSLIWYIINAGKYTSSVVSIWMIILVMVVTLSGGYAFYKYRIQRYMDTEIRAIMAQYMPLDNQPLIVPNPNQVHHDI*