AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1455680

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1455680 MtrunA17_Chr3g0135051 95.402 87 4 0 8 94 308 394 6.59e-55 174
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1455680 AT1G59520.3 64.286 84 29 1 11 94 305 387 8.83e-18 76.6
Msa1455680 AT1G59520.1 64.286 84 29 1 11 94 305 387 9.37e-18 76.6
Msa1455680 AT1G59520.4 63.636 77 27 1 11 87 305 380 1.58e-13 64.7
Msa1455680 AT1G59520.5 71.053 38 11 0 57 94 315 352 5.98e-13 63.2

Find 41 sgRNAs with CRISPR-Local

Find 128 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GTGATCATCTCATATATTTC+TGG 0.228833 tig0036439:+1263 Msa1455680:exon
TCTCCAGTTGTATCAAATAA+AGG 0.233028 tig0036439:+775 Msa1455680:CDS
AGCGTATGATCTTATGTTTA+AGG 0.304447 tig0036439:+954 Msa1455680:CDS
GCAGATGTAACAAATTCTAT+TGG 0.325232 tig0036439:-1414 Msa1455680:intergenic
GATCAAAGCCAGCAGGATTC+AGG 0.333189 tig0036439:+745 Msa1455680:CDS
AACCCTTTATTTGATACAAC+TGG 0.334616 tig0036439:-778 Msa1455680:intergenic
TGTATAGGACTGTGCATATT+TGG 0.334660 tig0036439:+1375 Msa1455680:three_prime_UTR
CTCCAGTTGTATCAAATAAA+GGG 0.364902 tig0036439:+776 Msa1455680:CDS
ATATTCCCAAGGCAATGATA+TGG 0.384495 tig0036439:-929 Msa1455680:intergenic
GTTGTATCAAATAAAGGGTT+CGG 0.390728 tig0036439:+781 Msa1455680:CDS
CTTACAGGGAACTAAGGAAT+TGG 0.407541 tig0036439:-1508 Msa1455680:intergenic
TTGTATCAAATAAAGGGTTC+GGG 0.422955 tig0036439:+782 Msa1455680:CDS
ATATTGAGAGATGGATGAAA+TGG 0.425277 tig0036439:+701 Msa1455680:exon
TCAAATAAAGGGTTCGGGCT+TGG 0.433966 tig0036439:+787 Msa1455680:CDS
TAATGTCCATATCATTGCCT+TGG 0.441902 tig0036439:+923 Msa1455680:CDS
TGATAACATCAGGTTTGAAA+AGG 0.442132 tig0036439:-1589 Msa1455680:intergenic
CAGATGTAACAAATTCTATT+GGG 0.442466 tig0036439:-1413 Msa1455680:intergenic
CATGCTGCACGTGCATGTAT+AGG 0.453172 tig0036439:+1360 Msa1455680:three_prime_UTR
AATGTCCATATCATTGCCTT+GGG 0.455539 tig0036439:+924 Msa1455680:CDS
GACTGTGCATATTTGGTAGT+GGG 0.456442 tig0036439:+1382 Msa1455680:three_prime_UTR
AAAATTTGAGCTAGAGGAAG+AGG 0.477255 tig0036439:-872 Msa1455680:intergenic
CTCATATATTTCTGGCCACA+TGG 0.495271 tig0036439:+1271 Msa1455680:three_prime_UTR
TTCATCAAAATTTGAGCTAG+AGG 0.499203 tig0036439:-878 Msa1455680:intergenic
ATCGAGGCTGTGATAACATC+AGG 0.504440 tig0036439:-1599 Msa1455680:intergenic
GTTTATCTTACAGGGAACTA+AGG 0.508808 tig0036439:-1514 Msa1455680:intergenic
GGCCACATGGAAAATTGAAT+CGG 0.510881 tig0036439:+1284 Msa1455680:three_prime_UTR
GGACTGTGCATATTTGGTAG+TGG 0.515540 tig0036439:+1381 Msa1455680:three_prime_UTR
GACATTAAGCTGCATTTCAA+CGG 0.538504 tig0036439:-907 Msa1455680:intergenic
GATAACATCAGGTTTGAAAA+GGG 0.538562 tig0036439:-1588 Msa1455680:intergenic
AATGTGGTCCTGAATCCTGC+TGG 0.541467 tig0036439:-753 Msa1455680:intergenic
TGATATGTAAGTATATAAGA+TGG 0.544997 tig0036439:+1463 Msa1455680:three_prime_UTR
TGAGATGATCACATGTTGAC+TGG 0.553030 tig0036439:-1252 Msa1455680:intergenic
CGGAGATGATATCTAAGTCA+TGG 0.555155 tig0036439:+1304 Msa1455680:three_prime_UTR
TTTGATACAACTGGAGAATG+TGG 0.555890 tig0036439:-769 Msa1455680:intergenic
AAAAGGTATATATTGAGAGA+TGG 0.564701 tig0036439:+692 Msa1455680:five_prime_UTR
AAAACTGGGTTTATCTTACA+GGG 0.579919 tig0036439:-1522 Msa1455680:intergenic
AATGTCAGATCAAAGCCAGC+AGG 0.605391 tig0036439:+738 Msa1455680:CDS
TCATACGCTATATATTCCCA+AGG 0.658657 tig0036439:-940 Msa1455680:intergenic
ACTGTGCATATTTGGTAGTG+GGG 0.667252 tig0036439:+1383 Msa1455680:three_prime_UTR
GAACTAAGGAATTGGCAGTG+TGG 0.683589 tig0036439:-1500 None:intergenic
GATGATCACATGTTGACTGG+AGG 0.738848 tig0036439:-1249 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! CTCTAATTTTATTATTTAAA+AGG + tig0036439:675-694 Msa1455680:five_prime_UTR 10.0%
!!! CTCTAATTTTATTATTTAAA+AGG + tig0036439:675-694 Msa1455680:five_prime_UTR 10.0%
!!! ATAATCTGATTTTCATATTT+AGG + tig0036439:1221-1240 Msa1455680:intron 15.0%
!!! TAATCTGATTTTCATATTTA+GGG + tig0036439:1222-1241 Msa1455680:intron 15.0%
!!! ATAATCTGATTTTCATATTT+AGG + tig0036439:1221-1240 Msa1455680:intron 15.0%
!!! TAATCTGATTTTCATATTTA+GGG + tig0036439:1222-1241 Msa1455680:intron 15.0%
!!! CAAACTTTACAACATATTTT+TGG - tig0036439:642-661 None:intergenic 20.0%
!! TGATATGTAAGTATATAAGA+TGG + tig0036439:1463-1482 Msa1455680:three_prime_UTR 20.0%
!!! CAATTGTTTTTAAGAAAGAA+AGG - tig0036439:1563-1582 Msa1455680:intergenic 20.0%
!!! CAAACTTTACAACATATTTT+TGG - tig0036439:642-661 Msa1455680:intergenic 20.0%
!! TGATATGTAAGTATATAAGA+TGG + tig0036439:1463-1482 Msa1455680:three_prime_UTR 20.0%
!!! CAATTGTTTTTAAGAAAGAA+AGG - tig0036439:1563-1582 Msa1455680:intergenic 20.0%
!! AAAAGGTATATATTGAGAGA+TGG + tig0036439:692-711 Msa1455680:five_prime_UTR 25.0%
! CTTCAAAATTTGTATGATTC+CGG + tig0036439:1059-1078 Msa1455680:intron 25.0%
! AAAGAAAACCACTGAAAAAT+GGG - tig0036439:1156-1175 Msa1455680:intergenic 25.0%
! CAGATGTAACAAATTCTATT+GGG - tig0036439:1416-1435 Msa1455680:intergenic 25.0%
!! AAAAGGTATATATTGAGAGA+TGG + tig0036439:692-711 Msa1455680:five_prime_UTR 25.0%
! CTTCAAAATTTGTATGATTC+CGG + tig0036439:1059-1078 Msa1455680:intron 25.0%
! AAAGAAAACCACTGAAAAAT+GGG - tig0036439:1156-1175 Msa1455680:intergenic 25.0%
! CAGATGTAACAAATTCTATT+GGG - tig0036439:1416-1435 Msa1455680:intergenic 25.0%
ATATTGAGAGATGGATGAAA+TGG + tig0036439:701-720 Msa1455680:exon 30.0%
TCTCCAGTTGTATCAAATAA+AGG + tig0036439:775-794 Msa1455680:CDS 30.0%
CTCCAGTTGTATCAAATAAA+GGG + tig0036439:776-795 Msa1455680:CDS 30.0%
! AACCCTTTATTTGATACAAC+TGG - tig0036439:781-800 Msa1455680:intergenic 30.0%
GTTGTATCAAATAAAGGGTT+CGG + tig0036439:781-800 Msa1455680:CDS 30.0%
TTGTATCAAATAAAGGGTTC+GGG + tig0036439:782-801 Msa1455680:CDS 30.0%
TTCATCAAAATTTGAGCTAG+AGG - tig0036439:881-900 Msa1455680:intergenic 30.0%
AGCGTATGATCTTATGTTTA+AGG + tig0036439:954-973 Msa1455680:CDS 30.0%
! ATGATCTTATGTTTAAGGTG+AGG + tig0036439:959-978 Msa1455680:intron 30.0%
GGAAAATATTTCTTTGCATC+TGG + tig0036439:1035-1054 Msa1455680:intron 30.0%
!! TTTGTTGGTAACTTGAATTC+CGG - tig0036439:1081-1100 Msa1455680:intergenic 30.0%
! AGTGCAAAGAAATGTTTTGT+TGG - tig0036439:1096-1115 Msa1455680:intergenic 30.0%
CAAAGAAAACCACTGAAAAA+TGG - tig0036439:1157-1176 Msa1455680:intergenic 30.0%
GTGATCATCTCATATATTTC+TGG + tig0036439:1263-1282 Msa1455680:exon 30.0%
!!! TCTGTTCTGAAAGTTCTTTT+TGG + tig0036439:1335-1354 Msa1455680:three_prime_UTR 30.0%
GCAGATGTAACAAATTCTAT+TGG - tig0036439:1417-1436 Msa1455680:intergenic 30.0%
AAAACTGGGTTTATCTTACA+GGG - tig0036439:1525-1544 Msa1455680:intergenic 30.0%
AAAAACTGGGTTTATCTTAC+AGG - tig0036439:1526-1545 Msa1455680:intergenic 30.0%
GATAACATCAGGTTTGAAAA+GGG - tig0036439:1591-1610 Msa1455680:intergenic 30.0%
TGATAACATCAGGTTTGAAA+AGG - tig0036439:1592-1611 Msa1455680:intergenic 30.0%
!!! CATTTTGAAATACACAATCG+AGG - tig0036439:1618-1637 Msa1455680:intergenic 30.0%
ATATTGAGAGATGGATGAAA+TGG + tig0036439:701-720 Msa1455680:exon 30.0%
TCTCCAGTTGTATCAAATAA+AGG + tig0036439:775-794 Msa1455680:CDS 30.0%
CTCCAGTTGTATCAAATAAA+GGG + tig0036439:776-795 Msa1455680:CDS 30.0%
! AACCCTTTATTTGATACAAC+TGG - tig0036439:781-800 Msa1455680:intergenic 30.0%
GTTGTATCAAATAAAGGGTT+CGG + tig0036439:781-800 Msa1455680:CDS 30.0%
TTGTATCAAATAAAGGGTTC+GGG + tig0036439:782-801 Msa1455680:CDS 30.0%
TTCATCAAAATTTGAGCTAG+AGG - tig0036439:881-900 Msa1455680:intergenic 30.0%
AGCGTATGATCTTATGTTTA+AGG + tig0036439:954-973 Msa1455680:CDS 30.0%
! ATGATCTTATGTTTAAGGTG+AGG + tig0036439:959-978 Msa1455680:intron 30.0%
GGAAAATATTTCTTTGCATC+TGG + tig0036439:1035-1054 Msa1455680:intron 30.0%
!! TTTGTTGGTAACTTGAATTC+CGG - tig0036439:1081-1100 Msa1455680:intergenic 30.0%
! AGTGCAAAGAAATGTTTTGT+TGG - tig0036439:1096-1115 Msa1455680:intergenic 30.0%
CAAAGAAAACCACTGAAAAA+TGG - tig0036439:1157-1176 Msa1455680:intergenic 30.0%
GTGATCATCTCATATATTTC+TGG + tig0036439:1263-1282 Msa1455680:exon 30.0%
!!! TCTGTTCTGAAAGTTCTTTT+TGG + tig0036439:1335-1354 Msa1455680:three_prime_UTR 30.0%
GCAGATGTAACAAATTCTAT+TGG - tig0036439:1417-1436 Msa1455680:intergenic 30.0%
AAAACTGGGTTTATCTTACA+GGG - tig0036439:1525-1544 Msa1455680:intergenic 30.0%
AAAAACTGGGTTTATCTTAC+AGG - tig0036439:1526-1545 Msa1455680:intergenic 30.0%
GATAACATCAGGTTTGAAAA+GGG - tig0036439:1591-1610 Msa1455680:intergenic 30.0%
TGATAACATCAGGTTTGAAA+AGG - tig0036439:1592-1611 Msa1455680:intergenic 30.0%
!!! CATTTTGAAATACACAATCG+AGG - tig0036439:1618-1637 Msa1455680:intergenic 30.0%
TTTGATACAACTGGAGAATG+TGG - tig0036439:772-791 Msa1455680:intergenic 35.0%
AAAATTTGAGCTAGAGGAAG+AGG - tig0036439:875-894 Msa1455680:intergenic 35.0%
GACATTAAGCTGCATTTCAA+CGG - tig0036439:910-929 Msa1455680:intergenic 35.0%
TAATGTCCATATCATTGCCT+TGG + tig0036439:923-942 Msa1455680:CDS 35.0%
AATGTCCATATCATTGCCTT+GGG + tig0036439:924-943 Msa1455680:CDS 35.0%
ATATTCCCAAGGCAATGATA+TGG - tig0036439:932-951 Msa1455680:intergenic 35.0%
TCATACGCTATATATTCCCA+AGG - tig0036439:943-962 Msa1455680:intergenic 35.0%
TTCTTTGCACTAAGCTGAAA+TGG + tig0036439:1105-1124 Msa1455680:intron 35.0%
TAAGCTGAAATGGCTTTCAA+GGG + tig0036439:1115-1134 Msa1455680:intron 35.0%
!! TTTCTGTTCCCATTTTTCAG+TGG + tig0036439:1145-1164 Msa1455680:intron 35.0%
TGTATAGGACTGTGCATATT+TGG + tig0036439:1375-1394 Msa1455680:three_prime_UTR 35.0%
GTTTATCTTACAGGGAACTA+AGG - tig0036439:1517-1536 Msa1455680:intergenic 35.0%
TTTGATACAACTGGAGAATG+TGG - tig0036439:772-791 Msa1455680:intergenic 35.0%
AAAATTTGAGCTAGAGGAAG+AGG - tig0036439:875-894 Msa1455680:intergenic 35.0%
GACATTAAGCTGCATTTCAA+CGG - tig0036439:910-929 Msa1455680:intergenic 35.0%
TAATGTCCATATCATTGCCT+TGG + tig0036439:923-942 Msa1455680:CDS 35.0%
AATGTCCATATCATTGCCTT+GGG + tig0036439:924-943 Msa1455680:CDS 35.0%
ATATTCCCAAGGCAATGATA+TGG - tig0036439:932-951 Msa1455680:intergenic 35.0%
TCATACGCTATATATTCCCA+AGG - tig0036439:943-962 Msa1455680:intergenic 35.0%
TTCTTTGCACTAAGCTGAAA+TGG + tig0036439:1105-1124 Msa1455680:intron 35.0%
TAAGCTGAAATGGCTTTCAA+GGG + tig0036439:1115-1134 Msa1455680:intron 35.0%
!! TTTCTGTTCCCATTTTTCAG+TGG + tig0036439:1145-1164 Msa1455680:intron 35.0%
TGTATAGGACTGTGCATATT+TGG + tig0036439:1375-1394 Msa1455680:three_prime_UTR 35.0%
GTTTATCTTACAGGGAACTA+AGG - tig0036439:1517-1536 Msa1455680:intergenic 35.0%
CTAAGCTGAAATGGCTTTCA+AGG + tig0036439:1114-1133 Msa1455680:intron 40.0%
TGAGATGATCACATGTTGAC+TGG - tig0036439:1255-1274 Msa1455680:intergenic 40.0%
!! CTCATATATTTCTGGCCACA+TGG + tig0036439:1271-1290 Msa1455680:three_prime_UTR 40.0%
GGCCACATGGAAAATTGAAT+CGG + tig0036439:1284-1303 Msa1455680:three_prime_UTR 40.0%
! CTCCGATTCAATTTTCCATG+TGG - tig0036439:1289-1308 Msa1455680:intergenic 40.0%
CGGAGATGATATCTAAGTCA+TGG + tig0036439:1304-1323 Msa1455680:three_prime_UTR 40.0%
! GACTGTGCATATTTGGTAGT+GGG + tig0036439:1382-1401 Msa1455680:three_prime_UTR 40.0%
!! ACTGTGCATATTTGGTAGTG+GGG + tig0036439:1383-1402 Msa1455680:three_prime_UTR 40.0%
CTTACAGGGAACTAAGGAAT+TGG - tig0036439:1511-1530 Msa1455680:intergenic 40.0%
CTAAGCTGAAATGGCTTTCA+AGG + tig0036439:1114-1133 Msa1455680:intron 40.0%
TGAGATGATCACATGTTGAC+TGG - tig0036439:1255-1274 Msa1455680:intergenic 40.0%
!! CTCATATATTTCTGGCCACA+TGG + tig0036439:1271-1290 Msa1455680:three_prime_UTR 40.0%
GGCCACATGGAAAATTGAAT+CGG + tig0036439:1284-1303 Msa1455680:three_prime_UTR 40.0%
! CTCCGATTCAATTTTCCATG+TGG - tig0036439:1289-1308 Msa1455680:intergenic 40.0%
CGGAGATGATATCTAAGTCA+TGG + tig0036439:1304-1323 Msa1455680:three_prime_UTR 40.0%
! GACTGTGCATATTTGGTAGT+GGG + tig0036439:1382-1401 Msa1455680:three_prime_UTR 40.0%
!! ACTGTGCATATTTGGTAGTG+GGG + tig0036439:1383-1402 Msa1455680:three_prime_UTR 40.0%
CTTACAGGGAACTAAGGAAT+TGG - tig0036439:1511-1530 Msa1455680:intergenic 40.0%
AATGTCAGATCAAAGCCAGC+AGG + tig0036439:738-757 Msa1455680:CDS 45.0%
TCAAATAAAGGGTTCGGGCT+TGG + tig0036439:787-806 Msa1455680:CDS 45.0%
GACACAATGTCAGTGCTTCT+AGG + tig0036439:1014-1033 Msa1455680:intron 45.0%
! GATGATCACATGTTGACTGG+AGG - tig0036439:1252-1271 Msa1455680:intergenic 45.0%
GGACTGTGCATATTTGGTAG+TGG + tig0036439:1381-1400 Msa1455680:three_prime_UTR 45.0%
GAACTAAGGAATTGGCAGTG+TGG - tig0036439:1503-1522 Msa1455680:intergenic 45.0%
ATCGAGGCTGTGATAACATC+AGG - tig0036439:1602-1621 Msa1455680:intergenic 45.0%
AATGTCAGATCAAAGCCAGC+AGG + tig0036439:738-757 Msa1455680:CDS 45.0%
TCAAATAAAGGGTTCGGGCT+TGG + tig0036439:787-806 Msa1455680:CDS 45.0%
GACACAATGTCAGTGCTTCT+AGG + tig0036439:1014-1033 Msa1455680:intron 45.0%
! GATGATCACATGTTGACTGG+AGG - tig0036439:1252-1271 Msa1455680:intergenic 45.0%
GGACTGTGCATATTTGGTAG+TGG + tig0036439:1381-1400 Msa1455680:three_prime_UTR 45.0%
GAACTAAGGAATTGGCAGTG+TGG - tig0036439:1503-1522 Msa1455680:intergenic 45.0%
ATCGAGGCTGTGATAACATC+AGG - tig0036439:1602-1621 Msa1455680:intergenic 45.0%
!! AAAAAAAAAAAAAAAAAACT+GGG - tig0036439:1539-1558 Msa1455680:intergenic 5.0%
!! AAAAAAAAAAAAAAAAAAAC+TGG - tig0036439:1540-1559 Msa1455680:intergenic 5.0%
!! AAAAAAAAAAAAAAAAAACT+GGG - tig0036439:1539-1558 Msa1455680:intergenic 5.0%
!! AAAAAAAAAAAAAAAAAAAC+TGG - tig0036439:1540-1559 Msa1455680:intergenic 5.0%
GATCAAAGCCAGCAGGATTC+AGG + tig0036439:745-764 Msa1455680:CDS 50.0%
AATGTGGTCCTGAATCCTGC+TGG - tig0036439:756-775 Msa1455680:intergenic 50.0%
CATGCTGCACGTGCATGTAT+AGG + tig0036439:1360-1379 Msa1455680:three_prime_UTR 50.0%
GATCAAAGCCAGCAGGATTC+AGG + tig0036439:745-764 Msa1455680:CDS 50.0%
AATGTGGTCCTGAATCCTGC+TGG - tig0036439:756-775 Msa1455680:intergenic 50.0%
CATGCTGCACGTGCATGTAT+AGG + tig0036439:1360-1379 Msa1455680:three_prime_UTR 50.0%
Chromosome Type Strat End Strand Name
tig0036439 gene 568 1653 568 ID=Msa1455680;Name=Msa1455680
tig0036439 mRNA 568 1653 568 ID=Msa1455680-mRNA-1;Parent=Msa1455680;Name=Msa1455680-mRNA-1;_AED=0.00;_eAED=0.00;_QI=147|1|1|1|1|1|2|387|94
tig0036439 exon 568 975 568 ID=Msa1455680-mRNA-1:exon:20356;Parent=Msa1455680-mRNA-1
tig0036439 exon 1243 1653 1243 ID=Msa1455680-mRNA-1:exon:20357;Parent=Msa1455680-mRNA-1
tig0036439 five_prime_UTR 568 714 568 ID=Msa1455680-mRNA-1:five_prime_utr;Parent=Msa1455680-mRNA-1
tig0036439 CDS 715 975 715 ID=Msa1455680-mRNA-1:cds;Parent=Msa1455680-mRNA-1
tig0036439 CDS 1243 1266 1243 ID=Msa1455680-mRNA-1:cds;Parent=Msa1455680-mRNA-1
tig0036439 three_prime_UTR 1267 1653 1267 ID=Msa1455680-mRNA-1:three_prime_utr;Parent=Msa1455680-mRNA-1
Gene Sequence

>Msa1455680

ATGAAATGGAATCTGTCTGTTGCAATGTCAGATCAAAGCCAGCAGGATTCAGGACCACATTCTCCAGTTGTATCAAATAAAGGGTTCGGGCTTGGTGTAATCGTTCGCAGAGCTGCAACAGTTGCATCAGTAGCAGCAAGACATGCTTACGCTGCTGCCTCTTCCTCTAGCTCAAATTTTGATGAAATGATTCCGTTGAAATGCAGCTTAATGTCCATATCATTGCCTTGGGAATATATAGCGTATGATCTTATGTTTAAGGGAGCTCCTCCAGTCAACATGTGA
Protein sequence

>Msa1455680

MKWNLSVAMSDQSQQDSGPHSPVVSNKGFGLGVIVRRAATVASVAARHAYAAASSSSSNFDEMIPLKCSLMSISLPWEYIAYDLMFKGAPPVNM*