AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1394380


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1394380 MtrunA17_Chr6g0485841 97.980 99 2 0 1 99 624 722 3.98e-64 205
Msa1394380 MtrunA17_Chr4g0067521 68.966 87 27 0 1 87 628 714 6.98e-40 139
Msa1394380 MtrunA17_Chr2g0295671 67.816 87 28 0 1 87 626 712 2.51e-39 137
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1394380 AT4G29010.1 76.923 91 21 0 1 91 627 717 1.19e-43 150
Msa1394380 AT3G06860.1 61.364 88 34 0 1 88 630 717 3.38e-36 129

Find 36 sgRNAs with CRISPR-Local

Find 98 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTATAAACCATCAAGGTATT+TGG 0.237844 tig0021787:+866 Msa1394380:CDS
CTTTCTTCCAAATACCTTGA+TGG 0.286598 tig0021787:-873 None:intergenic
TCTTGGTCGGTGATAGAAAT+AGG 0.325992 tig0021787:-389 None:intergenic
TTTCTCATGTTGGATGTTCT+AGG 0.334747 tig0021787:+1408 Msa1394380:three_prime_UTR
TCTCACCCCTACCAGCAAAA+TGG 0.337112 tig0021787:+1481 Msa1394380:three_prime_UTR
TTGAGCAATGAGGAGAAATA+GGG 0.382711 tig0021787:-1682 None:intergenic
AACCGTTTCGCTTTCAACTT+TGG 0.390445 tig0021787:+1642 Msa1394380:three_prime_UTR
GAATGAGCTTCCCAAGTTAT+CGG 0.391451 tig0021787:+516 Msa1394380:CDS
CAATCTCACTAACTTCTTTG+AGG 0.395866 tig0021787:-1584 None:intergenic
CTTGACATTGCATCTGTCCT+TGG 0.405307 tig0021787:+494 Msa1394380:CDS
CAGCAAAATGGAAAATTCAT+AGG 0.421349 tig0021787:+1493 Msa1394380:three_prime_UTR
CGACAAGCCTCGTTCACTAC+TGG 0.423547 tig0021787:-434 None:intergenic
CATAGACGCGCCTTTGATGT+TGG 0.455260 tig0021787:-1356 None:intergenic
GTATCATCTCCACGATCTCT+TGG 0.461518 tig0021787:-406 None:intergenic
AGCAACAAAAGGCATTCCTT+TGG 0.468936 tig0021787:+896 Msa1394380:CDS
CATGTTGGATGTTCTAGGAT+AGG 0.502007 tig0021787:+1413 Msa1394380:three_prime_UTR
GTGAGAATATTATTTAAACT+TGG 0.502936 tig0021787:-1464 None:intergenic
TTGGAAGAAAGAGCAACAAA+AGG 0.543685 tig0021787:+885 Msa1394380:CDS
GAATATTATTTAAACTTGGT+AGG 0.545080 tig0021787:-1460 None:intergenic
ACACAGAGTGTTTCTCATGT+TGG 0.545275 tig0021787:+1398 Msa1394380:three_prime_UTR
AACCAAAGTTGAAAGCGAAA+CGG 0.547237 tig0021787:-1644 None:intergenic
GATGTTGGATTTGTTGAAGC+CGG 0.552564 tig0021787:-1341 None:intergenic
GTATTGCCTGCAGAGTGCAC+CGG 0.569946 tig0021787:+1322 Msa1394380:intron
TTCAACAAATCCAACATCAA+AGG 0.570396 tig0021787:+1346 Msa1394380:CDS
TCAAAGGCGCGTCTATGAGA+AGG 0.586995 tig0021787:+1362 Msa1394380:exon
TGAGCAATGAGGAGAAATAG+GGG 0.598862 tig0021787:-1681 None:intergenic
CATCTCCACGATCTCTTGGT+CGG 0.598867 tig0021787:-402 None:intergenic
ACATGAGAAACACTCTGTGT+AGG 0.620951 tig0021787:-1395 None:intergenic
GTGAGGCCTACCGATAACTT+GGG 0.631765 tig0021787:-526 None:intergenic
AACTTGGGAAGCTCATTCCA+AGG 0.639897 tig0021787:-511 None:intergenic
CAAGGACAGATGCAATGTCA+AGG 0.645468 tig0021787:-493 None:intergenic
TATCACCGACCAAGAGATCG+TGG 0.651409 tig0021787:+397 Msa1394380:five_prime_UTR
ACTACATAAGAGTTCAACAA+GGG 0.680113 tig0021787:-1616 None:intergenic
ACTCTTTCCAGTAGTGAACG+AGG 0.701898 tig0021787:+427 Msa1394380:CDS
CTACATAAGAGTTCAACAAG+GGG 0.706623 tig0021787:-1615 None:intergenic
TACTACATAAGAGTTCAACA+AGG 0.720082 tig0021787:-1617 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAAAATACATTAACAATTAT+GGG - tig0021787:719-738 None:intergenic 10.0%
!! TAAAAATACATTAACAATTA+TGG - tig0021787:720-739 None:intergenic 10.0%
!! AATTATAATAAAATTACAGA+AGG - tig0021787:1097-1116 None:intergenic 10.0%
!! ATTAAGAAAACTAAATTTCA+TGG - tig0021787:959-978 None:intergenic 15.0%
!!! TAGGAAAATAAATGTTTTTA+TGG + tig0021787:1512-1531 Msa1394380:three_prime_UTR 15.0%
!!! AGGAAAATAAATGTTTTTAT+GGG + tig0021787:1513-1532 Msa1394380:three_prime_UTR 15.0%
!!! CACTAATTTTCATTTTACAA+CGG + tig0021787:1185-1204 Msa1394380:intron 20.0%
!! GAATATTATTTAAACTTGGT+AGG - tig0021787:1463-1482 None:intergenic 20.0%
!! GTGAGAATATTATTTAAACT+TGG - tig0021787:1467-1486 None:intergenic 20.0%
! ATCCTCAATCATTAAAAGAA+GGG - tig0021787:554-573 None:intergenic 25.0%
! ATAATTTAGAGAGTTCAATG+AGG + tig0021787:584-603 Msa1394380:intron 25.0%
! TAATTTAGAGAGTTCAATGA+GGG + tig0021787:585-604 Msa1394380:intron 25.0%
! TATATAGCAGCCTAAAAAAA+TGG + tig0021787:823-842 Msa1394380:CDS 25.0%
! ATATAGCAGCCTAAAAAAAT+GGG + tig0021787:824-843 Msa1394380:CDS 25.0%
!!! ATAATTGTGCCCATTTTTTT+AGG - tig0021787:836-855 None:intergenic 25.0%
! AAAAAATGGGCACAATTATA+TGG + tig0021787:837-856 Msa1394380:CDS 25.0%
!! GTAACTTTTATAAACCATCA+AGG + tig0021787:859-878 Msa1394380:CDS 25.0%
!! TTATAAACCATCAAGGTATT+TGG + tig0021787:866-885 Msa1394380:CDS 25.0%
! AATAATGATCCCTTTCATAA+GGG - tig0021787:1151-1170 None:intergenic 25.0%
! TAATAATGATCCCTTTCATA+AGG - tig0021787:1152-1171 None:intergenic 25.0%
!!! TGTTACATTTTGAAAATGCA+TGG + tig0021787:1558-1577 Msa1394380:three_prime_UTR 25.0%
! TTCCCTTCTTTTAATGATTG+AGG + tig0021787:549-568 Msa1394380:intron 30.0%
CATCCTCAATCATTAAAAGA+AGG - tig0021787:555-574 None:intergenic 30.0%
!! TTCTAAAATAGTCTTGACCT+TGG + tig0021787:616-635 Msa1394380:intron 30.0%
TAACAATTATGGGTGAGAAT+AGG - tig0021787:709-728 None:intergenic 30.0%
!!! CTCATTGCAATCATTTTTTG+TGG + tig0021787:753-772 Msa1394380:intron 30.0%
!!! TTGCAATCATTTTTTGTGGT+AGG + tig0021787:757-776 Msa1394380:intron 30.0%
!!! TGCAATCATTTTTTGTGGTA+GGG + tig0021787:758-777 Msa1394380:intron 30.0%
TTCAACAAATCCAACATCAA+AGG + tig0021787:1346-1365 Msa1394380:CDS 30.0%
! AATTTTCCATTTTGCTGGTA+GGG - tig0021787:1490-1509 None:intergenic 30.0%
! CTATGAATTTTCCATTTTGC+TGG - tig0021787:1495-1514 None:intergenic 30.0%
CAGCAAAATGGAAAATTCAT+AGG + tig0021787:1493-1512 Msa1394380:three_prime_UTR 30.0%
!! AATGTTTTTATGGGTTCATG+AGG + tig0021787:1522-1541 Msa1394380:three_prime_UTR 30.0%
ACTACATAAGAGTTCAACAA+GGG - tig0021787:1619-1638 None:intergenic 30.0%
TACTACATAAGAGTTCAACA+AGG - tig0021787:1620-1639 None:intergenic 30.0%
TCATTAAAAGAAGGGAAGTG+AGG - tig0021787:546-565 None:intergenic 35.0%
!!! GCAATCATTTTTTGTGGTAG+GGG + tig0021787:759-778 Msa1394380:intron 35.0%
CTTTCTTCCAAATACCTTGA+TGG - tig0021787:876-895 None:intergenic 35.0%
TTGGAAGAAAGAGCAACAAA+AGG + tig0021787:885-904 Msa1394380:CDS 35.0%
GAACATTGTTGTCTTACCAA+AGG - tig0021787:915-934 None:intergenic 35.0%
! AGATGTCATTTCATGCACAA+AGG - tig0021787:984-1003 None:intergenic 35.0%
CATAAGCATGTATAGTTGCT+AGG + tig0021787:1017-1036 Msa1394380:intron 35.0%
TTTCTCATGTTGGATGTTCT+AGG + tig0021787:1408-1427 Msa1394380:three_prime_UTR 35.0%
! ATTTTCCATTTTGCTGGTAG+GGG - tig0021787:1489-1508 None:intergenic 35.0%
! GAATTTTCCATTTTGCTGGT+AGG - tig0021787:1491-1510 None:intergenic 35.0%
CAATCTCACTAACTTCTTTG+AGG - tig0021787:1587-1606 None:intergenic 35.0%
CTACATAAGAGTTCAACAAG+GGG - tig0021787:1618-1637 None:intergenic 35.0%
AACCAAAGTTGAAAGCGAAA+CGG - tig0021787:1647-1666 None:intergenic 35.0%
TCTTGGTCGGTGATAGAAAT+AGG - tig0021787:392-411 None:intergenic 40.0%
!!! GCTTGTCGTGTTTTAGAAGA+AGG + tig0021787:449-468 Msa1394380:CDS 40.0%
GAATGAGCTTCCCAAGTTAT+CGG + tig0021787:516-535 Msa1394380:CDS 40.0%
! AGGTTTTCTTTCGATAGCCA+AGG - tig0021787:636-655 None:intergenic 40.0%
TATCGAAAGAAAACCTAGCC+TGG + tig0021787:640-659 Msa1394380:intron 40.0%
ATCGAAAGAAAACCTAGCCT+GGG + tig0021787:641-660 Msa1394380:intron 40.0%
ATTATGGGTGAGAATAGGTC+AGG - tig0021787:704-723 None:intergenic 40.0%
!!! ATCATTTTTTGTGGTAGGGG+TGG + tig0021787:762-781 Msa1394380:intron 40.0%
!! AGCAACAAAAGGCATTCCTT+TGG + tig0021787:896-915 Msa1394380:CDS 40.0%
ACACACTTCACCCTTATGAA+AGG + tig0021787:1138-1157 Msa1394380:intron 40.0%
CACACTTCACCCTTATGAAA+GGG + tig0021787:1139-1158 Msa1394380:intron 40.0%
AGATGATGTTCAAACTCCCT+CGG - tig0021787:1214-1233 None:intergenic 40.0%
ACCACTTAACTGACACTTCA+TGG + tig0021787:1235-1254 Msa1394380:intron 40.0%
! TCCATGAAGTGTCAGTTAAG+TGG - tig0021787:1239-1258 None:intergenic 40.0%
!! GATGTTGGATTTGTTGAAGC+CGG - tig0021787:1344-1363 None:intergenic 40.0%
ACATGAGAAACACTCTGTGT+AGG - tig0021787:1398-1417 None:intergenic 40.0%
! ACACAGAGTGTTTCTCATGT+TGG + tig0021787:1398-1417 Msa1394380:three_prime_UTR 40.0%
!! CATGTTGGATGTTCTAGGAT+AGG + tig0021787:1413-1432 Msa1394380:three_prime_UTR 40.0%
AACCGTTTCGCTTTCAACTT+TGG + tig0021787:1642-1661 Msa1394380:three_prime_UTR 40.0%
GTATCATCTCCACGATCTCT+TGG - tig0021787:409-428 None:intergenic 45.0%
ACTCTTTCCAGTAGTGAACG+AGG + tig0021787:427-446 Msa1394380:CDS 45.0%
CAAGGACAGATGCAATGTCA+AGG - tig0021787:496-515 None:intergenic 45.0%
CTTGACATTGCATCTGTCCT+TGG + tig0021787:494-513 Msa1394380:CDS 45.0%
AACTTGGGAAGCTCATTCCA+AGG - tig0021787:514-533 None:intergenic 45.0%
!! GATTGGCCATTGACTCCTAT+TGG + tig0021787:674-693 Msa1394380:intron 45.0%
! TAGGGGTGGCATTGTTTTCT+GGG + tig0021787:776-795 Msa1394380:intron 45.0%
! GTTTTCTGGGCTGATCTAGT+TGG + tig0021787:789-808 Msa1394380:CDS 45.0%
! TCATTTTACAACGGTCTCCG+AGG + tig0021787:1194-1213 Msa1394380:intron 45.0%
! CATTTTACAACGGTCTCCGA+GGG + tig0021787:1195-1214 Msa1394380:intron 45.0%
TATCACCGACCAAGAGATCG+TGG + tig0021787:397-416 Msa1394380:five_prime_UTR 50.0%
CATCTCCACGATCTCTTGGT+CGG - tig0021787:405-424 None:intergenic 50.0%
GAGCTTCCCAAGTTATCGGT+AGG + tig0021787:520-539 Msa1394380:intron 50.0%
GTGAGGCCTACCGATAACTT+GGG - tig0021787:529-548 None:intergenic 50.0%
AGTGAGGCCTACCGATAACT+TGG - tig0021787:530-549 None:intergenic 50.0%
!! GGCCATTGACTCCTATTGGT+CGG + tig0021787:678-697 Msa1394380:intron 50.0%
AATAGGTCAGGCCGACCAAT+AGG - tig0021787:692-711 None:intergenic 50.0%
! GTAGGGGTGGCATTGTTTTC+TGG + tig0021787:775-794 Msa1394380:intron 50.0%
CATAGACGCGCCTTTGATGT+TGG - tig0021787:1359-1378 None:intergenic 50.0%
! TCAAAGGCGCGTCTATGAGA+AGG + tig0021787:1362-1381 Msa1394380:exon 50.0%
TCTCACCCCTACCAGCAAAA+TGG + tig0021787:1481-1500 Msa1394380:three_prime_UTR 50.0%
CGACAAGCCTCGTTCACTAC+TGG - tig0021787:437-456 None:intergenic 55.0%
AAGAAAACCTAGCCTGGGCC+AGG + tig0021787:646-665 Msa1394380:intron 55.0%
TCAATGGCCAATCCTACGCC+TGG - tig0021787:667-686 None:intergenic 55.0%
GGCCGACCAATAGGAGTCAA+TGG - tig0021787:683-702 None:intergenic 55.0%
GTATTGCCTGCAGAGTGCAC+CGG + tig0021787:1322-1341 Msa1394380:intron 55.0%
TTGAAGCCGGTGCACTCTGC+AGG - tig0021787:1331-1350 None:intergenic 60.0%
ACCTAGCCTGGGCCAGGCGT+AGG + tig0021787:652-671 Msa1394380:intron 70.0%
TCCTACGCCTGGCCCAGGCT+AGG - tig0021787:656-675 None:intergenic 70.0%
GCCTGGGCCAGGCGTAGGAT+TGG + tig0021787:657-676 Msa1394380:intron 70.0%
GCCAATCCTACGCCTGGCCC+AGG - tig0021787:661-680 None:intergenic 70.0%
Chromosome Type Strat End Strand Name
tig0021787 gene 369 1689 369 ID=Msa1394380;Name=Msa1394380
tig0021787 mRNA 369 1689 369 ID=Msa1394380-mRNA-1;Parent=Msa1394380;Name=Msa1394380-mRNA-1;_AED=0.00;_eAED=0.00;_QI=53|1|1|1|1|1|3|310|99
tig0021787 exon 369 537 369 ID=Msa1394380-mRNA-1:exon:14316;Parent=Msa1394380-mRNA-1
tig0021787 exon 779 917 779 ID=Msa1394380-mRNA-1:exon:14317;Parent=Msa1394380-mRNA-1
tig0021787 exon 1335 1689 1335 ID=Msa1394380-mRNA-1:exon:14318;Parent=Msa1394380-mRNA-1
tig0021787 five_prime_UTR 369 421 369 ID=Msa1394380-mRNA-1:five_prime_utr;Parent=Msa1394380-mRNA-1
tig0021787 CDS 422 537 422 ID=Msa1394380-mRNA-1:cds;Parent=Msa1394380-mRNA-1
tig0021787 CDS 779 917 779 ID=Msa1394380-mRNA-1:cds;Parent=Msa1394380-mRNA-1
tig0021787 CDS 1335 1379 1335 ID=Msa1394380-mRNA-1:cds;Parent=Msa1394380-mRNA-1
tig0021787 three_prime_UTR 1380 1689 1380 ID=Msa1394380-mRNA-1:three_prime_utr;Parent=Msa1394380-mRNA-1
Gene Sequence

>Msa1394380

ATGATACTCTTTCCAGTAGTGAACGAGGCTTGTCGTGTTTTAGAAGAAGGAATTGTTATTCGCGCATCAGACCTTGACATTGCATCTGTCCTTGGAATGAGCTTCCCAAGTTATCGGGGTGGCATTGTTTTCTGGGCTGATCTAGTTGGAGCTAAGCATATATATAGCAGCCTAAAAAAATGGGCACAATTATATGGTAACTTTTATAAACCATCAAGGTATTTGGAAGAAAGAGCAACAAAAGGCATTCCTTTGAGTGCACCGGCTTCAACAAATCCAACATCAAAGGCGCGTCTATGA

Protein sequence

>Msa1394380

MILFPVVNEACRVLEEGIVIRASDLDIASVLGMSFPSYRGGIVFWADLVGAKHIYSSLKKWAQLYGNFYKPSRYLEERATKGIPLSAPASTNPTSKARL*