AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0317280


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0317280 MtrunA17_Chr2g0290471 97.849 93 1 1 1 93 1 92 3.03e-52 164
Msa0317280 MtrunA17_Chr8g0386231 67.213 61 20 0 33 93 50 110 9.21e-22 86.7
Msa0317280 MtrunA17_Chr3g0132061 66.102 59 20 0 35 93 35 93 1.74e-19 80.1
Msa0317280 MtrunA17_Chr4g0001151 67.797 59 19 0 35 93 169 227 1.89e-19 80.1
Msa0317280 MtrunA17_Chr3g0132051 64.407 59 21 0 35 93 35 93 2.87e-19 79.0
Msa0317280 MtrunA17_Chr7g0264601 44.286 70 37 2 23 92 3 70 4.11e-13 63.2
Msa0317280 MtrunA17_Chr3g0094841 43.103 58 32 1 36 92 28 85 1.29e-12 60.8
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0317280 AT5G50740.2 70.690 58 17 0 36 93 29 86 1.21e-23 88.6
Msa0317280 AT5G50740.4 70.690 58 17 0 36 93 36 93 2.47e-23 87.8
Msa0317280 AT5G50740.5 70.690 58 17 0 36 93 29 86 6.06e-23 89.4
Msa0317280 AT5G50740.1 70.690 58 17 0 36 93 29 86 6.06e-23 89.4
Msa0317280 AT5G50740.3 70.690 58 17 0 36 93 36 93 9.59e-23 89.0
Msa0317280 AT5G63530.2 67.797 59 19 0 35 93 59 117 4.03e-21 85.5
Msa0317280 AT5G63530.1 67.797 59 19 0 35 93 74 132 4.84e-21 85.5
Msa0317280 AT3G02960.1 43.820 89 50 0 4 92 6 94 1.14e-18 77.4
Msa0317280 AT2G36950.1 50.000 58 28 1 36 93 52 108 1.41e-13 64.7
Msa0317280 AT2G28090.1 37.879 66 41 0 20 85 15 80 5.73e-12 59.7
Msa0317280 AT5G60800.1 50.000 50 24 1 36 85 28 76 4.49e-11 57.4
Msa0317280 AT5G60800.2 50.000 50 24 1 36 85 28 76 4.54e-11 57.4

Find 19 sgRNAs with CRISPR-Local

Find 106 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GAAGAAGGAAGAAGAGAAAA+AGG 0.176799 2_4:-14948499 Msa0317280:CDS
TCAACCTTGAGTACTATTTC+TGG 0.234887 2_4:+14948450 None:intergenic
AAAGAAAGAAGAAACCAAAA+AGG 0.312807 2_4:-14948523 Msa0317280:CDS
GGAGGTGACCGCAGATAGTA+AGG 0.417983 2_4:-14947536 Msa0317280:CDS
AAAGCATTGAAAGGATTTGA+AGG 0.510804 2_4:-14948393 Msa0317280:intron
TGAAAGGAGAACAAGGAAGA+AGG 0.511133 2_4:-14948546 Msa0317280:intron
AAAGGCAGCAGACCCCATAA+AGG 0.514781 2_4:-14947491 Msa0317280:CDS
AAAGTTGCAAAAGCATTGAA+AGG 0.535218 2_4:-14948402 Msa0317280:CDS
AAAAGACTACAAAAGAAAAG+TGG 0.555223 2_4:-14947463 None:intergenic
ACCTCCAGAAATAGTACTCA+AGG 0.560038 2_4:-14948454 Msa0317280:CDS
GTGTGTGAAAGGAGTGGAGG+AGG 0.602247 2_4:-14947554 Msa0317280:intron
GGCAGCAAAGTGGTAGTGAA+AGG 0.606418 2_4:-14947514 Msa0317280:CDS
ACCTTGAGTACTATTTCTGG+AGG 0.614898 2_4:+14948453 None:intergenic
AGATAGTAAGGGCAGCAAAG+TGG 0.627174 2_4:-14947524 Msa0317280:CDS
TTTGCTGCCCTTACTATCTG+CGG 0.627410 2_4:+14947528 None:intergenic
TGCATTGTGAAGCTTGTGCA+AGG 0.638724 2_4:-14948425 Msa0317280:CDS
GAGGTGACCGCAGATAGTAA+GGG 0.644356 2_4:-14947535 Msa0317280:CDS
CAAAGTGGTAGTGAAAGGAA+AGG 0.648004 2_4:-14947509 Msa0317280:CDS
GTTGTGTGTGAAAGGAGTGG+AGG 0.667974 2_4:-14947557 Msa0317280:intron

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! CATTTTTCATAAAAAAATAA+AGG - chr2_4:14948493-14948512 Msa0317280:CDS 10.0%
!!! CATTTTTCATAAAAAAATAA+AGG - chr2_4:14948493-14948512 Msa0317280:CDS 10.0%
!!! ATATGTACATTATTTTTTTG+AGG + chr2_4:14948077-14948096 None:intergenic 15.0%
!!! TATAAAATTCTAACTTTTAC+AGG - chr2_4:14948243-14948262 Msa0317280:intron 15.0%
!!! ATATGTACATTATTTTTTTG+AGG + chr2_4:14948077-14948096 None:intergenic 15.0%
!!! TATAAAATTCTAACTTTTAC+AGG - chr2_4:14948243-14948262 Msa0317280:intron 15.0%
!!! TATAGTTGATATTTTCTACT+TGG - chr2_4:14947544-14947563 Msa0317280:CDS 20.0%
!! GATTTATTAGATTATTGTCT+TGG + chr2_4:14947852-14947871 None:intergenic 20.0%
!! AAGTAATATGTACTACATTA+TGG + chr2_4:14948053-14948072 None:intergenic 20.0%
!! TCATAAAAAAATAAAGGTCT+AGG - chr2_4:14948499-14948518 Msa0317280:CDS 20.0%
!!! TATAGTTGATATTTTCTACT+TGG - chr2_4:14947544-14947563 Msa0317280:CDS 20.0%
!! GATTTATTAGATTATTGTCT+TGG + chr2_4:14947852-14947871 None:intergenic 20.0%
!! AAGTAATATGTACTACATTA+TGG + chr2_4:14948053-14948072 None:intergenic 20.0%
!! TCATAAAAAAATAAAGGTCT+AGG - chr2_4:14948499-14948518 Msa0317280:CDS 20.0%
!!! GCTTTTTTTTTTTGTGTGAA+AGG - chr2_4:14947575-14947594 Msa0317280:intron 25.0%
! AAAGAAAGAAGAAACCAAAA+AGG - chr2_4:14947614-14947633 Msa0317280:intron 25.0%
! AATATGTACTACATTATGGT+TGG + chr2_4:14948049-14948068 None:intergenic 25.0%
!! AGGTAAATTTTATACACGAT+AGG - chr2_4:14948263-14948282 Msa0317280:intron 25.0%
! TAAAAAAATAAAGGTCTAGG+TGG - chr2_4:14948502-14948521 Msa0317280:CDS 25.0%
! AAAAAAATAAAGGTCTAGGT+GGG - chr2_4:14948503-14948522 Msa0317280:CDS 25.0%
!!! GCTTTTTTTTTTTGTGTGAA+AGG - chr2_4:14947575-14947594 Msa0317280:intron 25.0%
! AAAGAAAGAAGAAACCAAAA+AGG - chr2_4:14947614-14947633 Msa0317280:intron 25.0%
! AATATGTACTACATTATGGT+TGG + chr2_4:14948049-14948068 None:intergenic 25.0%
!! AGGTAAATTTTATACACGAT+AGG - chr2_4:14948263-14948282 Msa0317280:intron 25.0%
! TAAAAAAATAAAGGTCTAGG+TGG - chr2_4:14948502-14948521 Msa0317280:CDS 25.0%
! AAAAAAATAAAGGTCTAGGT+GGG - chr2_4:14948503-14948522 Msa0317280:CDS 25.0%
!! AAAGTTGCAAAAGCATTGAA+AGG - chr2_4:14947735-14947754 Msa0317280:intron 30.0%
!! AAAGCATTGAAAGGATTTGA+AGG - chr2_4:14947744-14947763 Msa0317280:intron 30.0%
TGACAATGGATCATACAAAT+TGG + chr2_4:14948105-14948124 None:intergenic 30.0%
GTGAAATTCAAAAGCAATCA+TGG + chr2_4:14948191-14948210 None:intergenic 30.0%
! TTTTGTTAACGAGTGTCTTA+AGG - chr2_4:14948330-14948349 Msa0317280:intron 30.0%
AAAAAATAAAGGTCTAGGTG+GGG - chr2_4:14948504-14948523 Msa0317280:CDS 30.0%
TTGAAAATGTTGTGTGTGAA+AGG - chr2_4:14948572-14948591 Msa0317280:intron 30.0%
!! AAAGTTGCAAAAGCATTGAA+AGG - chr2_4:14947735-14947754 Msa0317280:intron 30.0%
!! AAAGCATTGAAAGGATTTGA+AGG - chr2_4:14947744-14947763 Msa0317280:intron 30.0%
TGACAATGGATCATACAAAT+TGG + chr2_4:14948105-14948124 None:intergenic 30.0%
GTGAAATTCAAAAGCAATCA+TGG + chr2_4:14948191-14948210 None:intergenic 30.0%
! TTTTGTTAACGAGTGTCTTA+AGG - chr2_4:14948330-14948349 Msa0317280:intron 30.0%
AAAAAATAAAGGTCTAGGTG+GGG - chr2_4:14948504-14948523 Msa0317280:CDS 30.0%
TTGAAAATGTTGTGTGTGAA+AGG - chr2_4:14948572-14948591 Msa0317280:intron 30.0%
! TTTTGTGTGAAAGGAGAACA+AGG - chr2_4:14947584-14947603 Msa0317280:intron 35.0%
AGAAACCAAAAAGGAGAAGA+AGG - chr2_4:14947623-14947642 Msa0317280:intron 35.0%
! TTCTTCCTTCTTCTCCTTTT+TGG + chr2_4:14947631-14947650 None:intergenic 35.0%
GAAGAAGGAAGAAGAGAAAA+AGG - chr2_4:14947638-14947657 Msa0317280:intron 35.0%
TCAACCTTGAGTACTATTTC+TGG + chr2_4:14947690-14947709 None:intergenic 35.0%
!! ACAAAAGTACTAGCTGACAA+TGG + chr2_4:14948119-14948138 None:intergenic 35.0%
CTCTAACAAGGAAAAAAGGA+GGG + chr2_4:14948155-14948174 None:intergenic 35.0%
!!! CTCCTTTTTTCCTTGTTAGA+GGG - chr2_4:14948154-14948173 Msa0317280:intron 35.0%
ATCCCTCTAACAAGGAAAAA+AGG + chr2_4:14948159-14948178 None:intergenic 35.0%
! AGTCTTTTGAGCACCTTTAT+GGG + chr2_4:14948662-14948681 None:intergenic 35.0%
! TAGTCTTTTGAGCACCTTTA+TGG + chr2_4:14948663-14948682 None:intergenic 35.0%
! TTTTGTGTGAAAGGAGAACA+AGG - chr2_4:14947584-14947603 Msa0317280:intron 35.0%
AGAAACCAAAAAGGAGAAGA+AGG - chr2_4:14947623-14947642 Msa0317280:intron 35.0%
! TTCTTCCTTCTTCTCCTTTT+TGG + chr2_4:14947631-14947650 None:intergenic 35.0%
GAAGAAGGAAGAAGAGAAAA+AGG - chr2_4:14947638-14947657 Msa0317280:intron 35.0%
TCAACCTTGAGTACTATTTC+TGG + chr2_4:14947690-14947709 None:intergenic 35.0%
!! ACAAAAGTACTAGCTGACAA+TGG + chr2_4:14948119-14948138 None:intergenic 35.0%
CTCTAACAAGGAAAAAAGGA+GGG + chr2_4:14948155-14948174 None:intergenic 35.0%
!!! CTCCTTTTTTCCTTGTTAGA+GGG - chr2_4:14948154-14948173 Msa0317280:intron 35.0%
ATCCCTCTAACAAGGAAAAA+AGG + chr2_4:14948159-14948178 None:intergenic 35.0%
! AGTCTTTTGAGCACCTTTAT+GGG + chr2_4:14948662-14948681 None:intergenic 35.0%
! TAGTCTTTTGAGCACCTTTA+TGG + chr2_4:14948663-14948682 None:intergenic 35.0%
TGAAAGGAGAACAAGGAAGA+AGG - chr2_4:14947591-14947610 Msa0317280:intron 40.0%
GAAGGAAGAAGAGAAAAAGG+AGG - chr2_4:14947641-14947660 Msa0317280:intron 40.0%
ACCTCCAGAAATAGTACTCA+AGG - chr2_4:14947683-14947702 Msa0317280:intron 40.0%
!! ACCTTGAGTACTATTTCTGG+AGG + chr2_4:14947687-14947706 None:intergenic 40.0%
CCTCTAACAAGGAAAAAAGG+AGG + chr2_4:14948156-14948175 None:intergenic 40.0%
!!! CCTCCTTTTTTCCTTGTTAG+AGG - chr2_4:14948153-14948172 Msa0317280:intron 40.0%
TTGTGTAGATCCCTCTAACA+AGG + chr2_4:14948167-14948186 None:intergenic 40.0%
AATGTTGTGTGTGAAAGGAG+TGG - chr2_4:14948577-14948596 Msa0317280:intron 40.0%
! CAAAGTGGTAGTGAAAGGAA+AGG - chr2_4:14948628-14948647 Msa0317280:intron 40.0%
! GTCTTTTGAGCACCTTTATG+GGG + chr2_4:14948661-14948680 None:intergenic 40.0%
TGAAAGGAGAACAAGGAAGA+AGG - chr2_4:14947591-14947610 Msa0317280:intron 40.0%
GAAGGAAGAAGAGAAAAAGG+AGG - chr2_4:14947641-14947660 Msa0317280:intron 40.0%
ACCTCCAGAAATAGTACTCA+AGG - chr2_4:14947683-14947702 Msa0317280:intron 40.0%
!! ACCTTGAGTACTATTTCTGG+AGG + chr2_4:14947687-14947706 None:intergenic 40.0%
CCTCTAACAAGGAAAAAAGG+AGG + chr2_4:14948156-14948175 None:intergenic 40.0%
!!! CCTCCTTTTTTCCTTGTTAG+AGG - chr2_4:14948153-14948172 Msa0317280:intron 40.0%
TTGTGTAGATCCCTCTAACA+AGG + chr2_4:14948167-14948186 None:intergenic 40.0%
AATGTTGTGTGTGAAAGGAG+TGG - chr2_4:14948577-14948596 Msa0317280:intron 40.0%
! CAAAGTGGTAGTGAAAGGAA+AGG - chr2_4:14948628-14948647 Msa0317280:intron 40.0%
! GTCTTTTGAGCACCTTTATG+GGG + chr2_4:14948661-14948680 None:intergenic 40.0%
TGCATTGTGAAGCTTGTGCA+AGG - chr2_4:14947712-14947731 Msa0317280:intron 45.0%
TCTAGGTGGGGAAAAGAGTA+TGG - chr2_4:14948516-14948535 Msa0317280:CDS 45.0%
TTTGCTGCCCTTACTATCTG+CGG + chr2_4:14948612-14948631 None:intergenic 45.0%
AGATAGTAAGGGCAGCAAAG+TGG - chr2_4:14948613-14948632 Msa0317280:intron 45.0%
TGCATTGTGAAGCTTGTGCA+AGG - chr2_4:14947712-14947731 Msa0317280:intron 45.0%
TCTAGGTGGGGAAAAGAGTA+TGG - chr2_4:14948516-14948535 Msa0317280:CDS 45.0%
TTTGCTGCCCTTACTATCTG+CGG + chr2_4:14948612-14948631 None:intergenic 45.0%
AGATAGTAAGGGCAGCAAAG+TGG - chr2_4:14948613-14948632 Msa0317280:intron 45.0%
!!! TTAAAACTTTAATAAAATTT+TGG + chr2_4:14947959-14947978 None:intergenic 5.0%
!!! TCATAAAATTTTAATATTTA+AGG - chr2_4:14948438-14948457 Msa0317280:CDS 5.0%
!!! TTAAAACTTTAATAAAATTT+TGG + chr2_4:14947959-14947978 None:intergenic 5.0%
!!! TCATAAAATTTTAATATTTA+AGG - chr2_4:14948438-14948457 Msa0317280:CDS 5.0%
GTTGTGTGTGAAAGGAGTGG+AGG - chr2_4:14948580-14948599 Msa0317280:intron 50.0%
GAGGTGACCGCAGATAGTAA+GGG - chr2_4:14948602-14948621 Msa0317280:intron 50.0%
! GGCAGCAAAGTGGTAGTGAA+AGG - chr2_4:14948623-14948642 Msa0317280:intron 50.0%
AAAGGCAGCAGACCCCATAA+AGG - chr2_4:14948646-14948665 Msa0317280:intron 50.0%
GTTGTGTGTGAAAGGAGTGG+AGG - chr2_4:14948580-14948599 Msa0317280:intron 50.0%
GAGGTGACCGCAGATAGTAA+GGG - chr2_4:14948602-14948621 Msa0317280:intron 50.0%
! GGCAGCAAAGTGGTAGTGAA+AGG - chr2_4:14948623-14948642 Msa0317280:intron 50.0%
AAAGGCAGCAGACCCCATAA+AGG - chr2_4:14948646-14948665 Msa0317280:intron 50.0%
GTGTGTGAAAGGAGTGGAGG+AGG - chr2_4:14948583-14948602 Msa0317280:intron 55.0%
GGAGGTGACCGCAGATAGTA+AGG - chr2_4:14948601-14948620 Msa0317280:intron 55.0%
GTGTGTGAAAGGAGTGGAGG+AGG - chr2_4:14948583-14948602 Msa0317280:intron 55.0%
GGAGGTGACCGCAGATAGTA+AGG - chr2_4:14948601-14948620 Msa0317280:intron 55.0%
Chromosome Type Strat End Strand Name
chr2_4 gene 14947465 14948694 14947465 ID=Msa0317280;Name=Msa0317280
chr2_4 mRNA 14947465 14948694 14947465 ID=Msa0317280-mRNA-1;Parent=Msa0317280;Name=Msa0317280-mRNA-1;_AED=0.08;_eAED=0.08;_QI=0|0.5|0|0.66|0.5|0.33|3|0|93
chr2_4 exon 14948686 14948694 14948686 ID=Msa0317280-mRNA-1:exon:5602;Parent=Msa0317280-mRNA-1
chr2_4 exon 14948394 14948562 14948394 ID=Msa0317280-mRNA-1:exon:5601;Parent=Msa0317280-mRNA-1
chr2_4 exon 14947465 14947565 14947465 ID=Msa0317280-mRNA-1:exon:5600;Parent=Msa0317280-mRNA-1
chr2_4 CDS 14948686 14948694 14948686 ID=Msa0317280-mRNA-1:cds;Parent=Msa0317280-mRNA-1
chr2_4 CDS 14948394 14948562 14948394 ID=Msa0317280-mRNA-1:cds;Parent=Msa0317280-mRNA-1
chr2_4 CDS 14947465 14947565 14947465 ID=Msa0317280-mRNA-1:cds;Parent=Msa0317280-mRNA-1
Gene Sequence

>Msa0317280

ATGGGTGAAGAGAACAAGGAAGAAGGAAAGAAAGAAGAAACCAAAAAGGAGAAGAAGGAAGAAGAGAAAAAGGAGGAAAAGAAAGATGAAGAACAACCTCCAGAAATAGTACTCAAGGTTGATATGCATTGTGAAGCTTGTGCAAGGAAAGTTGCAAAAGCATTGAAAGGATTTGAAGGAGTGGAGGAGGTGACCGCAGATAGTAAGGGCAGCAAAGTGGTAGTGAAAGGAAAGGCAGCAGACCCCATAAAGGTGCTCAAAAGACTACAAAAGAAAAGT

Protein sequence

>Msa0317280

MGEENKEEGKKEETKKEKKEEEKKEEKKDEEQPPEIVLKVDMHCEACARKVAKALKGFEGVEEVTADSKGSKVVVKGKAADPIKVLKRLQKKS