AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1430130


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1430130 MtrunA17_Chr8g0390061 89.855 207 21 0 24 230 1 207 6.68e-141 392
Msa1430130 MtrunA17_Chr8g0390051 60.924 238 62 3 24 230 1 238 5.33e-98 285
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 35 sgRNAs with CRISPR-Local

Find 136 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTTCTTGTCTTCCTTGTTCT+TGG 0.156350 tig0026637:+30915 None:intergenic
TAATGATATTGAAATGAATT+TGG 0.220117 tig0026637:-29835 Msa1430130:CDS
AAGACAGAAACAAAGAAATT+TGG 0.303541 tig0026637:-30221 Msa1430130:CDS
ATTGAAGATGATGCTACTTT+TGG 0.318948 tig0026637:-30276 Msa1430130:CDS
CAAAGCTTTCATGATGAAAA+TGG 0.325691 tig0026637:-29954 Msa1430130:CDS
CAGGTTTGCAATCAAGAAAT+AGG 0.331402 tig0026637:-29743 Msa1430130:CDS
ACTGTTCATGTTGATACTTC+AGG 0.350166 tig0026637:-29762 Msa1430130:CDS
ATTCAAATCAAGCTTGTTGC+TGG 0.398775 tig0026637:-30197 Msa1430130:CDS
ATCTATTACACCATTATTTG+CGG 0.399079 tig0026637:+29983 None:intergenic
GGATGTGGACATAAATTGTT+TGG 0.414508 tig0026637:-30176 Msa1430130:CDS
GAATCTACCTTTCCTGAGTC+AGG 0.424703 tig0026637:+30113 None:intergenic
AAAAGGGTCTAACGTAAAAC+AGG 0.453639 tig0026637:-30300 Msa1430130:CDS
ATCAAGCTTGTTGCTGGATG+TGG 0.461106 tig0026637:-30191 Msa1430130:CDS
GTGGAGAGTGCCGCAAATAA+TGG 0.466076 tig0026637:-29993 Msa1430130:CDS
AGAATGGAGTATCAATCTCT+TGG 0.471194 tig0026637:-30338 Msa1430130:CDS
CATAAATTGTTTGGACGGAA+AGG 0.490271 tig0026637:-30167 Msa1430130:CDS
GTTGAATTAATGCAGAAGAA+TGG 0.500286 tig0026637:-30354 Msa1430130:intron
GATATTGAAATGAATTTGGA+AGG 0.502773 tig0026637:-29831 Msa1430130:CDS
TCAGGAAAAGCTCTTTCATC+GGG 0.511579 tig0026637:+30131 None:intergenic
ATAAATTGTTTGGACGGAAA+GGG 0.528425 tig0026637:-30166 Msa1430130:CDS
GTCAGGAAAAGCTCTTTCAT+CGG 0.531583 tig0026637:+30130 None:intergenic
AGTATTTATGAAGTCACGTA+TGG 0.536293 tig0026637:-29864 Msa1430130:CDS
TCAGGAAAGGTAGATTCTGT+TGG 0.537763 tig0026637:-30107 Msa1430130:CDS
GTAGACGAAGAAATTAATAC+AGG 0.538396 tig0026637:-29789 Msa1430130:CDS
GTGGACATAAATTGTTTGGA+CGG 0.566125 tig0026637:-30172 Msa1430130:CDS
TGGAGTATCAATCTCTTGGA+AGG 0.588423 tig0026637:-30334 Msa1430130:CDS
ACAACTTGGAGTTGAAGAGA+AGG 0.600247 tig0026637:-30039 Msa1430130:CDS
CAACTTGGAGTTGAAGAGAA+GGG 0.601023 tig0026637:-30038 Msa1430130:CDS
AATACTGAACACCAAGAACA+AGG 0.614953 tig0026637:-30926 None:intergenic
CTTGATTTGATATAACAACC+AGG 0.620765 tig0026637:+30244 None:intergenic
GTTTGCAATCAAGAAATAGG+TGG 0.639196 tig0026637:-29740 Msa1430130:CDS
AAATAATGGTGTAATAGATG+AGG 0.639630 tig0026637:-29979 Msa1430130:CDS
GAAAATGGTGTTCCGCCTGA+CGG 0.653575 tig0026637:-29939 Msa1430130:CDS
AATGGTGTTCCGCCTGACGG+TGG 0.691121 tig0026637:-29936 Msa1430130:CDS
CCGTTGAGAAAACAAAACAA+AGG 0.712405 tig0026637:-30879 Msa1430130:intron

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TAATGATATTGAAATGAATT+TGG - tig0026637:30821-30840 Msa1430130:intron 15.0%
!! TAATGATATTGAAATGAATT+TGG - tig0026637:30821-30840 Msa1430130:intron 15.0%
!! TTGTTACATAGAAAATTCAA+CGG + tig0026637:29845-29864 None:intergenic 20.0%
!! AAACTAAGAATCAAATCAAT+AGG + tig0026637:30048-30067 None:intergenic 20.0%
!!! CAACTTTTAGAATAGTAAAT+TGG - tig0026637:30757-30776 Msa1430130:intron 20.0%
!! TTGTTACATAGAAAATTCAA+CGG + tig0026637:29845-29864 None:intergenic 20.0%
!! AAACTAAGAATCAAATCAAT+AGG + tig0026637:30048-30067 None:intergenic 20.0%
!!! CAACTTTTAGAATAGTAAAT+TGG - tig0026637:30757-30776 Msa1430130:intron 20.0%
! GAAAATTCAACGGTAAAATA+AGG + tig0026637:29835-29854 None:intergenic 25.0%
! AAATCAATAGGCAAATATGT+TGG + tig0026637:30036-30055 None:intergenic 25.0%
!! AAAGAAAGACTTTTCTTTCA+TGG + tig0026637:30096-30115 None:intergenic 25.0%
! CATTAGTGTATATAGTTAGT+TGG - tig0026637:30165-30184 Msa1430130:CDS 25.0%
!!! AGTAACTTAACTTGTTGATT+TGG + tig0026637:30235-30254 None:intergenic 25.0%
! AAGACAGAAACAAAGAAATT+TGG - tig0026637:30435-30454 Msa1430130:intron 25.0%
!! AAAGAAAAAGAAGTACAACT+TGG - tig0026637:30603-30622 Msa1430130:intron 25.0%
! ATCTATTACACCATTATTTG+CGG + tig0026637:30676-30695 None:intergenic 25.0%
! AAATAATGGTGTAATAGATG+AGG - tig0026637:30677-30696 Msa1430130:intron 25.0%
! GATATTGAAATGAATTTGGA+AGG - tig0026637:30825-30844 Msa1430130:intron 25.0%
! GAAAATTCAACGGTAAAATA+AGG + tig0026637:29835-29854 None:intergenic 25.0%
! AAATCAATAGGCAAATATGT+TGG + tig0026637:30036-30055 None:intergenic 25.0%
!! AAAGAAAGACTTTTCTTTCA+TGG + tig0026637:30096-30115 None:intergenic 25.0%
! CATTAGTGTATATAGTTAGT+TGG - tig0026637:30165-30184 Msa1430130:CDS 25.0%
!!! AGTAACTTAACTTGTTGATT+TGG + tig0026637:30235-30254 None:intergenic 25.0%
! AAGACAGAAACAAAGAAATT+TGG - tig0026637:30435-30454 Msa1430130:intron 25.0%
!! AAAGAAAAAGAAGTACAACT+TGG - tig0026637:30603-30622 Msa1430130:intron 25.0%
! ATCTATTACACCATTATTTG+CGG + tig0026637:30676-30695 None:intergenic 25.0%
! AAATAATGGTGTAATAGATG+AGG - tig0026637:30677-30696 Msa1430130:intron 25.0%
! GATATTGAAATGAATTTGGA+AGG - tig0026637:30825-30844 Msa1430130:intron 25.0%
!!! CCTTTGTTTTGTTTTCTCAA+CGG + tig0026637:29780-29799 None:intergenic 30.0%
GATAGATAGTTAAGAGTTGT+TGG - tig0026637:29986-30005 Msa1430130:CDS 30.0%
TAGATCAGATAAACATTCAG+AGG + tig0026637:30274-30293 None:intergenic 30.0%
GTTGAATTAATGCAGAAGAA+TGG - tig0026637:30302-30321 Msa1430130:CDS 30.0%
!!! ATTGAAGATGATGCTACTTT+TGG - tig0026637:30380-30399 Msa1430130:intron 30.0%
! CTTGATTTGATATAACAACC+AGG + tig0026637:30415-30434 None:intergenic 30.0%
ATAAATTGTTTGGACGGAAA+GGG - tig0026637:30490-30509 Msa1430130:intron 30.0%
AAACAAGATGCAGAAAAATG+AGG - tig0026637:30641-30660 Msa1430130:intron 30.0%
! CATTTTCATCATGAAAGCTT+TGG + tig0026637:30704-30723 None:intergenic 30.0%
CAAAGCTTTCATGATGAAAA+TGG - tig0026637:30702-30721 Msa1430130:intron 30.0%
AGTATTTATGAAGTCACGTA+TGG - tig0026637:30792-30811 Msa1430130:intron 30.0%
GTAGACGAAGAAATTAATAC+AGG - tig0026637:30867-30886 Msa1430130:intron 30.0%
!!! CCTTTGTTTTGTTTTCTCAA+CGG + tig0026637:29780-29799 None:intergenic 30.0%
GATAGATAGTTAAGAGTTGT+TGG - tig0026637:29986-30005 Msa1430130:CDS 30.0%
TAGATCAGATAAACATTCAG+AGG + tig0026637:30274-30293 None:intergenic 30.0%
GTTGAATTAATGCAGAAGAA+TGG - tig0026637:30302-30321 Msa1430130:CDS 30.0%
!!! ATTGAAGATGATGCTACTTT+TGG - tig0026637:30380-30399 Msa1430130:intron 30.0%
! CTTGATTTGATATAACAACC+AGG + tig0026637:30415-30434 None:intergenic 30.0%
ATAAATTGTTTGGACGGAAA+GGG - tig0026637:30490-30509 Msa1430130:intron 30.0%
AAACAAGATGCAGAAAAATG+AGG - tig0026637:30641-30660 Msa1430130:intron 30.0%
! CATTTTCATCATGAAAGCTT+TGG + tig0026637:30704-30723 None:intergenic 30.0%
CAAAGCTTTCATGATGAAAA+TGG - tig0026637:30702-30721 Msa1430130:intron 30.0%
AGTATTTATGAAGTCACGTA+TGG - tig0026637:30792-30811 Msa1430130:intron 30.0%
GTAGACGAAGAAATTAATAC+AGG - tig0026637:30867-30886 Msa1430130:intron 30.0%
TTTCTTGTCTTCCTTGTTCT+TGG + tig0026637:29744-29763 None:intergenic 35.0%
CCGTTGAGAAAACAAAACAA+AGG - tig0026637:29777-29796 Msa1430130:CDS 35.0%
CATGATGATTGATGGGAAAT+TGG + tig0026637:29922-29941 None:intergenic 35.0%
CAATTTCCCATCAATCATCA+TGG - tig0026637:29920-29939 Msa1430130:CDS 35.0%
TTGTAGCCATGATGATTGAT+GGG + tig0026637:29929-29948 None:intergenic 35.0%
ATTGTAGCCATGATGATTGA+TGG + tig0026637:29930-29949 None:intergenic 35.0%
GAGTTGTTGGAAATCATACT+TGG - tig0026637:29999-30018 Msa1430130:CDS 35.0%
! AGTCTTTCTTTTCCTACGTT+TGG - tig0026637:30105-30124 Msa1430130:CDS 35.0%
! GTCTTTCTTTTCCTACGTTT+GGG - tig0026637:30106-30125 Msa1430130:CDS 35.0%
! TTTTGCATTTGCAACAAGAG+AGG + tig0026637:30201-30220 None:intergenic 35.0%
! AGAATGGAGTATCAATCTCT+TGG - tig0026637:30318-30337 Msa1430130:CDS 35.0%
!! GAAGGTACCAAAAACCAAAA+GGG - tig0026637:30340-30359 Msa1430130:CDS 35.0%
! TGTTTTACGTTAGACCCTTT+TGG + tig0026637:30357-30376 None:intergenic 35.0%
AAAAGGGTCTAACGTAAAAC+AGG - tig0026637:30356-30375 Msa1430130:intron 35.0%
!! ATTCAAATCAAGCTTGTTGC+TGG - tig0026637:30459-30478 Msa1430130:intron 35.0%
GGATGTGGACATAAATTGTT+TGG - tig0026637:30480-30499 Msa1430130:intron 35.0%
GTGGACATAAATTGTTTGGA+CGG - tig0026637:30484-30503 Msa1430130:intron 35.0%
CATAAATTGTTTGGACGGAA+AGG - tig0026637:30489-30508 Msa1430130:intron 35.0%
ACTGTTCATGTTGATACTTC+AGG - tig0026637:30894-30913 Msa1430130:CDS 35.0%
CAGGTTTGCAATCAAGAAAT+AGG - tig0026637:30913-30932 Msa1430130:CDS 35.0%
GTTTGCAATCAAGAAATAGG+TGG - tig0026637:30916-30935 Msa1430130:CDS 35.0%
TTTCTTGTCTTCCTTGTTCT+TGG + tig0026637:29744-29763 None:intergenic 35.0%
CCGTTGAGAAAACAAAACAA+AGG - tig0026637:29777-29796 Msa1430130:CDS 35.0%
CATGATGATTGATGGGAAAT+TGG + tig0026637:29922-29941 None:intergenic 35.0%
CAATTTCCCATCAATCATCA+TGG - tig0026637:29920-29939 Msa1430130:CDS 35.0%
TTGTAGCCATGATGATTGAT+GGG + tig0026637:29929-29948 None:intergenic 35.0%
ATTGTAGCCATGATGATTGA+TGG + tig0026637:29930-29949 None:intergenic 35.0%
GAGTTGTTGGAAATCATACT+TGG - tig0026637:29999-30018 Msa1430130:CDS 35.0%
! AGTCTTTCTTTTCCTACGTT+TGG - tig0026637:30105-30124 Msa1430130:CDS 35.0%
! GTCTTTCTTTTCCTACGTTT+GGG - tig0026637:30106-30125 Msa1430130:CDS 35.0%
! TTTTGCATTTGCAACAAGAG+AGG + tig0026637:30201-30220 None:intergenic 35.0%
! AGAATGGAGTATCAATCTCT+TGG - tig0026637:30318-30337 Msa1430130:CDS 35.0%
!! GAAGGTACCAAAAACCAAAA+GGG - tig0026637:30340-30359 Msa1430130:CDS 35.0%
! TGTTTTACGTTAGACCCTTT+TGG + tig0026637:30357-30376 None:intergenic 35.0%
AAAAGGGTCTAACGTAAAAC+AGG - tig0026637:30356-30375 Msa1430130:intron 35.0%
!! ATTCAAATCAAGCTTGTTGC+TGG - tig0026637:30459-30478 Msa1430130:intron 35.0%
GGATGTGGACATAAATTGTT+TGG - tig0026637:30480-30499 Msa1430130:intron 35.0%
GTGGACATAAATTGTTTGGA+CGG - tig0026637:30484-30503 Msa1430130:intron 35.0%
CATAAATTGTTTGGACGGAA+AGG - tig0026637:30489-30508 Msa1430130:intron 35.0%
ACTGTTCATGTTGATACTTC+AGG - tig0026637:30894-30913 Msa1430130:CDS 35.0%
CAGGTTTGCAATCAAGAAAT+AGG - tig0026637:30913-30932 Msa1430130:CDS 35.0%
GTTTGCAATCAAGAAATAGG+TGG - tig0026637:30916-30935 Msa1430130:CDS 35.0%
! TGTTTTCTCAACGGAGAAAG+TGG + tig0026637:29771-29790 None:intergenic 40.0%
AAGTCAAACAACCCAAACGT+AGG + tig0026637:30120-30139 None:intergenic 40.0%
! TGGAGTATCAATCTCTTGGA+AGG - tig0026637:30322-30341 Msa1430130:CDS 40.0%
!! GGAAGGTACCAAAAACCAAA+AGG - tig0026637:30339-30358 Msa1430130:CDS 40.0%
!!! CGTTAGACCCTTTTGGTTTT+TGG + tig0026637:30350-30369 None:intergenic 40.0%
TCAGGAAAAGCTCTTTCATC+GGG + tig0026637:30528-30547 None:intergenic 40.0%
GTCAGGAAAAGCTCTTTCAT+CGG + tig0026637:30529-30548 None:intergenic 40.0%
TCAGGAAAGGTAGATTCTGT+TGG - tig0026637:30549-30568 Msa1430130:intron 40.0%
ACAACTTGGAGTTGAAGAGA+AGG - tig0026637:30617-30636 Msa1430130:intron 40.0%
CAACTTGGAGTTGAAGAGAA+GGG - tig0026637:30618-30637 Msa1430130:intron 40.0%
CAAGATGCAGAAAAATGAGG+TGG - tig0026637:30644-30663 Msa1430130:intron 40.0%
! TGTTTTCTCAACGGAGAAAG+TGG + tig0026637:29771-29790 None:intergenic 40.0%
AAGTCAAACAACCCAAACGT+AGG + tig0026637:30120-30139 None:intergenic 40.0%
! TGGAGTATCAATCTCTTGGA+AGG - tig0026637:30322-30341 Msa1430130:CDS 40.0%
!! GGAAGGTACCAAAAACCAAA+AGG - tig0026637:30339-30358 Msa1430130:CDS 40.0%
!!! CGTTAGACCCTTTTGGTTTT+TGG + tig0026637:30350-30369 None:intergenic 40.0%
TCAGGAAAAGCTCTTTCATC+GGG + tig0026637:30528-30547 None:intergenic 40.0%
GTCAGGAAAAGCTCTTTCAT+CGG + tig0026637:30529-30548 None:intergenic 40.0%
TCAGGAAAGGTAGATTCTGT+TGG - tig0026637:30549-30568 Msa1430130:intron 40.0%
ACAACTTGGAGTTGAAGAGA+AGG - tig0026637:30617-30636 Msa1430130:intron 40.0%
CAACTTGGAGTTGAAGAGAA+GGG - tig0026637:30618-30637 Msa1430130:intron 40.0%
CAAGATGCAGAAAAATGAGG+TGG - tig0026637:30644-30663 Msa1430130:intron 40.0%
!! TACTTTTGGCTGTTTGTGCC+TGG - tig0026637:30394-30413 Msa1430130:intron 45.0%
!! ATCAAGCTTGTTGCTGGATG+TGG - tig0026637:30465-30484 Msa1430130:intron 45.0%
! GAAAGAGCTTTTCCTGACTC+AGG - tig0026637:30531-30550 Msa1430130:intron 45.0%
! AGCTTTTCCTGACTCAGGAA+AGG - tig0026637:30536-30555 Msa1430130:intron 45.0%
GAATCTACCTTTCCTGAGTC+AGG + tig0026637:30546-30565 None:intergenic 45.0%
! ATGTTTTCTTCACCACCGTC+AGG + tig0026637:30735-30754 None:intergenic 45.0%
!! TACTTTTGGCTGTTTGTGCC+TGG - tig0026637:30394-30413 Msa1430130:intron 45.0%
!! ATCAAGCTTGTTGCTGGATG+TGG - tig0026637:30465-30484 Msa1430130:intron 45.0%
! GAAAGAGCTTTTCCTGACTC+AGG - tig0026637:30531-30550 Msa1430130:intron 45.0%
! AGCTTTTCCTGACTCAGGAA+AGG - tig0026637:30536-30555 Msa1430130:intron 45.0%
GAATCTACCTTTCCTGAGTC+AGG + tig0026637:30546-30565 None:intergenic 45.0%
! ATGTTTTCTTCACCACCGTC+AGG + tig0026637:30735-30754 None:intergenic 45.0%
!! GTGGAGAGTGCCGCAAATAA+TGG - tig0026637:30663-30682 Msa1430130:intron 50.0%
GAAAATGGTGTTCCGCCTGA+CGG - tig0026637:30717-30736 Msa1430130:intron 50.0%
! TTTTCTTCACCACCGTCAGG+CGG + tig0026637:30732-30751 None:intergenic 50.0%
!! GTGGAGAGTGCCGCAAATAA+TGG - tig0026637:30663-30682 Msa1430130:intron 50.0%
GAAAATGGTGTTCCGCCTGA+CGG - tig0026637:30717-30736 Msa1430130:intron 50.0%
! TTTTCTTCACCACCGTCAGG+CGG + tig0026637:30732-30751 None:intergenic 50.0%
AATGGTGTTCCGCCTGACGG+TGG - tig0026637:30720-30739 Msa1430130:intron 60.0%
AATGGTGTTCCGCCTGACGG+TGG - tig0026637:30720-30739 Msa1430130:intron 60.0%
Chromosome Type Strat End Strand Name
tig0026637 gene 29734 30944 29734 ID=Msa1430130;Name=Msa1430130
tig0026637 mRNA 29734 30944 29734 ID=Msa1430130-mRNA-1;Parent=Msa1430130;Name=Msa1430130-mRNA-1;_AED=0.30;_eAED=0.30;_QI=0|1|0|1|0|0|2|0|230
tig0026637 exon 30880 30944 30880 ID=Msa1430130-mRNA-1:exon:6848;Parent=Msa1430130-mRNA-1
tig0026637 exon 29734 30361 29734 ID=Msa1430130-mRNA-1:exon:6847;Parent=Msa1430130-mRNA-1
tig0026637 CDS 30880 30944 30880 ID=Msa1430130-mRNA-1:cds;Parent=Msa1430130-mRNA-1
tig0026637 CDS 29734 30361 29734 ID=Msa1430130-mRNA-1:cds;Parent=Msa1430130-mRNA-1
Gene Sequence

>Msa1430130

CTGAACACCAAGAACAAGGAAGACAAGAAAGAAACCACTTTCTCCGTTGAGAAAACAAAACAAAGAAGAATGGAGTATCAATCTCTTGGAAGGTACCAAAAACCAAAAGGGTCTAACGTAAAACAGGTATTGAAGATGATGCTACTTTTGGCTGTTTGTGCCTGGTTGTTATATCAAATCAAGAAGACAGAAACAAAGAAATTTGGTATTCAAATCAAGCTTGTTGCTGGATGTGGACATAAATTGTTTGGACGGAAAGGGATGCTATCACGTCCCGATGAAAGAGCTTTTCCTGACTCAGGAAAGGTAGATTCTGTTGGAGAAGTAACAAATGAGTTTAAAAGTAATGACAAAGAAAAAGAAGTACAACTTGGAGTTGAAGAGAAGGGAAACAAGATGCAGAAAAATGAGGTGGAGAGTGCCGCAAATAATGGTGTAATAGATGAGGTCCAAAGCTTTCATGATGAAAATGGTGTTCCGCCTGACGGTGGTGAAGAAAACATGTCAACTTTTAGAATAGTAAATTGGCTTAAAAAGATCAGTATTTATGAAGTCACGTATGGAGAAGATAATGATATTGAAATGAATTTGGAAGGAACGACGAATGCTACAACAGTAGACGAAGAAATTAATACAGGAACTACTGTTCATGTTGATACTTCAGGTTTGCAATCAAGAAATAGGTGGAGATAA

Protein sequence

>Msa1430130

LNTKNKEDKKETTFSVEKTKQRRMEYQSLGRYQKPKGSNVKQVLKMMLLLAVCAWLLYQIKKTETKKFGIQIKLVAGCGHKLFGRKGMLSRPDERAFPDSGKVDSVGEVTNEFKSNDKEKEVQLGVEEKGNKMQKNEVESAANNGVIDEVQSFHDENGVPPDGGEENMSTFRIVNWLKKISIYEVTYGEDNDIEMNLEGTTNATTVDEEINTGTTVHVDTSGLQSRNRWR*