AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1088790

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1088790 MtrunA17_Chr8g0359161 96.569 204 7 0 1 204 1 204 1.03e-147 408
Msa1088790 MtrunA17_Chr8g0359111 66.832 202 67 0 3 204 1 202 1.50e-103 296
Msa1088790 MtrunA17_Chr1g0173431 68.317 202 61 2 5 204 1 201 4.63e-98 283
Msa1088790 MtrunA17_Chr4g0022761 67.327 202 60 2 5 204 1 198 1.82e-94 273
Msa1088790 MtrunA17_Chr3g0082651 66.667 204 63 3 5 204 1 203 4.02e-94 273
Msa1088790 MtrunA17_Chr3g0082661 67.157 204 62 3 5 204 1 203 5.00e-94 273
Msa1088790 MtrunA17_Chr3g0082681 66.667 204 63 3 5 204 1 203 8.74e-94 272
Msa1088790 MtrunA17_Chr3g0082641 65.686 204 67 2 3 204 1 203 1.70e-93 271
Msa1088790 MtrunA17_Chr3g0082671 65.686 204 67 2 3 204 1 203 6.48e-93 270
Msa1088790 MtrunA17_Chr4g0022751 63.366 202 72 1 5 204 1 202 2.05e-90 263
Msa1088790 MtrunA17_Chr7g0269461 63.054 203 72 3 3 204 1 201 5.23e-89 260
Msa1088790 MtrunA17_Chr2g0314441 55.789 190 71 3 16 201 15 195 2.58e-71 215
Msa1088790 MtrunA17_Chr2g0314431 45.274 201 84 7 5 193 1 187 8.02e-45 147
Msa1088790 MtrunA17_Chr6g0482041 33.511 188 104 8 29 202 30 210 2.39e-17 77.0
Msa1088790 MtrunA17_Chr6g0481911 28.351 194 123 9 9 193 4 190 8.08e-14 67.4
Msa1088790 MtrunA17_Chr6g0467771 29.775 178 113 6 29 201 31 201 5.75e-12 62.8
Msa1088790 MtrunA17_Chr6g0481941 28.571 203 124 10 1 193 1 192 5.00e-11 59.7
Msa1088790 MtrunA17_Chr6g0467761 29.545 176 117 6 29 201 32 203 6.84e-11 59.7
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1088790 AT1G17860.1 30.481 187 115 6 20 203 20 194 1.60e-15 72.0
Msa1088790 AT1G73260.1 31.548 168 106 7 41 203 41 204 5.81e-14 68.2

Find 54 sgRNAs with CRISPR-Local

Find 57 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GATCATATGGTAACTTCTTT+AGG 0.202488 7_3:-2150138 Msa1088790:CDS
CCTCCTTTGTTTGTGATAAC+TGG 0.265337 7_3:+2150424 None:intergenic
ATCACGACTTCGACGATGTT+AGG 0.298935 7_3:-2150294 Msa1088790:CDS
CGACTGTGTCGAAGACAAAC+TGG 0.334067 7_3:+2150485 None:intergenic
TATTCCTCGTCGCCTTCAAC+TGG 0.432772 7_3:+2150457 None:intergenic
AGTGCTACTAATGGATCATA+TGG 0.432987 7_3:-2150151 Msa1088790:CDS
GGAAGAGATAGTGCTACTAA+TGG 0.447916 7_3:-2150160 Msa1088790:CDS
GGTCTTGAGAACACTGGCTT+AGG 0.457139 7_3:-2150355 Msa1088790:CDS
TTCTCAAGACCAACATGTAA+AGG 0.464201 7_3:+2150367 None:intergenic
TCACGACTTCGACGATGTTA+GGG 0.467925 7_3:-2150293 Msa1088790:CDS
TTCATTTCTGCTGATCATAG+TGG 0.471060 7_3:+2150396 None:intergenic
ATACATGAGCAAGAATTATG+AGG 0.476793 7_3:+2150536 None:intergenic
CAATCAACAGAATGGAGATT+GGG 0.482818 7_3:-2150223 Msa1088790:CDS
AGGGAGGGGACCACCATCAA+GGG 0.484944 7_3:+2149991 None:intergenic
GAGGGAGGGGACCACCATCA+AGG 0.485248 7_3:+2149990 None:intergenic
GGAAGAAGGTTGATTATCAC+TGG 0.495698 7_3:-2150181 Msa1088790:CDS
TTCTGGAAAACAAGAGGGAG+GGG 0.496214 7_3:+2149977 None:intergenic
GTACACAACTTGATGAAGCT+TGG 0.498312 7_3:+2150245 None:intergenic
AAGTCGTGATGGGGAGCAAA+AGG 0.500088 7_3:+2150307 None:intergenic
TCTCAAGACCAACATGTAAA+GGG 0.503765 7_3:+2150368 None:intergenic
ACAATCAACAGAATGGAGAT+TGG 0.508137 7_3:-2150224 Msa1088790:CDS
AACATCGTCGAAGTCGTGAT+GGG 0.515072 7_3:+2150297 None:intergenic
ATTGTAGAGACCCCACTTGA+AGG 0.515965 7_3:-2150115 Msa1088790:CDS
CACTGGCTTAGGACACGGTC+TGG 0.532480 7_3:-2150344 Msa1088790:CDS
CAACTAGGACATACCTCTGT+AGG 0.534967 7_3:+2150070 None:intergenic
GAATCATGCCCTTTACATGT+TGG 0.540282 7_3:-2150376 Msa1088790:CDS
GTTGTGTACAATCAACAGAA+TGG 0.542722 7_3:-2150231 Msa1088790:CDS
TAACATCGTCGAAGTCGTGA+TGG 0.545399 7_3:+2150296 None:intergenic
GACTGTGTCGAAGACAAACT+GGG 0.554983 7_3:+2150486 None:intergenic
ATTCTTTCTGGAAAACAAGA+GGG 0.555637 7_3:+2149972 None:intergenic
CTTTGTTTGTGATAACTGGA+CGG 0.556090 7_3:+2150428 None:intergenic
GTTGATATGCTGAATGAGAA+TGG 0.566614 7_3:-2150028 Msa1088790:CDS
AAGATACTAAGAGTGGAAGA+AGG 0.571477 7_3:-2150195 Msa1088790:CDS
CCACATTCAAATCTACAACT+AGG 0.573570 7_3:+2150055 None:intergenic
TTTCTGGAAAACAAGAGGGA+GGG 0.581340 7_3:+2149976 None:intergenic
TATTCTTTCTGGAAAACAAG+AGG 0.582397 7_3:+2149971 None:intergenic
CAGTTTGTCTTCGACACAGT+CGG 0.584758 7_3:-2150484 Msa1088790:CDS
TACATGAGCAAGAATTATGA+GGG 0.589317 7_3:+2150537 None:intergenic
TATTATACATACCTTCAAGT+GGG 0.589842 7_3:+2150104 None:intergenic
AAACTGGGCTATTGTTGTTG+TGG 0.592731 7_3:+2150501 None:intergenic
CGTCCAGTTATCACAAACAA+AGG 0.595247 7_3:-2150427 Msa1088790:CDS
ACAGTCGGAGAACCAGTTGA+AGG 0.605474 7_3:-2150469 Msa1088790:CDS
CATGTTGGTCTTGAGAACAC+TGG 0.606261 7_3:-2150361 Msa1088790:CDS
AGTAGATAATCTCATTGACA+TGG 0.610571 7_3:+2150564 None:intergenic
ACATCGTCGAAGTCGTGATG+GGG 0.622395 7_3:+2150298 None:intergenic
GAGAACACTGGCTTAGGACA+CGG 0.624273 7_3:-2150349 Msa1088790:CDS
CTTTCTGGAAAACAAGAGGG+AGG 0.626753 7_3:+2149975 None:intergenic
ATATTATACATACCTTCAAG+TGG 0.635907 7_3:+2150103 None:intergenic
CCTAGTTGTAGATTTGAATG+TGG 0.636625 7_3:-2150055 Msa1088790:CDS
TATACAGTGGTGTCCTACAG+AGG 0.674639 7_3:-2150083 Msa1088790:CDS
ATTATACATACCTTCAAGTG+GGG 0.680213 7_3:+2150105 None:intergenic
AGAACCAGTTGAAGGCGACG+AGG 0.683558 7_3:-2150461 Msa1088790:CDS
CCAGTTATCACAAACAAAGG+AGG 0.688592 7_3:-2150424 Msa1088790:CDS
AAGGTATGTATAATATACAG+TGG 0.689864 7_3:-2150096 Msa1088790:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! TATTATACATACCTTCAAGT+GGG + chr7_3:2150431-2150450 None:intergenic 25.0%
! ATATTATACATACCTTCAAG+TGG + chr7_3:2150432-2150451 None:intergenic 25.0%
! AAGGTATGTATAATATACAG+TGG - chr7_3:2150436-2150455 Msa1088790:CDS 25.0%
TACATGAGCAAGAATTATGA+GGG + chr7_3:2149998-2150017 None:intergenic 30.0%
ATACATGAGCAAGAATTATG+AGG + chr7_3:2149999-2150018 None:intergenic 30.0%
GATCATATGGTAACTTCTTT+AGG - chr7_3:2150394-2150413 Msa1088790:CDS 30.0%
ATTATACATACCTTCAAGTG+GGG + chr7_3:2150430-2150449 None:intergenic 30.0%
! ATTCTTTCTGGAAAACAAGA+GGG + chr7_3:2150563-2150582 None:intergenic 30.0%
! TATTCTTTCTGGAAAACAAG+AGG + chr7_3:2150564-2150583 None:intergenic 30.0%
! CTTTGTTTGTGATAACTGGA+CGG + chr7_3:2150107-2150126 None:intergenic 35.0%
TTCATTTCTGCTGATCATAG+TGG + chr7_3:2150139-2150158 None:intergenic 35.0%
TCTCAAGACCAACATGTAAA+GGG + chr7_3:2150167-2150186 None:intergenic 35.0%
TTCTCAAGACCAACATGTAA+AGG + chr7_3:2150168-2150187 None:intergenic 35.0%
GTTGTGTACAATCAACAGAA+TGG - chr7_3:2150301-2150320 Msa1088790:CDS 35.0%
ACAATCAACAGAATGGAGAT+TGG - chr7_3:2150308-2150327 Msa1088790:CDS 35.0%
CAATCAACAGAATGGAGATT+GGG - chr7_3:2150309-2150328 Msa1088790:CDS 35.0%
GGTGAAAAAGATACTAAGAG+TGG - chr7_3:2150330-2150349 Msa1088790:CDS 35.0%
AAGATACTAAGAGTGGAAGA+AGG - chr7_3:2150337-2150356 Msa1088790:CDS 35.0%
! AGTGCTACTAATGGATCATA+TGG - chr7_3:2150381-2150400 Msa1088790:CDS 35.0%
CCACATTCAAATCTACAACT+AGG + chr7_3:2150480-2150499 None:intergenic 35.0%
CCTAGTTGTAGATTTGAATG+TGG - chr7_3:2150477-2150496 Msa1088790:CDS 35.0%
GTTGATATGCTGAATGAGAA+TGG - chr7_3:2150504-2150523 Msa1088790:CDS 35.0%
! TGAGAATGGTAAGATTTTGC+TGG - chr7_3:2150518-2150537 Msa1088790:CDS 35.0%
! AAACTGGGCTATTGTTGTTG+TGG + chr7_3:2150034-2150053 None:intergenic 40.0%
CGTCCAGTTATCACAAACAA+AGG - chr7_3:2150105-2150124 Msa1088790:CDS 40.0%
! CCTCCTTTGTTTGTGATAAC+TGG + chr7_3:2150111-2150130 None:intergenic 40.0%
CCAGTTATCACAAACAAAGG+AGG - chr7_3:2150108-2150127 Msa1088790:CDS 40.0%
GAATCATGCCCTTTACATGT+TGG - chr7_3:2150156-2150175 Msa1088790:CDS 40.0%
GTACACAACTTGATGAAGCT+TGG + chr7_3:2150290-2150309 None:intergenic 40.0%
! GGAAGAAGGTTGATTATCAC+TGG - chr7_3:2150351-2150370 Msa1088790:CDS 40.0%
! GGAAGAGATAGTGCTACTAA+TGG - chr7_3:2150372-2150391 Msa1088790:CDS 40.0%
! TTTCTGGAAAACAAGAGGGA+GGG + chr7_3:2150559-2150578 None:intergenic 40.0%
GACTGTGTCGAAGACAAACT+GGG + chr7_3:2150049-2150068 None:intergenic 45.0%
CAGTTTGTCTTCGACACAGT+CGG - chr7_3:2150048-2150067 Msa1088790:CDS 45.0%
!! CATGTTGGTCTTGAGAACAC+TGG - chr7_3:2150171-2150190 Msa1088790:CDS 45.0%
AACATCGTCGAAGTCGTGAT+GGG + chr7_3:2150238-2150257 None:intergenic 45.0%
TAACATCGTCGAAGTCGTGA+TGG + chr7_3:2150239-2150258 None:intergenic 45.0%
ATCACGACTTCGACGATGTT+AGG - chr7_3:2150238-2150257 Msa1088790:CDS 45.0%
TCACGACTTCGACGATGTTA+GGG - chr7_3:2150239-2150258 Msa1088790:CDS 45.0%
ATTGTAGAGACCCCACTTGA+AGG - chr7_3:2150417-2150436 Msa1088790:CDS 45.0%
TATACAGTGGTGTCCTACAG+AGG - chr7_3:2150449-2150468 Msa1088790:CDS 45.0%
CAACTAGGACATACCTCTGT+AGG + chr7_3:2150465-2150484 None:intergenic 45.0%
! AAGATTTTGCTGGCCCTTGA+TGG - chr7_3:2150528-2150547 Msa1088790:CDS 45.0%
! TTCTGGAAAACAAGAGGGAG+GGG + chr7_3:2150558-2150577 None:intergenic 45.0%
! CTTTCTGGAAAACAAGAGGG+AGG + chr7_3:2150560-2150579 None:intergenic 45.0%
CGACTGTGTCGAAGACAAAC+TGG + chr7_3:2150050-2150069 None:intergenic 50.0%
ACAGTCGGAGAACCAGTTGA+AGG - chr7_3:2150063-2150082 Msa1088790:CDS 50.0%
TATTCCTCGTCGCCTTCAAC+TGG + chr7_3:2150078-2150097 None:intergenic 50.0%
!! GGTCTTGAGAACACTGGCTT+AGG - chr7_3:2150177-2150196 Msa1088790:CDS 50.0%
!! GAGAACACTGGCTTAGGACA+CGG - chr7_3:2150183-2150202 Msa1088790:CDS 50.0%
! AAGTCGTGATGGGGAGCAAA+AGG + chr7_3:2150228-2150247 None:intergenic 50.0%
ACATCGTCGAAGTCGTGATG+GGG + chr7_3:2150237-2150256 None:intergenic 50.0%
! ATTTTGCTGGCCCTTGATGG+TGG - chr7_3:2150531-2150550 Msa1088790:CDS 50.0%
AGAACCAGTTGAAGGCGACG+AGG - chr7_3:2150071-2150090 Msa1088790:CDS 55.0%
!! CACTGGCTTAGGACACGGTC+TGG - chr7_3:2150188-2150207 Msa1088790:CDS 60.0%
AGGGAGGGGACCACCATCAA+GGG + chr7_3:2150544-2150563 None:intergenic 60.0%
GAGGGAGGGGACCACCATCA+AGG + chr7_3:2150545-2150564 None:intergenic 65.0%
Chromosome Type Strat End Strand Name
chr7_3 gene 2149970 2150584 2149970 ID=Msa1088790;Name=Msa1088790
chr7_3 mRNA 2149970 2150584 2149970 ID=Msa1088790-mRNA-1;Parent=Msa1088790;Name=Msa1088790-mRNA-1;_AED=0.19;_eAED=0.19;_QI=0|-1|0|1|-1|1|1|0|204
chr7_3 exon 2149970 2150584 2149970 ID=Msa1088790-mRNA-1:exon:859;Parent=Msa1088790-mRNA-1
chr7_3 CDS 2149970 2150584 2149970 ID=Msa1088790-mRNA-1:cds;Parent=Msa1088790-mRNA-1
Gene Sequence

>Msa1088790

ATGTCAATGAGATTATCTACTAGAACCCTCATAATTCTTGCTCATGTATGTCTCTTTATAACCACAACAACAATAGCCCAGTTTGTCTTCGACACAGTCGGAGAACCAGTTGAAGGCGACGAGGAATATTTTATCCGTCCAGTTATCACAAACAAAGGAGGACGTTCCACTATGATCAGCAGAAATGAATCATGCCCTTTACATGTTGGTCTTGAGAACACTGGCTTAGGACACGGTCTGGTTGTGAAATTCACACCTTTTGCTCCCCATCACGACTTCGACGATGTTAGGGTTAACAGAGACTTAAGAATAACATTCCAAGCTTCATCAAGTTGTGTACAATCAACAGAATGGAGATTGGGTGAAAAAGATACTAAGAGTGGAAGAAGGTTGATTATCACTGGAAGAGATAGTGCTACTAATGGATCATATGGTAACTTCTTTAGGATTGTAGAGACCCCACTTGAAGGTATGTATAATATACAGTGGTGTCCTACAGAGGTATGTCCTAGTTGTAGATTTGAATGTGGAACTGTTGATATGCTGAATGAGAATGGTAAGATTTTGCTGGCCCTTGATGGTGGTCCCCTCCCTCTTGTTTTCCAGAAAGAATAA
Protein sequence

>Msa1088790

MSMRLSTRTLIILAHVCLFITTTTIAQFVFDTVGEPVEGDEEYFIRPVITNKGGRSTMISRNESCPLHVGLENTGLGHGLVVKFTPFAPHHDFDDVRVNRDLRITFQASSSCVQSTEWRLGEKDTKSGRRLIITGRDSATNGSYGNFFRIVETPLEGMYNIQWCPTEVCPSCRFECGTVDMLNENGKILLALDGGPLPLVFQKE*