AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene046062

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene046062.t1 MTR_4g045977 81.395 344 42 4 1 333 1 333 0.0 546
MS.gene046062.t1 MTR_4g045977 66.667 63 12 2 224 286 329 382 1.28e-13 71.6
MS.gene046062.t1 MTR_4g107170 53.265 291 86 4 1 277 1 255 3.49e-97 288
MS.gene046062.t1 MTR_2g049610 47.619 210 103 4 1 209 1 204 4.78e-61 195
MS.gene046062.t1 MTR_1g115290 57.576 165 49 4 38 200 2 147 6.99e-56 179
MS.gene046062.t1 MTR_2g049630 36.438 365 152 12 2 287 4 367 5.38e-53 179
MS.gene046062.t1 MTR_2g049530 46.561 189 95 3 3 190 5 188 6.94e-50 165
MS.gene046062.t1 MTR_6g005440 37.113 194 108 3 1 190 1 184 5.83e-36 132
MS.gene046062.t1 MTR_6g018920 34.197 193 124 1 1 190 1 193 3.27e-32 123
MS.gene046062.t1 MTR_1g114730 35.323 201 126 2 1 198 1 200 1.70e-31 121
MS.gene046062.t1 MTR_6g005450 36.471 170 105 1 1 167 1 170 6.12e-30 117
MS.gene046062.t1 MTR_2g016210 25.641 156 106 2 1 148 1 154 4.54e-13 68.6
MS.gene046062.t1 MTR_3g466980 28.676 136 91 4 1 135 1 131 8.72e-13 67.4
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene046062.t1 AT5G55690 32.877 146 87 2 1 142 1 139 9.57e-16 76.6
MS.gene046062.t1 AT5G55690 32.877 146 87 2 1 142 1 139 9.57e-16 76.6

Find 52 sgRNAs with CRISPR-Local

Find 63 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GCATTCAGATTTCCTTAATA+TGG 0.236107 4.4:+57100490 MS.gene046062:CDS
TTTACAATTGTAGGGTCTTC+TGG 0.267825 4.4:-57100317 None:intergenic
GTGAAGAGGGCAATGAAATT+TGG 0.269654 4.4:+57101122 MS.gene046062:CDS
TTGTGGACATCAAATATTTC+AGG 0.290143 4.4:-57100383 None:intergenic
CAATGCTCTCATGCAAAATA+TGG 0.294005 4.4:+57100628 MS.gene046062:CDS
TCTAAATTTGTTAGCAAGAC+TGG 0.334083 4.4:+57100233 MS.gene046062:CDS
AAGTTGGATACTTCTTCTTA+AGG 0.361888 4.4:-57100466 None:intergenic
TTTAACCAATCGTCAAAATC+AGG 0.377207 4.4:-57100875 None:intergenic
AGTTGGATACTTCTTCTTAA+GGG 0.378758 4.4:-57100465 None:intergenic
ATGATTGATTTCACTAATCT+TGG 0.384115 4.4:+57100812 MS.gene046062:CDS
GGGTCTTCTGGCCATGTCAT+TGG 0.398342 4.4:-57100305 None:intergenic
TCTTAATTTCAAAGTATTTG+TGG 0.402565 4.4:-57100400 None:intergenic
AACTTAGCCAACCACATGAT+TGG 0.404058 4.4:+57101035 MS.gene046062:CDS
TCTTTCCATGCAAACTGATC+AGG 0.410075 4.4:-57100935 None:intergenic
TGATGTGTTGTTGCATTTGA+GGG 0.426219 4.4:-57100712 None:intergenic
GAGGGCAATGCAAGTTATCT+TGG 0.432079 4.4:+57100983 MS.gene046062:CDS
TGCTATGCATGGCGTTAACT+TGG 0.433866 4.4:-57100682 None:intergenic
AAGGGTATCTTTCCTCACTT+TGG 0.441633 4.4:-57100447 None:intergenic
TTGATGTGTTGTTGCATTTG+AGG 0.449551 4.4:-57100713 None:intergenic
AGCATGGAGTTTACAATTGT+AGG 0.450184 4.4:-57100326 None:intergenic
ATGAGGCAAATCAACATGAT+TGG 0.473560 4.4:-57100753 None:intergenic
GCATGGAGTTTACAATTGTA+GGG 0.478326 4.4:-57100325 None:intergenic
GATTGGTTAAATCAACTAGA+TGG 0.481740 4.4:+57100887 MS.gene046062:CDS
AGTTGCATTGTTGATGAACT+AGG 0.485117 4.4:-57101016 None:intergenic
GATTTACCCAATCATGTGGT+TGG 0.489852 4.4:-57101042 None:intergenic
TTGCCCTCTTCACTTTGAGA+TGG 0.492565 4.4:-57101112 None:intergenic
ACTTAGCCAACCACATGATT+GGG 0.501075 4.4:+57101036 MS.gene046062:CDS
AGTTGCTTTGTAGATGAACT+AGG 0.501324 4.4:-57100845 None:intergenic
TGGTTTGTTGATGAATTATG+AGG 0.510382 4.4:-57100770 None:intergenic
AGGAAATCTGAATGCCAAGT+TGG 0.511291 4.4:-57100482 None:intergenic
TCTCACTAATATCATGAGGT+TGG 0.521834 4.4:-57100790 None:intergenic
TGGAAAAGAAATATCTTTCG+AGG 0.525349 4.4:-57101092 None:intergenic
TTGATTGTGTATGATGATGA+TGG 0.536425 4.4:+57100269 MS.gene046062:CDS
ATATGAGCATAAGAAGATTG+AGG 0.542149 4.4:+57100355 MS.gene046062:CDS
TTTCCATCTCAAAGTGAAGA+GGG 0.553124 4.4:+57101109 MS.gene046062:CDS
GTCAACCTGATCAGTTTGCA+TGG 0.562911 4.4:+57100930 MS.gene046062:CDS
ATGCTCATATTCTTGAAGCA+TGG 0.569236 4.4:-57100342 None:intergenic
TGATGATGATGGTAATAATG+TGG 0.569879 4.4:+57100280 MS.gene046062:CDS
AGGGATGCTATTGCTATGCA+TGG 0.574776 4.4:-57100693 None:intergenic
AGTTGATTTACCCAATCATG+TGG 0.604044 4.4:-57101046 None:intergenic
AATCAACTAGATGATGGTGT+TGG 0.609634 4.4:+57101061 MS.gene046062:CDS
GTTAACTTGGCTTGAATGTG+AGG 0.614041 4.4:-57100669 None:intergenic
GCAACAACACATCAATGAGA+TGG 0.623711 4.4:+57100721 MS.gene046062:CDS
GATGATGATGGTAATAATGT+GGG 0.631187 4.4:+57100281 MS.gene046062:CDS
TTAAGAAGAAGTATCCAACT+TGG 0.637255 4.4:+57100468 MS.gene046062:CDS
TGGGTAAATCAACTAGATGA+TGG 0.641321 4.4:+57101055 MS.gene046062:CDS
ATCATCTCACTAATATCATG+AGG 0.641661 4.4:-57100794 None:intergenic
ACAACACATCAATGAGATGG+TGG 0.646608 4.4:+57100724 MS.gene046062:CDS
ATAATGTGGGACCAATGACA+TGG 0.658982 4.4:+57100294 MS.gene046062:CDS
AAGCTAAGATAACCAAAGTG+AGG 0.659175 4.4:+57100435 MS.gene046062:CDS
TGGTTAAATCAACTAGATGG+TGG 0.663107 4.4:+57100890 MS.gene046062:CDS
TGCTTTGTAGATGAACTAGG+AGG 0.674710 4.4:-57100842 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! CTTTGAAATTAAGAAAAAAA+AGG + chr4.4:57100409-57100428 MS.gene046062:CDS 15.0%
!!! TCATTTTGAATGTATTTCAT+TGG - chr4.4:57100158-57100177 None:intergenic 20.0%
!!! TCTTAATTTCAAAGTATTTG+TGG - chr4.4:57100403-57100422 None:intergenic 20.0%
! GCTTTCAAAGAAAGAAAAAA+TGG + chr4.4:57100194-57100213 MS.gene046062:CDS 25.0%
!! ATGATTGATTTCACTAATCT+TGG + chr4.4:57100812-57100831 MS.gene046062:CDS 25.0%
!! TTTTCATCTCAAAATGAAGA+GGG + chr4.4:57100965-57100984 MS.gene046062:CDS 25.0%
!! TTTTTCATCTCAAAATGAAG+AGG + chr4.4:57100964-57100983 MS.gene046062:CDS 25.0%
!!! AAAGAAAAAATGGATTAGCA+AGG + chr4.4:57100204-57100223 MS.gene046062:CDS 25.0%
!!! GTTGATTTTCTTCCATATTA+AGG - chr4.4:57100505-57100524 None:intergenic 25.0%
AAGTTGGATACTTCTTCTTA+AGG - chr4.4:57100469-57100488 None:intergenic 30.0%
AGTTGGATACTTCTTCTTAA+GGG - chr4.4:57100468-57100487 None:intergenic 30.0%
ATATGAGCATAAGAAGATTG+AGG + chr4.4:57100355-57100374 MS.gene046062:CDS 30.0%
ATCATCTCACTAATATCATG+AGG - chr4.4:57100797-57100816 None:intergenic 30.0%
GCATTCAGATTTCCTTAATA+TGG + chr4.4:57100490-57100509 MS.gene046062:CDS 30.0%
TGGAAAAGAAATATCTTTCG+AGG - chr4.4:57101095-57101114 None:intergenic 30.0%
TTGTGGACATCAAATATTTC+AGG - chr4.4:57100386-57100405 None:intergenic 30.0%
TTTAACCAATCGTCAAAATC+AGG - chr4.4:57100878-57100897 None:intergenic 30.0%
! GATTGGTTAAATCAACTAGA+TGG + chr4.4:57100887-57100906 MS.gene046062:CDS 30.0%
! TTGATTGTGTATGATGATGA+TGG + chr4.4:57100269-57100288 MS.gene046062:CDS 30.0%
!! GATGATGATGGTAATAATGT+GGG + chr4.4:57100281-57100300 MS.gene046062:CDS 30.0%
!! TCTAAATTTGTTAGCAAGAC+TGG + chr4.4:57100233-57100252 MS.gene046062:CDS 30.0%
!! TGATGATGATGGTAATAATG+TGG + chr4.4:57100280-57100299 MS.gene046062:CDS 30.0%
!! TGGTTTGTTGATGAATTATG+AGG - chr4.4:57100773-57100792 None:intergenic 30.0%
!! TTAAGAAGAAGTATCCAACT+TGG + chr4.4:57100468-57100487 MS.gene046062:CDS 30.0%
AAGCTAAGATAACCAAAGTG+AGG + chr4.4:57100435-57100454 MS.gene046062:CDS 35.0%
AGCATGGAGTTTACAATTGT+AGG - chr4.4:57100329-57100348 None:intergenic 35.0%
ATGAGGCAAATCAACATGAT+TGG - chr4.4:57100756-57100775 None:intergenic 35.0%
ATGCTCATATTCTTGAAGCA+TGG - chr4.4:57100345-57100364 None:intergenic 35.0%
CAATGCTCTCATGCAAAATA+TGG + chr4.4:57100628-57100647 MS.gene046062:CDS 35.0%
GCATGGAGTTTACAATTGTA+GGG - chr4.4:57100328-57100347 None:intergenic 35.0%
TCTCACTAATATCATGAGGT+TGG - chr4.4:57100793-57100812 None:intergenic 35.0%
TGGGTAAATCAACTAGATGA+TGG + chr4.4:57101055-57101074 MS.gene046062:CDS 35.0%
TGGTTAAATCAACTAGATGG+TGG + chr4.4:57100890-57100909 MS.gene046062:CDS 35.0%
TTTACAATTGTAGGGTCTTC+TGG - chr4.4:57100320-57100339 None:intergenic 35.0%
TTTCCATCTCAAAGTGAAGA+GGG + chr4.4:57101109-57101128 MS.gene046062:CDS 35.0%
! AATCAACTAGATGATGGTGT+TGG + chr4.4:57101061-57101080 MS.gene046062:CDS 35.0%
! AGTTGATTTACCCAATCATG+TGG - chr4.4:57101049-57101068 None:intergenic 35.0%
! AGTTGCATTGTTGATGAACT+AGG - chr4.4:57101019-57101038 None:intergenic 35.0%
! AGTTGCTTTGTAGATGAACT+AGG - chr4.4:57100848-57100867 None:intergenic 35.0%
! TGATGTGTTGTTGCATTTGA+GGG - chr4.4:57100715-57100734 None:intergenic 35.0%
! TGATTTTGTGATCACAAGCT+TGG - chr4.4:57100562-57100581 None:intergenic 35.0%
! TTGATGTGTTGTTGCATTTG+AGG - chr4.4:57100716-57100735 None:intergenic 35.0%
! TTTTCCATCTCAAAGTGAAG+AGG + chr4.4:57101108-57101127 MS.gene046062:CDS 35.0%
AACTTAGCCAACCACATGAT+TGG + chr4.4:57101035-57101054 MS.gene046062:CDS 40.0%
ACAACACATCAATGAGATGG+TGG + chr4.4:57100724-57100743 MS.gene046062:CDS 40.0%
ACTTAGCCAACCACATGATT+GGG + chr4.4:57101036-57101055 MS.gene046062:CDS 40.0%
AGGAAATCTGAATGCCAAGT+TGG - chr4.4:57100485-57100504 None:intergenic 40.0%
ATAATGTGGGACCAATGACA+TGG + chr4.4:57100294-57100313 MS.gene046062:CDS 40.0%
GATTTACCCAATCATGTGGT+TGG - chr4.4:57101045-57101064 None:intergenic 40.0%
GCAACAACACATCAATGAGA+TGG + chr4.4:57100721-57100740 MS.gene046062:CDS 40.0%
GTGAAGAGGGCAATGAAATT+TGG + chr4.4:57101122-57101141 MS.gene046062:CDS 40.0%
TCTTTCCATGCAAACTGATC+AGG - chr4.4:57100938-57100957 None:intergenic 40.0%
TGCTTTGTAGATGAACTAGG+AGG - chr4.4:57100845-57100864 None:intergenic 40.0%
! GTTAACTTGGCTTGAATGTG+AGG - chr4.4:57100672-57100691 None:intergenic 40.0%
!! AAGGGTATCTTTCCTCACTT+TGG - chr4.4:57100450-57100469 None:intergenic 40.0%
!! AGATGGTGGTGTTTTGAATC+AGG + chr4.4:57100904-57100923 MS.gene046062:CDS 40.0%
AGGGATGCTATTGCTATGCA+TGG - chr4.4:57100696-57100715 None:intergenic 45.0%
GAGGGCAATGCAAGTTATCT+TGG + chr4.4:57100983-57101002 MS.gene046062:CDS 45.0%
GTCAACCTGATCAGTTTGCA+TGG + chr4.4:57100930-57100949 MS.gene046062:CDS 45.0%
TGCTATGCATGGCGTTAACT+TGG - chr4.4:57100685-57100704 None:intergenic 45.0%
! TTGCCCTCTTCACTTTGAGA+TGG - chr4.4:57101115-57101134 None:intergenic 45.0%
!! GTCAGCCTGATTTTGACGAT+TGG + chr4.4:57100870-57100889 MS.gene046062:CDS 45.0%
GGGTCTTCTGGCCATGTCAT+TGG - chr4.4:57100308-57100327 None:intergenic 55.0%


Chromosome Type Strat End Strand Name
chr4.4 gene 57100137 57101153 57100137 ID=MS.gene046062
chr4.4 mRNA 57100137 57101153 57100137 ID=MS.gene046062.t1;Parent=MS.gene046062
chr4.4 exon 57100137 57101153 57100137 ID=MS.gene046062.t1.exon1;Parent=MS.gene046062.t1
chr4.4 CDS 57100137 57101153 57100137 ID=cds.MS.gene046062.t1;Parent=MS.gene046062.t1
Gene Sequence

>MS.gene046062

ATGGGTCGTAAAAAAATACCAATGAAATACATTCAAAATGAGAAATCTCGCAAAATAGCTTTCAAAGAAAGAAAAAATGGATTAGCAAGGAAACTTTCTAAATTTGTTAGCAAGACTGGAGCAAGAGCTTGTTTGATTGTGTATGATGATGATGGTAATAATGTGGGACCAATGACATGGCCAGAAGACCCTACAATTGTAAACTCCATGCTTCAAGAATATGAGCATAAGAAGATTGAGGAAACTCCTGAAATATTTGATGTCCACAAATACTTTGAAATTAAGAAAAAAAAGGTTGAAGCTAAGATAACCAAAGTGAGGAAAGATACCCTTAAGAAGAAGTATCCAACTTGGCATTCAGATTTCCTTAATATGGAAGAAAATCAACTCAGAGACTTCATTGCTACTGTAAATGATAAGATCCAAGCTTGTGATCACAAAATCAGCATGTTGAAAAATATGCAACATAGTGAAACTAGTTTCTTGCAAAACAATGCTCTCATGCAAAATATGGTTCAAGAGAGTGTTGTTTCCTCACATTCAAGCCAAGTTAACGCCATGCATAGCAATAGCATCCCTCAAATGCAACAACACATCAATGAGATGGTGGATTTGACCAATCATGTTGATTTGCCTCATAATTCATCAACAAACCAACCTCATGATATTAGTGAGATGATTGATTTCACTAATCTTGGTGATTTGCCTCCTAGTTCATCTACAAAGCAACTTAGTCAGCCTGATTTTGACGATTGGTTAAATCAACTAGATGGTGGTGTTTTGAATCAGGCTAGTCAACCTGATCAGTTTGCATGGAAAGATCTTTCTTTTTCATCTCAAAATGAAGAGGGCAATGCAAGTTATCTTGGTAATTTTCTTCCTAGTTCATCAACAATGCAACTTAGCCAACCACATGATTGGGTAAATCAACTAGATGATGGTGTTGGTCAGTTTGCCTCGAAAGATATTTCTTTTCCATCTCAAAGTGAAGAGGGCAATGAAATTTGGATGATTTGA
Protein sequence

>MS.gene046062.t1

MGRKKIPMKYIQNEKSRKIAFKERKNGLARKLSKFVSKTGARACLIVYDDDGNNVGPMTWPEDPTIVNSMLQEYEHKKIEETPEIFDVHKYFEIKKKKVEAKITKVRKDTLKKKYPTWHSDFLNMEENQLRDFIATVNDKIQACDHKISMLKNMQHSETSFLQNNALMQNMVQESVVSSHSSQVNAMHSNSIPQMQQHINEMVDLTNHVDLPHNSSTNQPHDISEMIDFTNLGDLPPSSSTKQLSQPDFDDWLNQLDGGVLNQASQPDQFAWKDLSFSSQNEEGNASYLGNFLPSSSTMQLSQPHDWVNQLDDGVGQFASKDISFPSQSEEGNEIWMI