AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene63043


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene63043.t1 MTR_5g056480 92.790 319 18 2 1 319 1 314 0.0 538
MS.gene63043.t1 MTR_1g110550 40.411 292 109 10 1 281 4 241 1.46e-51 171
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene63043.t1 AT1G68440 34.557 327 174 11 1 310 1 304 9.05e-36 131
MS.gene63043.t1 AT1G25400 31.250 304 179 9 1 300 1 278 2.62e-27 108
MS.gene63043.t1 AT1G25400 31.250 304 179 9 1 300 1 278 2.62e-27 108

Find 74 sgRNAs with CRISPR-Local

Find 79 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCGTTGAGTCTATCGATTAA+TGG 0.309567 5.4:-44723369 None:intergenic
GTAATCTCGCAGTCGAGATA+TGG 0.314723 5.4:+44724045 MS.gene63043:CDS
ACGAAGGTGGACGATGAAAA+TGG 0.314900 5.4:-44723562 None:intergenic
CTTAACAACGTTATCACTAT+TGG 0.316917 5.4:-44723862 None:intergenic
GTGATAACGTTGTTAAGCTT+TGG 0.325270 5.4:+44723868 MS.gene63043:CDS
CTTTGGGACAGTATAGGATT+TGG 0.332824 5.4:+44723885 MS.gene63043:CDS
TTGCTTTCAATTTCTGCAAA+TGG 0.333771 5.4:+44723484 MS.gene63043:CDS
AACACGCTGCGCGTGGAATC+TGG 0.336904 5.4:+44724128 MS.gene63043:CDS
TGCTTTCAATTTCTGCAAAT+GGG 0.348348 5.4:+44723485 MS.gene63043:CDS
TGATAACGTTGTTAAGCTTT+GGG 0.361870 5.4:+44723869 MS.gene63043:CDS
GACAGTATAGGATTTGGTTT+AGG 0.399313 5.4:+44723891 MS.gene63043:CDS
TTGTTACAGATGAATCTTAC+GGG 0.418397 5.4:+44724288 MS.gene63043:CDS
GCAGCAGCCGCAGAAGTTGA+AGG 0.439563 5.4:-44723981 None:intergenic
ATCACAACCACTTCCTTCAA+TGG 0.443517 5.4:+44723444 MS.gene63043:CDS
GTTAAGCTTTGGGACAGTAT+AGG 0.445462 5.4:+44723879 MS.gene63043:CDS
AACGGATTGGATTCCATTGA+AGG 0.457478 5.4:-44723457 None:intergenic
CTTGATGAAGATGACATAGA+TGG 0.461410 5.4:-44723711 None:intergenic
TGAAAGCAATGGAAACGGAT+TGG 0.472954 5.4:-44723470 None:intergenic
TCGTTGTCGAAGGTGATTGA+TGG 0.476471 5.4:-44723603 None:intergenic
GTGATTTGTGAAGGGAAAGA+TGG 0.477961 5.4:-44723426 None:intergenic
CCTGCGGAGACAATCACATC+TGG 0.481257 5.4:-44724008 None:intergenic
TGACGGACGTCAACGTTTGA+CGG 0.481919 5.4:+44724178 MS.gene63043:CDS
TGATTTGTGAAGGGAAAGAT+GGG 0.488143 5.4:-44723425 None:intergenic
AATCTGACGCGGATAATACT+TGG 0.488206 5.4:+44724246 MS.gene63043:CDS
AGACTCAACGATTTCCAAGC+AGG 0.489396 5.4:+44723381 MS.gene63043:CDS
GATTTCGATGATTACGAGGA+TGG 0.489828 5.4:+44723918 MS.gene63043:CDS
ATTGTTACAGATGAATCTTA+CGG 0.491552 5.4:+44724287 MS.gene63043:CDS
TTGGATTCCATTGAAGGAAG+TGG 0.497956 5.4:-44723451 None:intergenic
GCCGTCGGTCGTAGCTGAGT+GGG 0.499438 5.4:+44724091 MS.gene63043:CDS
TTTGCAGAAATTGAAAGCAA+TGG 0.502375 5.4:-44723481 None:intergenic
GGACGTCAACGTTTGACGGT+TGG 0.515827 5.4:+44724182 MS.gene63043:CDS
TAATCTCGCAGTCGAGATAT+GGG 0.515982 5.4:+44724046 MS.gene63043:CDS
CGTTAGTTTATCTTCGTCAT+CGG 0.519809 5.4:+44723671 MS.gene63043:CDS
CATAGACGACAACGTAGTAT+TGG 0.523774 5.4:+44723813 MS.gene63043:CDS
GCTGAGTGGGGACCCACGGT+GGG 0.524570 5.4:+44724104 MS.gene63043:CDS
GAAATCATCGTCGTTGTCGA+AGG 0.525729 5.4:-44723613 None:intergenic
GTGATTGTCTCCGCAGGAGA+AGG 0.526686 5.4:+44724014 MS.gene63043:CDS
GAAATTGAAAGCAATGGAAA+CGG 0.527809 5.4:-44723475 None:intergenic
AACGTGTTCCAAACTCAAAA+CGG 0.533078 5.4:+44723786 MS.gene63043:CDS
AGAAAAGTCAGTGTTCCGTT+AGG 0.537364 5.4:+44724212 MS.gene63043:CDS
CGACCGACGGCTTCCGTCGT+CGG 0.539535 5.4:-44724079 None:intergenic
GGTGACTTTGTTGATGATGC+TGG 0.548195 5.4:-44723541 None:intergenic
AAAGTTTATGTAAGAGATGA+CGG 0.550055 5.4:+44724161 MS.gene63043:CDS
GCTTTCAATTTCTGCAAATG+GGG 0.560368 5.4:+44723486 MS.gene63043:CDS
GGTGGGGAACACGCTGCGCG+TGG 0.563432 5.4:+44724121 MS.gene63043:CDS
GTCGAAGGTGATTGATGGAA+GGG 0.564506 5.4:-44723598 None:intergenic
CCAGATGTGATTGTCTCCGC+AGG 0.566568 5.4:+44724008 MS.gene63043:CDS
CGTAGCTGAGTGGGGACCCA+CGG 0.568010 5.4:+44724100 MS.gene63043:CDS
GGGACACTCGTCTCCGACGA+CGG 0.568741 5.4:+44724066 MS.gene63043:CDS
AGCTGAGTGGGGACCCACGG+TGG 0.572221 5.4:+44724103 MS.gene63043:CDS
GCAATGAATTGAAACCTGCT+TGG 0.577118 5.4:-44723395 None:intergenic
CGCAGCGTGTTCCCCACCGT+GGG 0.591309 5.4:-44724116 None:intergenic
GAAGTGGTTGTGATTTGTGA+AGG 0.591968 5.4:-44723435 None:intergenic
TGTCGAAGGTGATTGATGGA+AGG 0.594870 5.4:-44723599 None:intergenic
CTGACGCGGATAATACTTGG+TGG 0.603373 5.4:+44724249 MS.gene63043:CDS
ACCACGTGCGCCTTCTCCTG+CGG 0.604226 5.4:-44724024 None:intergenic
TCTCCGACGACGGAAGCCGT+CGG 0.605600 5.4:+44724076 MS.gene63043:CDS
AGCCGTCGGTCGTAGCTGAG+TGG 0.610080 5.4:+44724090 MS.gene63043:CDS
GCAGAAGTTGAAGGCGCATG+TGG 0.619563 5.4:-44723972 None:intergenic
TCCGCAGGAGAAGGCGCACG+TGG 0.627475 5.4:+44724023 MS.gene63043:CDS
CCGTCGGTCGTAGCTGAGTG+GGG 0.632234 5.4:+44724092 MS.gene63043:CDS
TGACGCGGATAATACTTGGT+GGG 0.643095 5.4:+44724250 MS.gene63043:CDS
CTGAGTGGGGACCCACGGTG+GGG 0.648350 5.4:+44724105 MS.gene63043:CDS
TTTGTTTATCATGTCATACG+TGG 0.648765 5.4:-44723949 None:intergenic
CCCCACTCAGCTACGACCGA+CGG 0.650159 5.4:-44724092 None:intergenic
ACGCTGCGCGTGGAATCTGG+CGG 0.651618 5.4:+44724131 MS.gene63043:CDS
AAGTGGTTGTGATTTGTGAA+GGG 0.653510 5.4:-44723434 None:intergenic
GCGCAGCGTGTTCCCCACCG+TGG 0.659108 5.4:-44724117 None:intergenic
GATTCCGTTACGTTACCTAA+CGG 0.659410 5.4:-44724227 None:intergenic
TTTAGATTTCGATGATTACG+AGG 0.676604 5.4:+44723914 MS.gene63043:CDS
TAACGTAACGGAATCTGACG+CGG 0.701362 5.4:+44724235 MS.gene63043:CDS
GTGTTCCAAACTCAAAACGG+TGG 0.704795 5.4:+44723789 MS.gene63043:CDS
TGTTCCGTTAGGTAACGTAA+CGG 0.710318 5.4:+44724223 MS.gene63043:CDS
ACATGCGCCTTCAACTTCTG+CGG 0.738730 5.4:+44723974 MS.gene63043:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! AAAGTTTATGTAAGAGATGA+CGG + chr5.4:44724161-44724180 MS.gene63043:CDS 25.0%
! ATTGTTACAGATGAATCTTA+CGG + chr5.4:44724287-44724306 MS.gene63043:CDS 25.0%
CTTAACAACGTTATCACTAT+TGG - chr5.4:44723865-44723884 None:intergenic 30.0%
GAAATTGAAAGCAATGGAAA+CGG - chr5.4:44723478-44723497 None:intergenic 30.0%
TGCTTTCAATTTCTGCAAAT+GGG + chr5.4:44723485-44723504 MS.gene63043:CDS 30.0%
TTGCTTTCAATTTCTGCAAA+TGG + chr5.4:44723484-44723503 MS.gene63043:CDS 30.0%
TTGTTACAGATGAATCTTAC+GGG + chr5.4:44724288-44724307 MS.gene63043:CDS 30.0%
TTTAGATTTCGATGATTACG+AGG + chr5.4:44723914-44723933 MS.gene63043:CDS 30.0%
TTTGCAGAAATTGAAAGCAA+TGG - chr5.4:44723484-44723503 None:intergenic 30.0%
TTTGTTTATCATGTCATACG+TGG - chr5.4:44723952-44723971 None:intergenic 30.0%
! TGATAACGTTGTTAAGCTTT+GGG + chr5.4:44723869-44723888 MS.gene63043:CDS 30.0%
AACGTGTTCCAAACTCAAAA+CGG + chr5.4:44723786-44723805 MS.gene63043:CDS 35.0%
CTTGATGAAGATGACATAGA+TGG - chr5.4:44723714-44723733 None:intergenic 35.0%
GCTTTCAATTTCTGCAAATG+GGG + chr5.4:44723486-44723505 MS.gene63043:CDS 35.0%
! AAGTGGTTGTGATTTGTGAA+GGG - chr5.4:44723437-44723456 None:intergenic 35.0%
! CGTTAGTTTATCTTCGTCAT+CGG + chr5.4:44723671-44723690 MS.gene63043:CDS 35.0%
! GACAGTATAGGATTTGGTTT+AGG + chr5.4:44723891-44723910 MS.gene63043:CDS 35.0%
! GTGATAACGTTGTTAAGCTT+TGG + chr5.4:44723868-44723887 MS.gene63043:CDS 35.0%
! GTTTTCGTTATCTTCGTCAT+CGG - chr5.4:44723643-44723662 None:intergenic 35.0%
! TCGTTGAGTCTATCGATTAA+TGG - chr5.4:44723372-44723391 None:intergenic 35.0%
! TGATTTGTGAAGGGAAAGAT+GGG - chr5.4:44723428-44723447 None:intergenic 35.0%
!!! AAAGATTTTTTTCGCGTTGC+AGG + chr5.4:44723738-44723757 MS.gene63043:CDS 35.0%
!!! AAGAAGCTTTTTTACGAAGG+TGG - chr5.4:44723578-44723597 None:intergenic 35.0%
AATCTGACGCGGATAATACT+TGG + chr5.4:44724246-44724265 MS.gene63043:CDS 40.0%
AGAAAAGTCAGTGTTCCGTT+AGG + chr5.4:44724212-44724231 MS.gene63043:CDS 40.0%
ATCACAACCACTTCCTTCAA+TGG + chr5.4:44723444-44723463 MS.gene63043:CDS 40.0%
CATAGACGACAACGTAGTAT+TGG + chr5.4:44723813-44723832 MS.gene63043:CDS 40.0%
GATTCCGTTACGTTACCTAA+CGG - chr5.4:44724230-44724249 None:intergenic 40.0%
GATTTCGATGATTACGAGGA+TGG + chr5.4:44723918-44723937 MS.gene63043:CDS 40.0%
GCAATGAATTGAAACCTGCT+TGG - chr5.4:44723398-44723417 None:intergenic 40.0%
TAATCTCGCAGTCGAGATAT+GGG + chr5.4:44724046-44724065 MS.gene63043:CDS 40.0%
TGAAAGCAATGGAAACGGAT+TGG - chr5.4:44723473-44723492 None:intergenic 40.0%
TGTTCCGTTAGGTAACGTAA+CGG + chr5.4:44724223-44724242 MS.gene63043:CDS 40.0%
TTGGATTCCATTGAAGGAAG+TGG - chr5.4:44723454-44723473 None:intergenic 40.0%
! GAAGTGGTTGTGATTTGTGA+AGG - chr5.4:44723438-44723457 None:intergenic 40.0%
! GTGATTTGTGAAGGGAAAGA+TGG - chr5.4:44723429-44723448 None:intergenic 40.0%
!! AACGGATTGGATTCCATTGA+AGG - chr5.4:44723460-44723479 None:intergenic 40.0%
!! CTTTGGGACAGTATAGGATT+TGG + chr5.4:44723885-44723904 MS.gene63043:CDS 40.0%
!! GTTAAGCTTTGGGACAGTAT+AGG + chr5.4:44723879-44723898 MS.gene63043:CDS 40.0%
!!! GGGAAGAAGCTTTTTTACGA+AGG - chr5.4:44723581-44723600 None:intergenic 40.0%
!!! TATGTCCACCGTTTTGAGTT+TGG - chr5.4:44723797-44723816 None:intergenic 40.0%
ACGAAGGTGGACGATGAAAA+TGG - chr5.4:44723565-44723584 None:intergenic 45.0%
AGACTCAACGATTTCCAAGC+AGG + chr5.4:44723381-44723400 MS.gene63043:CDS 45.0%
GAAATCATCGTCGTTGTCGA+AGG - chr5.4:44723616-44723635 None:intergenic 45.0%
GTAATCTCGCAGTCGAGATA+TGG + chr5.4:44724045-44724064 MS.gene63043:CDS 45.0%
GTCGAAGGTGATTGATGGAA+GGG - chr5.4:44723601-44723620 None:intergenic 45.0%
GTGTTCCAAACTCAAAACGG+TGG + chr5.4:44723789-44723808 MS.gene63043:CDS 45.0%
TCGTTGTCGAAGGTGATTGA+TGG - chr5.4:44723606-44723625 None:intergenic 45.0%
TGACGCGGATAATACTTGGT+GGG + chr5.4:44724250-44724269 MS.gene63043:CDS 45.0%
TGTCGAAGGTGATTGATGGA+AGG - chr5.4:44723602-44723621 None:intergenic 45.0%
! TAACGTAACGGAATCTGACG+CGG + chr5.4:44724235-44724254 MS.gene63043:CDS 45.0%
!! GGTGACTTTGTTGATGATGC+TGG - chr5.4:44723544-44723563 None:intergenic 45.0%
ACATGCGCCTTCAACTTCTG+CGG + chr5.4:44723974-44723993 MS.gene63043:CDS 50.0%
CTGACGCGGATAATACTTGG+TGG + chr5.4:44724249-44724268 MS.gene63043:CDS 50.0%
! TGACGGACGTCAACGTTTGA+CGG + chr5.4:44724178-44724197 MS.gene63043:CDS 50.0%
CCAGATGTGATTGTCTCCGC+AGG + chr5.4:44724008-44724027 MS.gene63043:CDS 55.0%
CCTGCGGAGACAATCACATC+TGG - chr5.4:44724011-44724030 None:intergenic 55.0%
GGACGTCAACGTTTGACGGT+TGG + chr5.4:44724182-44724201 MS.gene63043:CDS 55.0%
GTGATTGTCTCCGCAGGAGA+AGG + chr5.4:44724014-44724033 MS.gene63043:CDS 55.0%
! GCAGAAGTTGAAGGCGCATG+TGG - chr5.4:44723975-44723994 None:intergenic 55.0%
AACACGCTGCGCGTGGAATC+TGG + chr5.4:44724128-44724147 MS.gene63043:CDS 60.0%
GCAGCAGCCGCAGAAGTTGA+AGG - chr5.4:44723984-44724003 None:intergenic 60.0%
ACCACGTGCGCCTTCTCCTG+CGG - chr5.4:44724027-44724046 None:intergenic 65.0%
ACGCTGCGCGTGGAATCTGG+CGG + chr5.4:44724131-44724150 MS.gene63043:CDS 65.0%
AGCCGTCGGTCGTAGCTGAG+TGG + chr5.4:44724090-44724109 MS.gene63043:CDS 65.0%
CCCCACTCAGCTACGACCGA+CGG - chr5.4:44724095-44724114 None:intergenic 65.0%
CCGTCGGTCGTAGCTGAGTG+GGG + chr5.4:44724092-44724111 MS.gene63043:CDS 65.0%
CGTAGCTGAGTGGGGACCCA+CGG + chr5.4:44724100-44724119 MS.gene63043:CDS 65.0%
GCCGTCGGTCGTAGCTGAGT+GGG + chr5.4:44724091-44724110 MS.gene63043:CDS 65.0%
GGGACACTCGTCTCCGACGA+CGG + chr5.4:44724066-44724085 MS.gene63043:CDS 65.0%
TCTCCGACGACGGAAGCCGT+CGG + chr5.4:44724076-44724095 MS.gene63043:CDS 65.0%
AGCTGAGTGGGGACCCACGG+TGG + chr5.4:44724103-44724122 MS.gene63043:CDS 70.0%
CGACCGACGGCTTCCGTCGT+CGG - chr5.4:44724082-44724101 None:intergenic 70.0%
CGCAGCGTGTTCCCCACCGT+GGG - chr5.4:44724119-44724138 None:intergenic 70.0%
CTGAGTGGGGACCCACGGTG+GGG + chr5.4:44724105-44724124 MS.gene63043:CDS 70.0%
GCTGAGTGGGGACCCACGGT+GGG + chr5.4:44724104-44724123 MS.gene63043:CDS 70.0%
! TCCGCAGGAGAAGGCGCACG+TGG + chr5.4:44724023-44724042 MS.gene63043:CDS 70.0%
GCGCAGCGTGTTCCCCACCG+TGG - chr5.4:44724120-44724139 None:intergenic 75.0%
GGTGGGGAACACGCTGCGCG+TGG + chr5.4:44724121-44724140 MS.gene63043:CDS 75.0%


Chromosome Type Strat End Strand Name
chr5.4 gene 44723360 44724319 44723360 ID=MS.gene63043
chr5.4 mRNA 44723360 44724319 44723360 ID=MS.gene63043.t1;Parent=MS.gene63043
chr5.4 exon 44723360 44724319 44723360 ID=MS.gene63043.t1.exon1;Parent=MS.gene63043.t1
chr5.4 CDS 44723360 44724319 44723360 ID=cds.MS.gene63043.t1;Parent=MS.gene63043.t1
Gene Sequence

>MS.gene63043

ATGCAAGTTCCATTAATCGATAGACTCAACGATTTCCAAGCAGGTTTCAATTCATTGCAACAAAACCCATCTTTCCCTTCACAAATCACAACCACTTCCTTCAATGGAATCCAATCCGTTTCCATTGCTTTCAATTTCTGCAAATGGGGTGCTGTCATTCTTGCTTTAGTCGCAACTTTCACCAGCATCATCAACAAAGTCACCATTTTCATCGTCCACCTTCGTAAAAAAGCTTCTTCCCTTCCATCAATCACCTTCGACAACGACGATGATTTCAGCTCCGATGACGAAGATAACGAAAACGATGACATCGTTAGTTTATCTTCGTCATCGGAATTCGAAGACGATGAACCATCTATGTCATCTTCATCAAGCTTCAAAGATTTTTTTCGCGTTGCAGGAAACAGTTTTGATTATGATGTAAACAACGTGTTCCAAACTCAAAACGGTGGACATAGACGACAACGTAGTATTGGTGATTTTTTTTCTCTTTTAGAATTAGCCAATAGTGATAACGTTGTTAAGCTTTGGGACAGTATAGGATTTGGTTTAGGTTTAGATTTCGATGATTACGAGGATGGAGTTGTATCCACGTATGACATGATAAACAAACCACATGCGCCTTCAACTTCTGCGGCTGCTGCATCACCAGATGTGATTGTCTCCGCAGGAGAAGGCGCACGTGGTAATCTCGCAGTCGAGATATGGGACACTCGTCTCCGACGACGGAAGCCGTCGGTCGTAGCTGAGTGGGGACCCACGGTGGGGAACACGCTGCGCGTGGAATCTGGCGGCGTTCAGAAAGTTTATGTAAGAGATGACGGACGTCAACGTTTGACGGTTGGTGATATGAGAAAAGTCAGTGTTCCGTTAGGTAACGTAACGGAATCTGACGCGGATAATACTTGGTGGGATGCTGATGCTGTTATTGTTACAGATGAATCTTACGGGAAACATTAA

Protein sequence

>MS.gene63043.t1

MQVPLIDRLNDFQAGFNSLQQNPSFPSQITTTSFNGIQSVSIAFNFCKWGAVILALVATFTSIINKVTIFIVHLRKKASSLPSITFDNDDDFSSDDEDNENDDIVSLSSSSEFEDDEPSMSSSSSFKDFFRVAGNSFDYDVNNVFQTQNGGHRRQRSIGDFFSLLELANSDNVVKLWDSIGFGLGLDFDDYEDGVVSTYDMINKPHAPSTSAAAASPDVIVSAGEGARGNLAVEIWDTRLRRRKPSVVAEWGPTVGNTLRVESGGVQKVYVRDDGRQRLTVGDMRKVSVPLGNVTESDADNTWWDADAVIVTDESYGKH