AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene059840


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene059840.t1 MTR_4g021290 95.187 187 9 0 1 187 1 187 3.77e-126 353
MS.gene059840.t1 MTR_3g005450 95.187 187 9 0 1 187 1 187 3.77e-126 353
MS.gene059840.t1 MTR_3g005430 95.187 187 9 0 1 187 1 187 3.77e-126 353
MS.gene059840.t1 MTR_7g067490 94.118 187 11 0 1 187 1 187 2.04e-124 349
MS.gene059840.t1 MTR_1g068965 93.855 179 11 0 1 179 28 206 3.45e-123 347
MS.gene059840.t1 MTR_4g108310 91.304 115 10 0 1 115 1 115 6.32e-74 218
MS.gene059840.t1 MTR_4g108305 100.000 38 0 0 138 175 21 58 3.07e-22 85.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene059840.t1 AT5G39850 87.166 187 24 0 1 187 1 187 9.02e-120 337
MS.gene059840.t1 AT5G15200 83.333 198 32 1 1 197 1 198 1.80e-115 327
MS.gene059840.t1 AT5G15200 87.591 137 17 0 1 137 1 137 4.74e-84 246

Find 65 sgRNAs with CRISPR-Local

Find 93 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CCCTTTGGTGGTGGTCTTCC+TGG 0.197404 2.4:-18202458 MS.gene059840:CDS
ATCACCACCAGAAGCCTTCT+TGG 0.218725 2.4:+18202403 None:intergenic
TTCCCATAGTTTCGGTAAAC+TGG 0.287392 2.4:+18203319 None:intergenic
CAGACTCTTGTCTTCAAATC+TGG 0.288805 2.4:-18202998 MS.gene059840:CDS
ATTCCAGTTTACCGAAACTA+TGG 0.305962 2.4:-18203322 MS.gene059840:CDS
TTGAAGCTGGTCGGAGAGTA+TGG 0.314070 2.4:-18203244 MS.gene059840:CDS
CCTTCTTGGTTGCAGCCTTA+AGG 0.336380 2.4:+18202417 None:intergenic
ACCATGCTAGGGTTCTTATC+AGG 0.369101 2.4:-18202958 MS.gene059840:CDS
GCTGCAACCAAGAAGGCTTC+TGG 0.408125 2.4:-18202410 MS.gene059840:CDS
TGGACGACGTGGCTTCTTGA+AGG 0.409761 2.4:+18203294 None:intergenic
TCTTCTCATCCAATGTCAAA+AGG 0.432229 2.4:+18203152 None:intergenic
TCCATACGAGAAGGAGCGTT+TGG 0.432310 2.4:-18203275 MS.gene059840:CDS
TCCCTCACCAGTCCCTTTGG+TGG 0.444838 2.4:-18202470 MS.gene059840:CDS
TTATCAGGCAGAGACACATT+AGG 0.445935 2.4:-18202943 MS.gene059840:intron
CCTAGCATGGTGAATGGACT+TGG 0.448468 2.4:+18202970 None:intergenic
CATTGTTACGGATACGGCTC+AGG 0.451453 2.4:+18203182 None:intergenic
TTCTTTCGCTTCACGCGACC+AGG 0.452567 2.4:+18202440 None:intergenic
TTCTAGCATTGTTACGGATA+CGG 0.467109 2.4:+18203176 None:intergenic
CTCACCAGTCCCTTTGGTGG+TGG 0.469552 2.4:-18202467 MS.gene059840:CDS
ACCAGGAAGACCACCACCAA+AGG 0.473047 2.4:+18202457 None:intergenic
AAAGGGTTCTAGCATTGTTA+CGG 0.475438 2.4:+18203170 None:intergenic
AGTGAACATCCCATCCTTCA+TGG 0.476720 2.4:-18202525 MS.gene059840:CDS
GAGCCCTCGTCGGATCTTTG+AGG 0.482488 2.4:-18203131 MS.gene059840:CDS
AAGAAGGCTTCTGGTGGTGA+TGG 0.495137 2.4:-18202401 MS.gene059840:CDS
TCCAAACGCTCCTTCTCGTA+TGG 0.519540 2.4:+18203274 None:intergenic
CTTCTCATCCAATGTCAAAA+GGG 0.523313 2.4:+18203153 None:intergenic
AGCCCTCGTCGGATCTTTGA+GGG 0.524524 2.4:-18203130 MS.gene059840:CDS
CCAAGTCCATTCACCATGCT+AGG 0.525789 2.4:-18202970 MS.gene059840:CDS
GTTTCGGTAAACTGGAATGT+GGG 0.529716 2.4:+18203327 None:intergenic
TCAACCCTCACCATGAAGGA+TGG 0.531047 2.4:+18202515 None:intergenic
AAGAACCCTAGCATGGTGAA+TGG 0.539163 2.4:+18202964 None:intergenic
CGTGAAGCGAAAGAACCTTA+AGG 0.541128 2.4:-18202432 MS.gene059840:CDS
TGGTCGGAGAGTATGGTCTT+CGG 0.541482 2.4:-18203237 MS.gene059840:CDS
TTCCAGTTTACCGAAACTAT+GGG 0.556730 2.4:-18203321 MS.gene059840:CDS
TTGAGGAGAATGTTTAAGCA+TGG 0.560766 2.4:-18203097 MS.gene059840:CDS
CAACCCTCACCATGAAGGAT+GGG 0.569875 2.4:+18202516 None:intergenic
AAGACCACCACCAAAGGGAC+TGG 0.570564 2.4:+18202463 None:intergenic
TGAATCAACCCTCACCATGA+AGG 0.571223 2.4:+18202511 None:intergenic
CCTTAAGGCTGCAACCAAGA+AGG 0.573742 2.4:-18202417 MS.gene059840:CDS
ACCACCAAAGGGACTGGTGA+GGG 0.576930 2.4:+18202469 None:intergenic
GAACAAGCTCGATTATGTGT+TGG 0.578338 2.4:-18203056 MS.gene059840:CDS
TTTGGATGCTGAGTTGAAGC+TGG 0.579570 2.4:-18203257 MS.gene059840:CDS
CCAGGAAGACCACCACCAAA+GGG 0.581024 2.4:+18202458 None:intergenic
GGTGTAAGAGAGAGCTGTGG+AGG 0.589621 2.4:-18203216 MS.gene059840:CDS
TTCTGGTGGTGATGGAGATG+AGG 0.590267 2.4:-18202393 MS.gene059840:CDS
AGTTTCGGTAAACTGGAATG+TGG 0.592077 2.4:+18203326 None:intergenic
CATCCCATCCTTCATGGTGA+GGG 0.593258 2.4:-18202519 MS.gene059840:CDS
TCTTGTCTTCAAATCTGGCA+TGG 0.593384 2.4:-18202993 MS.gene059840:CDS
ATTGTTACGGATACGGCTCA+GGG 0.599593 2.4:+18203183 None:intergenic
CAAGTCCATTCACCATGCTA+GGG 0.599707 2.4:-18202969 MS.gene059840:CDS
ACATCCCATCCTTCATGGTG+AGG 0.616704 2.4:-18202520 MS.gene059840:CDS
GCCACGTCGTCCATACGAGA+AGG 0.630150 2.4:-18203284 MS.gene059840:CDS
TGAAGACAAGAGTCTGAAGA+CGG 0.630423 2.4:+18203005 None:intergenic
GATGCTGAGTTGAAGCTGGT+CGG 0.640820 2.4:-18203253 MS.gene059840:CDS
TTTCGGTAAACTGGAATGTG+GGG 0.641183 2.4:+18203328 None:intergenic
GCAACCAAGAAGGCTTCTGG+TGG 0.643072 2.4:-18202407 MS.gene059840:CDS
GCCTGATAAGAACCCTAGCA+TGG 0.650504 2.4:+18202957 None:intergenic
CACCACCAAAGGGACTGGTG+AGG 0.654247 2.4:+18202468 None:intergenic
TGGTGGTGATGGAGATGAGG+AGG 0.657794 2.4:-18202390 MS.gene059840:CDS
GTGTAAGAGAGAGCTGTGGA+GGG 0.669438 2.4:-18203215 MS.gene059840:CDS
CACCCTCAAAGATCCGACGA+GGG 0.691605 2.4:+18203128 None:intergenic
TTCGGTGTAAGAGAGAGCTG+TGG 0.694839 2.4:-18203219 MS.gene059840:CDS
TCCTTCTCGTATGGACGACG+TGG 0.696550 2.4:+18203283 None:intergenic
TGGATGAGAAGAGCCCTCGT+CGG 0.701475 2.4:-18203141 MS.gene059840:CDS
TCACCCTCAAAGATCCGACG+AGG 0.706908 2.4:+18203127 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TAATTATTTAATTGTAAGTT+TGG - chr2.4:18202809-18202828 MS.gene059840:intron 10.0%
!!! ATATCATTTTTTGTTTTCAT+AGG - chr2.4:18203148-18203167 MS.gene059840:CDS 15.0%
!!! TATCATTTTTTGTTTTCATA+GGG - chr2.4:18203149-18203168 MS.gene059840:CDS 15.0%
! ATAAAAGGCAGAAATAAACT+AGG + chr2.4:18203070-18203089 None:intergenic 25.0%
!! ATGTCAATAGAACTTACTTT+TGG - chr2.4:18202895-18202914 MS.gene059840:intron 25.0%
!! GTAAAGGTTTAAGCAAATTT+TGG + chr2.4:18203026-18203045 None:intergenic 25.0%
!!! ATTTTTTGTTTTCATAGGGT+TGG - chr2.4:18203153-18203172 MS.gene059840:CDS 25.0%
!!! GTTTATTTCTGCCTTTTATT+TGG - chr2.4:18203071-18203090 MS.gene059840:CDS 25.0%
!!! TGTCAATAGAACTTACTTTT+GGG - chr2.4:18202896-18202915 MS.gene059840:intron 25.0%
!!! TTTTTTGTTTTCATAGGGTT+GGG - chr2.4:18203154-18203173 MS.gene059840:CDS 25.0%
AAACACAAAATTGTGCAAAC+AGG + chr2.4:18202940-18202959 None:intergenic 30.0%
AACACAAAATTGTGCAAACA+GGG + chr2.4:18202939-18202958 None:intergenic 30.0%
AGAAAACCCAACCAAATAAA+AGG + chr2.4:18203085-18203104 None:intergenic 30.0%
! ATCTGAGAGTTCGAATTTTT+GGG - chr2.4:18202853-18202872 MS.gene059840:intron 30.0%
!! ATTTCTGCCTTTTATTTGGT+TGG - chr2.4:18203075-18203094 MS.gene059840:CDS 30.0%
!! GTTTAAGCAAATTTTGGCAA+TGG + chr2.4:18203020-18203039 None:intergenic 30.0%
!! TTTCTGCCTTTTATTTGGTT+GGG - chr2.4:18203076-18203095 MS.gene059840:CDS 30.0%
ATTCCAGTTTACCGAAACTA+TGG - chr2.4:18202388-18202407 MS.gene059840:CDS 35.0%
CTTCTCATCCAATGTCAAAA+GGG + chr2.4:18202560-18202579 None:intergenic 35.0%
GATCAGATAATCAACGGTAA+AGG + chr2.4:18203042-18203061 None:intergenic 35.0%
TCATCGTTGTGAAACATGTT+TGG - chr2.4:18203113-18203132 MS.gene059840:CDS 35.0%
TCTTCTCATCCAATGTCAAA+AGG + chr2.4:18202561-18202580 None:intergenic 35.0%
TTCCAGTTTACCGAAACTAT+GGG - chr2.4:18202389-18202408 MS.gene059840:CDS 35.0%
TTCTAGCATTGTTACGGATA+CGG + chr2.4:18202537-18202556 None:intergenic 35.0%
TTGAGGAGAATGTTTAAGCA+TGG - chr2.4:18202613-18202632 MS.gene059840:intron 35.0%
! AAAGGGTTCTAGCATTGTTA+CGG + chr2.4:18202543-18202562 None:intergenic 35.0%
! CATCTGAGAGTTCGAATTTT+TGG - chr2.4:18202852-18202871 MS.gene059840:intron 35.0%
! GTCTAGGATCAGATAATCAA+CGG + chr2.4:18203048-18203067 None:intergenic 35.0%
! TGAAGGTTTTCCCATAGTTT+CGG + chr2.4:18202402-18202421 None:intergenic 35.0%
AGTTTCGGTAAACTGGAATG+TGG + chr2.4:18202387-18202406 None:intergenic 40.0%
CAGACTCTTGTCTTCAAATC+TGG - chr2.4:18202712-18202731 MS.gene059840:intron 40.0%
GAACAAGCTCGATTATGTGT+TGG - chr2.4:18202654-18202673 MS.gene059840:intron 40.0%
GGCAGAAATAAACTAGGTCT+AGG + chr2.4:18203064-18203083 None:intergenic 40.0%
GTTTCGGTAAACTGGAATGT+GGG + chr2.4:18202386-18202405 None:intergenic 40.0%
TCTTGTCTTCAAATCTGGCA+TGG - chr2.4:18202717-18202736 MS.gene059840:intron 40.0%
TGAAGACAAGAGTCTGAAGA+CGG + chr2.4:18202708-18202727 None:intergenic 40.0%
TTATCAGGCAGAGACACATT+AGG - chr2.4:18202767-18202786 MS.gene059840:intron 40.0%
TTCCCATAGTTTCGGTAAAC+TGG + chr2.4:18202394-18202413 None:intergenic 40.0%
TTTCGGTAAACTGGAATGTG+GGG + chr2.4:18202385-18202404 None:intergenic 40.0%
! TGCTAGAACCCTTTTGACAT+TGG - chr2.4:18202549-18202568 MS.gene059840:intron 40.0%
!! TTTGTTTTCATAGGGTTGGG+AGG - chr2.4:18203157-18203176 MS.gene059840:CDS 40.0%
AAGAACCCTAGCATGGTGAA+TGG + chr2.4:18202749-18202768 None:intergenic 45.0%
ACCATGCTAGGGTTCTTATC+AGG - chr2.4:18202752-18202771 MS.gene059840:intron 45.0%
AGTGAACATCCCATCCTTCA+TGG - chr2.4:18203185-18203204 MS.gene059840:CDS 45.0%
ATTGTTACGGATACGGCTCA+GGG + chr2.4:18202530-18202549 None:intergenic 45.0%
CAAGTCCATTCACCATGCTA+GGG - chr2.4:18202741-18202760 MS.gene059840:intron 45.0%
CGTGAAGCGAAAGAACCTTA+AGG - chr2.4:18203278-18203297 MS.gene059840:CDS 45.0%
TGAATCAACCCTCACCATGA+AGG + chr2.4:18203202-18203221 None:intergenic 45.0%
! TTTGGATGCTGAGTTGAAGC+TGG - chr2.4:18202453-18202472 MS.gene059840:CDS 45.0%
ACATCCCATCCTTCATGGTG+AGG - chr2.4:18203190-18203209 MS.gene059840:CDS 50.0%
ATCACCACCAGAAGCCTTCT+TGG + chr2.4:18203310-18203329 None:intergenic 50.0%
CAACCCTCACCATGAAGGAT+GGG + chr2.4:18203197-18203216 None:intergenic 50.0%
CATCCCATCCTTCATGGTGA+GGG - chr2.4:18203191-18203210 MS.gene059840:CDS 50.0%
CATTGTTACGGATACGGCTC+AGG + chr2.4:18202531-18202550 None:intergenic 50.0%
CCAAGTCCATTCACCATGCT+AGG - chr2.4:18202740-18202759 MS.gene059840:intron 50.0%
CCTTAAGGCTGCAACCAAGA+AGG - chr2.4:18203293-18203312 MS.gene059840:CDS 50.0%
CCTTCTTGGTTGCAGCCTTA+AGG + chr2.4:18203296-18203315 None:intergenic 50.0%
GCCTGATAAGAACCCTAGCA+TGG + chr2.4:18202756-18202775 None:intergenic 50.0%
GTGTAAGAGAGAGCTGTGGA+GGG - chr2.4:18202495-18202514 MS.gene059840:CDS 50.0%
TCAACCCTCACCATGAAGGA+TGG + chr2.4:18203198-18203217 None:intergenic 50.0%
TCCAAACGCTCCTTCTCGTA+TGG + chr2.4:18202439-18202458 None:intergenic 50.0%
TTGAAGCTGGTCGGAGAGTA+TGG - chr2.4:18202466-18202485 MS.gene059840:CDS 50.0%
! AAGAAGGCTTCTGGTGGTGA+TGG - chr2.4:18203309-18203328 MS.gene059840:CDS 50.0%
! CCTAGCATGGTGAATGGACT+TGG + chr2.4:18202743-18202762 None:intergenic 50.0%
! GATGCTGAGTTGAAGCTGGT+CGG - chr2.4:18202457-18202476 MS.gene059840:CDS 50.0%
! TGGTCGGAGAGTATGGTCTT+CGG - chr2.4:18202473-18202492 MS.gene059840:CDS 50.0%
! TTCGGTGTAAGAGAGAGCTG+TGG - chr2.4:18202491-18202510 MS.gene059840:CDS 50.0%
! TTGAGGGTGACGCACTTTTG+AGG - chr2.4:18202596-18202615 MS.gene059840:intron 50.0%
! TTTTCATAGGGTTGGGAGGC+AGG - chr2.4:18203161-18203180 MS.gene059840:CDS 50.0%
! TTTTCCCTCACCAGTCCCTT+TGG - chr2.4:18203237-18203256 MS.gene059840:CDS 50.0%
!! TCCATACGAGAAGGAGCGTT+TGG - chr2.4:18202435-18202454 MS.gene059840:CDS 50.0%
!! TTCTGGTGGTGATGGAGATG+AGG - chr2.4:18203317-18203336 MS.gene059840:CDS 50.0%
AAGACCACCACCAAAGGGAC+TGG + chr2.4:18203250-18203269 None:intergenic 55.0%
ACCAGGAAGACCACCACCAA+AGG + chr2.4:18203256-18203275 None:intergenic 55.0%
AGCCCTCGTCGGATCTTTGA+GGG - chr2.4:18202580-18202599 MS.gene059840:intron 55.0%
CACCCTCAAAGATCCGACGA+GGG + chr2.4:18202585-18202604 None:intergenic 55.0%
CCAGGAAGACCACCACCAAA+GGG + chr2.4:18203255-18203274 None:intergenic 55.0%
GCAACCAAGAAGGCTTCTGG+TGG - chr2.4:18203303-18203322 MS.gene059840:CDS 55.0%
GCTGCAACCAAGAAGGCTTC+TGG - chr2.4:18203300-18203319 MS.gene059840:CDS 55.0%
GGTGTAAGAGAGAGCTGTGG+AGG - chr2.4:18202494-18202513 MS.gene059840:CDS 55.0%
TCACCCTCAAAGATCCGACG+AGG + chr2.4:18202586-18202605 None:intergenic 55.0%
TCCTTCTCGTATGGACGACG+TGG + chr2.4:18202430-18202449 None:intergenic 55.0%
TGGACGACGTGGCTTCTTGA+AGG + chr2.4:18202419-18202438 None:intergenic 55.0%
TGGATGAGAAGAGCCCTCGT+CGG - chr2.4:18202569-18202588 MS.gene059840:intron 55.0%
TTCTTTCGCTTCACGCGACC+AGG + chr2.4:18203273-18203292 None:intergenic 55.0%
! ACCACCAAAGGGACTGGTGA+GGG + chr2.4:18203244-18203263 None:intergenic 55.0%
!! TGGTGGTGATGGAGATGAGG+AGG - chr2.4:18203320-18203339 MS.gene059840:CDS 55.0%
CTCACCAGTCCCTTTGGTGG+TGG - chr2.4:18203243-18203262 MS.gene059840:CDS 60.0%
GAGCCCTCGTCGGATCTTTG+AGG - chr2.4:18202579-18202598 MS.gene059840:intron 60.0%
GCCACGTCGTCCATACGAGA+AGG - chr2.4:18202426-18202445 MS.gene059840:CDS 60.0%
TCCCTCACCAGTCCCTTTGG+TGG - chr2.4:18203240-18203259 MS.gene059840:CDS 60.0%
! CACCACCAAAGGGACTGGTG+AGG + chr2.4:18203245-18203264 None:intergenic 60.0%
!! CCCTTTGGTGGTGGTCTTCC+TGG - chr2.4:18203252-18203271 MS.gene059840:CDS 60.0%


Chromosome Type Strat End Strand Name
chr2.4 gene 18202379 18203353 18202379 ID=MS.gene059840
chr2.4 mRNA 18202379 18203353 18202379 ID=MS.gene059840.t1;Parent=MS.gene059840
chr2.4 exon 18202944 18203353 18202944 ID=MS.gene059840.t1.exon1;Parent=MS.gene059840.t1
chr2.4 CDS 18202944 18203353 18202944 ID=cds.MS.gene059840.t1;Parent=MS.gene059840.t1
chr2.4 exon 18202379 18202562 18202379 ID=MS.gene059840.t1.exon2;Parent=MS.gene059840.t1
chr2.4 CDS 18202379 18202562 18202379 ID=cds.MS.gene059840.t1;Parent=MS.gene059840.t1
Gene Sequence

>MS.gene059840

ATGCCCCACATTCCAGTTTACCGAAACTATGGGAAAACCTTCAAGAAGCCACGTCGTCCATACGAGAAGGAGCGTTTGGATGCTGAGTTGAAGCTGGTCGGAGAGTATGGTCTTCGGTGTAAGAGAGAGCTGTGGAGGGTTCAATACTCCCTGAGCCGTATCCGTAACAATGCTAGAACCCTTTTGACATTGGATGAGAAGAGCCCTCGTCGGATCTTTGAGGGTGACGCACTTTTGAGGAGAATGTTTAAGCATGGTCTTCTCGATGATACTCAGAACAAGCTCGATTATGTGTTGGCTCTCACTGTTGAGAATTTTCTCGAGCGCCGTCTTCAGACTCTTGTCTTCAAATCTGGCATGGCCAAGTCCATTCACCATGCTAGGGTTCTTATCAGGCAGAGACACATTAGGTAATCTTTTGATTTCATGTTAATTATTTAATTGTAAGTTTGGATCAATGTCTTTAATATAATCATCTGAGAGTTCGAATTTTTGGGTTTGCTTTGTGATTAATTGATGTCAATAGAACTTACTTTTGGGTTTGCTGCTTTGTGATGCCCTGTTTGCACAATTTTGTGTTTTGTCTTATTTACTATACAAGATTTTTCTTTTCGTTCGAAGACAAAAATGTTTTGTTGCCATTGCCAAAATTTGCTTAAACCTTTACCGTTGATTATCTGATCCTAGACCTAGTTTATTTCTGCCTTTTATTTGGTTGGGTTTTCTTTCATAAATCATCGTTGTGAAACATGTTTGGATATGATTGATAATATCATTTTTTGTTTTCATAGGGTTGGGAGGCAGGTAGTGAACATCCCATCCTTCATGGTGAGGGTTGATTCACAGAAGCACATTGACTTTTCCCTCACCAGTCCCTTTGGTGGTGGTCTTCCTGGTCGCGTGAAGCGAAAGAACCTTAAGGCTGCAACCAAGAAGGCTTCTGGTGGTGATGGAGATGAGGAGGATGAAGATTAA

Protein sequence

>MS.gene059840.t1

MPHIPVYRNYGKTFKKPRRPYEKERLDAELKLVGEYGLRCKRELWRVQYSLSRIRNNARTLLTLDEKSPRRIFEGDALLRRMFKHGLLDDTQNKLDYVLALTVENFLERRLQTLVFKSGMAKSIHHARVLIRQRHIRVGRQVVNIPSFMVRVDSQKHIDFSLTSPFGGGLPGRVKRKNLKAATKKASGGDGDEEDED