AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene060253


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene060253.t1 MTR_7g062720 40.541 148 80 3 1 146 1 142 1.74e-31 116
MS.gene060253.t1 MTR_4g037355 39.706 136 62 4 155 290 1 116 1.73e-21 89.4
MS.gene060253.t1 MTR_5g061150 35.354 99 64 0 52 150 38 136 3.68e-18 80.5
MS.gene060253.t1 MTR_4g112730 56.522 69 29 1 143 211 2 69 8.33e-17 75.1
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 65 sgRNAs with CRISPR-Local

Find 90 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGGATCAATGGAACAAATTA+AGG 0.196151 5.4:+60126591 MS.gene060253:CDS
AGTCTTATTGCCCTCATTAA+TGG 0.201947 5.4:+60126571 MS.gene060253:CDS
AAAGTTGTGGCGTTTATTTC+AGG 0.203868 5.4:-60126887 None:intergenic
GACAAAATTAAGGCAAGATT+TGG 0.257188 5.4:+60126536 MS.gene060253:CDS
GATTCTTGAGGGAGACGATT+TGG 0.271296 5.4:+60126394 MS.gene060253:CDS
CTCAATTAAGTTGTTGTTCC+AGG 0.274617 5.4:-60126345 None:intergenic
CACGGCCTCCACCACGAAAA+TGG 0.277262 5.4:-60127003 None:intergenic
CATAGGAGAAGATATTAATA+TGG 0.311554 5.4:+60127297 MS.gene060253:CDS
ATTTACTGAATACTCTGATT+TGG 0.313227 5.4:+60126781 MS.gene060253:CDS
GATTTCTTGAGGGACCTTCC+TGG 0.314207 5.4:-60127102 None:intergenic
CTTGATGATTCTTGTTGGTT+TGG 0.339105 5.4:-60127063 None:intergenic
GAAGAGGTTATATGAATTAT+AGG 0.339571 5.4:+60127026 MS.gene060253:CDS
GGGAGATGTCCCAGAGGAAT+TGG 0.345733 5.4:+60126415 MS.gene060253:CDS
ATTCTTGAGGGAGACGATTT+GGG 0.354692 5.4:+60126395 MS.gene060253:CDS
CGTGGTGGCTATGCTCGTTT+TGG 0.359061 5.4:+60126947 MS.gene060253:CDS
TTTACCTTGATGATTCTTGT+TGG 0.362649 5.4:-60127068 None:intergenic
CTTGAGGCTGCTGATTTCAT+AGG 0.363536 5.4:+60127280 MS.gene060253:CDS
CATAGCCACCACGTCCTCTT+TGG 0.374275 5.4:-60126937 None:intergenic
ACAAAATTAAGGCAAGATTT+GGG 0.416566 5.4:+60126537 MS.gene060253:CDS
TATAACTGAAAAGGAAAAGT+TGG 0.422757 5.4:+60126694 MS.gene060253:CDS
CGTGGTGGAGGCCGTGGAAG+AGG 0.431707 5.4:+60127010 MS.gene060253:CDS
TGCCCTCATTAATGGATCAA+TGG 0.432677 5.4:+60126579 MS.gene060253:CDS
AGATACAAAGAATCTGTTGA+TGG 0.446469 5.4:+60127202 MS.gene060253:CDS
TGGCAAAACTATAACTGAAA+AGG 0.467052 5.4:+60126685 MS.gene060253:CDS
ATCTGTTGATGGAAAGGAAA+AGG 0.477668 5.4:+60127213 MS.gene060253:CDS
AACCACCAGTTGCGTCCTAC+AGG 0.478404 5.4:+60126851 MS.gene060253:CDS
TTGTTCCTGTAGGACGCAAC+TGG 0.480977 5.4:-60126856 None:intergenic
ATCAAGCACCACATTGATGA+TGG 0.492315 5.4:+60126467 MS.gene060253:CDS
TGCAACAACAATATAGAATG+AGG 0.496917 5.4:+60126756 MS.gene060253:CDS
CTGGAGACAACTACATAACC+TGG 0.502040 5.4:+60126327 MS.gene060253:CDS
AACAAGAATCATCAAGGTAA+AGG 0.504207 5.4:+60127070 MS.gene060253:CDS
GTTCCATTGATCCATTAATG+AGG 0.509644 5.4:-60126582 None:intergenic
CAAAGAATCTGTTGATGGAA+AGG 0.510693 5.4:+60127207 MS.gene060253:CDS
CGATCATCATGATTTCTTGA+GGG 0.512195 5.4:-60127112 None:intergenic
TGTTATAGATGCGGAAAGAA+AGG 0.513070 5.4:+60127136 MS.gene060253:CDS
TTCCATTGATCCATTAATGA+GGG 0.533283 5.4:-60126581 None:intergenic
GATGCGGAAAGAAAGGTCAT+TGG 0.533423 5.4:+60127143 MS.gene060253:CDS
GGACTCGACAAGATTCTTGA+GGG 0.539594 5.4:+60126383 MS.gene060253:CDS
TTGGTTTGGTCATATTTGAG+AGG 0.544297 5.4:-60127049 None:intergenic
GAAATCAGCAGCCTCAAGAC+AGG 0.558951 5.4:-60127275 None:intergenic
AATTGAGTATCTTGCATGTG+AGG 0.565013 5.4:+60126361 MS.gene060253:CDS
ACGATCATCATGATTTCTTG+AGG 0.565496 5.4:-60127113 None:intergenic
CGTGGTCGAGGCAGAAGTCA+TGG 0.572503 5.4:+60126974 MS.gene060253:CDS
CAAACCAACAAGAATCATCA+AGG 0.574004 5.4:+60127064 MS.gene060253:CDS
TTTGGTTACAGCTCTTCTAG+TGG 0.574259 5.4:+60126799 MS.gene060253:CDS
AGGTAAAGGTAAAAGCATCC+AGG 0.575090 5.4:+60127084 MS.gene060253:CDS
ATTGAGTATCTTGCATGTGA+GGG 0.575966 5.4:+60126362 MS.gene060253:CDS
GGATATGCCATTGTTCCTGT+AGG 0.578642 5.4:-60126866 None:intergenic
GCAACAACAATATAGAATGA+GGG 0.579939 5.4:+60126757 MS.gene060253:CDS
TTCCTGTAGGACGCAACTGG+TGG 0.593030 5.4:-60126853 None:intergenic
AATTCATATAACCTCTTCCA+CGG 0.595635 5.4:-60127021 None:intergenic
ACGCCCTTGATTAAAAGTTG+TGG 0.608515 5.4:-60126900 None:intergenic
GCAATATCACTTGAGATGCA+TGG 0.608661 5.4:-60126736 None:intergenic
TATAATCGCCAAAGAGGACG+TGG 0.608957 5.4:+60126929 MS.gene060253:CDS
GGGACTCGACAAGATTCTTG+AGG 0.610766 5.4:+60126382 MS.gene060253:CDS
TGTTGATGGAAAGGAAAAGG+AGG 0.612844 5.4:+60127216 MS.gene060253:CDS
AAATGATACTACCTGTCTTG+AGG 0.616100 5.4:+60127264 MS.gene060253:CDS
GTCATTGGTCTAAAGCATGT+AGG 0.629444 5.4:+60127158 MS.gene060253:CDS
GATGATCGTTGTTATAGATG+CGG 0.637106 5.4:+60127127 MS.gene060253:CDS
GGTGGTTATAATCGCCAAAG+AGG 0.642086 5.4:+60126923 MS.gene060253:CDS
GTTGCGTCCTACAGGAACAA+TGG 0.661047 5.4:+60126859 MS.gene060253:CDS
AAAGGTAAAAGCATCCAGGA+AGG 0.661440 5.4:+60127088 MS.gene060253:CDS
AATCGCCAAAGAGGACGTGG+TGG 0.698905 5.4:+60126932 MS.gene060253:CDS
TTTGTAATCCATCATCAATG+TGG 0.715751 5.4:-60126475 None:intergenic
CGATTTGGGAGATGTCCCAG+AGG 0.725435 5.4:+60126409 MS.gene060253:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTATGTTTAAAATTTTGAAT+TGG - chr5.4:60126307-60126326 None:intergenic 10.0%
!!! TTCAAAATTTTAAACATAAC+TGG + chr5.4:60126308-60126327 MS.gene060253:CDS 15.0%
! ACAAAATTAAGGCAAGATTT+GGG + chr5.4:60126537-60126556 MS.gene060253:CDS 25.0%
! ATTTACTGAATACTCTGATT+TGG + chr5.4:60126781-60126800 MS.gene060253:CDS 25.0%
! CATAGGAGAAGATATTAATA+TGG + chr5.4:60127297-60127316 MS.gene060253:CDS 25.0%
! GAAGAGGTTATATGAATTAT+AGG + chr5.4:60127026-60127045 MS.gene060253:CDS 25.0%
! TATAACTGAAAAGGAAAAGT+TGG + chr5.4:60126694-60126713 MS.gene060253:CDS 25.0%
!! AAAAGATCCCAAGATTTTAT+GGG + chr5.4:60126514-60126533 MS.gene060253:CDS 25.0%
!! AATTTTGTCCCATAAAATCT+TGG - chr5.4:60126525-60126544 None:intergenic 25.0%
!! ATTCTTTGTATCTTTTACAC+AGG - chr5.4:60127195-60127214 None:intergenic 25.0%
!! ATTGCACAATTAGAATTTTG+TGG + chr5.4:60126665-60126684 MS.gene060253:CDS 25.0%
!! ATTTTGTCCCATAAAATCTT+GGG - chr5.4:60126524-60126543 None:intergenic 25.0%
!! GATTTTATGGGACAAAATTA+AGG + chr5.4:60126526-60126545 MS.gene060253:CDS 25.0%
!!! CAACAACAGTTTTATAATCT+TGG - chr5.4:60126619-60126638 None:intergenic 25.0%
AACAAGAATCATCAAGGTAA+AGG + chr5.4:60127070-60127089 MS.gene060253:CDS 30.0%
AATTCATATAACCTCTTCCA+CGG - chr5.4:60127024-60127043 None:intergenic 30.0%
AGATACAAAGAATCTGTTGA+TGG + chr5.4:60127202-60127221 MS.gene060253:CDS 30.0%
GACAAAATTAAGGCAAGATT+TGG + chr5.4:60126536-60126555 MS.gene060253:CDS 30.0%
GCAACAACAATATAGAATGA+GGG + chr5.4:60126757-60126776 MS.gene060253:CDS 30.0%
TGCAACAACAATATAGAATG+AGG + chr5.4:60126756-60126775 MS.gene060253:CDS 30.0%
TGGATCAATGGAACAAATTA+AGG + chr5.4:60126591-60126610 MS.gene060253:CDS 30.0%
TGGCAAAACTATAACTGAAA+AGG + chr5.4:60126685-60126704 MS.gene060253:CDS 30.0%
TTCCATTGATCCATTAATGA+GGG - chr5.4:60126584-60126603 None:intergenic 30.0%
TTTGTAATCCATCATCAATG+TGG - chr5.4:60126478-60126497 None:intergenic 30.0%
! AAGACAGGTAGTATCATTTT+TGG - chr5.4:60127263-60127282 None:intergenic 30.0%
! CAAAAGATCCCAAGATTTTA+TGG + chr5.4:60126513-60126532 MS.gene060253:CDS 30.0%
! TTTACCTTGATGATTCTTGT+TGG - chr5.4:60127071-60127090 None:intergenic 30.0%
!! AGACAGGTAGTATCATTTTT+GGG - chr5.4:60127262-60127281 None:intergenic 30.0%
AAAGTTGTGGCGTTTATTTC+AGG - chr5.4:60126890-60126909 None:intergenic 35.0%
AAATGATACTACCTGTCTTG+AGG + chr5.4:60127264-60127283 MS.gene060253:CDS 35.0%
AATTGAGTATCTTGCATGTG+AGG + chr5.4:60126361-60126380 MS.gene060253:CDS 35.0%
ACGATCATCATGATTTCTTG+AGG - chr5.4:60127116-60127135 None:intergenic 35.0%
ATTGAGTATCTTGCATGTGA+GGG + chr5.4:60126362-60126381 MS.gene060253:CDS 35.0%
CAAACCAACAAGAATCATCA+AGG + chr5.4:60127064-60127083 MS.gene060253:CDS 35.0%
CGATCATCATGATTTCTTGA+GGG - chr5.4:60127115-60127134 None:intergenic 35.0%
GATGATCGTTGTTATAGATG+CGG + chr5.4:60127127-60127146 MS.gene060253:CDS 35.0%
GTTCCATTGATCCATTAATG+AGG - chr5.4:60126585-60126604 None:intergenic 35.0%
TGTTATAGATGCGGAAAGAA+AGG + chr5.4:60127136-60127155 MS.gene060253:CDS 35.0%
! AACGCCACAACTTTTAATCA+AGG + chr5.4:60126896-60126915 MS.gene060253:CDS 35.0%
! ACGCCACAACTTTTAATCAA+GGG + chr5.4:60126897-60126916 MS.gene060253:CDS 35.0%
! ATCTGTTGATGGAAAGGAAA+AGG + chr5.4:60127213-60127232 MS.gene060253:CDS 35.0%
! CAAAGAATCTGTTGATGGAA+AGG + chr5.4:60127207-60127226 MS.gene060253:CDS 35.0%
! CTCAATTAAGTTGTTGTTCC+AGG - chr5.4:60126348-60126367 None:intergenic 35.0%
! CTTGATGATTCTTGTTGGTT+TGG - chr5.4:60127066-60127085 None:intergenic 35.0%
! TATCTTTTACACAGGTACTC+TGG - chr5.4:60127187-60127206 None:intergenic 35.0%
! TTTTCTTTGCCAATTCCTCT+GGG - chr5.4:60126427-60126446 None:intergenic 35.0%
! TTTTTCTTTGCCAATTCCTC+TGG - chr5.4:60126428-60126447 None:intergenic 35.0%
!! AGTCTTATTGCCCTCATTAA+TGG + chr5.4:60126571-60126590 MS.gene060253:CDS 35.0%
!! TTGGTTTGGTCATATTTGAG+AGG - chr5.4:60127052-60127071 None:intergenic 35.0%
ACGCCCTTGATTAAAAGTTG+TGG - chr5.4:60126903-60126922 None:intergenic 40.0%
ATCAAGCACCACATTGATGA+TGG + chr5.4:60126467-60126486 MS.gene060253:CDS 40.0%
ATTCTTGAGGGAGACGATTT+GGG + chr5.4:60126395-60126414 MS.gene060253:CDS 40.0%
GCAATATCACTTGAGATGCA+TGG - chr5.4:60126739-60126758 None:intergenic 40.0%
TTTGGTTACAGCTCTTCTAG+TGG + chr5.4:60126799-60126818 MS.gene060253:CDS 40.0%
! ACAACTTTTAATCAAGGGCG+TGG + chr5.4:60126902-60126921 MS.gene060253:CDS 40.0%
! GTCATTGGTCTAAAGCATGT+AGG + chr5.4:60127158-60127177 MS.gene060253:CDS 40.0%
! TGCCCTCATTAATGGATCAA+TGG + chr5.4:60126579-60126598 MS.gene060253:CDS 40.0%
! TGTTGATGGAAAGGAAAAGG+AGG + chr5.4:60127216-60127235 MS.gene060253:CDS 40.0%
!! AAAGGTAAAAGCATCCAGGA+AGG + chr5.4:60127088-60127107 MS.gene060253:CDS 40.0%
!! AGGTAAAGGTAAAAGCATCC+AGG + chr5.4:60127084-60127103 MS.gene060253:CDS 40.0%
CTGGAGACAACTACATAACC+TGG + chr5.4:60126327-60126346 MS.gene060253:CDS 45.0%
GATGCGGAAAGAAAGGTCAT+TGG + chr5.4:60127143-60127162 MS.gene060253:CDS 45.0%
GATTCTTGAGGGAGACGATT+TGG + chr5.4:60126394-60126413 MS.gene060253:CDS 45.0%
GGACTCGACAAGATTCTTGA+GGG + chr5.4:60126383-60126402 MS.gene060253:CDS 45.0%
GGATATGCCATTGTTCCTGT+AGG - chr5.4:60126869-60126888 None:intergenic 45.0%
GGTGGTTATAATCGCCAAAG+AGG + chr5.4:60126923-60126942 MS.gene060253:CDS 45.0%
TATAATCGCCAAAGAGGACG+TGG + chr5.4:60126929-60126948 MS.gene060253:CDS 45.0%
! CATGGTCGAAACCATTTTCG+TGG + chr5.4:60126992-60127011 MS.gene060253:CDS 45.0%
!! ACTTTTAATCAAGGGCGTGG+TGG + chr5.4:60126905-60126924 MS.gene060253:CDS 45.0%
!! CTTGAGGCTGCTGATTTCAT+AGG + chr5.4:60127280-60127299 MS.gene060253:CDS 45.0%
!! TATGCTCGTTTTGGTAGTCG+TGG + chr5.4:60126956-60126975 MS.gene060253:CDS 45.0%
GAAATCAGCAGCCTCAAGAC+AGG - chr5.4:60127278-60127297 None:intergenic 50.0%
GATTTCTTGAGGGACCTTCC+TGG - chr5.4:60127105-60127124 None:intergenic 50.0%
GGGACTCGACAAGATTCTTG+AGG + chr5.4:60126382-60126401 MS.gene060253:CDS 50.0%
GTTGCGTCCTACAGGAACAA+TGG + chr5.4:60126859-60126878 MS.gene060253:CDS 50.0%
TTGTTCCTGTAGGACGCAAC+TGG - chr5.4:60126859-60126878 None:intergenic 50.0%
! CGAAACCATTTTCGTGGTGG+AGG + chr5.4:60126998-60127017 MS.gene060253:CDS 50.0%
! GGTCGAAACCATTTTCGTGG+TGG + chr5.4:60126995-60127014 MS.gene060253:CDS 50.0%
AACCACCAGTTGCGTCCTAC+AGG + chr5.4:60126851-60126870 MS.gene060253:CDS 55.0%
AATCGCCAAAGAGGACGTGG+TGG + chr5.4:60126932-60126951 MS.gene060253:CDS 55.0%
CATAGCCACCACGTCCTCTT+TGG - chr5.4:60126940-60126959 None:intergenic 55.0%
GGGAGATGTCCCAGAGGAAT+TGG + chr5.4:60126415-60126434 MS.gene060253:CDS 55.0%
TTCCTGTAGGACGCAACTGG+TGG - chr5.4:60126856-60126875 None:intergenic 55.0%
! CGATTTGGGAGATGTCCCAG+AGG + chr5.4:60126409-60126428 MS.gene060253:CDS 55.0%
! CGTGGTGGCTATGCTCGTTT+TGG + chr5.4:60126947-60126966 MS.gene060253:CDS 55.0%
!! CGTTTTGGTAGTCGTGGTCG+AGG + chr5.4:60126962-60126981 MS.gene060253:CDS 55.0%
CACGGCCTCCACCACGAAAA+TGG - chr5.4:60127006-60127025 None:intergenic 60.0%
CGTGGTCGAGGCAGAAGTCA+TGG + chr5.4:60126974-60126993 MS.gene060253:CDS 60.0%
!! CATTTTCGTGGTGGAGGCCG+TGG + chr5.4:60127004-60127023 MS.gene060253:CDS 60.0%
! CGTGGTGGAGGCCGTGGAAG+AGG + chr5.4:60127010-60127029 MS.gene060253:CDS 70.0%


Chromosome Type Strat End Strand Name
chr5.4 gene 60126287 60127324 60126287 ID=MS.gene060253
chr5.4 mRNA 60126287 60127324 60126287 ID=MS.gene060253.t1;Parent=MS.gene060253
chr5.4 exon 60126287 60127324 60126287 ID=MS.gene060253.t1.exon1;Parent=MS.gene060253.t1
chr5.4 CDS 60126287 60127324 60126287 ID=cds.MS.gene060253.t1;Parent=MS.gene060253.t1
Gene Sequence

>MS.gene060253

ATGTCAAATGTTAAGCACCAATTCAAAATTTTAAACATAACTGGAGACAACTACATAACCTGGAACAACAACTTAATTGAGTATCTTGCATGTGAGGGACTCGACAAGATTCTTGAGGGAGACGATTTGGGAGATGTCCCAGAGGAATTGGCAAAGAAAAAATCAAAAGTAAATCGTATAATCAAGCACCACATTGATGATGGATTACAAACAGAGTATTCGAATGCAAAAGATCCCAAGATTTTATGGGACAAAATTAAGGCAAGATTTGGGCATCAGAAGAAAGTCTTATTGCCCTCATTAATGGATCAATGGAACAAATTAAGGTTCCAAGATTATAAAACTGTTGTTGCATATAACTCTGCTATGCATCAAATTATTGCACAATTAGAATTTTGTGGCAAAACTATAACTGAAAAGGAAAAGTTGGAGAAAACATTCTCAACTTTCCATGCATCTCAAGTGATATTGCAACAACAATATAGAATGAGGGAATTTACTGAATACTCTGATTTGGTTACAGCTCTTCTAGTGGCTGAACAAAATAATGTACTGCTCATTAAAAACCACCAGTTGCGTCCTACAGGAACAATGGCATATCCTGAAATAAACGCCACAACTTTTAATCAAGGGCGTGGTGGTTATAATCGCCAAAGAGGACGTGGTGGCTATGCTCGTTTTGGTAGTCGTGGTCGAGGCAGAAGTCATGGTCGAAACCATTTTCGTGGTGGAGGCCGTGGAAGAGGTTATATGAATTATAGGCCTCTCAAATATGACCAAACCAACAAGAATCATCAAGGTAAAGGTAAAAGCATCCAGGAAGGTCCCTCAAGAAATCATGATGATCGTTGTTATAGATGCGGAAAGAAAGGTCATTGGTCTAAAGCATGTAGGACACCAGAGTACCTGTGTAAAAGATACAAAGAATCTGTTGATGGAAAGGAAAAGGAGGTTAATTTTAATGAAATTGAACCCAAAAATGATACTACCTGTCTTGAGGCTGCTGATTTCATAGGAGAAGATATTAATATGGATTAA

Protein sequence

>MS.gene060253.t1

MSNVKHQFKILNITGDNYITWNNNLIEYLACEGLDKILEGDDLGDVPEELAKKKSKVNRIIKHHIDDGLQTEYSNAKDPKILWDKIKARFGHQKKVLLPSLMDQWNKLRFQDYKTVVAYNSAMHQIIAQLEFCGKTITEKEKLEKTFSTFHASQVILQQQYRMREFTEYSDLVTALLVAEQNNVLLIKNHQLRPTGTMAYPEINATTFNQGRGGYNRQRGRGGYARFGSRGRGRSHGRNHFRGGGRGRGYMNYRPLKYDQTNKNHQGKGKSIQEGPSRNHDDRCYRCGKKGHWSKACRTPEYLCKRYKESVDGKEKEVNFNEIEPKNDTTCLEAADFIGEDINMD