AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene022106

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene022106.t1 MTR_7g021030 100.000 112 0 0 1 112 1 112 1.89e-79 229
MS.gene022106.t1 MTR_0024s0220 98.214 112 2 0 1 112 1 112 4.04e-78 225
MS.gene022106.t1 MTR_5g088740 92.857 112 8 0 1 112 1 112 1.27e-74 216
MS.gene022106.t1 MTR_0024s0220 97.030 101 3 0 1 101 1 101 7.17e-69 202
MS.gene022106.t1 MTR_7g021030 96.203 79 3 0 1 79 1 79 3.58e-50 154
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene022106.t1 AT1G36240 88.393 112 13 0 1 112 1 112 9.26e-72 209
MS.gene022106.t1 AT1G77940 87.500 112 14 0 1 112 1 112 6.12e-71 207
MS.gene022106.t1 AT3G18740 87.500 112 14 0 1 112 1 112 6.98e-71 207

Find 26 sgRNAs with CRISPR-Local

Find 84 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTAACAACTGTCCTCCTTTG+AGG 0.365472 7.4:-80682572 MS.gene022106:CDS
GACATCATCAAGACAATTCC+TGG 0.382525 7.4:-80681335 MS.gene022106:CDS
ACAACTTACTTCCATTGTAA+TGG 0.429111 7.4:+80682502 None:intergenic
CTCATGAGAGCATCAACAAC+AGG 0.462326 7.4:-80683023 MS.gene022106:CDS
TGCCTCAGCATTGTTGATCC+TGG 0.466033 7.4:-80681453 MS.gene022106:intron
GAAGCTTACGGTCTTCTTTG+CGG 0.470686 7.4:+80683144 None:intergenic
TACTACGTTTACTGATCTCC+AGG 0.471605 7.4:+80681317 None:intergenic
AATTACCTTTAGAACTCCTA+AGG 0.474325 7.4:+80682941 None:intergenic
AAGAGTGGAAAATATACCCT+TGG 0.505811 7.4:-80682985 MS.gene022106:CDS
GTTGACCTTGGCACTGCTTG+TGG 0.506943 7.4:-80681495 MS.gene022106:CDS
AAACCGTTCTCAAATCCCTT+AGG 0.509696 7.4:-80682957 MS.gene022106:CDS
ATTACCTTTAGAACTCCTAA+GGG 0.521637 7.4:+80682942 None:intergenic
TATGCTATGTTGGCTAAGGT+TGG 0.529938 7.4:-80682531 MS.gene022106:CDS
AAATCCCTTAGGAGTTCTAA+AGG 0.532626 7.4:-80682946 MS.gene022106:intron
ATCATAGACAATGTTGACCT+TGG 0.543023 7.4:-80681507 MS.gene022106:intron
CTCGCTCTTGTCATGAAGAG+TGG 0.545906 7.4:-80683000 MS.gene022106:CDS
AATTGAGTACTATGCTATGT+TGG 0.552970 7.4:-80682541 MS.gene022106:CDS
AGAGTGGAAAATATACCCTT+GGG 0.553555 7.4:-80682984 MS.gene022106:CDS
GTACTATGCTATGTTGGCTA+AGG 0.556485 7.4:-80682535 MS.gene022106:CDS
ACTCCTAAGGGATTTGAGAA+CGG 0.577693 7.4:+80682954 None:intergenic
ATTTCAGACTTCCTCAAAGG+AGG 0.587118 7.4:+80682561 None:intergenic
TCAATTTCAGACTTCCTCAA+AGG 0.597003 7.4:+80682558 None:intergenic
GTTGGAGTTCACCATTACAA+TGG 0.600433 7.4:-80682513 MS.gene022106:CDS
AGGAATTGTCTTGATGATGT+CGG 0.611366 7.4:+80681337 None:intergenic
ACTTTCCACAAGCAGTGCCA+AGG 0.620377 7.4:+80681490 None:intergenic
TACCAGGATCAACAATGCTG+AGG 0.662178 7.4:+80681451 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TGTAAATTAAATTAAATTGT+CGG - chr7.4:80681829-80681848 MS.gene022106:intron 10.0%
!! AATAACAAATAAAATTAGAG+AGG + chr7.4:80683101-80683120 None:intergenic 15.0%
!! ATAACAAATAAAATTAGAGA+GGG + chr7.4:80683100-80683119 None:intergenic 15.0%
!!! AACTTTATTTTATAAGATTC+TGG - chr7.4:80682485-80682504 MS.gene022106:intron 15.0%
!!! ATTTTGATTTGATTATTTGT+AGG - chr7.4:80681864-80681883 MS.gene022106:intron 15.0%
!!! CTCTAATTTTATTTGTTATT+TGG - chr7.4:80683101-80683120 MS.gene022106:intron 15.0%
!!! TTTTGATTTGATTATTTGTA+GGG - chr7.4:80681865-80681884 MS.gene022106:intron 15.0%
!! AAATTAAATTAAATTGTCGG+TGG - chr7.4:80681832-80681851 MS.gene022106:intron 20.0%
!! ATGTTTGGATTAATGATATA+GGG + chr7.4:80682252-80682271 None:intergenic 20.0%
!! TACTGGAAAAATATTATACA+TGG - chr7.4:80682410-80682429 MS.gene022106:intron 20.0%
!! TATAATTATCTATCAGTAGT+TGG - chr7.4:80682590-80682609 MS.gene022106:CDS 20.0%
!! TATGTTTGGATTAATGATAT+AGG + chr7.4:80682253-80682272 None:intergenic 20.0%
!! TGTTGAAAGAATATTATACA+TGG - chr7.4:80682356-80682375 MS.gene022106:intron 20.0%
!! TTAATCCAAACATAATGTTA+CGG - chr7.4:80682259-80682278 MS.gene022106:intron 20.0%
!!! AGCTAGTTATACTTTAAAAA+TGG - chr7.4:80682195-80682214 MS.gene022106:intron 20.0%
! ATGATTTCGTTTCAGATTTA+GGG - chr7.4:80681384-80681403 MS.gene022106:intron 25.0%
! TACACATTTCAACAACAAAA+TGG + chr7.4:80681569-80681588 None:intergenic 25.0%
! TAGAATGAAATGAAATGTAG+TGG - chr7.4:80682155-80682174 MS.gene022106:intron 25.0%
! TATGATTTCGTTTCAGATTT+AGG - chr7.4:80681383-80681402 MS.gene022106:intron 25.0%
!! AATATTTTTCCAGTATGACA+AGG + chr7.4:80682405-80682424 None:intergenic 25.0%
!! TACATTAACAGAAGCATATT+TGG + chr7.4:80682648-80682667 None:intergenic 25.0%
!! TAGTTTGATGATTATGCATA+TGG - chr7.4:80682718-80682737 MS.gene022106:intron 25.0%
!! TTGTTGTTGAAATGTGTATT+GGG - chr7.4:80681571-80681590 MS.gene022106:intron 25.0%
!! TTTTGTAATGTTGAATTTGC+TGG - chr7.4:80681794-80681813 MS.gene022106:intron 25.0%
!!! ATTTGTTATTTGGTGTTTTC+AGG - chr7.4:80683111-80683130 MS.gene022106:intron 25.0%
!!! GAAATGTAGTGGATTAAAAT+GGG - chr7.4:80682166-80682185 MS.gene022106:intron 25.0%
!!! TGAAATGTAGTGGATTAAAA+TGG - chr7.4:80682165-80682184 MS.gene022106:intron 25.0%
!!! TTTGTTGTTGAAATGTGTAT+TGG - chr7.4:80681570-80681589 MS.gene022106:intron 25.0%
AATTATTGCATGTGACCATA+AGG + chr7.4:80682312-80682331 None:intergenic 30.0%
AATTGAGTACTATGCTATGT+TGG - chr7.4:80681935-80681954 MS.gene022106:intron 30.0%
ACAACTTACTTCCATTGTAA+TGG + chr7.4:80681977-80681996 None:intergenic 30.0%
ATTATTGCATGTGACCATAA+GGG + chr7.4:80682311-80682330 None:intergenic 30.0%
ATTGTGTATGTATACCCTTA+TGG - chr7.4:80682294-80682313 MS.gene022106:intron 30.0%
TAAAGAAAGCAACATATACC+AGG + chr7.4:80683044-80683063 None:intergenic 30.0%
TATGCATAGATTAGATTGCA+AGG - chr7.4:80681617-80681636 MS.gene022106:intron 30.0%
TCAATGTTGATATGCATTCA+GGG - chr7.4:80682032-80682051 MS.gene022106:intron 30.0%
TTCAATGTTGATATGCATTC+AGG - chr7.4:80682031-80682050 MS.gene022106:intron 30.0%
TTTGGATTAATGATATAGGG+TGG + chr7.4:80682249-80682268 None:intergenic 30.0%
!! AATTACCTTTAGAACTCCTA+AGG + chr7.4:80681538-80681557 None:intergenic 30.0%
!! ATTACCTTTAGAACTCCTAA+GGG + chr7.4:80681537-80681556 None:intergenic 30.0%
AAGAGTGGAAAATATACCCT+TGG - chr7.4:80681491-80681510 MS.gene022106:CDS 35.0%
AGAGTGGAAAATATACCCTT+GGG - chr7.4:80681492-80681511 MS.gene022106:CDS 35.0%
ATCATAGACAATGTTGACCT+TGG - chr7.4:80682969-80682988 MS.gene022106:CDS 35.0%
CTAATCGAACTATGCATATG+CGG + chr7.4:80682686-80682705 None:intergenic 35.0%
TAAGAAGAATCCCAACGATT+TGG + chr7.4:80682843-80682862 None:intergenic 35.0%
TACATCTAACCTTGTCATAC+TGG - chr7.4:80682393-80682412 MS.gene022106:intron 35.0%
TATCTATCAGTAGTTGGATG+TGG - chr7.4:80682596-80682615 MS.gene022106:intron 35.0%
TATGCATTCAGGGATTGTTT+AGG - chr7.4:80682042-80682061 MS.gene022106:intron 35.0%
TCAATTTCAGACTTCCTCAA+AGG + chr7.4:80681921-80681940 None:intergenic 35.0%
TGCTGAATGAAAGAAGCTTA+CGG + chr7.4:80681347-80681366 None:intergenic 35.0%
TGTGACCGTAACATTATGTT+TGG + chr7.4:80682267-80682286 None:intergenic 35.0%
! AAATCCCTTAGGAGTTCTAA+AGG - chr7.4:80681530-80681549 MS.gene022106:intron 35.0%
! AATTGACGACACAGAAGTAT+AGG + chr7.4:80682010-80682029 None:intergenic 35.0%
! TCTGTTATCAGTTGACTCTA+AGG - chr7.4:80682890-80682909 MS.gene022106:intron 35.0%
!! AGGAATTGTCTTGATGATGT+CGG + chr7.4:80683142-80683161 None:intergenic 35.0%
!! ATAGTAACAAGTGCTGATCA+AGG + chr7.4:80682799-80682818 None:intergenic 35.0%
!! TGTTGTTTCTCCAAATCGTT+GGG - chr7.4:80682830-80682849 MS.gene022106:intron 35.0%
!! TTGTTGTTTCTCCAAATCGT+TGG - chr7.4:80682829-80682848 MS.gene022106:intron 35.0%
AAACCGTTCTCAAATCCCTT+AGG - chr7.4:80681519-80681538 MS.gene022106:intron 40.0%
AAATGACACTACTGTACGAC+AGG + chr7.4:80682460-80682479 None:intergenic 40.0%
AATGACACTACTGTACGACA+GGG + chr7.4:80682459-80682478 None:intergenic 40.0%
ACTCCTAAGGGATTTGAGAA+CGG + chr7.4:80681525-80681544 None:intergenic 40.0%
ATTTCAGACTTCCTCAAAGG+AGG + chr7.4:80681918-80681937 None:intergenic 40.0%
ATTTGATCTTACGCTGCTGT+TGG - chr7.4:80682524-80682543 MS.gene022106:CDS 40.0%
CACTGATACACACTAAAGCT+CGG + chr7.4:80682132-80682151 None:intergenic 40.0%
GACATCATCAAGACAATTCC+TGG - chr7.4:80683141-80683160 MS.gene022106:intron 40.0%
GTTGGAGTTCACCATTACAA+TGG - chr7.4:80681963-80681982 MS.gene022106:intron 40.0%
GTTGTAGAGTGATGTTGTAG+TGG - chr7.4:80681746-80681765 MS.gene022106:intron 40.0%
TTTGATCTTACGCTGCTGTT+GGG - chr7.4:80682525-80682544 MS.gene022106:CDS 40.0%
! AGAGTGATGTTGTAGTGGAA+TGG - chr7.4:80681751-80681770 MS.gene022106:intron 40.0%
! GTACTATGCTATGTTGGCTA+AGG - chr7.4:80681941-80681960 MS.gene022106:intron 40.0%
! TATGCTATGTTGGCTAAGGT+TGG - chr7.4:80681945-80681964 MS.gene022106:intron 40.0%
!! GAGAACGGTTTTATACCCAA+GGG + chr7.4:80681510-80681529 None:intergenic 40.0%
!! TGAGAACGGTTTTATACCCA+AGG + chr7.4:80681511-80681530 None:intergenic 40.0%
CTAACAACTGTCCTCCTTTG+AGG - chr7.4:80681904-80681923 MS.gene022106:intron 45.0%
GAAGCTTACGGTCTTCTTTG+CGG + chr7.4:80681335-80681354 None:intergenic 45.0%
TACCAGGATCAACAATGCTG+AGG + chr7.4:80683028-80683047 None:intergenic 45.0%
! CGAGCTTTAGTGTGTATCAG+TGG - chr7.4:80682130-80682149 MS.gene022106:intron 45.0%
! TCGGCTAGCTAGAATCAATC+AGG + chr7.4:80682113-80682132 None:intergenic 45.0%
!! CTCATGAGAGCATCAACAAC+AGG - chr7.4:80681453-80681472 MS.gene022106:intron 45.0%
ACTTTCCACAAGCAGTGCCA+AGG + chr7.4:80682989-80683008 None:intergenic 50.0%
CTCGCTCTTGTCATGAAGAG+TGG - chr7.4:80681476-80681495 MS.gene022106:CDS 50.0%
TGCCTCAGCATTGTTGATCC+TGG - chr7.4:80683023-80683042 MS.gene022106:CDS 50.0%
GTTGACCTTGGCACTGCTTG+TGG - chr7.4:80682981-80683000 MS.gene022106:CDS 55.0%


Chromosome Type Strat End Strand Name
chr7.4 gene 80681325 80683173 80681325 ID=MS.gene022106
chr7.4 mRNA 80681325 80683173 80681325 ID=MS.gene022106.t1;Parent=MS.gene022106
chr7.4 exon 80683153 80683173 80683153 ID=MS.gene022106.t1.exon1;Parent=MS.gene022106.t1
chr7.4 CDS 80683153 80683173 80683153 ID=cds.MS.gene022106.t1;Parent=MS.gene022106.t1
chr7.4 exon 80682947 80683052 80682947 ID=MS.gene022106.t1.exon2;Parent=MS.gene022106.t1
chr7.4 CDS 80682947 80683052 80682947 ID=cds.MS.gene022106.t1;Parent=MS.gene022106.t1
chr7.4 exon 80682511 80682612 80682511 ID=MS.gene022106.t1.exon3;Parent=MS.gene022106.t1
chr7.4 CDS 80682511 80682612 80682511 ID=cds.MS.gene022106.t1;Parent=MS.gene022106.t1
chr7.4 exon 80681454 80681522 80681454 ID=MS.gene022106.t1.exon4;Parent=MS.gene022106.t1
chr7.4 CDS 80681454 80681522 80681454 ID=cds.MS.gene022106.t1;Parent=MS.gene022106.t1
chr7.4 exon 80681325 80681365 80681325 ID=MS.gene022106.t1.exon5;Parent=MS.gene022106.t1
chr7.4 CDS 80681325 80681365 80681325 ID=cds.MS.gene022106.t1;Parent=MS.gene022106.t1
Gene Sequence

>MS.gene022106

ATGGTGGCCGCAAAGAAGACCGTAAGCTTCTTTCATTCAGCATTTGTTGATTTTTCATTATGATTTCGTTTCAGATTTAGGGTTTTTGATTCTGAATCGAATTTTTGATTGATTTTTACAGAAGAAGACTCATGAGAGCATCAACAACAGGCTCGCTCTTGTCATGAAGAGTGGAAAATATACCCTTGGGTATAAAACCGTTCTCAAATCCCTTAGGAGTTCTAAAGGTAATTTTTTTTATCCATTTTGTTGTTGAAATGTGTATTGGGACGTTTTTGTTTTGCTGATAAGCTATGCATAGATTAGATTGCAAGGACTTGTTTGAAATTGTTTACATGCTTTGTAATTTGAACTGTTGAAGATTGATTTTGTAGTTGAATTAAGTGATTAGTGAAATTAAGTGATTATTTTAGATTGAACTGTTGTAGAGTGATGTTGTAGTGGAATGGAAATCAGTGATTATACTTGATTTTGTAATGTTGAATTTGCTGGTTTGTGAACTGTTGTAAATTAAATTAAATTGTCGGTGGAATTAAGTGATTTTGATTTGATTATTTGTAGGGAAATTGATTATCATTGCTAACAACTGTCCTCCTTTGAGGAAGTCTGAAATTGAGTACTATGCTATGTTGGCTAAGGTTGGAGTTCACCATTACAATGGAAGTAAGTTGTTTATCTAGCTCCTATACTTCTGTGTCGTCAATTTTTCAATGTTGATATGCATTCAGGGATTGTTTAGGATCATTATTTTATTTTTATCGTGTTGTGTTTTTCTTTGCTTTAGTCCTGATTGATTCTAGCTAGCCGAGCTTTAGTGTGTATCAGTGGTATAGAATGAAATGAAATGTAGTGGATTAAAATGGGATAAGAAGCTAGTTATACTTTAAAAATGGATGTTATTTCATTTCATTCTACTCTATTCCACCCTATATCATTAATCCAAACATAATGTTACGGTCACATGTAGTAATTGTGTATGTATACCCTTATGGTCACATGCAATAATTGTCTATGCATTGATTTGTCAGTCATGTTGAAAGAATATTATACATGGTTGAATGTATGTGATACATCTAACCTTGTCATACTGGAAAAATATTATACATGGTTGAACGAATGTGATGCAACGAACCCTGTCGTACAGTAGTGTCATTTGACTTAACTTTATTTTATAAGATTCTGGTAAATGAAATAATATGATTTGATCTTACGCTGCTGTTGGGAACATTTTTATTGTATATGATTTTGCGATGTTTATTAGAAATTATAATTATCTATCAGTAGTTGGATGTGGAACTAATTTTTAGTGATGCGTTGTTTCCAAATATGCTTCTGTTAATGTATGCATGCACTTATTACCGCATATGCATAGTTCGATTAGTATGCATATGCTTAGTTTGATGATTATGCATATGGCTTAGTTTGATGATTATGCATATATGCTTAGTTTGATGATTATGCATATGGCTTACCTTGATCAGCACTTGTTACTATTCTTGTTGTATTGTTGTTTCTCCAAATCGTTGGGATTCTTCTTATTGATGTTAATTGTCAAATATAATGTGTCTGTTATCAGTTGACTCTAAGGTTTCTGCATATATATTTGTAAGACACTTTTATTGACAAGTTGAACTTTTATGTATTATCATAGACAATGTTGACCTTGGCACTGCTTGTGGAAAGTACTACAGAGTGTGCTGCCTCAGCATTGTTGATCCTGGTATATGTTGCTTTCTTTAACTGTTTTAGTATTAAAAACTAGTTTTTTTTTTCCCTCTCTAATTTTATTTGTTATTTGGTGTTTTCAGGTGATTCCGACATCATCAAGACAATTCCTGGAGATCAGTAA
Protein sequence

>MS.gene022106.t1

MVAAKKTKKTHESINNRLALVMKSGKYTLGYKTVLKSLRSSKGKLIIIANNCPPLRKSEIEYYAMLAKVGVHHYNGNNVDLGTACGKYYRVCCLSIVDPGDSDIIKTIPGDQ