AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene35160


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene35160.t1 MTR_5g004830 41.429 140 71 3 6 142 11 142 3.49e-33 115
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 44 sgRNAs with CRISPR-Local

Find 102 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ACTTCAAACTCGCAGTTATA+CGG 0.304728 4.4:-19272966 None:intergenic
TGGGAGGTGCTGATTCATTC+TGG 0.307310 4.4:+19271449 MS.gene35160:CDS
CTTCTCTGCATCAACCTTAC+TGG 0.321088 4.4:-19271306 None:intergenic
GTTTAAGATGGACAGTAATC+CGG 0.386700 4.4:+19271798 MS.gene35160:CDS
TACATTTGTTGAAGCGAGTA+AGG 0.420870 4.4:+19271753 MS.gene35160:CDS
AGACATGGAGGAACCGGTAT+TGG 0.457153 4.4:-19271407 None:intergenic
TGAATGTTCGAACAAATTCA+TGG 0.458298 4.4:+19271429 MS.gene35160:CDS
CGAATTCCATTCCACATCAA+TGG 0.458515 4.4:+19271589 MS.gene35160:CDS
GCAGGTTCTACATCAATTTG+AGG 0.461169 4.4:-19271368 None:intergenic
TGACAGATTGTTGTTTAAGA+TGG 0.463808 4.4:+19271786 MS.gene35160:CDS
ACATTCAGACATGGAGGAAC+CGG 0.479236 4.4:-19271413 None:intergenic
AATGTCAGAGTCTCTTTCCC+AGG 0.481300 4.4:-19271625 None:intergenic
TTTAAGATGGACAGTAATCC+GGG 0.497303 4.4:+19271799 MS.gene35160:CDS
AAAGATCCATTGATGTGGAA+TGG 0.510519 4.4:-19271595 None:intergenic
TATGTGCAGAAGAAATTCAT+AGG 0.511115 4.4:+19271718 MS.gene35160:CDS
TTCGACGGTGTTGCCTCCAC+CGG 0.514992 4.4:-19272940 None:intergenic
ATGCAATATTCGAATGAAGA+AGG 0.515264 4.4:+19271329 MS.gene35160:CDS
GGCTCACGGTAATCATCTGC+AGG 0.521858 4.4:-19271386 None:intergenic
AAGATGCAGTTGATGCGATC+TGG 0.525388 4.4:+19271668 MS.gene35160:CDS
TGCAGAAGAAATTCATAGGA+AGG 0.530136 4.4:+19271722 MS.gene35160:CDS
TAGATTACCAGCTTATGAGT+TGG 0.531267 4.4:-19271482 None:intergenic
GTAATCAATAACGCCGGTGG+AGG 0.535659 4.4:+19272927 MS.gene35160:CDS
TTCTTCTGCACATAATCACC+AGG 0.548008 4.4:-19271709 None:intergenic
TTTACGTCCAACTCATAAGC+TGG 0.553121 4.4:+19271475 MS.gene35160:CDS
CAGAAGAAATTCATAGGAAG+GGG 0.562018 4.4:+19271724 MS.gene35160:CDS
TGATTACCGTGAGCCAATAC+CGG 0.564459 4.4:+19271394 MS.gene35160:CDS
AGAAATTCATAGGAAGGGGT+TGG 0.574152 4.4:+19271728 MS.gene35160:CDS
GAAGCGAGTAAGGTGAAAGT+TGG 0.578483 4.4:+19271763 MS.gene35160:CDS
GCAGAAGAAATTCATAGGAA+GGG 0.580030 4.4:+19271723 MS.gene35160:CDS
GAATGTTCGAACAAATTCAT+GGG 0.580892 4.4:+19271430 MS.gene35160:CDS
AGAGACTCTGACATTGACAT+TGG 0.584037 4.4:+19271633 MS.gene35160:CDS
TTACTGCAGTGAGTCCAGTA+AGG 0.589344 4.4:+19271292 MS.gene35160:intron
CACGAAAAGATCCATTGATG+TGG 0.608405 4.4:-19271600 None:intergenic
TTTGTTCGAACATTCAGACA+TGG 0.613761 4.4:-19271422 None:intergenic
TGAGAATGGCAACATTGAAG+AGG 0.623240 4.4:+19271195 None:intergenic
GAGGAACCGGTATTGGCTCA+CGG 0.632876 4.4:-19271400 None:intergenic
CAATATTCGAATGAAGAAGG+AGG 0.651295 4.4:+19271332 MS.gene35160:CDS
ATTGTAATCAATAACGCCGG+TGG 0.653478 4.4:+19272924 MS.gene35160:CDS
TGTGATATTGATGTTGAACC+TGG 0.654348 4.4:+19271691 MS.gene35160:CDS
GCAGTTATACGGTGGTTCGA+CGG 0.660300 4.4:-19272955 None:intergenic
GTTCGAACATTCAGACATGG+AGG 0.688432 4.4:-19271419 None:intergenic
TGTTCGAACAAATTCATGGG+AGG 0.689256 4.4:+19271433 MS.gene35160:CDS
GCAATTGTAATCAATAACGC+CGG 0.690508 4.4:+19272921 MS.gene35160:CDS
TCAAACTCGCAGTTATACGG+TGG 0.708422 4.4:-19272963 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! AATTTTATATATAATAAATA+AGG + chr4.4:19272068-19272087 MS.gene35160:intron 0.0%
!!! TATTTTCATCTTTTAAAATA+AGG - chr4.4:19272734-19272753 None:intergenic 10.0%
!! ATAAAACTAACATAAAGTAA+GGG - chr4.4:19271516-19271535 None:intergenic 15.0%
!! TATAAAACTAACATAAAGTA+AGG - chr4.4:19271517-19271536 None:intergenic 15.0%
!! TTAAAAGATGAAAATAGAAA+GGG + chr4.4:19272738-19272757 MS.gene35160:intron 15.0%
!! TTTAAAAGATGAAAATAGAA+AGG + chr4.4:19272737-19272756 MS.gene35160:intron 15.0%
!!! AAAAGCTAAAAAAATGTTTT+TGG + chr4.4:19272329-19272348 MS.gene35160:intron 15.0%
!!! AAAGTTGATTATTAATGAAA+TGG + chr4.4:19272137-19272156 MS.gene35160:intron 15.0%
!!! TATTTTAAACTTTGTAGTAA+TGG + chr4.4:19271970-19271989 MS.gene35160:intron 15.0%
!!! TTTTCTAATTTATTAATTCC+AGG - chr4.4:19272532-19272551 None:intergenic 15.0%
!! ACGAAAAGACTTAAATATAT+AGG + chr4.4:19272200-19272219 MS.gene35160:intron 20.0%
!! TAAAAGATGAAAATAGAAAG+GGG + chr4.4:19272739-19272758 MS.gene35160:intron 20.0%
!! TAATTGCTATGTTAAATTTC+TGG + chr4.4:19271822-19271841 MS.gene35160:intron 20.0%
!! TATTATGAATAAGAATAGCA+TGG + chr4.4:19272092-19272111 MS.gene35160:intron 20.0%
!! TTGATTATTAATGAAATGGT+TGG + chr4.4:19272141-19272160 MS.gene35160:intron 20.0%
! AAAAAGAATAAGAAGATGAG+AGG - chr4.4:19272837-19272856 None:intergenic 25.0%
! AAAAGATGAAAATAGAAAGG+GGG + chr4.4:19272740-19272759 MS.gene35160:intron 25.0%
! AAGACTTAAATATATAGGAG+TGG + chr4.4:19272205-19272224 MS.gene35160:intron 25.0%
! AATTTAACATAGCAATTACC+CGG - chr4.4:19271820-19271839 None:intergenic 25.0%
! ACCTGTAAATATAGTGAATT+TGG + chr4.4:19272353-19272372 MS.gene35160:intron 25.0%
! AGTATCAAGTCAACATAAAA+TGG - chr4.4:19271263-19271282 None:intergenic 25.0%
! CCTGTAAATATAGTGAATTT+GGG + chr4.4:19272354-19272373 MS.gene35160:intron 25.0%
! GTATTAAGTACTAAAAGATC+AGG + chr4.4:19271920-19271939 MS.gene35160:intron 25.0%
! TACAGGAAGAAGAATAATAA+TGG - chr4.4:19272788-19272807 None:intergenic 25.0%
! TGAAGAGGTAATAAAGTTTA+TGG + chr4.4:19271210-19271229 MS.gene35160:intron 25.0%
! TGATATATAAAACTGGTAAG+TGG + chr4.4:19271849-19271868 MS.gene35160:intron 25.0%
! TGGAAAGTGATATATAAAAC+TGG + chr4.4:19271842-19271861 MS.gene35160:intron 25.0%
!!! TTGATGATTCAACACATTTT+CGG + chr4.4:19272460-19272479 MS.gene35160:intron 25.0%
!!! TTGTTTTTTAAAATAGCCTC+TGG + chr4.4:19272427-19272446 MS.gene35160:intron 25.0%
ATGCAATATTCGAATGAAGA+AGG + chr4.4:19271329-19271348 MS.gene35160:CDS 30.0%
CCCAAATTCACTATATTTAC+AGG - chr4.4:19272357-19272376 None:intergenic 30.0%
GAATGTTCGAACAAATTCAT+GGG + chr4.4:19271430-19271449 MS.gene35160:CDS 30.0%
TATGTGCAGAAGAAATTCAT+AGG + chr4.4:19271718-19271737 MS.gene35160:CDS 30.0%
TGAATGTTCGAACAAATTCA+TGG + chr4.4:19271429-19271448 MS.gene35160:CDS 30.0%
TTTCTTCTTATTCACAATCC+TGG + chr4.4:19272854-19272873 MS.gene35160:intron 30.0%
!! AATATAGTGAATTTGGGTTG+TGG + chr4.4:19272360-19272379 MS.gene35160:intron 30.0%
!! TGACAGATTGTTGTTTAAGA+TGG + chr4.4:19271786-19271805 MS.gene35160:CDS 30.0%
AAAGATCCATTGATGTGGAA+TGG - chr4.4:19271598-19271617 None:intergenic 35.0%
AAAGGGGGAGATTAAAAATG+AGG + chr4.4:19272755-19272774 MS.gene35160:intron 35.0%
AACCAATCAAGATTGTGTTG+TGG + chr4.4:19272884-19272903 MS.gene35160:intron 35.0%
AAGGGGGAGATTAAAAATGA+GGG + chr4.4:19272756-19272775 MS.gene35160:intron 35.0%
ACTTCAAACTCGCAGTTATA+CGG - chr4.4:19272969-19272988 None:intergenic 35.0%
CAATATTCGAATGAAGAAGG+AGG + chr4.4:19271332-19271351 MS.gene35160:CDS 35.0%
CAGAAGAAATTCATAGGAAG+GGG + chr4.4:19271724-19271743 MS.gene35160:CDS 35.0%
CCACTCATAAAGAAAAGAGA+TGG + chr4.4:19272291-19272310 MS.gene35160:intron 35.0%
GATTGTACAAAACTGTCAAG+TGG + chr4.4:19272637-19272656 MS.gene35160:intron 35.0%
GCAATTGTAATCAATAACGC+CGG + chr4.4:19272921-19272940 MS.gene35160:CDS 35.0%
GCAGAAGAAATTCATAGGAA+GGG + chr4.4:19271723-19271742 MS.gene35160:CDS 35.0%
TAGATTACCAGCTTATGAGT+TGG - chr4.4:19271485-19271504 None:intergenic 35.0%
TGCAGAAGAAATTCATAGGA+AGG + chr4.4:19271722-19271741 MS.gene35160:CDS 35.0%
TGTGATATTGATGTTGAACC+TGG + chr4.4:19271691-19271710 MS.gene35160:CDS 35.0%
TTTGTTCGAACATTCAGACA+TGG - chr4.4:19271425-19271444 None:intergenic 35.0%
! CCATCTCTTTTCTTTATGAG+TGG - chr4.4:19272294-19272313 None:intergenic 35.0%
! GATCAGGTTGCTTAAGATAA+TGG + chr4.4:19271936-19271955 MS.gene35160:intron 35.0%
! GTTTAAGATGGACAGTAATC+CGG + chr4.4:19271798-19271817 MS.gene35160:CDS 35.0%
! TACATTTGTTGAAGCGAGTA+AGG + chr4.4:19271753-19271772 MS.gene35160:CDS 35.0%
! TTTAAGATGGACAGTAATCC+GGG + chr4.4:19271799-19271818 MS.gene35160:CDS 35.0%
!!! CTTGATTGGTTTTGATTTCC+AGG - chr4.4:19272875-19272894 None:intergenic 35.0%
ACTGGTAAGTGGTGTTTGTT+TGG + chr4.4:19271860-19271879 MS.gene35160:intron 40.0%
ACTGTCAAGTGGCATTTACT+TGG + chr4.4:19272648-19272667 MS.gene35160:intron 40.0%
AGAAATTCATAGGAAGGGGT+TGG + chr4.4:19271728-19271747 MS.gene35160:CDS 40.0%
AGAAGATGAGAGGAGAAACA+AGG - chr4.4:19272827-19272846 None:intergenic 40.0%
AGAGACTCTGACATTGACAT+TGG + chr4.4:19271633-19271652 MS.gene35160:CDS 40.0%
ATAGGAGTGGATGATGAATG+TGG + chr4.4:19272218-19272237 MS.gene35160:intron 40.0%
ATTGGACAAAACTGTCAACG+TGG + chr4.4:19272500-19272519 MS.gene35160:intron 40.0%
ATTGTAATCAATAACGCCGG+TGG + chr4.4:19272924-19272943 MS.gene35160:CDS 40.0%
CACGAAAAGATCCATTGATG+TGG - chr4.4:19271603-19271622 None:intergenic 40.0%
CGAATTCCATTCCACATCAA+TGG + chr4.4:19271589-19271608 MS.gene35160:CDS 40.0%
GAGGAAGAGAAAACGATTAC+AGG - chr4.4:19272805-19272824 None:intergenic 40.0%
GCAGGTTCTACATCAATTTG+AGG - chr4.4:19271371-19271390 None:intergenic 40.0%
GTCCACAACACAATCTTGAT+TGG - chr4.4:19272889-19272908 None:intergenic 40.0%
TGTTCGAACAAATTCATGGG+AGG + chr4.4:19271433-19271452 MS.gene35160:CDS 40.0%
TTCTTCTGCACATAATCACC+AGG - chr4.4:19271712-19271731 None:intergenic 40.0%
TTTACGTCCAACTCATAAGC+TGG + chr4.4:19271475-19271494 MS.gene35160:CDS 40.0%
TTTGTTTGGAGACAGTGTGT+TGG + chr4.4:19271874-19271893 MS.gene35160:intron 40.0%
! AATGGATCTTTTCGTGAACC+TGG + chr4.4:19271607-19271626 MS.gene35160:CDS 40.0%
! ATGGATCTTTTCGTGAACCT+GGG + chr4.4:19271608-19271627 MS.gene35160:CDS 40.0%
AATGTCAGAGTCTCTTTCCC+AGG - chr4.4:19271628-19271647 None:intergenic 45.0%
ACATTCAGACATGGAGGAAC+CGG - chr4.4:19271416-19271435 None:intergenic 45.0%
AGATGAGAGGAGAAACAAGG+AGG - chr4.4:19272824-19272843 None:intergenic 45.0%
CATCAAGAAAGTGAGTCCAG+AGG - chr4.4:19272446-19272465 None:intergenic 45.0%
CTTCTCTGCATCAACCTTAC+TGG - chr4.4:19271309-19271328 None:intergenic 45.0%
GAAGCGAGTAAGGTGAAAGT+TGG + chr4.4:19271763-19271782 MS.gene35160:CDS 45.0%
GTTCGAACATTCAGACATGG+AGG - chr4.4:19271422-19271441 None:intergenic 45.0%
TCAAACTCGCAGTTATACGG+TGG - chr4.4:19272966-19272985 None:intergenic 45.0%
TGATTACCGTGAGCCAATAC+CGG + chr4.4:19271394-19271413 MS.gene35160:CDS 45.0%
TTACTGCAGTGAGTCCAGTA+AGG + chr4.4:19271292-19271311 MS.gene35160:intron 45.0%
! AAGATGCAGTTGATGCGATC+TGG + chr4.4:19271668-19271687 MS.gene35160:CDS 45.0%
AGACATGGAGGAACCGGTAT+TGG - chr4.4:19271410-19271429 None:intergenic 50.0%
CTGTCAACGTGGCATTTACC+TGG + chr4.4:19272511-19272530 MS.gene35160:intron 50.0%
GCAGTTATACGGTGGTTCGA+CGG - chr4.4:19272958-19272977 None:intergenic 50.0%
GTAATCAATAACGCCGGTGG+AGG + chr4.4:19272927-19272946 MS.gene35160:CDS 50.0%
! TCAACACATTTTCGGCCACG+CGG + chr4.4:19272468-19272487 MS.gene35160:intron 50.0%
! TCAACACATTTTCGGCCACG+TGG + chr4.4:19272468-19272487 MS.gene35160:intron 50.0%
!! TGAATTTGGGTTGTGGCAGC+TGG + chr4.4:19272367-19272386 MS.gene35160:intron 50.0%
!! TGGGAGGTGCTGATTCATTC+TGG + chr4.4:19271449-19271468 MS.gene35160:CDS 50.0%
GGCTCACGGTAATCATCTGC+AGG - chr4.4:19271389-19271408 None:intergenic 55.0%
TCCAATCAGCAAGTGCCACG+TGG - chr4.4:19272486-19272505 None:intergenic 55.0%
! TACAATCAGCAAGTGCCGCG+TGG - chr4.4:19272624-19272643 None:intergenic 55.0%
!! GAGGAACCGGTATTGGCTCA+CGG - chr4.4:19271403-19271422 None:intergenic 55.0%
! GCCACGTGGCACTTGCTGAT+TGG + chr4.4:19272482-19272501 MS.gene35160:intron 60.0%
!! TTCGACGGTGTTGCCTCCAC+CGG - chr4.4:19272943-19272962 None:intergenic 60.0%


Chromosome Type Strat End Strand Name
chr4.4 gene 19271200 19273001 19271200 ID=MS.gene35160
chr4.4 mRNA 19271200 19273001 19271200 ID=MS.gene35160.t1;Parent=MS.gene35160
chr4.4 exon 19271200 19271216 19271200 ID=MS.gene35160.t1.exon1;Parent=MS.gene35160.t1
chr4.4 CDS 19271200 19271216 19271200 ID=cds.MS.gene35160.t1;Parent=MS.gene35160.t1
chr4.4 exon 19271301 19271496 19271301 ID=MS.gene35160.t1.exon2;Parent=MS.gene35160.t1
chr4.4 CDS 19271301 19271496 19271301 ID=cds.MS.gene35160.t1;Parent=MS.gene35160.t1
chr4.4 exon 19271589 19271820 19271589 ID=MS.gene35160.t1.exon3;Parent=MS.gene35160.t1
chr4.4 CDS 19271589 19271820 19271589 ID=cds.MS.gene35160.t1;Parent=MS.gene35160.t1
chr4.4 exon 19272919 19273001 19272919 ID=MS.gene35160.t1.exon4;Parent=MS.gene35160.t1
chr4.4 CDS 19272919 19273001 19272919 ID=cds.MS.gene35160.t1;Parent=MS.gene35160.t1
Gene Sequence

>MS.gene35160

ATGGCAACATTGAAGAGGTAATAAAGTTTATGGTATGAAGTTAAGAAATCGTTGATTGAACCATTTTATGTTGACTTGATACTATGATTTAATTACTGCAGTGAGTCCAGTAAGGTTGATGCAGAGAAGATGCAATATTCGAATGAAGAAGGAGGAAGATCTGCAGAACCTCAAATTGATGTAGAACCTGCAGATGATTACCGTGAGCCAATACCGGTTCCTCCATGTCTGAATGTTCGAACAAATTCATGGGAGGTGCTGATTCATTCTGGTCATTTACGTCCAACTCATAAGCTGGTAATCTAAAGATATTCCCTTACTTTATGTTAGTTTTATAAGTAAACAAAGAATGTTTTTGAATTGACATATTTGTAATTGATATGATGTAGCGAATTCCATTCCACATCAATGGATCTTTTCGTGAACCTGGGAAAGAGACTCTGACATTGACATTGGTTGATTATGAAGAAGATGCAGTTGATGCGATCTGGTGTGATATTGATGTTGAACCTGGTGATTATGTGCAGAAGAAATTCATAGGAAGGGGTTGGCATACATTTGTTGAAGCGAGTAAGGTGAAAGTTGGTGACAGATTGTTGTTTAAGATGGACAGTAATCCGGGTAATTGCTATGTTAAATTTCTGGAAAGTGATATATAAAACTGGTAAGTGGTGTTTGTTTGGAGACAGTGTGTTGGTTGTACTATGTATTTGTTTAGTTGTATTAAGTACTAAAAGATCAGGTTGCTTAAGATAATGGTTTGTAATGTTTATTTTAAACTTTGTAGTAATGGTTGTTCTGAAGAATATCTACGTGTTTATTATGTTATGAAATTCGTTATTTTTATTGACAGCTGAATTATAAGTATAATTTTATATATAATAAATAAGGATATTATGAATAAGAATAGCATGGTACATGAGAAAAATATGAAGTGAAAGTTGATTATTAATGAAATGGTTGGCGAAAAATTCATTGTAAAATTGTTAAATATATATAAACGAAAAGACTTAAATATATAGGAGTGGATGATGAATGTGGCAATATTTTGTATTCATTTGTGTTACTGTAAAATGTAGAACTTGACTTGACCACTCATAAAGAAAAGAGATGGATTTAGTTAAAAAATAAAAGCTAAAAAAATGTTTTTGGTACCTGTAAATATAGTGAATTTGGGTTGTGGCAGCTGGTAAAAAAAACTTTTGAAACACGTCTATGTAAAATTTTTTGTTTTTTAAAATAGCCTCTGGACTCACTTTCTTGATGATTCAACACATTTTCGGCCACGTGGCACTTGCTGATTGGACAAAACTGTCAACGTGGCATTTACCTGGAATTAATAAATTAGAAAATAAAATAAAAAAACAGTTTTTTAAAATAGTCTCTAGACTCACTTTCTTGATGATTCAACACATTTTCGGCCACGCGGCACTTGCTGATTGTACAAAACTGTCAAGTGGCATTTACTTGGAATTAATAAATTAGAAAATAAAATAAAAAAACATAAAAAGATTTATTATTATTTTTATTTCCTTATTTTAAAAGATGAAAATAGAAAGGGGGAGATTAAAAATGAGGGTATATGCCATTATTATTCTTCTTCCTGTAATCGTTTTCTCTTCCTCCTTGTTTCTCCTCTCATCTTCTTATTCTTTTTCTTCTTATTCACAATCCTGGAAATCAAAACCAATCAAGATTGTGTTGTGGACAACAACTCAGATGCAATTGTAATCAATAACGCCGGTGGAGGCAACACCGTCGAACCACCGTATAACTGCGAGTTTGAAGTCGAGATTTGTTGA

Protein sequence

>MS.gene35160.t1

MATLKSESSKVDAEKMQYSNEEGGRSAEPQIDVEPADDYREPIPVPPCLNVRTNSWEVLIHSGHLRPTHKLRIPFHINGSFREPGKETLTLTLVDYEEDAVDAIWCDIDVEPGDYVQKKFIGRGWHTFVEASKVKVGDRLLFKMDSNPDAIVINNAGGGNTVEPPYNCEFEVEIC