AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene052078


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene052078.t1 MTR_2g097680 92.398 171 7 4 1 170 18 183 5.09e-80 235
MS.gene052078.t1 MTR_1g071380 90.643 171 8 6 1 170 1 164 8.29e-77 226
MS.gene052078.t1 MTR_2g097680 89.831 118 6 4 1 117 18 130 2.81e-57 176
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene052078.t1 AT2G29180 41.772 158 75 5 20 163 5 159 4.46e-24 92.8

Find 29 sgRNAs with CRISPR-Local

Find 84 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GGCTTATCCGTTATCACTAT+TGG 0.245133 2.2:+4834179 MS.gene052078:CDS
GCTTATCCGTTATCACTATT+GGG 0.260636 2.2:+4834180 MS.gene052078:CDS
TCTGGTTGTAGTAGTGATAA+TGG 0.300412 2.2:-4833985 None:intergenic
GAAAGGAAGGTTGCAATCTT+TGG 0.300675 2.2:-4833888 None:intergenic
GCTGTAGCAGCAACAGGATT+TGG 0.334339 2.2:-4834044 None:intergenic
TTCAAAGGAAGTCCAAACTA+TGG 0.343791 2.2:+4834021 MS.gene052078:CDS
CATTGATGCTTCGGAGCAAT+TGG 0.360695 2.2:+4834088 MS.gene052078:CDS
CTGGTTGTAGTAGTGATAAT+GGG 0.369858 2.2:-4833984 None:intergenic
AACAGGATTTGGCCATAGTT+TGG 0.372494 2.2:-4834033 None:intergenic
AAAAGAAAAGAAAAGTAGTA+AGG 0.384781 2.2:+4835330 MS.gene052078:CDS
AGGGCAGGACCTAAAGGATT+TGG 0.404020 2.2:+4835350 MS.gene052078:CDS
GAGAAAGATGAAGAAGTTGT+TGG 0.423658 2.2:-4833960 None:intergenic
TGCTACAGCCATTGATGCTT+CGG 0.431580 2.2:+4834079 MS.gene052078:CDS
TCAACAGCTGTAGCAGCAAC+AGG 0.437132 2.2:-4834050 None:intergenic
CAATTGCTCCGAAGCATCAA+TGG 0.447559 2.2:-4834087 None:intergenic
AGAAGATGATGTTGAAAGGA+AGG 0.478894 2.2:-4833901 None:intergenic
TCATCAACTACCACTGATGA+TGG 0.480753 2.2:+4834113 MS.gene052078:CDS
AAAGAAAAGAAAAGTAGTAA+GGG 0.491413 2.2:+4835331 MS.gene052078:CDS
AAGAAGAAGATGATGTTGAA+AGG 0.496918 2.2:-4833905 None:intergenic
GTAGTAAGGGCAGGACCTAA+AGG 0.510055 2.2:+4835344 MS.gene052078:CDS
CTTATCCGTTATCACTATTG+GGG 0.525510 2.2:+4834181 MS.gene052078:CDS
CATCAACTACCACTGATGAT+GGG 0.525641 2.2:+4834114 MS.gene052078:CDS
AAAAGAAAAGTAGTAAGGGC+AGG 0.536130 2.2:+4835335 MS.gene052078:CDS
ATATACCCCAATAGTGATAA+CGG 0.550650 2.2:-4834186 None:intergenic
TTTCTTGACAAAGAGAGAGA+AGG 0.571247 2.2:+4835268 MS.gene052078:CDS
ATCAACTACCACTGATGATG+GGG 0.608198 2.2:+4834115 MS.gene052078:CDS
AAGAGACACCCCATCATCAG+TGG 0.647668 2.2:-4834123 None:intergenic
GAGAAAGAAGAAGCAGCTAG+CGG 0.687353 2.2:+4835299 MS.gene052078:CDS
TGATGATGCAAATAATGCAG+TGG 0.718262 2.2:-4833856 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! CTCTATATTAATAAAAGAAT+TGG - chr2.2:4834246-4834265 None:intergenic 15.0%
!! TATTCAAAATGAACTAATTA+GGG - chr2.2:4834605-4834624 None:intergenic 15.0%
!!! AAATGATTATGAACTAATTT+TGG - chr2.2:4834578-4834597 None:intergenic 15.0%
!!! AATAGAATTTTACAATATTG+AGG + chr2.2:4834621-4834640 MS.gene052078:intron 15.0%
!!! CAATTCTTTTATTAATATAG+AGG + chr2.2:4834244-4834263 MS.gene052078:intron 15.0%
!!! TTTTATAAATGTAAATGACT+TGG + chr2.2:4835116-4835135 MS.gene052078:intron 15.0%
!!! TTTTTCGTTTTGTAATTTTA+TGG + chr2.2:4834975-4834994 MS.gene052078:intron 15.0%
!! AAAAGAAAAGAAAAGTAGTA+AGG + chr2.2:4835330-4835349 MS.gene052078:CDS 20.0%
!! AAAGAAAAGAAAAGTAGTAA+GGG + chr2.2:4835331-4835350 MS.gene052078:CDS 20.0%
!! CTAAATTGATTATGAAAGTT+AGG - chr2.2:4834519-4834538 None:intergenic 20.0%
!! CTATTCAAAATGAACTAATT+AGG - chr2.2:4834606-4834625 None:intergenic 20.0%
!!! GAAAATCCATAATTTTTCAA+AGG + chr2.2:4834006-4834025 MS.gene052078:CDS 20.0%
!!! TATTGACATTACATGTTTTA+GGG + chr2.2:4834438-4834457 MS.gene052078:intron 20.0%
!!! TTATTGACATTACATGTTTT+AGG + chr2.2:4834437-4834456 MS.gene052078:intron 20.0%
!!! TTGAAAAATTATGGATTTTC+TGG - chr2.2:4834006-4834025 None:intergenic 20.0%
!!! TTGCGATTTTAATACATTAA+GGG - chr2.2:4834939-4834958 None:intergenic 20.0%
!!! TTTGCGATTTTAATACATTA+AGG - chr2.2:4834940-4834959 None:intergenic 20.0%
!!! TTTTTGTTTATAATAGTGAC+CGG - chr2.2:4834658-4834677 None:intergenic 20.0%
! CATTCATTAAATGATGTATG+TGG - chr2.2:4834713-4834694 None:intergenic 25.0%
! TAAGCAAAAATCAACATTCT+AGG - chr2.2:4834758-4834777 None:intergenic 25.0%
! TTACTTAGCATTAGTATTCA+GGG + chr2.2:4835190-4835209 MS.gene052078:intron 25.0%
! TTAGTGAAAATTATTTCCCT+TGG + chr2.2:4834354-4834373 MS.gene052078:intron 25.0%
!! TTTTGATCTTTGAATATGTG+AGG - chr2.2:4835082-4835101 None:intergenic 25.0%
!! TTTTTGCTTATAATAGTGAC+CGG + chr2.2:4834768-4834787 MS.gene052078:intron 25.0%
AAGAAGAAGATGATGTTGAA+AGG - chr2.2:4833908-4833927 None:intergenic 30.0%
AGTAAAAACGTGTGTTGAAA+TGG - chr2.2:4833935-4833954 None:intergenic 30.0%
ATATACCCCAATAGTGATAA+CGG - chr2.2:4834189-4834208 None:intergenic 30.0%
CACATATTTAGAGACCTAAA+TGG - chr2.2:4834898-4834917 None:intergenic 30.0%
CTAGTTTATACTTTGTAGTG+TGG - chr2.2:4834412-4834431 None:intergenic 30.0%
GTTACTTAGCATTAGTATTC+AGG + chr2.2:4835189-4835208 MS.gene052078:intron 30.0%
TTTAGGTCTCTAAATATGTG+AGG + chr2.2:4834898-4834917 MS.gene052078:intron 30.0%
! ATCTTTTGACCAAATCCTTT+AGG - chr2.2:4835362-4835381 None:intergenic 30.0%
! CCTCCTATCTAAAACTATTT+CGG + chr2.2:4835165-4835184 MS.gene052078:intron 30.0%
! CTTTTCTTCATTGCTTTCAT+TGG + chr2.2:4834158-4834177 MS.gene052078:CDS 30.0%
! GGACTTCCTTTGAAAAATTA+TGG - chr2.2:4834015-4834034 None:intergenic 30.0%
! TTTAAAGCAAACAGCCATTT+AGG + chr2.2:4834881-4834900 MS.gene052078:intron 30.0%
!! TTTTTGTTTGTTTGTGTTGC+AGG + chr2.2:4835223-4835242 MS.gene052078:intron 30.0%
!!! ACACCGAAATAGTTTTAGAT+AGG - chr2.2:4835171-4835190 None:intergenic 30.0%
AAAAGAAAAGTAGTAAGGGC+AGG + chr2.2:4835335-4835354 MS.gene052078:CDS 35.0%
AGAAGATGATGTTGAAAGGA+AGG - chr2.2:4833904-4833923 None:intergenic 35.0%
ATTCCATGTCATATTGTCCA+AGG - chr2.2:4834374-4834393 None:intergenic 35.0%
CTGGTTGTAGTAGTGATAAT+GGG - chr2.2:4833987-4834006 None:intergenic 35.0%
CTTATCCGTTATCACTATTG+GGG + chr2.2:4834181-4834200 MS.gene052078:CDS 35.0%
GAGAAAGATGAAGAAGTTGT+TGG - chr2.2:4833963-4833982 None:intergenic 35.0%
GCTTATCCGTTATCACTATT+GGG + chr2.2:4834180-4834199 MS.gene052078:CDS 35.0%
TCTGGTTGTAGTAGTGATAA+TGG - chr2.2:4833988-4834007 None:intergenic 35.0%
TGTTTATAATAGTGACCGGA+GGG - chr2.2:4834654-4834673 None:intergenic 35.0%
TTCAAAGGAAGTCCAAACTA+TGG + chr2.2:4834021-4834040 MS.gene052078:CDS 35.0%
TTCCATGTCATATTGTCCAA+GGG - chr2.2:4834373-4834392 None:intergenic 35.0%
TTGAGACATGCTTGCAATTT+CGG - chr2.2:4834281-4834300 None:intergenic 35.0%
TTGTTTATAATAGTGACCGG+AGG - chr2.2:4834655-4834674 None:intergenic 35.0%
TTTCTTGACAAAGAGAGAGA+AGG + chr2.2:4835268-4835287 MS.gene052078:CDS 35.0%
! TGATGATGCAAATAATGCAG+TGG - chr2.2:4833859-4833878 None:intergenic 35.0%
!!! CCGAAATAGTTTTAGATAGG+AGG - chr2.2:4835168-4835187 None:intergenic 35.0%
AACAGGATTTGGCCATAGTT+TGG - chr2.2:4834036-4834055 None:intergenic 40.0%
AATCGCAAACACATCTCTAG+TGG + chr2.2:4834951-4834970 MS.gene052078:intron 40.0%
CATCAACTACCACTGATGAT+GGG + chr2.2:4834114-4834133 MS.gene052078:CDS 40.0%
CTTAGCATTAGTATTCAGGG+AGG + chr2.2:4835193-4835212 MS.gene052078:intron 40.0%
GAAAGGAAGGTTGCAATCTT+TGG - chr2.2:4833891-4833910 None:intergenic 40.0%
GAATTGACATATACACCCTC+CGG - chr2.2:4834790-4834809 None:intergenic 40.0%
GGCAAATGGTCACGATTTAA+AGG + chr2.2:4834831-4834850 MS.gene052078:intron 40.0%
GGCTTATCCGTTATCACTAT+TGG + chr2.2:4834179-4834198 MS.gene052078:CDS 40.0%
TCATCAACTACCACTGATGA+TGG + chr2.2:4834113-4834132 MS.gene052078:CDS 40.0%
TGCTTATAATAGTGACCGGA+GGG + chr2.2:4834772-4834791 MS.gene052078:intron 40.0%
TTCCCTTGGACAATATGACA+TGG + chr2.2:4834368-4834387 MS.gene052078:intron 40.0%
TTGCTTATAATAGTGACCGG+AGG + chr2.2:4834771-4834790 MS.gene052078:intron 40.0%
! ATCAACTACCACTGATGATG+GGG + chr2.2:4834115-4834134 MS.gene052078:CDS 40.0%
ACACATGCGGTCAACTTACT+AGG - chr2.2:4834544-4834563 None:intergenic 45.0%
CACATGCGGTCAACTTACTA+GGG - chr2.2:4834543-4834562 None:intergenic 45.0%
CATTGATGCTTCGGAGCAAT+TGG + chr2.2:4834088-4834107 MS.gene052078:CDS 45.0%
GAGAAAGAAGAAGCAGCTAG+CGG + chr2.2:4835299-4835318 MS.gene052078:CDS 45.0%
TATTGAGGATGTACACCCTC+CGG + chr2.2:4834636-4834655 MS.gene052078:intron 45.0%
TGCTACAGCCATTGATGCTT+CGG + chr2.2:4834079-4834098 MS.gene052078:CDS 45.0%
! AGTAAGTTGACCGCATGTGT+TGG + chr2.2:4834544-4834563 MS.gene052078:intron 45.0%
! CAATTGCTCCGAAGCATCAA+TGG - chr2.2:4834090-4834109 None:intergenic 45.0%
! GCCAAAACGAGTGACTAGTT+TGG + chr2.2:4834810-4834829 MS.gene052078:intron 45.0%
! GCCAAACTAGTCACTCGTTT+TGG - chr2.2:4834814-4834833 None:intergenic 45.0%
!! CGAGTGACTAGTTTGGCAAA+TGG + chr2.2:4834817-4834836 MS.gene052078:intron 45.0%
AAGAGACACCCCATCATCAG+TGG - chr2.2:4834126-4834145 None:intergenic 50.0%
AGGGCAGGACCTAAAGGATT+TGG + chr2.2:4835350-4835369 MS.gene052078:CDS 50.0%
GCTGTAGCAGCAACAGGATT+TGG - chr2.2:4834047-4834066 None:intergenic 50.0%
GGACGTTGATCCAACACATG+CGG - chr2.2:4834557-4834576 None:intergenic 50.0%
GTAGTAAGGGCAGGACCTAA+AGG + chr2.2:4835344-4835363 MS.gene052078:CDS 50.0%
TCAACAGCTGTAGCAGCAAC+AGG - chr2.2:4834053-4834072 None:intergenic 50.0%


Chromosome Type Strat End Strand Name
chr2.2 gene 4833852 4835406 4833852 ID=MS.gene052078
chr2.2 mRNA 4833852 4835406 4833852 ID=MS.gene052078.t1;Parent=MS.gene052078
chr2.2 exon 4833852 4834202 4833852 ID=MS.gene052078.t1.exon1;Parent=MS.gene052078.t1
chr2.2 CDS 4833852 4834202 4833852 ID=cds.MS.gene052078.t1;Parent=MS.gene052078.t1
chr2.2 exon 4835245 4835406 4835245 ID=MS.gene052078.t1.exon2;Parent=MS.gene052078.t1
chr2.2 CDS 4835245 4835406 4835245 ID=cds.MS.gene052078.t1;Parent=MS.gene052078.t1
Gene Sequence

>MS.gene052078

ATGGCCACTGCATTATTTGCATCATCATCATCATCTCCAAAGATTGCAACCTTCCTTTCAACATCATCTTCTTCTTCTTTCCATTTCAACACACGTTTTTACTCACTTCCAACAACTTCTTCATCTTTCTCTCCCATTATCACTACTACAACCAGAAAATCCATAATTTTTCAAAGGAAGTCCAAACTATGGCCAAATCCTGTTGCTGCTACAGCTGTTGAAGATGCTGCTACAGCCATTGATGCTTCGGAGCAATTGGTTTCATCAACTACCACTGATGATGGGGTGTCTCTTATCGTATCAGCTCTTTTCTTCATTGCTTTCATTGGCTTATCCGTTATCACTATTGGGGTATATTCGTCATTTTCTTCTATTCTCACTTTTTTGTTTTCCAATTCTTTTATTAATATAGAGGTAAATTATCATCCGAAATTGCAAGCATGTCTCAAAATAGTGTTTGATTTTTGTGAATTGACAAACATATTTGTGAAATTGTAAAATGTTAGTGAAAATTATTTCCCTTGGACAATATGACATGGAATCTAACATCAATGTTACCACACTACAAAGTATAAACTAGTTTGTTTATTGACATTACATGTTTTAGGGACTAATTTGTCAATAATTAATTAGTTCATGTATATTTGTAATTATTGATAAATTACCTAACTTTCATAATCAATTTAGTCCCTAGTAAGTTGACCGCATGTGTTGGATCAACGTCCAAAATTAGTTCATAATCATTTTAGTCCCTAATTAGTTCATTTTGAATAGAATTTTACAATATTGAGGATGTACACCCTCCGGTCACTATTATAAACAAAAAAACAACATTTTAGATTCATTCATTAAATGATGTATGTAGTCTTTATTATAAACCACATACATCATTTAATGAATGAACCTAGAATGTTGATTTTTGCTTATAATAGTGACCGGAGGGTGTATATGTCAATTCGCCAAAACGAGTGACTAGTTTGGCAAATGGTCACGATTTAAAGGATCAATTTGACTATGCGCACTCATTTGTTTAAAGCAAACAGCCATTTAGGTCTCTAAATATGTGAGGTGTTGTTAGTACAGTCCCTTAATGTATTAAAATCGCAAACACATCTCTAGTGGCTTTTTCGTTTTGTAATTTTATGGATTATATTGACTAACGAATAAAAAAAAAAAACATGTTGATGTGCTTGTAATTCGATTCACTCAGTGACTATAGTGACAACACCTCACATATTCAAAGATCAAAATGATTGATTATCGTTTTTATAAATGTAAATGACTTGGTAAGTTAGTAGTATTTGAACTTTTGACCTCCTATCTAAAACTATTTCGGTGTTACTTAGCATTAGTATTCAGGGAGGTTCTGTATTTTTGTTTGTTTGTGTTGCAGGTTATCTATTTAGCAGTAACAGATTTCTTGACAAAGAGAGAGAAGGAAAAATTTGAGAAAGAAGAAGCAGCTAGCGGAAAGAAGAAAAAGAAAAGAAAAGTAGTAAGGGCAGGACCTAAAGGATTTGGTCAAAAGATTGTTCAAACTGAAGATGATGATTGA

Protein sequence

>MS.gene052078.t1

MATALFASSSSSPKIATFLSTSSSSSFHFNTRFYSLPTTSSSFSPIITTTTRKSIIFQRKSKLWPNPVAATAVEDAATAIDASEQLVSSTTTDDGVSLIVSALFFIAFIGLSVITIGVIYLAVTDFLTKREKEKFEKEEAASGKKKKKRKVVRAGPKGFGQKIVQTEDDD