AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1095680


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1095680 MtrunA17_Chr6g0475971 34.409 93 58 2 37 128 318 408 8.94e-15 70.9
Msa1095680 MtrunA17_Chr5g0422561 34.409 93 58 2 37 128 183 273 1.69e-14 69.7
Msa1095680 MtrunA17_Chr5g0406671 29.600 125 58 2 37 131 272 396 2.44e-14 69.3
Msa1095680 MtrunA17_Chr0c01g0489381 50.877 57 28 0 83 139 301 357 5.42e-13 65.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 31 sgRNAs with CRISPR-Local

Find 118 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CCATTTAGACTCCCACTTTA+AGG 0.122895 7_3:-18702589 Msa1095680:CDS
AGTCTAAATGGTAAATCTTT+TGG 0.209864 7_3:+18702601 None:intergenic
GTTCCTCTCAACTTTGAAAA+TGG 0.240069 7_3:+18703255 None:intergenic
CCTTAAAGTGGGAGTCTAAA+TGG 0.278922 7_3:+18702589 None:intergenic
CTGGGATACCCAACTATAAA+AGG 0.290874 7_3:+18702486 None:intergenic
AATACAAATATATTGTTCAT+AGG 0.347711 7_3:+18703337 None:intergenic
TGGCCATTAGTGTCTTCTAT+TGG 0.376530 7_3:+18702654 None:intergenic
TGATGGCGCTCAAGGTATCT+TGG 0.429487 7_3:-18703013 Msa1095680:CDS
GTGTCTACCACCATCCTTCT+CGG 0.435405 7_3:-18702958 Msa1095680:intron
TTACAATAAGAAACATTGTA+AGG 0.437196 7_3:-18702542 Msa1095680:CDS
CCAAGGCTTCTTCCTTAAAG+TGG 0.451553 7_3:+18702577 None:intergenic
CCACTTTAAGGAAGAAGCCT+TGG 0.472640 7_3:-18702577 Msa1095680:CDS
TACATAGATAATACTAATGA+TGG 0.480788 7_3:-18703030 Msa1095680:intron
GTATCTGATGGTGGTTTCAA+TGG 0.489751 7_3:-18702628 Msa1095680:CDS
TGTAAAACGTCTTTCTTCCA+AGG 0.493557 7_3:+18702560 None:intergenic
GTTCCAATAGAAGACACTAA+TGG 0.519961 7_3:-18702657 Msa1095680:CDS
CAAGGCTTCTTCCTTAAAGT+GGG 0.522231 7_3:+18702578 None:intergenic
TAAATCAAATTATACCGAGA+AGG 0.524272 7_3:+18702944 None:intergenic
TGAATGCATGTGTTCGGGAC+TGG 0.528106 7_3:-18703212 Msa1095680:CDS
AATACTAATGATGGCGCTCA+AGG 0.547857 7_3:-18703021 Msa1095680:CDS
CAACTCAGCATTATATGTAG+TGG 0.561364 7_3:-18702440 None:intergenic
TCAAATTATACCGAGAAGGA+TGG 0.573375 7_3:+18702948 None:intergenic
TGTGACATTGTCAATGCCAC+TGG 0.579217 7_3:+18702467 None:intergenic
TGGCCACTGGTATCTGATGG+TGG 0.602522 7_3:-18702637 Msa1095680:CDS
TAGAAGACACTAATGGCCAC+TGG 0.621867 7_3:-18702650 Msa1095680:CDS
AATTATACCGAGAAGGATGG+TGG 0.650578 7_3:+18702951 None:intergenic
GTGACATTGTCAATGCCACT+GGG 0.652854 7_3:+18702468 None:intergenic
TAATGGCCACTGGTATCTGA+TGG 0.658056 7_3:-18702640 Msa1095680:CDS
TTTATAGTTGGGTATCCCAG+TGG 0.659756 7_3:-18702483 Msa1095680:CDS
GGGACTGGTAGTGTCTAGAG+AGG 0.699395 7_3:-18703197 Msa1095680:intron
AAACCACCATCAGATACCAG+TGG 0.728616 7_3:+18702634 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! AAGTTTTATGGTTATATTAT+AGG - chr7_3:18702495-18702514 Msa1095680:CDS 15.0%
!!! AGTTTTATGGTTATATTATA+GGG - chr7_3:18702496-18702515 Msa1095680:CDS 15.0%
!!! TGATTTATGTTTAAAACATA+GGG + chr7_3:18702692-18702711 None:intergenic 15.0%
!!! TTGATTTATGTTTAAAACAT+AGG + chr7_3:18702693-18702712 None:intergenic 15.0%
!! TTGATTTAAAAACAGTTTAA+AGG - chr7_3:18702848-18702867 Msa1095680:intron 15.0%
!!! TACTACTGATTATTTAATAA+AGG - chr7_3:18702910-18702929 Msa1095680:intron 15.0%
!!! AAGTTTTATGGTTATATTAT+AGG - chr7_3:18702495-18702514 Msa1095680:CDS 15.0%
!!! AGTTTTATGGTTATATTATA+GGG - chr7_3:18702496-18702515 Msa1095680:CDS 15.0%
!!! TGATTTATGTTTAAAACATA+GGG + chr7_3:18702692-18702711 None:intergenic 15.0%
!!! TTGATTTATGTTTAAAACAT+AGG + chr7_3:18702693-18702712 None:intergenic 15.0%
!! TTGATTTAAAAACAGTTTAA+AGG - chr7_3:18702848-18702867 Msa1095680:intron 15.0%
!!! TACTACTGATTATTTAATAA+AGG - chr7_3:18702910-18702929 Msa1095680:intron 15.0%
!!! GTTATATAACACAAGTTTTA+TGG - chr7_3:18702483-18702502 Msa1095680:CDS 20.0%
!! TACATAGATAATACTAATGA+TGG - chr7_3:18702747-18702766 Msa1095680:intron 20.0%
!! GAATAAATATGAAAAACAAG+TGG + chr7_3:18703048-18703067 None:intergenic 20.0%
!! TTACAATAAGAAACATTGTA+AGG - chr7_3:18703235-18703254 Msa1095680:CDS 20.0%
!!! ATTACAAAACCTTTTATAGT+TGG - chr7_3:18703282-18703301 Msa1095680:CDS 20.0%
!!! TTACAAAACCTTTTATAGTT+GGG - chr7_3:18703283-18703302 Msa1095680:CDS 20.0%
!!! GTTATATAACACAAGTTTTA+TGG - chr7_3:18702483-18702502 Msa1095680:CDS 20.0%
!! TACATAGATAATACTAATGA+TGG - chr7_3:18702747-18702766 Msa1095680:intron 20.0%
!! GAATAAATATGAAAAACAAG+TGG + chr7_3:18703048-18703067 None:intergenic 20.0%
!! TTACAATAAGAAACATTGTA+AGG - chr7_3:18703235-18703254 Msa1095680:CDS 20.0%
!!! ATTACAAAACCTTTTATAGT+TGG - chr7_3:18703282-18703301 Msa1095680:CDS 20.0%
!!! TTACAAAACCTTTTATAGTT+GGG - chr7_3:18703283-18703302 Msa1095680:CDS 20.0%
! AAGCCATAAATCAACTAATA+TGG - chr7_3:18702711-18702730 Msa1095680:intron 25.0%
!! ACTCCATATTAGTTGATTTA+TGG + chr7_3:18702717-18702736 None:intergenic 25.0%
! TAAATCAAATTATACCGAGA+AGG + chr7_3:18702836-18702855 None:intergenic 25.0%
!! GTCTAAATGGTAAATCTTTT+GGG + chr7_3:18703178-18703197 None:intergenic 25.0%
!! AGTCTAAATGGTAAATCTTT+TGG + chr7_3:18703179-18703198 None:intergenic 25.0%
! AAGCCATAAATCAACTAATA+TGG - chr7_3:18702711-18702730 Msa1095680:intron 25.0%
!! ACTCCATATTAGTTGATTTA+TGG + chr7_3:18702717-18702736 None:intergenic 25.0%
! TAAATCAAATTATACCGAGA+AGG + chr7_3:18702836-18702855 None:intergenic 25.0%
!! GTCTAAATGGTAAATCTTTT+GGG + chr7_3:18703178-18703197 None:intergenic 25.0%
!! AGTCTAAATGGTAAATCTTT+TGG + chr7_3:18703179-18703198 None:intergenic 25.0%
! TTATCGTTCTCATGCTTTTA+TGG - chr7_3:18702461-18702480 Msa1095680:CDS 30.0%
! ATACCATTTTCAAAGTTGAG+AGG - chr7_3:18702519-18702538 Msa1095680:CDS 30.0%
! TGATTTTGAATGCATGTGTT+CGG - chr7_3:18702559-18702578 Msa1095680:CDS 30.0%
! GCTTATGTTTTCTTCATGAA+AGG - chr7_3:18702656-18702675 Msa1095680:CDS 30.0%
! ACAACATTTGCAAGTTTTTG+TGG - chr7_3:18702797-18702816 Msa1095680:intron 30.0%
! TGGTAATGTTAAAACTCACA+TGG - chr7_3:18703010-18703029 Msa1095680:CDS 30.0%
! TTATCGTTCTCATGCTTTTA+TGG - chr7_3:18702461-18702480 Msa1095680:CDS 30.0%
! ATACCATTTTCAAAGTTGAG+AGG - chr7_3:18702519-18702538 Msa1095680:CDS 30.0%
! TGATTTTGAATGCATGTGTT+CGG - chr7_3:18702559-18702578 Msa1095680:CDS 30.0%
! GCTTATGTTTTCTTCATGAA+AGG - chr7_3:18702656-18702675 Msa1095680:CDS 30.0%
! ACAACATTTGCAAGTTTTTG+TGG - chr7_3:18702797-18702816 Msa1095680:intron 30.0%
! TGGTAATGTTAAAACTCACA+TGG - chr7_3:18703010-18703029 Msa1095680:CDS 30.0%
! GTTCCTCTCAACTTTGAAAA+TGG + chr7_3:18702525-18702544 None:intergenic 35.0%
! GATTTTGAATGCATGTGTTC+GGG - chr7_3:18702560-18702579 Msa1095680:CDS 35.0%
TCTTCATGAAAGGTTTACTG+TGG - chr7_3:18702666-18702685 Msa1095680:CDS 35.0%
TCAAATTATACCGAGAAGGA+TGG + chr7_3:18702832-18702851 None:intergenic 35.0%
!! ATAAAGGTTGATGTTGCTAG+AGG - chr7_3:18702926-18702945 Msa1095680:intron 35.0%
GATTACCCTTTGATCGATTA+AGG - chr7_3:18702986-18703005 Msa1095680:CDS 35.0%
GTTCCAATAGAAGACACTAA+TGG - chr7_3:18703120-18703139 Msa1095680:intron 35.0%
TGTAAAACGTCTTTCTTCCA+AGG + chr7_3:18703220-18703239 None:intergenic 35.0%
! GTTCCTCTCAACTTTGAAAA+TGG + chr7_3:18702525-18702544 None:intergenic 35.0%
! GATTTTGAATGCATGTGTTC+GGG - chr7_3:18702560-18702579 Msa1095680:CDS 35.0%
TCTTCATGAAAGGTTTACTG+TGG - chr7_3:18702666-18702685 Msa1095680:CDS 35.0%
TCAAATTATACCGAGAAGGA+TGG + chr7_3:18702832-18702851 None:intergenic 35.0%
!! ATAAAGGTTGATGTTGCTAG+AGG - chr7_3:18702926-18702945 Msa1095680:intron 35.0%
GATTACCCTTTGATCGATTA+AGG - chr7_3:18702986-18703005 Msa1095680:CDS 35.0%
GTTCCAATAGAAGACACTAA+TGG - chr7_3:18703120-18703139 Msa1095680:intron 35.0%
TGTAAAACGTCTTTCTTCCA+AGG + chr7_3:18703220-18703239 None:intergenic 35.0%
! AATACTAATGATGGCGCTCA+AGG - chr7_3:18702756-18702775 Msa1095680:intron 40.0%
AATTATACCGAGAAGGATGG+TGG + chr7_3:18702829-18702848 None:intergenic 40.0%
! AGGCTTTGCATGCGTTTTAT+GGG - chr7_3:18702960-18702979 Msa1095680:CDS 40.0%
ACCAGCCTTAATCGATCAAA+GGG + chr7_3:18702994-18703013 None:intergenic 40.0%
TACCAGCCTTAATCGATCAA+AGG + chr7_3:18702995-18703014 None:intergenic 40.0%
TGGCCATTAGTGTCTTCTAT+TGG + chr7_3:18703126-18703145 None:intergenic 40.0%
!! GTATCTGATGGTGGTTTCAA+TGG - chr7_3:18703149-18703168 Msa1095680:intron 40.0%
CCTTAAAGTGGGAGTCTAAA+TGG + chr7_3:18703191-18703210 None:intergenic 40.0%
CCATTTAGACTCCCACTTTA+AGG - chr7_3:18703188-18703207 Msa1095680:intron 40.0%
CAAGGCTTCTTCCTTAAAGT+GGG + chr7_3:18703202-18703221 None:intergenic 40.0%
CTGGGATACCCAACTATAAA+AGG + chr7_3:18703294-18703313 None:intergenic 40.0%
TTTATAGTTGGGTATCCCAG+TGG - chr7_3:18703294-18703313 Msa1095680:CDS 40.0%
! AATACTAATGATGGCGCTCA+AGG - chr7_3:18702756-18702775 Msa1095680:intron 40.0%
AATTATACCGAGAAGGATGG+TGG + chr7_3:18702829-18702848 None:intergenic 40.0%
! AGGCTTTGCATGCGTTTTAT+GGG - chr7_3:18702960-18702979 Msa1095680:CDS 40.0%
ACCAGCCTTAATCGATCAAA+GGG + chr7_3:18702994-18703013 None:intergenic 40.0%
TACCAGCCTTAATCGATCAA+AGG + chr7_3:18702995-18703014 None:intergenic 40.0%
TGGCCATTAGTGTCTTCTAT+TGG + chr7_3:18703126-18703145 None:intergenic 40.0%
!! GTATCTGATGGTGGTTTCAA+TGG - chr7_3:18703149-18703168 Msa1095680:intron 40.0%
CCTTAAAGTGGGAGTCTAAA+TGG + chr7_3:18703191-18703210 None:intergenic 40.0%
CCATTTAGACTCCCACTTTA+AGG - chr7_3:18703188-18703207 Msa1095680:intron 40.0%
CAAGGCTTCTTCCTTAAAGT+GGG + chr7_3:18703202-18703221 None:intergenic 40.0%
CTGGGATACCCAACTATAAA+AGG + chr7_3:18703294-18703313 None:intergenic 40.0%
TTTATAGTTGGGTATCCCAG+TGG - chr7_3:18703294-18703313 Msa1095680:CDS 40.0%
TAAAACGCATGCAAAGCCTC+TGG + chr7_3:18702959-18702978 None:intergenic 45.0%
! GAGGCTTTGCATGCGTTTTA+TGG - chr7_3:18702959-18702978 Msa1095680:CDS 45.0%
ACCCTTTGATCGATTAAGGC+TGG - chr7_3:18702990-18703009 Msa1095680:CDS 45.0%
TAGAAGACACTAATGGCCAC+TGG - chr7_3:18703127-18703146 Msa1095680:intron 45.0%
TAATGGCCACTGGTATCTGA+TGG - chr7_3:18703137-18703156 Msa1095680:intron 45.0%
AAACCACCATCAGATACCAG+TGG + chr7_3:18703146-18703165 None:intergenic 45.0%
CCAAGGCTTCTTCCTTAAAG+TGG + chr7_3:18703203-18703222 None:intergenic 45.0%
! CCACTTTAAGGAAGAAGCCT+TGG - chr7_3:18703200-18703219 Msa1095680:CDS 45.0%
GTGACATTGTCAATGCCACT+GGG + chr7_3:18703312-18703331 None:intergenic 45.0%
TGTGACATTGTCAATGCCAC+TGG + chr7_3:18703313-18703332 None:intergenic 45.0%
TAAAACGCATGCAAAGCCTC+TGG + chr7_3:18702959-18702978 None:intergenic 45.0%
! GAGGCTTTGCATGCGTTTTA+TGG - chr7_3:18702959-18702978 Msa1095680:CDS 45.0%
ACCCTTTGATCGATTAAGGC+TGG - chr7_3:18702990-18703009 Msa1095680:CDS 45.0%
TAGAAGACACTAATGGCCAC+TGG - chr7_3:18703127-18703146 Msa1095680:intron 45.0%
TAATGGCCACTGGTATCTGA+TGG - chr7_3:18703137-18703156 Msa1095680:intron 45.0%
AAACCACCATCAGATACCAG+TGG + chr7_3:18703146-18703165 None:intergenic 45.0%
CCAAGGCTTCTTCCTTAAAG+TGG + chr7_3:18703203-18703222 None:intergenic 45.0%
! CCACTTTAAGGAAGAAGCCT+TGG - chr7_3:18703200-18703219 Msa1095680:CDS 45.0%
GTGACATTGTCAATGCCACT+GGG + chr7_3:18703312-18703331 None:intergenic 45.0%
TGTGACATTGTCAATGCCAC+TGG + chr7_3:18703313-18703332 None:intergenic 45.0%
TGAATGCATGTGTTCGGGAC+TGG - chr7_3:18702565-18702584 Msa1095680:CDS 50.0%
! TGATGGCGCTCAAGGTATCT+TGG - chr7_3:18702764-18702783 Msa1095680:intron 50.0%
GTGTCTACCACCATCCTTCT+CGG - chr7_3:18702819-18702838 Msa1095680:intron 50.0%
TGCTAGAGGTTCAACTCCAG+AGG - chr7_3:18702940-18702959 Msa1095680:intron 50.0%
TGAATGCATGTGTTCGGGAC+TGG - chr7_3:18702565-18702584 Msa1095680:CDS 50.0%
! TGATGGCGCTCAAGGTATCT+TGG - chr7_3:18702764-18702783 Msa1095680:intron 50.0%
GTGTCTACCACCATCCTTCT+CGG - chr7_3:18702819-18702838 Msa1095680:intron 50.0%
TGCTAGAGGTTCAACTCCAG+AGG - chr7_3:18702940-18702959 Msa1095680:intron 50.0%
! GGGACTGGTAGTGTCTAGAG+AGG - chr7_3:18702580-18702599 Msa1095680:CDS 55.0%
TGGCCACTGGTATCTGATGG+TGG - chr7_3:18703140-18703159 Msa1095680:intron 55.0%
! GGGACTGGTAGTGTCTAGAG+AGG - chr7_3:18702580-18702599 Msa1095680:CDS 55.0%
TGGCCACTGGTATCTGATGG+TGG - chr7_3:18703140-18703159 Msa1095680:intron 55.0%
Chromosome Type Strat End Strand Name
chr7_3 gene 18702443 18703356 18702443 ID=Msa1095680;Name=Msa1095680
chr7_3 mRNA 18702443 18703356 18702443 ID=Msa1095680-mRNA-1;Parent=Msa1095680;Name=Msa1095680-mRNA-1;_AED=0.39;_eAED=0.53;_QI=0|0|0|1|0|0.66|3|0|162
chr7_3 exon 18703198 18703356 18703198 ID=Msa1095680-mRNA-1:exon:4089;Parent=Msa1095680-mRNA-1
chr7_3 exon 18702959 18703045 18702959 ID=Msa1095680-mRNA-1:exon:4088;Parent=Msa1095680-mRNA-1
chr7_3 exon 18702443 18702685 18702443 ID=Msa1095680-mRNA-1:exon:4087;Parent=Msa1095680-mRNA-1
chr7_3 CDS 18703198 18703356 18703198 ID=Msa1095680-mRNA-1:cds;Parent=Msa1095680-mRNA-1
chr7_3 CDS 18702959 18703045 18702959 ID=Msa1095680-mRNA-1:cds;Parent=Msa1095680-mRNA-1
chr7_3 CDS 18702443 18702685 18702443 ID=Msa1095680-mRNA-1:cds;Parent=Msa1095680-mRNA-1
Gene Sequence

>Msa1095680

ATGAACAATATATTTGTATTATCGTTCTCATGCTTTTATGGTTATATAACACAAGTTTTATGGTTATATTATAGGGATACCATTTTCAAAGTTGAGAGGAACGAGTATTCACGAGCTGATTTTGAATGCATGTGTTCGGGACTGGTAGTGTCTAGAGAGATAATACTAATGATGGCGCTCAAGGTATCTTGGACACAACACAACAACATTTGCAAGTTTTTGTGGTGTCTACCACCATCCTTCTCGATTTATGTTCCAATAGAAGACACTAATGGCCACTGGTATCTGATGGTGGTTTCAATGGACACCCAAAAGATTTACCATTTAGACTCCCACTTTAAGGAAGAAGCCTTGGAAGAAAGACGTTTTACAATAAGAAACATTGTAAGGCTACGAGTGTATATTTTAAGTCTTATTACAAAACCTTTTATAGTTGGGTATCCCAGTGGCATTGACAATGTCACAGTGACAACTCAGCATTATATGTAG

Protein sequence

>Msa1095680

MNNIFVLSFSCFYGYITQVLWLYYRDTIFKVERNEYSRADFECMCSGLVVSREIILMMALKVSWTQHNNICKFLWCLPPSFSIYVPIEDTNGHWYLMVVSMDTQKIYHLDSHFKEEALEERRFTIRNIVRLRVYILSLITKPFIVGYPSGIDNVTVTTQHYM*