AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene65821


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene65821.t1 MTR_3g018790 98.630 73 1 0 1 73 1 73 6.14e-47 151
MS.gene65821.t1 MTR_3g018920 94.521 73 4 0 1 73 1 73 6.59e-46 145
MS.gene65821.t1 MTR_8g038180 76.712 73 17 0 1 73 1 73 1.03e-34 120
MS.gene65821.t1 MTR_8g038220 73.973 73 19 0 1 73 1 73 1.83e-34 119
MS.gene65821.t1 MTR_3g018780 72.603 73 20 0 1 73 1 73 3.71e-32 113
MS.gene65821.t1 MTR_8g038210 69.863 73 22 0 1 73 1 73 1.32e-31 112
MS.gene65821.t1 MTR_8g038220 69.863 73 21 1 1 73 1 72 2.92e-31 111
MS.gene65821.t1 MTR_8g038210 57.534 73 31 0 1 73 1 73 2.34e-25 95.5
MS.gene65821.t1 MTR_2g031980 56.164 73 32 0 1 73 1 73 1.63e-24 93.2
MS.gene65821.t1 MTR_0276s0050 55.405 74 32 1 1 73 1 74 5.16e-20 81.3
MS.gene65821.t1 MTR_5g063670 52.703 74 34 1 1 73 1 74 1.19e-19 80.5
MS.gene65821.t1 MTR_8g107640 54.054 74 33 1 1 73 1 74 2.27e-19 79.7
MS.gene65821.t1 MTR_8g038150 54.795 73 32 1 1 72 1 73 1.65e-18 77.4
MS.gene65821.t1 MTR_6g071615 53.333 75 34 1 1 74 1 75 1.90e-17 74.3
MS.gene65821.t1 MTR_1g112520 49.333 75 37 1 1 74 1 75 1.52e-15 69.3
MS.gene65821.t1 MTR_6g071605 50.000 74 36 1 1 73 1 74 1.23e-14 66.6
MS.gene65821.t1 MTR_1g033560 44.595 74 40 1 1 73 1 74 1.58e-14 66.6
MS.gene65821.t1 MTR_6g071595 52.459 61 29 0 14 74 15 75 6.00e-14 64.7
MS.gene65821.t1 MTR_6g071595 52.459 61 29 0 14 74 15 75 7.20e-14 64.7
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene65821.t1 AT5G12380 61.644 73 28 0 1 73 1 73 5.26e-27 100
MS.gene65821.t1 AT5G65020 58.108 74 30 1 1 73 1 74 1.66e-21 85.5
MS.gene65821.t1 AT5G10220 58.108 74 30 1 1 73 1 74 1.75e-21 85.5
MS.gene65821.t1 AT5G10230 58.108 74 30 1 1 73 1 74 2.02e-21 85.1
MS.gene65821.t1 AT2G38760 52.055 73 34 1 1 72 1 73 5.19e-21 84.3
MS.gene65821.t1 AT1G35720 55.405 74 32 1 1 73 1 74 2.88e-20 82.0
MS.gene65821.t1 AT5G65020 61.224 49 19 0 25 73 11 59 1.00e-14 67.0
MS.gene65821.t1 AT1G68090 50.704 71 34 1 1 70 1 71 9.54e-14 63.9
MS.gene65821.t1 AT1G68090 50.704 71 34 1 1 70 1 71 1.34e-13 63.9

Find 17 sgRNAs with CRISPR-Local

Find 58 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CGTCTTGAGTCTGAGCTTTC+AGG 0.157675 3.2:+9282145 MS.gene65821:CDS
ATGACCTAATATTGCTATAA+TGG 0.265808 3.2:-9282053 None:intergenic
CTTGTCTGATTTGAGTCCTT+TGG 0.274325 3.2:-9282087 None:intergenic
AGTGGTTGGAAGGAGCAATA+AGG 0.292571 3.2:-9281286 None:intergenic
AAAGCCATTATAGCAATATT+AGG 0.311002 3.2:+9282049 MS.gene65821:CDS
GCTCTTCAAAGGGCTGTTAA+AGG 0.314120 3.2:+9281329 MS.gene65821:CDS
TTGTCTGATTTGAGTCCTTT+GGG 0.385685 3.2:-9282086 None:intergenic
GTGGTTGGAAGGAGCAATAA+GGG 0.389381 3.2:-9281285 None:intergenic
AGAGCTTCTGCATCTTCAAC+TGG 0.416203 3.2:-9281311 None:intergenic
CTGCATCTTCAACTGGAGAG+TGG 0.522358 3.2:-9281304 None:intergenic
AAGATGCAGAAGCTCTTCAA+AGG 0.524239 3.2:+9281318 MS.gene65821:CDS
ATCTTCAACTGGAGAGTGGT+TGG 0.525012 3.2:-9281300 None:intergenic
AGGAGCAATAAGGGAAGCCA+TGG 0.568515 3.2:-9281276 None:intergenic
TCAACTGGAGAGTGGTTGGA+AGG 0.576644 3.2:-9281296 None:intergenic
AGATGCAGAAGCTCTTCAAA+GGG 0.589809 3.2:+9281319 MS.gene65821:CDS
ATACTATGAACTCTATCAAG+AGG 0.590523 3.2:+9282111 MS.gene65821:CDS
GTCATAGAAATGCTACCCAA+AGG 0.630775 3.2:+9282071 MS.gene65821:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATTAATTATTAATTAAAATT+TGG - chr3.2:9281492-9281511 None:intergenic 0.0%
!! TAATTAATAATAATTAATTA+AGG + chr3.2:9281504-9281523 MS.gene65821:intron 0.0%
!! TTAATTATTAATTAAAATTT+GGG - chr3.2:9281491-9281510 None:intergenic 0.0%
!! TTGAAATTGATTAAATTACT+GGG + chr3.2:9281993-9282012 MS.gene65821:intron 15.0%
!!! AAAAAAATTGATAACCAAAT+TGG + chr3.2:9282481-9282500 MS.gene65821:intron 15.0%
!!! ATCAACAAAAGTTAATTTTT+CGG + chr3.2:9282457-9282476 MS.gene65821:intron 15.0%
!!! ATTTGTTTTTTTGTTAAGTA+TGG + chr3.2:9282282-9282301 MS.gene65821:intron 15.0%
!! ACATTAATATATGCAAAGAT+CGG - chr3.2:9282355-9282374 None:intergenic 20.0%
!! CTTGAAATTGATTAAATTAC+TGG + chr3.2:9281992-9282011 MS.gene65821:intron 20.0%
!!! AATCAATTTCTAAAACCTAA+AGG + chr3.2:9282535-9282554 MS.gene65821:intron 20.0%
! AAAGCCATTATAGCAATATT+AGG + chr3.2:9282049-9282068 MS.gene65821:CDS 25.0%
! AAGAAATGAAAAGATGGATA+TGG - chr3.2:9281364-9281383 None:intergenic 25.0%
! ACAACAATACGTTAGAAAAA+TGG - chr3.2:9281790-9281809 None:intergenic 25.0%
! ATGACCTAATATTGCTATAA+TGG - chr3.2:9282056-9282075 None:intergenic 25.0%
! TATAATCGGTGAGTTTATAT+GGG + chr3.2:9281928-9281947 MS.gene65821:intron 25.0%
! TATTCTTATGTGTGAATGAA+AGG - chr3.2:9281438-9281457 None:intergenic 25.0%
! TCAAAGAAGAAATGAAAAGA+TGG - chr3.2:9281370-9281389 None:intergenic 25.0%
! TGTTGTTCTTAGTTAAAAGT+TGG + chr3.2:9281580-9281599 MS.gene65821:intron 25.0%
! TTATAATCGGTGAGTTTATA+TGG + chr3.2:9281927-9281946 MS.gene65821:intron 25.0%
!!! TTGTCATTTTTTTTTTACCG+TGG - chr3.2:9282187-9282206 None:intergenic 25.0%
AATATTGGCACAAGGAAAAA+GGG - chr3.2:9281754-9281773 None:intergenic 30.0%
ACGATTCCATGTGTTATAAT+CGG + chr3.2:9281914-9281933 MS.gene65821:intron 30.0%
ATACTATGAACTCTATCAAG+AGG + chr3.2:9282111-9282130 MS.gene65821:CDS 30.0%
TTACAGTGAATAAACGTGTT+CGG + chr3.2:9282321-9282340 MS.gene65821:intron 30.0%
!! GGTTTGATGAATTTTCAAGA+TGG - chr3.2:9281417-9281436 None:intergenic 30.0%
!! TGAGTTTAGCTCAACTTTTA+CGG - chr3.2:9282378-9282397 None:intergenic 30.0%
ATCGAAGGTAAAGGACTAAA+GGG + chr3.2:9281699-9281718 MS.gene65821:intron 35.0%
GAATATTGGCACAAGGAAAA+AGG - chr3.2:9281755-9281774 None:intergenic 35.0%
GACTGATTAAGTCACCAATT+TGG - chr3.2:9282498-9282517 None:intergenic 35.0%
GGTGTAACATGTCAGAATAT+TGG - chr3.2:9281769-9281788 None:intergenic 35.0%
TTTAGTCCTTTACCTTCGAT+GGG - chr3.2:9281699-9281718 None:intergenic 35.0%
! AACTCACCGATTATAACACA+TGG - chr3.2:9281923-9281942 None:intergenic 35.0%
! CTTCGAAATTTTGTAGGTTG+GGG + chr3.2:9282016-9282035 MS.gene65821:intron 35.0%
! GCTTCGAAATTTTGTAGGTT+GGG + chr3.2:9282015-9282034 MS.gene65821:intron 35.0%
! TTGTCTGATTTGAGTCCTTT+GGG - chr3.2:9282089-9282108 None:intergenic 35.0%
AAGATGCAGAAGCTCTTCAA+AGG + chr3.2:9281318-9281337 MS.gene65821:CDS 40.0%
AATACTAATAGCCCCATCGA+AGG + chr3.2:9281684-9281703 MS.gene65821:intron 40.0%
AGATGCAGAAGCTCTTCAAA+GGG + chr3.2:9281319-9281338 MS.gene65821:CDS 40.0%
CATCGAAGGTAAAGGACTAA+AGG + chr3.2:9281698-9281717 MS.gene65821:intron 40.0%
CATGTCAGAATATTGGCACA+AGG - chr3.2:9281762-9281781 None:intergenic 40.0%
CGATGGGGCTATTAGTATTT+CGG - chr3.2:9281683-9281702 None:intergenic 40.0%
CTTTAGTCCTTTACCTTCGA+TGG - chr3.2:9281700-9281719 None:intergenic 40.0%
GTCATAGAAATGCTACCCAA+AGG + chr3.2:9282071-9282090 MS.gene65821:CDS 40.0%
TTAGTCCTTTACCTTCGATG+GGG - chr3.2:9281698-9281717 None:intergenic 40.0%
! ACTGGGCTTCGAAATTTTGT+AGG + chr3.2:9282010-9282029 MS.gene65821:intron 40.0%
! CTTGTCTGATTTGAGTCCTT+TGG - chr3.2:9282090-9282109 None:intergenic 40.0%
! GGCTTCGAAATTTTGTAGGT+TGG + chr3.2:9282014-9282033 MS.gene65821:intron 40.0%
!! TGAGCTTTCAGGTGATTTTG+AGG + chr3.2:9282156-9282175 MS.gene65821:CDS 40.0%
!!! GTGATTTTGAGGTACATCCA+CGG + chr3.2:9282167-9282186 MS.gene65821:CDS 40.0%
AATAGCCCCATCGAAGGTAA+AGG + chr3.2:9281690-9281709 MS.gene65821:intron 45.0%
AGAGCTTCTGCATCTTCAAC+TGG - chr3.2:9281314-9281333 None:intergenic 45.0%
AGTGGTTGGAAGGAGCAATA+AGG - chr3.2:9281289-9281308 None:intergenic 45.0%
ATCTTCAACTGGAGAGTGGT+TGG - chr3.2:9281303-9281322 None:intergenic 45.0%
GCTCTTCAAAGGGCTGTTAA+AGG + chr3.2:9281329-9281348 MS.gene65821:CDS 45.0%
GTGGTTGGAAGGAGCAATAA+GGG - chr3.2:9281288-9281307 None:intergenic 45.0%
CGTCTTGAGTCTGAGCTTTC+AGG + chr3.2:9282145-9282164 MS.gene65821:CDS 50.0%
CTGCATCTTCAACTGGAGAG+TGG - chr3.2:9281307-9281326 None:intergenic 50.0%
TCAACTGGAGAGTGGTTGGA+AGG - chr3.2:9281299-9281318 None:intergenic 50.0%


Chromosome Type Strat End Strand Name
chr3.2 gene 9281278 9282566 9281278 ID=MS.gene65821
chr3.2 mRNA 9281278 9282566 9281278 ID=MS.gene65821.t1;Parent=MS.gene65821
chr3.2 exon 9281278 9281350 9281278 ID=MS.gene65821.t1.exon1;Parent=MS.gene65821.t1
chr3.2 CDS 9281278 9281350 9281278 ID=cds.MS.gene65821.t1;Parent=MS.gene65821.t1
chr3.2 exon 9282032 9282188 9282032 ID=MS.gene65821.t1.exon2;Parent=MS.gene65821.t1
chr3.2 CDS 9282032 9282188 9282032 ID=cds.MS.gene65821.t1;Parent=MS.gene65821.t1
chr3.2 exon 9282557 9282566 9282557 ID=MS.gene65821.t1.exon3;Parent=MS.gene65821.t1
chr3.2 CDS 9282557 9282566 9282557 ID=cds.MS.gene65821.t1;Parent=MS.gene65821.t1
Gene Sequence

>MS.gene65821

ATGGCTTCCCTTATTGCTCCTTCCAACCACTCTCCAGTTGAAGATGCAGAAGCTCTTCAAAGGGCTGTTAAAGGTAATCACAACCATATCCATCTTTTCATTTCTTCTTTGAAAAATTCATTATTGTTTGTTTATTCCATCTTGAAAATTCATCAAACCTTTCATTCACACATAAGAATATTTTTTTTAATTAATAGTCATTATTCTTTTCCCAAATTTTAATTAATAATTAATAATAATTAATTAAGGTCATATTTGTTGCGATCTCAAGTTAGCTTTGAATCTCATACAAGTCATCACGATGTTGTTCTTAGTTAAAAGTTGGCTCATTGATTTGAAGAGAGTAAATACATAAACTATCTTTAATCTCGATTTTCAAATAATGTGAGACTTTTTGTTGTACCGAAATACTAATAGCCCCATCGAAGGTAAAGGACTAAAGGGTCTATGATAAGCTTTGTGCATAGCTTAAACCCTTTTTCCTTGTGCCAATATTCTGACATGTTACACCATTTTTCTAACGTATTGTTGTCTATTTTGAATCTTATATGTGCTCTTATGTTATTTGTTAGTCTATGTAGATTAAATCGTACTTAGTCTTGATTCTCAAACAATATGAAATTGTTGTGTAGCGAGACGATTCCATGTGTTATAATCGGTGAGTTTATATGGGATATTTTTTAAAAGATGTGCAAAAAGAAATAGTAATAATATCTTGAAATTGATTAAATTACTGGGCTTCGAAATTTTGTAGGTTGGGGAGCTGATGAAAAAGCCATTATAGCAATATTAGGTCATAGAAATGCTACCCAAAGGACTCAAATCAGACAAGCATACTATGAACTCTATCAAGAGGATCTCATCAAACGTCTTGAGTCTGAGCTTTCAGGTGATTTTGAGGTACATCCACGGTAAAAAAAAAATGACAATTAAATATATTTAAAATAGAAATTTTGTTGAAATTTTATTGTGCATGTCGATGTTTTTAATGTATACATTATTGTATTTGTTTTTTTGTTAAGTATGGTTAGAAATTCACTTTTTTACAGTGAATAAACGTGTTCGGAGTTCGAACCGATCTTTGCATATATTAATGTCCGTAAAAGTTGAGCTAAACTCACAAGACATACATCAATGTATTTTATTATGTATATTGTTGATATACACACACACACGATTATCAACAAAAGTTAATTTTTCGGAAAAAAAATTGATAACCAAATTGGTGACTTAATCAGTCTCTAAAACTAATCTCTGAATCAATTTCTAAAACCTAAAGGACAAACTGA

Protein sequence

>MS.gene65821.t1

MASLIAPSNHSPVEDAEALQRAVKGWGADEKAIIAILGHRNATQRTQIRQAYYELYQEDLIKRLESELSGDFEVHPRTN