AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1421130


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1421130 MtrunA17_Chr3g0084011 93.506 77 5 0 1 77 1 77 1.20e-49 151
Msa1421130 MtrunA17_Chr3g0083921 98.630 73 1 0 1 73 1 73 5.20e-47 151
Msa1421130 MtrunA17_Chr8g0352591 76.712 73 17 0 1 73 1 73 5.46e-35 120
Msa1421130 MtrunA17_Chr3g0083901 72.603 73 20 0 1 73 1 73 3.60e-32 113
Msa1421130 MtrunA17_Chr8g0352611 69.863 73 22 0 1 73 1 73 7.68e-32 112
Msa1421130 MtrunA17_Chr8g0352621 69.863 73 21 1 1 73 1 72 2.60e-31 110
Msa1421130 MtrunA17_Chr2g0293441 56.164 73 32 0 1 73 1 73 1.26e-24 93.2
Msa1421130 MtrunA17_Chr8g0382281 55.405 74 32 1 1 73 1 74 3.80e-20 81.3
Msa1421130 MtrunA17_Chr5g0425971 52.703 74 34 1 1 73 1 74 8.24e-20 80.5
Msa1421130 MtrunA17_Chr8g0393281 54.054 74 33 1 1 73 1 74 1.90e-19 79.3
Msa1421130 MtrunA17_Chr8g0352571 54.795 73 32 1 1 72 1 73 1.23e-18 77.4
Msa1421130 MtrunA17_Chr6g0479421 53.333 75 34 1 1 74 1 75 1.67e-17 74.3
Msa1421130 MtrunA17_Chr1g0210981 49.333 75 37 1 1 74 1 75 1.09e-15 69.3
Msa1421130 MtrunA17_Chr6g0479411 50.000 74 36 1 1 73 28 101 3.29e-15 68.2
Msa1421130 MtrunA17_Chr1g0162071 44.595 74 40 1 1 73 1 74 1.26e-14 66.2
Msa1421130 MtrunA17_Chr6g0479391 52.459 61 29 0 14 74 15 75 5.93e-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
Msa1421130 AT5G12380.1 61.644 73 28 0 1 73 1 73 4.55e-27 100
Msa1421130 AT5G10220.1 58.108 74 30 1 1 73 1 74 1.57e-21 85.5
Msa1421130 AT5G65020.1 58.108 74 30 1 1 73 1 74 1.72e-21 85.5
Msa1421130 AT5G10230.1 58.108 74 30 1 1 73 1 74 2.00e-21 85.1
Msa1421130 AT2G38760.1 52.055 73 34 1 1 72 1 73 5.95e-21 84.0
Msa1421130 AT1G35720.1 55.405 74 32 1 1 73 1 74 3.17e-20 82.0
Msa1421130 AT5G65020.2 61.224 49 19 0 25 73 11 59 9.87e-15 67.0
Msa1421130 AT1G68090.2 50.704 71 34 1 1 70 1 71 9.38e-14 63.9
Msa1421130 AT1G68090.1 50.704 71 34 1 1 70 1 71 1.39e-13 63.9

Find 16 sgRNAs with CRISPR-Local

Find 102 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CGTCTTGAGTCTGAGCTTTC+AGG 0.157675 tig0024910:+63313 Msa1421130:CDS
ATGACCTAATATTGCTATAA+TGG 0.265808 tig0024910:-63221 None:intergenic
CTTGTCTGATTTGAGTCCTT+TGG 0.274325 tig0024910:-63255 None:intergenic
AGTGGTTGGAAGGAGCAATA+AGG 0.292571 tig0024910:-62449 None:intergenic
AAAGCCATTATAGCAATATT+AGG 0.311002 tig0024910:+63217 Msa1421130:CDS
GCTCTTCAAAGGGCTGTTAA+AGG 0.314120 tig0024910:+62492 Msa1421130:CDS
TTGTCTGATTTGAGTCCTTT+GGG 0.385685 tig0024910:-63254 None:intergenic
GTGGTTGGAAGGAGCAATAA+GGG 0.389381 tig0024910:-62448 None:intergenic
AGAGCTTCTGCATCTTCAAC+TGG 0.416203 tig0024910:-62474 None:intergenic
CTGCATCTTCAACTGGAGAG+TGG 0.522358 tig0024910:-62467 None:intergenic
AAGATGCAGAAGCTCTTCAA+AGG 0.524239 tig0024910:+62481 Msa1421130:CDS
ATCTTCAACTGGAGAGTGGT+TGG 0.525012 tig0024910:-62463 None:intergenic
TCAACTGGAGAGTGGTTGGA+AGG 0.576644 tig0024910:-62459 None:intergenic
AGATGCAGAAGCTCTTCAAA+GGG 0.589809 tig0024910:+62482 Msa1421130:CDS
ATACTATGAACTCTATCAAG+AGG 0.590523 tig0024910:+63279 Msa1421130:CDS
GTCATAGAAATGCTACCCAA+AGG 0.630775 tig0024910:+63239 Msa1421130:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTAATTATTAATTAAAATTT+GGG - tig0024910:62653-62672 None:intergenic 0.0%
!! ATTAATTATTAATTAAAATT+TGG - tig0024910:62654-62673 None:intergenic 0.0%
!! TAATTAATAATAATTAATTA+AGG + tig0024910:62666-62685 Msa1421130:intron 0.0%
!! TTAATTATTAATTAAAATTT+GGG - tig0024910:62653-62672 None:intergenic 0.0%
!! ATTAATTATTAATTAAAATT+TGG - tig0024910:62654-62673 None:intergenic 0.0%
!! TAATTAATAATAATTAATTA+AGG + tig0024910:62666-62685 Msa1421130:intron 0.0%
!! TTGAAATTGATTAAATTACT+GGG + tig0024910:63161-63180 Msa1421130:intron 15.0%
!! TTGAAATTGATTAAATTACT+GGG + tig0024910:63161-63180 Msa1421130:intron 15.0%
!! TTAATTAAGGTCATATTTGT+TGG + tig0024910:62679-62698 Msa1421130:intron 20.0%
!! TAATTAAGGTCATATTTGTT+GGG + tig0024910:62680-62699 Msa1421130:intron 20.0%
!! CTTGAAATTGATTAAATTAC+TGG + tig0024910:63160-63179 Msa1421130:intron 20.0%
!! TTAATTAAGGTCATATTTGT+TGG + tig0024910:62679-62698 Msa1421130:intron 20.0%
!! TAATTAAGGTCATATTTGTT+GGG + tig0024910:62680-62699 Msa1421130:intron 20.0%
!! CTTGAAATTGATTAAATTAC+TGG + tig0024910:63160-63179 Msa1421130:intron 20.0%
! AAGAAATGAAAAGATGGATA+TGG - tig0024910:62527-62546 None:intergenic 25.0%
! TCAAAGAAGAAATGAAAAGA+TGG - tig0024910:62533-62552 None:intergenic 25.0%
! TATTCTTATGTGTGAATGAA+AGG - tig0024910:62601-62620 None:intergenic 25.0%
! TGTTGTTCTTAGTTAAAAGT+TGG + tig0024910:62742-62761 Msa1421130:intron 25.0%
! ACAACAATACGTTAGAAAAA+TGG - tig0024910:62952-62971 None:intergenic 25.0%
! TTATAATCGGTGAGTTTATA+TGG + tig0024910:63095-63114 Msa1421130:intron 25.0%
! TATAATCGGTGAGTTTATAT+GGG + tig0024910:63096-63115 Msa1421130:intron 25.0%
! AAAGCCATTATAGCAATATT+AGG + tig0024910:63217-63236 Msa1421130:CDS 25.0%
! ATGACCTAATATTGCTATAA+TGG - tig0024910:63224-63243 None:intergenic 25.0%
! AAGAAATGAAAAGATGGATA+TGG - tig0024910:62527-62546 None:intergenic 25.0%
! TCAAAGAAGAAATGAAAAGA+TGG - tig0024910:62533-62552 None:intergenic 25.0%
! TATTCTTATGTGTGAATGAA+AGG - tig0024910:62601-62620 None:intergenic 25.0%
! TGTTGTTCTTAGTTAAAAGT+TGG + tig0024910:62742-62761 Msa1421130:intron 25.0%
! ACAACAATACGTTAGAAAAA+TGG - tig0024910:62952-62971 None:intergenic 25.0%
! TTATAATCGGTGAGTTTATA+TGG + tig0024910:63095-63114 Msa1421130:intron 25.0%
! TATAATCGGTGAGTTTATAT+GGG + tig0024910:63096-63115 Msa1421130:intron 25.0%
! AAAGCCATTATAGCAATATT+AGG + tig0024910:63217-63236 Msa1421130:CDS 25.0%
! ATGACCTAATATTGCTATAA+TGG - tig0024910:63224-63243 None:intergenic 25.0%
!! GGTTTGATGAATTTTCAAGA+TGG - tig0024910:62580-62599 None:intergenic 30.0%
ACGATTCCATGTGTTATAAT+CGG + tig0024910:63082-63101 Msa1421130:intron 30.0%
ATACTATGAACTCTATCAAG+AGG + tig0024910:63279-63298 Msa1421130:CDS 30.0%
!! GGTTTGATGAATTTTCAAGA+TGG - tig0024910:62580-62599 None:intergenic 30.0%
ACGATTCCATGTGTTATAAT+CGG + tig0024910:63082-63101 Msa1421130:intron 30.0%
ATACTATGAACTCTATCAAG+AGG + tig0024910:63279-63298 Msa1421130:CDS 30.0%
TTTAGTCCTTTACCTTCGAT+GGG - tig0024910:62861-62880 None:intergenic 35.0%
ATCGAAGGTAAAGGACTAAA+GGG + tig0024910:62861-62880 Msa1421130:intron 35.0%
! ATAGCTTAGATCCTTTTTCC+TGG + tig0024910:62903-62922 Msa1421130:intron 35.0%
GGTGTAACATGTCAGAATAT+TGG - tig0024910:62931-62950 None:intergenic 35.0%
! AACTCACCGATTATAACACA+TGG - tig0024910:63091-63110 None:intergenic 35.0%
! GCTTCGAAATTTTGTAGGTT+GGG + tig0024910:63183-63202 Msa1421130:intron 35.0%
! CTTCGAAATTTTGTAGGTTG+GGG + tig0024910:63184-63203 Msa1421130:intron 35.0%
! TTGTCTGATTTGAGTCCTTT+GGG - tig0024910:63257-63276 None:intergenic 35.0%
TTTAGTCCTTTACCTTCGAT+GGG - tig0024910:62861-62880 None:intergenic 35.0%
ATCGAAGGTAAAGGACTAAA+GGG + tig0024910:62861-62880 Msa1421130:intron 35.0%
! ATAGCTTAGATCCTTTTTCC+TGG + tig0024910:62903-62922 Msa1421130:intron 35.0%
GGTGTAACATGTCAGAATAT+TGG - tig0024910:62931-62950 None:intergenic 35.0%
! AACTCACCGATTATAACACA+TGG - tig0024910:63091-63110 None:intergenic 35.0%
! GCTTCGAAATTTTGTAGGTT+GGG + tig0024910:63183-63202 Msa1421130:intron 35.0%
! CTTCGAAATTTTGTAGGTTG+GGG + tig0024910:63184-63203 Msa1421130:intron 35.0%
! TTGTCTGATTTGAGTCCTTT+GGG - tig0024910:63257-63276 None:intergenic 35.0%
AAGATGCAGAAGCTCTTCAA+AGG + tig0024910:62481-62500 Msa1421130:CDS 40.0%
AGATGCAGAAGCTCTTCAAA+GGG + tig0024910:62482-62501 Msa1421130:CDS 40.0%
CGATGGGGCTATTAGTATTT+CGG - tig0024910:62845-62864 None:intergenic 40.0%
AATACTAATAGCCCCATCGA+AGG + tig0024910:62846-62865 Msa1421130:intron 40.0%
TTAGTCCTTTACCTTCGATG+GGG - tig0024910:62860-62879 None:intergenic 40.0%
CTTTAGTCCTTTACCTTCGA+TGG - tig0024910:62862-62881 None:intergenic 40.0%
CATCGAAGGTAAAGGACTAA+AGG + tig0024910:62860-62879 Msa1421130:intron 40.0%
GAATATTGGCACCAGGAAAA+AGG - tig0024910:62917-62936 None:intergenic 40.0%
! ACTGGGCTTCGAAATTTTGT+AGG + tig0024910:63178-63197 Msa1421130:intron 40.0%
! GGCTTCGAAATTTTGTAGGT+TGG + tig0024910:63182-63201 Msa1421130:intron 40.0%
GTCATAGAAATGCTACCCAA+AGG + tig0024910:63239-63258 Msa1421130:CDS 40.0%
! CTTGTCTGATTTGAGTCCTT+TGG - tig0024910:63258-63277 None:intergenic 40.0%
!! TGAGCTTTCAGGTGATTTTG+AGG + tig0024910:63324-63343 Msa1421130:CDS 40.0%
!!! GTGATTTTGAGGTACATCCA+CGG + tig0024910:63335-63354 Msa1421130:CDS 40.0%
AAGATGCAGAAGCTCTTCAA+AGG + tig0024910:62481-62500 Msa1421130:CDS 40.0%
AGATGCAGAAGCTCTTCAAA+GGG + tig0024910:62482-62501 Msa1421130:CDS 40.0%
CGATGGGGCTATTAGTATTT+CGG - tig0024910:62845-62864 None:intergenic 40.0%
AATACTAATAGCCCCATCGA+AGG + tig0024910:62846-62865 Msa1421130:intron 40.0%
TTAGTCCTTTACCTTCGATG+GGG - tig0024910:62860-62879 None:intergenic 40.0%
CTTTAGTCCTTTACCTTCGA+TGG - tig0024910:62862-62881 None:intergenic 40.0%
CATCGAAGGTAAAGGACTAA+AGG + tig0024910:62860-62879 Msa1421130:intron 40.0%
GAATATTGGCACCAGGAAAA+AGG - tig0024910:62917-62936 None:intergenic 40.0%
! ACTGGGCTTCGAAATTTTGT+AGG + tig0024910:63178-63197 Msa1421130:intron 40.0%
! GGCTTCGAAATTTTGTAGGT+TGG + tig0024910:63182-63201 Msa1421130:intron 40.0%
GTCATAGAAATGCTACCCAA+AGG + tig0024910:63239-63258 Msa1421130:CDS 40.0%
! CTTGTCTGATTTGAGTCCTT+TGG - tig0024910:63258-63277 None:intergenic 40.0%
!! TGAGCTTTCAGGTGATTTTG+AGG + tig0024910:63324-63343 Msa1421130:CDS 40.0%
!!! GTGATTTTGAGGTACATCCA+CGG + tig0024910:63335-63354 Msa1421130:CDS 40.0%
GTGGTTGGAAGGAGCAATAA+GGG - tig0024910:62451-62470 None:intergenic 45.0%
AGTGGTTGGAAGGAGCAATA+AGG - tig0024910:62452-62471 None:intergenic 45.0%
ATCTTCAACTGGAGAGTGGT+TGG - tig0024910:62466-62485 None:intergenic 45.0%
AGAGCTTCTGCATCTTCAAC+TGG - tig0024910:62477-62496 None:intergenic 45.0%
GCTCTTCAAAGGGCTGTTAA+AGG + tig0024910:62492-62511 Msa1421130:CDS 45.0%
AATAGCCCCATCGAAGGTAA+AGG + tig0024910:62852-62871 Msa1421130:intron 45.0%
CATGTCAGAATATTGGCACC+AGG - tig0024910:62924-62943 None:intergenic 45.0%
GTGGTTGGAAGGAGCAATAA+GGG - tig0024910:62451-62470 None:intergenic 45.0%
AGTGGTTGGAAGGAGCAATA+AGG - tig0024910:62452-62471 None:intergenic 45.0%
ATCTTCAACTGGAGAGTGGT+TGG - tig0024910:62466-62485 None:intergenic 45.0%
AGAGCTTCTGCATCTTCAAC+TGG - tig0024910:62477-62496 None:intergenic 45.0%
GCTCTTCAAAGGGCTGTTAA+AGG + tig0024910:62492-62511 Msa1421130:CDS 45.0%
AATAGCCCCATCGAAGGTAA+AGG + tig0024910:62852-62871 Msa1421130:intron 45.0%
CATGTCAGAATATTGGCACC+AGG - tig0024910:62924-62943 None:intergenic 45.0%
TCAACTGGAGAGTGGTTGGA+AGG - tig0024910:62462-62481 None:intergenic 50.0%
CTGCATCTTCAACTGGAGAG+TGG - tig0024910:62470-62489 None:intergenic 50.0%
CGTCTTGAGTCTGAGCTTTC+AGG + tig0024910:63313-63332 Msa1421130:CDS 50.0%
TCAACTGGAGAGTGGTTGGA+AGG - tig0024910:62462-62481 None:intergenic 50.0%
CTGCATCTTCAACTGGAGAG+TGG - tig0024910:62470-62489 None:intergenic 50.0%
CGTCTTGAGTCTGAGCTTTC+AGG + tig0024910:63313-63332 Msa1421130:CDS 50.0%
Chromosome Type Strat End Strand Name
tig0024910 gene 62441 63360 62441 ID=Msa1421130;Name=Msa1421130
tig0024910 mRNA 62441 63360 62441 ID=Msa1421130-mRNA-1;Parent=Msa1421130;Name=Msa1421130-mRNA-1;_AED=0.45;_eAED=0.45;_QI=0|0|0|1|1|1|2|0|77
tig0024910 exon 62441 62513 62441 ID=Msa1421130-mRNA-1:exon:1929;Parent=Msa1421130-mRNA-1
tig0024910 exon 63200 63360 63200 ID=Msa1421130-mRNA-1:exon:1930;Parent=Msa1421130-mRNA-1
tig0024910 CDS 62441 62513 62441 ID=Msa1421130-mRNA-1:cds;Parent=Msa1421130-mRNA-1
tig0024910 CDS 63200 63360 63200 ID=Msa1421130-mRNA-1:cds;Parent=Msa1421130-mRNA-1
Gene Sequence

>Msa1421130

ATGGCTTCCCTTATTGCTCCTTCCAACCACTCTCCAGTTGAAGATGCAGAAGCTCTTCAAAGGGCTGTTAAAGGTTGGGGAGCTGATGAAAAAGCCATTATAGCAATATTAGGTCATAGAAATGCTACCCAAAGGACTCAAATCAGACAAGCATACTATGAACTCTATCAAGAGGATCTCATCAAACGTCTTGAGTCTGAGCTTTCAGGTGATTTTGAGGTACATCCACGGTAA

Protein sequence

>Msa1421130

MASLIAPSNHSPVEDAEALQRAVKGWGADEKAIIAILGHRNATQRTQIRQAYYELYQEDLIKRLESELSGDFEVHPR*