AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene016987

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene016987.t1 MTR_5g089720 97.489 438 10 1 1 438 1 437 0.0 889
MS.gene016987.t1 MTR_5g094340 51.795 195 81 4 32 218 53 242 6.08e-62 206
MS.gene016987.t1 MTR_3g055960 48.718 195 94 3 32 222 54 246 3.95e-61 205
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene016987.t1 AT5G12300 56.204 274 86 6 33 296 19 268 1.52e-87 271
MS.gene016987.t1 AT1G50570 40.389 411 189 11 29 438 33 388 1.02e-83 262
MS.gene016987.t1 AT1G50570 40.389 411 189 11 29 438 33 388 1.02e-83 262
MS.gene016987.t1 AT5G55530 49.746 197 93 3 32 224 48 242 8.06e-62 206
MS.gene016987.t1 AT5G55530 49.746 197 93 3 32 224 48 242 8.06e-62 206
MS.gene016987.t1 AT5G55530 49.746 197 93 3 32 224 48 242 8.06e-62 206

Find 59 sgRNAs with CRISPR-Local

Find 72 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTTCCAACAATTTGTGAAAT+TGG 0.112542 5.2:+76113768 None:intergenic
CCGCTATGATCTTGTCTTTC+GGG 0.138670 5.2:+76112946 None:intergenic
AACTTCTTGTTCTCATGATT+TGG 0.220949 5.2:+76112913 None:intergenic
TGTGTAGCTCTATTCAAATT+TGG 0.233288 5.2:+76114095 None:intergenic
ACCGCTATGATCTTGTCTTT+CGG 0.271993 5.2:+76112945 None:intergenic
CTGTTATGAAATGTGAAATT+TGG 0.279391 5.2:-76113848 MS.gene016987:CDS
AGAAATCGACAATAAGAAAA+AGG 0.318863 5.2:-76112890 MS.gene016987:CDS
AGCATAGAAGTAACAAAGTT+TGG 0.319974 5.2:-76113117 MS.gene016987:CDS
TTCCAACAATTTGTGAAATT+GGG 0.331184 5.2:+76113769 None:intergenic
TTCTTTGAAGTTGGTGTATC+GGG 0.348339 5.2:+76113216 None:intergenic
ATTATCTTTAGACACATCTT+TGG 0.351395 5.2:-76113670 MS.gene016987:CDS
TCAATTCTTGAATACTCAAT+TGG 0.352551 5.2:+76113567 None:intergenic
TTGCTGCCATTTCTTCATCT+TGG 0.384771 5.2:-76113450 MS.gene016987:CDS
TCAAGATTAATATTCCCTAA+TGG 0.389292 5.2:+76113078 None:intergenic
TCCTGACATAAGTATTGTTA+AGG 0.391070 5.2:-76113541 MS.gene016987:CDS
GGGACAAAGAGTAACAAAAT+TGG 0.398931 5.2:+76113236 None:intergenic
GGAATTGTGAAGGCTTTCAT+TGG 0.401534 5.2:+76113350 None:intergenic
ATTTCACAAATTGTTGGAAA+AGG 0.401795 5.2:-76113765 MS.gene016987:CDS
CTTGTAGAAAGAGTTTCATC+AGG 0.408913 5.2:+76113942 None:intergenic
AATGAAAGCCTTCACAATTC+CGG 0.426166 5.2:-76113348 MS.gene016987:CDS
GTCCCAATTTCACAAATTGT+TGG 0.426474 5.2:-76113771 MS.gene016987:CDS
TCACCTTCTTTCTTTGAAGT+TGG 0.429226 5.2:+76113207 None:intergenic
TTTCTTTGAAGTTGGTGTAT+CGG 0.431713 5.2:+76113215 None:intergenic
GAGTTCGCCAGATGAGAATC+AGG 0.437738 5.2:-76113388 MS.gene016987:CDS
GAATCCACCTGATTCTCATC+TGG 0.447663 5.2:+76113381 None:intergenic
TCCTTAACAATACTTATGTC+AGG 0.450696 5.2:+76113540 None:intergenic
GTCATCAAAACAACAGCTTT+AGG 0.454918 5.2:-76114124 MS.gene016987:CDS
AAGCCTTCACAATTCCGGTT+TGG 0.455785 5.2:-76113343 MS.gene016987:CDS
GCAACAGTTTACTGAGTCCT+TGG 0.468052 5.2:-76113001 MS.gene016987:CDS
GAAGCACCAAGATGAAGAAA+TGG 0.478364 5.2:+76113444 None:intergenic
AAAATTCTCAAACAAAGAAA+AGG 0.487388 5.2:-76113157 MS.gene016987:CDS
GAATTGTGAAGGCTTTCATT+GGG 0.490123 5.2:+76113351 None:intergenic
TGTTAAGGAGAATCAACAAA+TGG 0.492303 5.2:-76113526 MS.gene016987:CDS
TGCTATGCAGAAGCAAATAG+TGG 0.492416 5.2:-76113043 MS.gene016987:CDS
AAAGATATCTGAAGTTATGT+TGG 0.495670 5.2:-76113592 MS.gene016987:CDS
GATAGTAGAGCTTACCAAAC+CGG 0.496758 5.2:+76113329 None:intergenic
AAAAGGAATGCAAGAAGGAA+AGG 0.505483 5.2:-76113140 MS.gene016987:CDS
CAAAGAAAAGGAATGCAAGA+AGG 0.507838 5.2:-76113145 MS.gene016987:CDS
GAAGATGAAGCAGAGTTCAC+AGG 0.514799 5.2:-76114062 MS.gene016987:CDS
GGCGAAAATGAAGCTTCCTA+TGG 0.518944 5.2:-76112980 MS.gene016987:CDS
TCTTGAATTGTTGTTACTTG+AGG 0.524311 5.2:+76113476 None:intergenic
TCGGGTTTGTCAACGTCCAT+AGG 0.526209 5.2:+76112964 None:intergenic
TTTCATCAGGGTTGTAAGTG+AGG 0.531627 5.2:+76113955 None:intergenic
GTTAATTGAACAGTTCCAGC+TGG 0.532682 5.2:+76113693 None:intergenic
CTTTCTACAAGAATAATCAA+TGG 0.534660 5.2:-76113930 MS.gene016987:CDS
AAATAGTGGATATGTATATG+AGG 0.538443 5.2:-76113029 MS.gene016987:CDS
ACAAGAATAATCAATGGAGG+TGG 0.563554 5.2:-76113924 MS.gene016987:CDS
TTCATCAGGGTTGTAAGTGA+GGG 0.567857 5.2:+76113956 None:intergenic
ACACCAACTTCAAAGAAAGA+AGG 0.576636 5.2:-76113210 MS.gene016987:CDS
TTACCAAACCGGAATTGTGA+AGG 0.582333 5.2:+76113340 None:intergenic
CAACATTCAATGAAAACTTG+AGG 0.590629 5.2:-76113893 MS.gene016987:CDS
GAATATTAATCTTGAAGCTG+AGG 0.593724 5.2:-76113070 MS.gene016987:CDS
AAGATGAAGCAGAGTTCACA+GGG 0.598725 5.2:-76114061 MS.gene016987:CDS
TGTTATGAATGTTTCTAGCA+TGG 0.599484 5.2:+76114018 None:intergenic
TTGTAGAAAGAGTTTCATCA+GGG 0.607403 5.2:+76113943 None:intergenic
TAGTAGAGCAAGAATTCACA+TGG 0.626136 5.2:-76113820 MS.gene016987:CDS
TCTACAAGAATAATCAATGG+AGG 0.653951 5.2:-76113927 MS.gene016987:CDS
TTCGCCAGATGAGAATCAGG+TGG 0.666779 5.2:-76113385 MS.gene016987:CDS
CCCGAAAGACAAGATCATAG+CGG 0.770714 5.2:-76112946 MS.gene016987:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAAATTCTCAAACAAAGAAA+AGG - chr5.2:76113835-76113854 MS.gene016987:CDS 20.0%
!!! AAGTTTTTAATTCTCCATTA+GGG - chr5.2:76113900-76113919 MS.gene016987:CDS 20.0%
! AGAAATCGACAATAAGAAAA+AGG - chr5.2:76114102-76114121 MS.gene016987:CDS 25.0%
! ATTATCTTTAGACACATCTT+TGG - chr5.2:76113322-76113341 MS.gene016987:CDS 25.0%
! ATTTCACAAATTGTTGGAAA+AGG - chr5.2:76113227-76113246 MS.gene016987:CDS 25.0%
! CTGTTATGAAATGTGAAATT+TGG - chr5.2:76113144-76113163 MS.gene016987:CDS 25.0%
! CTTTCTACAAGAATAATCAA+TGG - chr5.2:76113062-76113081 MS.gene016987:CDS 25.0%
! TCAAGATTAATATTCCCTAA+TGG + chr5.2:76113917-76113936 None:intergenic 25.0%
! TCAATTCTTGAATACTCAAT+TGG + chr5.2:76113428-76113447 None:intergenic 25.0%
! TTCCAACAATTTGTGAAATT+GGG + chr5.2:76113226-76113245 None:intergenic 25.0%
! TTTCCAACAATTTGTGAAAT+TGG + chr5.2:76113227-76113246 None:intergenic 25.0%
! TTTGAGAAAAAGAATCATCT+AGG - chr5.2:76113722-76113741 MS.gene016987:CDS 25.0%
!! AAAGATATCTGAAGTTATGT+TGG - chr5.2:76113400-76113419 MS.gene016987:CDS 25.0%
!!! AAATAGTGGATATGTATATG+AGG - chr5.2:76113963-76113982 MS.gene016987:CDS 25.0%
!!! CAAGTTTTTAATTCTCCATT+AGG - chr5.2:76113899-76113918 MS.gene016987:CDS 25.0%
AACTTCTTGTTCTCATGATT+TGG + chr5.2:76114082-76114101 None:intergenic 30.0%
AGCATAGAAGTAACAAAGTT+TGG - chr5.2:76113875-76113894 MS.gene016987:CDS 30.0%
ATCGACAATAAGAAAAAGGA+TGG - chr5.2:76114106-76114125 MS.gene016987:CDS 30.0%
CAACATTCAATGAAAACTTG+AGG - chr5.2:76113099-76113118 MS.gene016987:CDS 30.0%
GAAAAAGATCAGTTGAAGAA+AGG + chr5.2:76113274-76113293 None:intergenic 30.0%
GAATATTAATCTTGAAGCTG+AGG - chr5.2:76113922-76113941 MS.gene016987:CDS 30.0%
TCCTTAACAATACTTATGTC+AGG + chr5.2:76113455-76113474 None:intergenic 30.0%
TCTACAAGAATAATCAATGG+AGG - chr5.2:76113065-76113084 MS.gene016987:CDS 30.0%
TGTTAAGGAGAATCAACAAA+TGG - chr5.2:76113466-76113485 MS.gene016987:CDS 30.0%
TTGTAGAAAGAGTTTCATCA+GGG + chr5.2:76113052-76113071 None:intergenic 30.0%
! ACATGGAAGATCAACTTTTA+GGG - chr5.2:76113189-76113208 MS.gene016987:CDS 30.0%
! CTCAAGTTTTCATTGAATGT+TGG + chr5.2:76113101-76113120 None:intergenic 30.0%
! TCCTGACATAAGTATTGTTA+AGG - chr5.2:76113451-76113470 MS.gene016987:CDS 30.0%
! TCTTGAATTGTTGTTACTTG+AGG + chr5.2:76113519-76113538 None:intergenic 30.0%
! TGTGTAGCTCTATTCAAATT+TGG + chr5.2:76112900-76112919 None:intergenic 30.0%
!! TGTTATGAATGTTTCTAGCA+TGG + chr5.2:76112977-76112996 None:intergenic 30.0%
!! TTTCTTTGAAGTTGGTGTAT+CGG + chr5.2:76113780-76113799 None:intergenic 30.0%
AAAAGGAATGCAAGAAGGAA+AGG - chr5.2:76113852-76113871 MS.gene016987:CDS 35.0%
AATGAAAGCCTTCACAATTC+CGG - chr5.2:76113644-76113663 MS.gene016987:CDS 35.0%
ACAAGAATAATCAATGGAGG+TGG - chr5.2:76113068-76113087 MS.gene016987:CDS 35.0%
ACACCAACTTCAAAGAAAGA+AGG - chr5.2:76113782-76113801 MS.gene016987:CDS 35.0%
CAAAGAAAAGGAATGCAAGA+AGG - chr5.2:76113847-76113866 MS.gene016987:CDS 35.0%
CTTGTAGAAAGAGTTTCATC+AGG + chr5.2:76113053-76113072 None:intergenic 35.0%
GAATTGTGAAGGCTTTCATT+GGG + chr5.2:76113644-76113663 None:intergenic 35.0%
GGGACAAAGAGTAACAAAAT+TGG + chr5.2:76113759-76113778 None:intergenic 35.0%
GTCATCAAAACAACAGCTTT+AGG - chr5.2:76112868-76112887 MS.gene016987:CDS 35.0%
GTCCCAATTTCACAAATTGT+TGG - chr5.2:76113221-76113240 MS.gene016987:CDS 35.0%
TAGTAGAGCAAGAATTCACA+TGG - chr5.2:76113172-76113191 MS.gene016987:CDS 35.0%
! CACATGGAAGATCAACTTTT+AGG - chr5.2:76113188-76113207 MS.gene016987:CDS 35.0%
!! TCACCTTCTTTCTTTGAAGT+TGG + chr5.2:76113788-76113807 None:intergenic 35.0%
!! TTCTTTGAAGTTGGTGTATC+GGG + chr5.2:76113779-76113798 None:intergenic 35.0%
!!! TCAACTTTTAGGGTTTGCTT+TGG - chr5.2:76113199-76113218 MS.gene016987:CDS 35.0%
AAGATGAAGCAGAGTTCACA+GGG - chr5.2:76112931-76112950 MS.gene016987:CDS 40.0%
ACCGCTATGATCTTGTCTTT+CGG + chr5.2:76114050-76114069 None:intergenic 40.0%
GATAGTAGAGCTTACCAAAC+CGG + chr5.2:76113666-76113685 None:intergenic 40.0%
GGAATTGTGAAGGCTTTCAT+TGG + chr5.2:76113645-76113664 None:intergenic 40.0%
GTTAATTGAACAGTTCCAGC+TGG + chr5.2:76113302-76113321 None:intergenic 40.0%
TGCTATGCAGAAGCAAATAG+TGG - chr5.2:76113949-76113968 MS.gene016987:CDS 40.0%
TTACCAAACCGGAATTGTGA+AGG + chr5.2:76113655-76113674 None:intergenic 40.0%
TTCATCAGGGTTGTAAGTGA+GGG + chr5.2:76113039-76113058 None:intergenic 40.0%
TTTCATCAGGGTTGTAAGTG+AGG + chr5.2:76113040-76113059 None:intergenic 40.0%
! CTTTTTCTCAAACGAGTCTG+CGG + chr5.2:76113714-76113733 None:intergenic 40.0%
! GAAGCACCAAGATGAAGAAA+TGG + chr5.2:76113551-76113570 None:intergenic 40.0%
! TTGCTGCCATTTCTTCATCT+TGG - chr5.2:76113542-76113561 MS.gene016987:CDS 40.0%
!! GATCTTTTTCATTCTCCAGC+TGG - chr5.2:76113284-76113303 MS.gene016987:CDS 40.0%
AAGCCTTCACAATTCCGGTT+TGG - chr5.2:76113649-76113668 MS.gene016987:CDS 45.0%
CCCGAAAGACAAGATCATAG+CGG - chr5.2:76114046-76114065 MS.gene016987:CDS 45.0%
CCGCTATGATCTTGTCTTTC+GGG + chr5.2:76114049-76114068 None:intergenic 45.0%
GAAGATGAAGCAGAGTTCAC+AGG - chr5.2:76112930-76112949 MS.gene016987:CDS 45.0%
GAATCCACCTGATTCTCATC+TGG + chr5.2:76113614-76113633 None:intergenic 45.0%
GCAACAGTTTACTGAGTCCT+TGG - chr5.2:76113991-76114010 MS.gene016987:CDS 45.0%
GGCGAAAATGAAGCTTCCTA+TGG - chr5.2:76114012-76114031 MS.gene016987:CDS 45.0%
! AGGAAGCTTCATTTTCGCCA+AGG + chr5.2:76114011-76114030 None:intergenic 45.0%
! GATGGTTCGCGTGTGTTTTA+TGG - chr5.2:76114124-76114143 MS.gene016987:CDS 45.0%
GAGTTCGCCAGATGAGAATC+AGG - chr5.2:76113604-76113623 MS.gene016987:CDS 50.0%
TCGGGTTTGTCAACGTCCAT+AGG + chr5.2:76114031-76114050 None:intergenic 50.0%
TTCGCCAGATGAGAATCAGG+TGG - chr5.2:76113607-76113626 MS.gene016987:CDS 50.0%


Chromosome Type Strat End Strand Name
chr5.2 gene 76112849 76114165 76112849 ID=MS.gene016987
chr5.2 mRNA 76112849 76114165 76112849 ID=MS.gene016987.t1;Parent=MS.gene016987
chr5.2 exon 76112849 76114165 76112849 ID=MS.gene016987.t1.exon1;Parent=MS.gene016987.t1
chr5.2 CDS 76112849 76114165 76112849 ID=cds.MS.gene016987.t1;Parent=MS.gene016987.t1
Gene Sequence

>MS.gene016987

ATGGATTCATTCAATCAGAGTCATCAAAACAACAGCTTTAGGTACAATCCAAATTTGAATAGAGCTACACAAGTAGATGATGAAGATGAAGCAGAGTTCACAGGGCTTCTTGATGTCTATGTTCACCATGCTAGAAACATTCATAACATTTGCATCTATGATAATCAAGATGTATATGCTAAATTCTCCCTCACTTACAACCCTGATGAAACTCTTTCTACAAGAATAATCAATGGAGGTGGAAAAAATCCAACATTCAATGAAAACTTGAGGATGAAGATAACTCAAATAGATGCTGTTATGAAATGTGAAATTTGGATGTTTAGTAGAGCAAGAATTCACATGGAAGATCAACTTTTAGGGTTTGCTTTGGTCCCAATTTCACAAATTGTTGGAAAAGGAAAAGTAACTGAAGACTATAGCCTTTCTTCAACTGATCTTTTTCATTCTCCAGCTGGAACTGTTCAATTAACATTATCTTTAGACACATCTTTGGTATCAGAATCAACAAATAGTTCGTCGATATCGTCAGAAGTTATTTTGCTTGATAGAAAGATATCTGAAGTTATGTTGGATCCAATTGAGTATTCAAGAATTGAATTTCCTGACATAAGTATTGTTAAGGAGAATCAACAAATGGTTTCTCAATACTTCAATCTTGCTTGTGCCTCAAGTAACAACAATTCAAGAAAGTTGCTGCCATTTCTTCATCTTGGTGCTTCTCATCAACTTGATGATTATGAAATGATGACTATGAGTTCGCCAGATGAGAATCAGGTGGATTCGATCTCTCCCAATGAAAGCCTTCACAATTCCGGTTTGGTAAGCTCTACTATCACAAGCTTAAGCGACGATAGAAATTCCGCAGACTCGTTTGAGAAAAAGAATCATCTAGGATGTGATTCAACCAATTTTGTTACTCTTTGTCCCGATACACCAACTTCAAAGAAAGAAGGTGATCAATCAAAAGATGATGAGAAAGAAGAAAAATTCTCAAACAAAGAAAAGGAATGCAAGAAGGAAAGGAGCATAGAAGTAACAAAGTTTGGACAAGTTTTTAATTCTCCATTAGGGAATATTAATCTTGAAGCTGAGGAATGTGCTATGCAGAAGCAAATAGTGGATATGTATATGAGGAGCATGCAACAGTTTACTGAGTCCTTGGCGAAAATGAAGCTTCCTATGGACGTTGACAAACCCGAAAGACAAGATCATAGCGGTGATGTGATTCCAAATCATGAGAACAAGAAGTTAGAAATCGACAATAAGAAAAAGGATGGTTCGCGTGTGTTTTATGGTAGTCGAGCGTTTTTCTAA
Protein sequence

>MS.gene016987.t1

MDSFNQSHQNNSFRYNPNLNRATQVDDEDEAEFTGLLDVYVHHARNIHNICIYDNQDVYAKFSLTYNPDETLSTRIINGGGKNPTFNENLRMKITQIDAVMKCEIWMFSRARIHMEDQLLGFALVPISQIVGKGKVTEDYSLSSTDLFHSPAGTVQLTLSLDTSLVSESTNSSSISSEVILLDRKISEVMLDPIEYSRIEFPDISIVKENQQMVSQYFNLACASSNNNSRKLLPFLHLGASHQLDDYEMMTMSSPDENQVDSISPNESLHNSGLVSSTITSLSDDRNSADSFEKKNHLGCDSTNFVTLCPDTPTSKKEGDQSKDDEKEEKFSNKEKECKKERSIEVTKFGQVFNSPLGNINLEAEECAMQKQIVDMYMRSMQQFTESLAKMKLPMDVDKPERQDHSGDVIPNHENKKLEIDNKKKDGSRVFYGSRAFF