AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene55615

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene55615.t1 MTR_4g088015 66.667 54 17 1 121 174 220 272 2.83e-17 78.6
MS.gene55615.t1 MTR_3g463400 57.407 54 22 1 121 174 132 184 4.95e-15 72.4
MS.gene55615.t1 MTR_5g070020 57.407 54 22 1 121 174 121 173 1.24e-14 70.9
MS.gene55615.t1 MTR_5g049190 52.542 59 27 1 116 174 13 70 1.56e-14 69.3
MS.gene55615.t1 MTR_7g451170 57.407 54 22 1 121 174 190 242 2.77e-14 70.1
MS.gene55615.t1 MTR_7g037260 55.556 54 23 1 121 174 144 196 2.98e-13 67.0
MS.gene55615.t1 MTR_7g035350 52.727 55 25 1 120 174 223 276 2.99e-13 67.0
MS.gene55615.t1 MTR_3g077650 55.556 54 23 1 121 174 180 232 4.26e-13 66.6
MS.gene55615.t1 MTR_1g057980 56.364 55 22 2 121 174 78 131 8.72e-13 65.1
MS.gene55615.t1 MTR_4g105660 44.156 77 35 2 108 177 159 234 2.87e-12 64.3
MS.gene55615.t1 MTR_7g037130 51.852 54 25 1 121 174 144 196 3.13e-11 61.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene55615.t1 AT3G27785 58.621 58 23 1 117 174 184 240 1.28e-15 73.9
MS.gene55615.t1 AT5G58850 53.704 54 24 1 121 174 104 156 3.53e-14 69.7
MS.gene55615.t1 AT5G11050 55.556 54 23 1 121 174 104 156 3.84e-14 69.7
MS.gene55615.t1 AT4G18770 47.541 61 31 1 114 174 209 268 1.24e-13 68.2
MS.gene55615.t1 AT5G40360 50.769 65 30 2 111 174 146 209 7.73e-12 62.8

Find 36 sgRNAs with CRISPR-Local

Find 51 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATATAGGGAACTTGTTAAAT+TGG 0.199609 6.2:-19223902 MS.gene55615:intron
TAGACGACTGTTTAAGATAT+TGG 0.218716 6.2:+19224309 None:intergenic
CGCTCCAAACATGGATATTC+TGG 0.220757 6.2:+19224448 None:intergenic
TTTAAGATATTGGGATTATT+AGG 0.225450 6.2:+19224319 None:intergenic
TCATCTCCGTCCAAACATTA+AGG 0.270772 6.2:-19223788 MS.gene55615:CDS
AGACGACTGTTTAAGATATT+GGG 0.328045 6.2:+19224310 None:intergenic
ATGATGACATGCCACATAAA+TGG 0.337358 6.2:+19224266 None:intergenic
GGAACATAAACCTTAATGTT+TGG 0.342814 6.2:+19223778 None:intergenic
TTCATCAATCTTGCAATTTG+AGG 0.352946 6.2:+19223853 None:intergenic
GCATAAGCTTTGTTGACGTC+TGG 0.422118 6.2:+19224166 None:intergenic
AAATGGATGACATGCATGTT+TGG 0.422300 6.2:+19224283 None:intergenic
CAAAACAGTGTCGTGATAGA+TGG 0.437524 6.2:-19223816 MS.gene55615:CDS
GAACGAGAATTGACCTTTGT+GGG 0.444047 6.2:+19224413 None:intergenic
TTGTTGACGTCTGGTACAAA+TGG 0.468340 6.2:+19224175 None:intergenic
TATTAGGTACACTCAAGATA+TGG 0.470686 6.2:+19224335 None:intergenic
ACCATCTCGATGGAAACATC+TGG 0.493183 6.2:+19224210 None:intergenic
CTTATGCAATCAGAAAGAAA+TGG 0.496059 6.2:-19224150 MS.gene55615:CDS
CATAAACCTTAATGTTTGGA+CGG 0.508200 6.2:+19223782 None:intergenic
GTTAAATTGGTGAATCAACA+TGG 0.522743 6.2:-19223889 MS.gene55615:CDS
AAGGGATTGTTCTGAGGAGG+TGG 0.523100 6.2:+19224391 None:intergenic
GGAACGAGAATTGACCTTTG+TGG 0.525598 6.2:+19224412 None:intergenic
ACCAGATGTTTCCATCGAGA+TGG 0.544531 6.2:-19224211 MS.gene55615:CDS
TCGAAAGATTGAGAAATGAC+AGG 0.547098 6.2:+19224235 None:intergenic
TGAATCACACGCTCCAAACA+TGG 0.559827 6.2:+19224439 None:intergenic
AACAAGGGATTGTTCTGAGG+AGG 0.564533 6.2:+19224388 None:intergenic
ATGCATGTCATCCATTTATG+TGG 0.566202 6.2:-19224277 MS.gene55615:CDS
TTGAGATGGTAGTTTAACAA+GGG 0.576755 6.2:+19224373 None:intergenic
TTTAACAAGGGATTGTTCTG+AGG 0.590649 6.2:+19224385 None:intergenic
CATGTAAATTAGTGTTGAGA+TGG 0.594522 6.2:+19224359 None:intergenic
TGTTAAGAAAACCATCTCGA+TGG 0.597227 6.2:+19224200 None:intergenic
GTTGAGATGGTAGTTTAACA+AGG 0.598487 6.2:+19224372 None:intergenic
AAAGAAATGGACAACCAATG+AGG 0.657128 6.2:-19224137 MS.gene55615:CDS
TTAAATTGGTGAATCAACAT+GGG 0.666593 6.2:-19223888 MS.gene55615:CDS
ATTGCAAGATTGATGAAGCG+AGG 0.667312 6.2:-19223847 MS.gene55615:CDS
AACGAGAATTGACCTTTGTG+GGG 0.672668 6.2:+19224414 None:intergenic
GTGTGATTCATACCCCACAA+AGG 0.701235 6.2:-19224426 MS.gene55615:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTAAATTGTGATTTCATATA+GGG - chr6.2:19224359-19224378 MS.gene55615:CDS 15.0%
!!! AGGTTTTTTTAATGTTAAAA+TGG - chr6.2:19224321-19224340 MS.gene55615:CDS 15.0%
!!! GGTTTTTTTAATGTTAAAAT+GGG - chr6.2:19224322-19224341 MS.gene55615:CDS 15.0%
!!! GTTTTTTTAATGTTAAAATG+GGG - chr6.2:19224323-19224342 MS.gene55615:CDS 15.0%
!! AACCTTATATTGATGAAAAA+TGG + chr6.2:19224306-19224325 None:intergenic 20.0%
!! CTTAAATTGTGATTTCATAT+AGG - chr6.2:19224358-19224377 MS.gene55615:CDS 20.0%
!! TATAGAAAAAATCCAAAGAA+AGG + chr6.2:19224217-19224236 None:intergenic 20.0%
!!! TACCATTTTTCATCAATATA+AGG - chr6.2:19224301-19224320 MS.gene55615:CDS 20.0%
!!! TATATCTTTTTTCCTTTCTT+TGG - chr6.2:19224202-19224221 MS.gene55615:CDS 20.0%
!!! TTTAAGATATTGGGATTATT+AGG + chr6.2:19223960-19223979 None:intergenic 20.0%
! TTAAATTGGTGAATCAACAT+GGG - chr6.2:19224388-19224407 MS.gene55615:CDS 25.0%
!! ATTCTGGAAAAAGATTCAAA+AGG + chr6.2:19223815-19223834 None:intergenic 25.0%
!! TTTTACATACATATCCTCAT+TGG + chr6.2:19224156-19224175 None:intergenic 25.0%
!!! ATATAGGGAACTTGTTAAAT+TGG - chr6.2:19224374-19224393 MS.gene55615:CDS 25.0%
CATAAACCTTAATGTTTGGA+CGG + chr6.2:19224497-19224516 None:intergenic 30.0%
CTTATGCAATCAGAAAGAAA+TGG - chr6.2:19224126-19224145 MS.gene55615:intron 30.0%
GGAACATAAACCTTAATGTT+TGG + chr6.2:19224501-19224520 None:intergenic 30.0%
GTTAAATTGGTGAATCAACA+TGG - chr6.2:19224387-19224406 MS.gene55615:CDS 30.0%
TATTAGGTACACTCAAGATA+TGG + chr6.2:19223944-19223963 None:intergenic 30.0%
TTCATCAATCTTGCAATTTG+AGG + chr6.2:19224426-19224445 None:intergenic 30.0%
TTGAGATGGTAGTTTAACAA+GGG + chr6.2:19223906-19223925 None:intergenic 30.0%
! AGACGACTGTTTAAGATATT+GGG + chr6.2:19223969-19223988 None:intergenic 30.0%
! CATGTAAATTAGTGTTGAGA+TGG + chr6.2:19223920-19223939 None:intergenic 30.0%
! TAGACGACTGTTTAAGATAT+TGG + chr6.2:19223970-19223989 None:intergenic 30.0%
! TTTTCCAGAATATCCATGTT+TGG - chr6.2:19223824-19223843 MS.gene55615:CDS 30.0%
AAAGAAATGGACAACCAATG+AGG - chr6.2:19224139-19224158 MS.gene55615:CDS 35.0%
AAATGGATGACATGCATGTT+TGG + chr6.2:19223996-19224015 None:intergenic 35.0%
ATGATGACATGCCACATAAA+TGG + chr6.2:19224013-19224032 None:intergenic 35.0%
ATGCATGTCATCCATTTATG+TGG - chr6.2:19223999-19224018 MS.gene55615:intron 35.0%
CTACCAATAATTGAACAGTG+CGG + chr6.2:19224272-19224291 None:intergenic 35.0%
GTTGAGATGGTAGTTTAACA+AGG + chr6.2:19223907-19223926 None:intergenic 35.0%
TAACCGCACTGTTCAATTAT+TGG - chr6.2:19224266-19224285 MS.gene55615:CDS 35.0%
TCGAAAGATTGAGAAATGAC+AGG + chr6.2:19224044-19224063 None:intergenic 35.0%
TGTTAAGAAAACCATCTCGA+TGG + chr6.2:19224079-19224098 None:intergenic 35.0%
TTTAACAAGGGATTGTTCTG+AGG + chr6.2:19223894-19223913 None:intergenic 35.0%
! ATCAACATGGGCTGAAAAAA+TGG - chr6.2:19224400-19224419 MS.gene55615:CDS 35.0%
AACGAGAATTGACCTTTGTG+GGG + chr6.2:19223865-19223884 None:intergenic 40.0%
ATTGCAAGATTGATGAAGCG+AGG - chr6.2:19224429-19224448 MS.gene55615:CDS 40.0%
CAAAACAGTGTCGTGATAGA+TGG - chr6.2:19224460-19224479 MS.gene55615:CDS 40.0%
GAACGAGAATTGACCTTTGT+GGG + chr6.2:19223866-19223885 None:intergenic 40.0%
TCATCTCCGTCCAAACATTA+AGG - chr6.2:19224488-19224507 MS.gene55615:CDS 40.0%
TTGTTGACGTCTGGTACAAA+TGG + chr6.2:19224104-19224123 None:intergenic 40.0%
ACCAGATGTTTCCATCGAGA+TGG - chr6.2:19224065-19224084 MS.gene55615:intron 45.0%
ACCATCTCGATGGAAACATC+TGG + chr6.2:19224069-19224088 None:intergenic 45.0%
CGCTCCAAACATGGATATTC+TGG + chr6.2:19223831-19223850 None:intergenic 45.0%
GGAACGAGAATTGACCTTTG+TGG + chr6.2:19223867-19223886 None:intergenic 45.0%
GTGTGATTCATACCCCACAA+AGG - chr6.2:19223850-19223869 MS.gene55615:CDS 45.0%
TGAATCACACGCTCCAAACA+TGG + chr6.2:19223840-19223859 None:intergenic 45.0%
!! AACAAGGGATTGTTCTGAGG+AGG + chr6.2:19223891-19223910 None:intergenic 45.0%
!! GCATAAGCTTTGTTGACGTC+TGG + chr6.2:19224113-19224132 None:intergenic 45.0%
!! AAGGGATTGTTCTGAGGAGG+TGG + chr6.2:19223888-19223907 None:intergenic 50.0%


Chromosome Type Strat End Strand Name
chr6.2 gene 19223774 19224524 19223774 ID=MS.gene55615
chr6.2 mRNA 19223774 19224524 19223774 ID=MS.gene55615.t1;Parent=MS.gene55615
chr6.2 exon 19224133 19224524 19224133 ID=MS.gene55615.t1.exon1;Parent=MS.gene55615.t1
chr6.2 CDS 19224133 19224524 19224133 ID=cds.MS.gene55615.t1;Parent=MS.gene55615.t1
chr6.2 exon 19223774 19223918 19223774 ID=MS.gene55615.t1.exon2;Parent=MS.gene55615.t1
chr6.2 CDS 19223774 19223918 19223774 ID=cds.MS.gene55615.t1;Parent=MS.gene55615.t1
Gene Sequence

>MS.gene55615

ATGGAACTCAATCTTAACAATCGAGCAAAGCATTCAAACCTTTTGAATCTTTTTCCAGAATATCCATGTTTGGAGCGTGTGATTCATACCCCACAAAGGTCAATTCTCGTTCCACCTCCTCAGAACAATCCCTTGTTAAACTACCATCTCAACACTAATTTACATGACCATATCTTGAGTGTACCTAATAATCCCAATATCTTAAACAGTCGTCTATCTCCAAACATGCATGTCATCCATTTATGTGGCATGTCATCATCATTATCGCCTGTCATTTCTCAATCTTTCGAAACCAGATGTTTCCATCGAGATGGTTTTCTTAACACTCCATTTGTACCAGACGTCAACAAAGCTTATGCAATCAGAAAGAAATGGACAACCAATGAGGATATGTATGTAAAATATTTATTCATTTCTTAATCTCTCTCTATATCTTTTTTCCTTTCTTTGGATTTTTTCTATAAAAAAAAATATAATAGAATTAAATTACATTAACCGCACTGTTCAATTATTGGTAGTTTTATAGATACCATTTTTCATCAATATAAGGTTTTTTTAATGTTAAAATGGGGTGAGTGTTTAATCTTAAATTGTGATTTCATATAGGGAACTTGTTAAATTGGTGAATCAACATGGGCTGAAAAAATGGCCTCAAATTGCAAGATTGATGAAGCGAGGAAGAAATGCAAAACAGTGTCGTGATAGATGGCTCAATCATCTCCGTCCAAACATTAAGGTTTATGTTCCCTAA
Protein sequence

>MS.gene55615.t1

MELNLNNRAKHSNLLNLFPEYPCLERVIHTPQRSILVPPPQNNPLLNYHLNTNLHDHILSVPNNPNILNSRLSPNMHVIHLCGMSSSLSPVISQSFETRCFHRDGFLNTPFVPDVNKAYAIRKKWTTNEDMELVKLVNQHGLKKWPQIARLMKRGRNAKQCRDRWLNHLRPNIKVYVP