Alfalfa Gene Editing Database
Alfalfa Gene Editing Database
| Query id | Subject id | identity % | alignment length | mis matches | gap openings | q. start | q. end | s. start | s. end | e-value | bit score |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Msa0268970 | RHN59635.1 | 98.171 | 164 | 3 | 0 | 6 | 169 | 196 | 359 | 1.28e-106 | 330 |
| Query id | Subject id | identity % | alignment length | mis matches | gap openings | q. start | q. end | s. start | s. end | e-value | bit score |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Msa0268970 | sp|P12227|RPOC2_PEA | 87.805 | 164 | 18 | 1 | 6 | 169 | 596 | 757 | 2.60e-93 | 297 |
| Query id | Subject id | identity % | alignment length | mis matches | gap openings | q. start | q. end | s. start | s. end | e-value | bit score |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Msa0268970 | A0A396I7L0 | 98.171 | 164 | 3 | 0 | 6 | 169 | 196 | 359 | 6.11e-107 | 330 |
| Gene ID | Type | Classification |
|---|
| Gene ID | Type | Classification |
|---|
Co-expression Network
| Gene1 | Gene2 | correlation coefficient | p_value | FDR |
|---|---|---|---|---|
| Msa0268770 | Msa0268970 | 0.859844 | 3.121226e-63 | -8.615850e-47 |
PPI
| Gene1 | Gene2 | Type |
|---|
| Query id | Subject id | identity % | alignment length | mismatches | gap openings | q. start | q. end | s. start | s. end | e-value | bit score |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Msa0268970 | MtrunA17_Chr4g0015591 | 98.171 | 164 | 3 | 0 | 6 | 169 | 196 | 359 | 1.18e-110 | 330 |
| Msa0268970 | MtrunA17_CPg0493001 | 98.171 | 164 | 3 | 0 | 6 | 169 | 804 | 967 | 5.20e-106 | 330 |
| Msa0268970 | MtrunA17_Chr4g0016671 | 98.171 | 164 | 3 | 0 | 6 | 169 | 804 | 967 | 5.20e-106 | 330 |
| Msa0268970 | MtrunA17_Chr3g0095741 | 98.276 | 58 | 1 | 0 | 6 | 63 | 416 | 473 | 6.71e-32 | 119 |
| Query id | Subject id | identity % | alignment length | mismatches | gap openings | q. start | q. end | s. start | s. end | e-value | bit score |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Msa0268970 | ATCG00170.1 | 60.571 | 175 | 60 | 3 | 6 | 179 | 802 | 968 | 1.12e-54 | 186 |
Find 35 sgRNAs with CRISPR-Local
Find 47 sgRNAs with CRISPR-GE
CRISPR-Local
| sgRNA_sequence | on_target_score | Position | Region |
|---|---|---|---|
| TACGAATAGTTCCGTGATTT+TGG | 0.168127 | 2_2:+70465469 | None:intergenic |
| AATGAATTATTATTATTAAT+TGG | 0.173312 | 2_2:+70465325 | None:intergenic |
| GTTGTCAATTATATTCTTTA+TGG | 0.179224 | 2_2:-70465804 | Msa0268970:CDS |
| AATTATATTCTTTATGGAAA+TGG | 0.289554 | 2_2:-70465798 | Msa0268970:CDS |
| AGAAATGACCCATCTGGTTT+AGG | 0.294953 | 2_2:-70465579 | Msa0268970:CDS |
| GGACTTGTTTAGTCTTGAAT+TGG | 0.302268 | 2_2:-70465731 | Msa0268970:CDS |
| ATTAATAATAATAATTCATT+AGG | 0.308918 | 2_2:-70465322 | None:intergenic |
| TATGTTGTTGAATAGAAATA+AGG | 0.351435 | 2_2:-70465448 | Msa0268970:CDS |
| ATTCCAGGAAAGAGATAATC+TGG | 0.369993 | 2_2:-70465835 | Msa0268970:intron |
| GAAATAAGGAATGCCGATCT+TGG | 0.386359 | 2_2:-70465434 | Msa0268970:CDS |
| GACTTGTTTAGTCTTGAATT+GGG | 0.395976 | 2_2:-70465730 | Msa0268970:CDS |
| TGGAAATGGAAAATCCATTC+GGG | 0.398927 | 2_2:-70465784 | Msa0268970:CDS |
| ATGGAAATGGAAAATCCATT+CGG | 0.440917 | 2_2:-70465785 | Msa0268970:CDS |
| ACACAAGGATTCAATTAGTT+CGG | 0.470880 | 2_2:-70465752 | Msa0268970:CDS |
| TTAGTCTTGAATTGGGATCA+AGG | 0.488756 | 2_2:-70465723 | Msa0268970:CDS |
| TTTGTTGAAGTAAGTACAAA+CGG | 0.490928 | 2_2:-70465663 | Msa0268970:CDS |
| ACAATGTTAAATATCACAAT+GGG | 0.519777 | 2_2:-70465368 | Msa0268970:CDS |
| TGATATTTAACATTGTTGAA+TGG | 0.522425 | 2_2:+70465375 | None:intergenic |
| ATTGATCGCGGATAATGAAT+CGG | 0.540104 | 2_2:-70465556 | Msa0268970:CDS |
| ACTTACTTCAACAAAGGAAG+AGG | 0.540450 | 2_2:+70465671 | None:intergenic |
| TTCGGGGAATTTCCGACACA+AGG | 0.543374 | 2_2:-70465767 | Msa0268970:CDS |
| ATGACAAAATTATCCAAGAT+CGG | 0.543980 | 2_2:+70465421 | None:intergenic |
| AACAATGTTAAATATCACAA+TGG | 0.560038 | 2_2:-70465369 | Msa0268970:CDS |
| GTTTGTACTTACTTCAACAA+AGG | 0.560389 | 2_2:+70465665 | None:intergenic |
| GCGATCAATCCTAAACCAGA+TGG | 0.564364 | 2_2:+70465570 | None:intergenic |
| AACTAATTGAATCCTTGTGT+CGG | 0.584495 | 2_2:+70465755 | None:intergenic |
| TGTGTCGGAAATTCCCCGAA+TGG | 0.589742 | 2_2:+70465770 | None:intergenic |
| CTTACTTCAACAAAGGAAGA+GGG | 0.610881 | 2_2:+70465672 | None:intergenic |
| TACTTCAACAAAGGAAGAGG+GGG | 0.611335 | 2_2:+70465674 | None:intergenic |
| CGATCAATCCTAAACCAGAT+GGG | 0.613760 | 2_2:+70465571 | None:intergenic |
| AAATCACTTAGCCAAAATCA+CGG | 0.641309 | 2_2:-70465480 | Msa0268970:CDS |
| ATCTGGTTTAGGATTGATCG+CGG | 0.648560 | 2_2:-70465568 | Msa0268970:CDS |
| TCGCGGATAATGAATCGGAT+CGG | 0.674619 | 2_2:-70465551 | Msa0268970:CDS |
| TTACTTCAACAAAGGAAGAG+GGG | 0.682642 | 2_2:+70465673 | None:intergenic |
| GGAAATGGAAAATCCATTCG+GGG | 0.695544 | 2_2:-70465783 | Msa0268970:CDS |
CRISPR-GE
| badsite warning | sgRNA_sequence | Strand | Position | Region | GC_content |
|---|---|---|---|---|---|
| !!! | TTATTATTAATTGGAATTTT+AGG | + | chr2_2:70465876-70465895 | None:intergenic | 10.0% |
| !! | AATTATATTCTTTATGGAAA+TGG | - | chr2_2:70465409-70465428 | Msa0268970:CDS | 15.0% |
| !! | GTTGTCAATTATATTCTTTA+TGG | - | chr2_2:70465403-70465422 | Msa0268970:CDS | 20.0% |
| !! | TTGGAATGAATAGAAAAAAA+TGG | + | chr2_2:70465694-70465713 | None:intergenic | 20.0% |
| !!! | ATTTTTTTCTATTCATTCCA+AGG | - | chr2_2:70465693-70465712 | Msa0268970:CDS | 20.0% |
| !!! | TGATTTTTTAATTTTTGCCT+TGG | + | chr2_2:70465713-70465732 | None:intergenic | 20.0% |
| !! | TATGTTGTTGAATAGAAATA+AGG | - | chr2_2:70465759-70465778 | Msa0268970:CDS | 20.0% |
| !! | TGATATTTAACATTGTTGAA+TGG | + | chr2_2:70465835-70465854 | None:intergenic | 20.0% |
| !! | AACAATGTTAAATATCACAA+TGG | - | chr2_2:70465838-70465857 | Msa0268970:intron | 20.0% |
| !! | ACAATGTTAAATATCACAAT+GGG | - | chr2_2:70465839-70465858 | Msa0268970:intron | 20.0% |
| !!! | CAAAAAAAGTACTTCTATTG+AGG | - | chr2_2:70465507-70465526 | Msa0268970:CDS | 25.0% |
| ! | TTTGTTGAAGTAAGTACAAA+CGG | - | chr2_2:70465544-70465563 | Msa0268970:CDS | 25.0% |
| ! | ATGACAAAATTATCCAAGAT+CGG | + | chr2_2:70465789-70465808 | None:intergenic | 25.0% |
| TTTACAAAATCGATACTGTC+CGG | + | chr2_2:70465334-70465353 | None:intergenic | 30.0% | |
| ATGGAAATGGAAAATCCATT+CGG | - | chr2_2:70465422-70465441 | Msa0268970:CDS | 30.0% | |
| AACTAATTGAATCCTTGTGT+CGG | + | chr2_2:70465455-70465474 | None:intergenic | 30.0% | |
| ACACAAGGATTCAATTAGTT+CGG | - | chr2_2:70465455-70465474 | Msa0268970:CDS | 30.0% | |
| !! | GACTTGTTTAGTCTTGAATT+GGG | - | chr2_2:70465477-70465496 | Msa0268970:CDS | 30.0% |
| !! | AAAAAGTACTTCTATTGAGG+AGG | - | chr2_2:70465510-70465529 | Msa0268970:CDS | 30.0% |
| GTTTGTACTTACTTCAACAA+AGG | + | chr2_2:70465545-70465564 | None:intergenic | 30.0% | |
| AAATCACTTAGCCAAAATCA+CGG | - | chr2_2:70465727-70465746 | Msa0268970:CDS | 30.0% | |
| TCTTTCCTGGAATAGATCTT+GGG | + | chr2_2:70465365-70465384 | None:intergenic | 35.0% | |
| ATTCCAGGAAAGAGATAATC+TGG | - | chr2_2:70465372-70465391 | Msa0268970:CDS | 35.0% | |
| TGGAAATGGAAAATCCATTC+GGG | - | chr2_2:70465423-70465442 | Msa0268970:CDS | 35.0% | |
| !! | GGACTTGTTTAGTCTTGAAT+TGG | - | chr2_2:70465476-70465495 | Msa0268970:CDS | 35.0% |
| !! | TTAGTCTTGAATTGGGATCA+AGG | - | chr2_2:70465484-70465503 | Msa0268970:CDS | 35.0% |
| TTACTTCAACAAAGGAAGAG+GGG | + | chr2_2:70465537-70465556 | None:intergenic | 35.0% | |
| CTTACTTCAACAAAGGAAGA+GGG | + | chr2_2:70465538-70465557 | None:intergenic | 35.0% | |
| ACTTACTTCAACAAAGGAAG+AGG | + | chr2_2:70465539-70465558 | None:intergenic | 35.0% | |
| AGAAAAAGAAATGACCCATC+TGG | - | chr2_2:70465622-70465641 | Msa0268970:CDS | 35.0% | |
| ATTGATCGCGGATAATGAAT+CGG | - | chr2_2:70465651-70465670 | Msa0268970:CDS | 35.0% | |
| ! | TACGAATAGTTCCGTGATTT+TGG | + | chr2_2:70465741-70465760 | None:intergenic | 35.0% |
| ! | TTTTCCCCAAGATCTATTCC+AGG | - | chr2_2:70465357-70465376 | Msa0268970:CDS | 40.0% |
| CTTTCCTGGAATAGATCTTG+GGG | + | chr2_2:70465364-70465383 | None:intergenic | 40.0% | |
| CTCTTTCCTGGAATAGATCT+TGG | + | chr2_2:70465366-70465385 | None:intergenic | 40.0% | |
| GTTCCAGATTATCTCTTTCC+TGG | + | chr2_2:70465378-70465397 | None:intergenic | 40.0% | |
| GGAAATGGAAAATCCATTCG+GGG | - | chr2_2:70465424-70465443 | Msa0268970:CDS | 40.0% | |
| TACTTCAACAAAGGAAGAGG+GGG | + | chr2_2:70465536-70465555 | None:intergenic | 40.0% | |
| ! | AGAAATGACCCATCTGGTTT+AGG | - | chr2_2:70465628-70465647 | Msa0268970:CDS | 40.0% |
| CGATCAATCCTAAACCAGAT+GGG | + | chr2_2:70465639-70465658 | None:intergenic | 40.0% | |
| ! | ATCTGGTTTAGGATTGATCG+CGG | - | chr2_2:70465639-70465658 | Msa0268970:CDS | 40.0% |
| GAAATAAGGAATGCCGATCT+TGG | - | chr2_2:70465773-70465792 | Msa0268970:CDS | 40.0% | |
| GCGATCAATCCTAAACCAGA+TGG | + | chr2_2:70465640-70465659 | None:intergenic | 45.0% | |
| TCGCGGATAATGAATCGGAT+CGG | - | chr2_2:70465656-70465675 | Msa0268970:CDS | 45.0% | |
| !! | AATGAATTATTATTATTAAT+TGG | + | chr2_2:70465885-70465904 | None:intergenic | 5.0% |
| TGTGTCGGAAATTCCCCGAA+TGG | + | chr2_2:70465440-70465459 | None:intergenic | 50.0% | |
| TTCGGGGAATTTCCGACACA+AGG | - | chr2_2:70465440-70465459 | Msa0268970:CDS | 50.0% |
| Chromosome | Type | Strat | End | Strand | Name |
|---|---|---|---|---|---|
| chr2_2 | gene | 70465323 | 70465906 | 70465323 | ID=Msa0268970;Name=Msa0268970 |
| chr2_2 | mRNA | 70465323 | 70465906 | 70465323 | ID=Msa0268970-mRNA-1;Parent=Msa0268970;Name=Msa0268970-mRNA-1;_AED=0.48;_eAED=0.49;_QI=0|0|0|1|0|0|2|0|180 |
| chr2_2 | exon | 70465892 | 70465906 | 70465892 | ID=Msa0268970-mRNA-1:exon:22682;Parent=Msa0268970-mRNA-1 |
| chr2_2 | exon | 70465323 | 70465850 | 70465323 | ID=Msa0268970-mRNA-1:exon:22681;Parent=Msa0268970-mRNA-1 |
| chr2_2 | CDS | 70465892 | 70465906 | 70465892 | ID=Msa0268970-mRNA-1:cds;Parent=Msa0268970-mRNA-1 |
| chr2_2 | CDS | 70465323 | 70465850 | 70465323 | ID=Msa0268970-mRNA-1:cds;Parent=Msa0268970-mRNA-1 |
| Gene Sequence |
| Protein sequence |
