AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene85140


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene85140.t1 MTR_2g101380 96.335 191 7 0 1 191 1 191 2.04e-137 382
MS.gene85140.t1 MTR_1g011510 53.846 104 46 2 72 174 60 162 2.92e-24 93.6
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene85140.t1 AT3G16250 63.536 181 53 5 18 186 20 199 1.93e-76 228
MS.gene85140.t1 AT4G32590 53.846 104 46 2 72 174 70 172 2.57e-25 96.7
MS.gene85140.t1 AT4G32590 49.074 108 53 2 57 163 55 161 5.13e-19 80.5

Find 42 sgRNAs with CRISPR-Local

Find 69 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CATGCTAATCTCCAATTCTT+TGG 0.246574 2.4:-3379537 None:intergenic
AGTGCCGACTGCTCTAATTT+TGG 0.281013 2.4:-3378717 None:intergenic
GAGAGACGTGTGAATGCATT+AGG 0.321958 2.4:-3378644 None:intergenic
GACAAATGCAAAACCTATAG+AGG 0.334673 2.4:-3378789 None:intergenic
CTTTATAGAAACCAAAGAAT+TGG 0.359961 2.4:+3379526 MS.gene85140:intron
GATTCTAACATTGAACTCTA+TGG 0.373731 2.4:+3379041 MS.gene85140:CDS
TAGGGGTTAGTTTGAGTTGG+AGG 0.393377 2.4:-3378625 None:intergenic
TCTAATGACCCTCCCTCTAT+AGG 0.394740 2.4:+3378776 MS.gene85140:CDS
CTTGTAAAGAGTGTTGTGTT+TGG 0.421734 2.4:-3378692 None:intergenic
CATTCATGTCCTTTCCACTC+TGG 0.430702 2.4:-3379743 None:intergenic
AGAGACGTGTGAATGCATTA+GGG 0.437849 2.4:-3378643 None:intergenic
TGCACATCTGGTGTTCCATC+TGG 0.437999 2.4:-3378972 None:intergenic
ACTTGCTATTAGGTTCTTGA+AGG 0.442328 2.4:+3379301 MS.gene85140:intron
CATTAGGGGTTAGTTTGAGT+TGG 0.450485 2.4:-3378628 None:intergenic
GCTGTACGATAATGCACATC+TGG 0.480063 2.4:-3378984 None:intergenic
GTGGGTGAAGCAGATTCTAC+AGG 0.486617 2.4:+3379570 MS.gene85140:CDS
CTATTAGGTTCTTGAAGGCA+AGG 0.501723 2.4:+3379306 MS.gene85140:intron
GAAGCTTAGGAACATAATGT+TGG 0.511451 2.4:+3379019 MS.gene85140:CDS
CGGCACTGTCCCTGAAAAGA+AGG 0.512597 2.4:+3378733 MS.gene85140:CDS
CTTGTGGTGGACAGAAGCTT+AGG 0.512735 2.4:+3379006 MS.gene85140:CDS
ACATGAATGGAAATATGAAA+AGG 0.521149 2.4:+3379757 MS.gene85140:CDS
CAGAGTGGAAAGGACATGAA+TGG 0.529406 2.4:+3379744 MS.gene85140:CDS
TAGTCTGTGTTGCTACCAGA+TGG 0.569681 2.4:+3378957 MS.gene85140:intron
TGGGTGAAGCAGATTCTACA+GGG 0.575014 2.4:+3379571 MS.gene85140:CDS
TGGAACTTGTGTTACATGTA+TGG 0.576257 2.4:+3379179 MS.gene85140:CDS
TCTTTCTCTTTGTCAGTGCG+AGG 0.589508 2.4:-3379340 None:intergenic
TTAGCATGTCAAACAACTGT+GGG 0.604116 2.4:+3379552 MS.gene85140:CDS
AGAACCAAAATTAGAGCAGT+CGG 0.615630 2.4:+3378713 MS.gene85140:CDS
TTGTGTTACATGTATGGTAG+AGG 0.617019 2.4:+3379185 MS.gene85140:CDS
ACAAATGCAAAACCTATAGA+GGG 0.622761 2.4:-3378788 None:intergenic
GACTCAGCAGACTCTTTGTG+AGG 0.642468 2.4:+3379788 MS.gene85140:CDS
GTGCATTATCGTACAGCTTG+TGG 0.644594 2.4:+3378990 MS.gene85140:CDS
CAACAATTACCAGAGTGGAA+AGG 0.648231 2.4:+3379734 MS.gene85140:CDS
TGAAGCAGATTCTACAGGGG+TGG 0.651914 2.4:+3379575 MS.gene85140:CDS
ATGCAAAACCTATAGAGGGA+GGG 0.653145 2.4:-3378784 None:intergenic
GAGACGTGTGAATGCATTAG+GGG 0.653996 2.4:-3378642 None:intergenic
AATGCAAAACCTATAGAGGG+AGG 0.655010 2.4:-3378785 None:intergenic
ATTAGCATGTCAAACAACTG+TGG 0.658456 2.4:+3379551 MS.gene85140:CDS
TGATTCAACAATTACCAGAG+TGG 0.670303 2.4:+3379729 MS.gene85140:CDS
CATTATCGTACAGCTTGTGG+TGG 0.680953 2.4:+3378993 MS.gene85140:CDS
AGGGTCATTAGAGTCACTAG+TGG 0.691443 2.4:-3378765 None:intergenic
GGGTGAAGCAGATTCTACAG+GGG 0.770570 2.4:+3379572 MS.gene85140:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTTTATTTTTAAGCAATAAT+TGG + chr2.4:3379096-3379115 MS.gene85140:intron 10.0%
!! CAGATTAGAAATTAATAAAA+TGG + chr2.4:3379632-3379651 MS.gene85140:intron 15.0%
!!! TTTTTTTTTAACTTGCTATT+AGG + chr2.4:3379291-3379310 MS.gene85140:intron 15.0%
!! ATTTATGTTGAGCAATATAT+TGG + chr2.4:3379677-3379696 MS.gene85140:intron 20.0%
!! TAATTCTACTTATATCTAGT+TGG + chr2.4:3378883-3378902 MS.gene85140:intron 20.0%
!!! AATTAATCTCTAATGTTTTG+TGG + chr2.4:3378932-3378951 MS.gene85140:intron 20.0%
!!! CAAAAAATGCACATTTTATT+GGG + chr2.4:3379239-3379258 MS.gene85140:intron 20.0%
!!! GTTAGTACTACTAATTTTTT+GGG + chr2.4:3379597-3379616 MS.gene85140:intron 20.0%
! AAGAGAAAGAAAAACTTAAG+AGG + chr2.4:3379353-3379372 MS.gene85140:CDS 25.0%
! AATTTAACAAAATTCTACCC+TGG - chr2.4:3379149-3379168 None:intergenic 25.0%
! ACATGAATGGAAATATGAAA+AGG + chr2.4:3379757-3379776 MS.gene85140:CDS 25.0%
! AGAGAAAGAAAAACTTAAGA+GGG + chr2.4:3379354-3379373 MS.gene85140:CDS 25.0%
! CTTTATAGAAACCAAAGAAT+TGG + chr2.4:3379526-3379545 MS.gene85140:intron 25.0%
! GTTAGTGAGATAATTACATA+AGG - chr2.4:3379068-3379087 None:intergenic 25.0%
!! AATTTTGTTAAATTGTGGAG+GGG + chr2.4:3379155-3379174 MS.gene85140:CDS 25.0%
!! AGAATTTTGTTAAATTGTGG+AGG + chr2.4:3379153-3379172 MS.gene85140:CDS 25.0%
!! GAATTTTGTTAAATTGTGGA+GGG + chr2.4:3379154-3379173 MS.gene85140:CDS 25.0%
!! GCAAAAAATGCACATTTTAT+TGG + chr2.4:3379238-3379257 MS.gene85140:intron 25.0%
!! GGTAGAATTTTGTTAAATTG+TGG + chr2.4:3379150-3379169 MS.gene85140:CDS 25.0%
!!! ATTTTGTTGTTGATTTTTCC+AGG + chr2.4:3379128-3379147 MS.gene85140:intron 25.0%
!!! GGTTAGTACTACTAATTTTT+TGG + chr2.4:3379596-3379615 MS.gene85140:intron 25.0%
!!! TTTTGTTGTTGATTTTTCCA+GGG + chr2.4:3379129-3379148 MS.gene85140:intron 25.0%
ACAAATGCAAAACCTATAGA+GGG - chr2.4:3378791-3378810 None:intergenic 30.0%
GATTCTAACATTGAACTCTA+TGG + chr2.4:3379041-3379060 MS.gene85140:CDS 30.0%
! ATTTTCATTCCATGTGATGT+AGG + chr2.4:3379703-3379722 MS.gene85140:intron 30.0%
! ATTTTGTTAAATTGTGGAGG+GGG + chr2.4:3379156-3379175 MS.gene85140:CDS 30.0%
!!! TGGTCTGAATTTTTTATGTG+AGG - chr2.4:3378675-3378694 None:intergenic 30.0%
AGAACCAAAATTAGAGCAGT+CGG + chr2.4:3378713-3378732 MS.gene85140:CDS 35.0%
ATGTGAAATGTGAACTCTTG+TGG + chr2.4:3379469-3379488 MS.gene85140:intron 35.0%
ATTAGCATGTCAAACAACTG+TGG + chr2.4:3379551-3379570 MS.gene85140:CDS 35.0%
CATGCTAATCTCCAATTCTT+TGG - chr2.4:3379540-3379559 None:intergenic 35.0%
GAAGCTTAGGAACATAATGT+TGG + chr2.4:3379019-3379038 MS.gene85140:CDS 35.0%
GACAAATGCAAAACCTATAG+AGG - chr2.4:3378792-3378811 None:intergenic 35.0%
TGATTCAACAATTACCAGAG+TGG + chr2.4:3379729-3379748 MS.gene85140:CDS 35.0%
TGGAACTTGTGTTACATGTA+TGG + chr2.4:3379179-3379198 MS.gene85140:CDS 35.0%
TTAGCATGTCAAACAACTGT+GGG + chr2.4:3379552-3379571 MS.gene85140:CDS 35.0%
TTGTGTTACATGTATGGTAG+AGG + chr2.4:3379185-3379204 MS.gene85140:CDS 35.0%
! TCTCTGAATCCTTCTTTTCA+GGG - chr2.4:3378745-3378764 None:intergenic 35.0%
!! ACTTGCTATTAGGTTCTTGA+AGG + chr2.4:3379301-3379320 MS.gene85140:intron 35.0%
!! CTTGTAAAGAGTGTTGTGTT+TGG - chr2.4:3378695-3378714 None:intergenic 35.0%
AATGCAAAACCTATAGAGGG+AGG - chr2.4:3378788-3378807 None:intergenic 40.0%
AGAGACGTGTGAATGCATTA+GGG - chr2.4:3378646-3378665 None:intergenic 40.0%
ATGCAAAACCTATAGAGGGA+GGG - chr2.4:3378787-3378806 None:intergenic 40.0%
CAACAATTACCAGAGTGGAA+AGG + chr2.4:3379734-3379753 MS.gene85140:CDS 40.0%
CTATTAGGTTCTTGAAGGCA+AGG + chr2.4:3379306-3379325 MS.gene85140:intron 40.0%
GAATCACAACCTACATCACA+TGG - chr2.4:3379715-3379734 None:intergenic 40.0%
! GTCTCTGAATCCTTCTTTTC+AGG - chr2.4:3378746-3378765 None:intergenic 40.0%
!! CATTAGGGGTTAGTTTGAGT+TGG - chr2.4:3378631-3378650 None:intergenic 40.0%
AGGGTCATTAGAGTCACTAG+TGG - chr2.4:3378768-3378787 None:intergenic 45.0%
CAGAGTGGAAAGGACATGAA+TGG + chr2.4:3379744-3379763 MS.gene85140:CDS 45.0%
CATTATCGTACAGCTTGTGG+TGG + chr2.4:3378993-3379012 MS.gene85140:CDS 45.0%
CATTCATGTCCTTTCCACTC+TGG - chr2.4:3379746-3379765 None:intergenic 45.0%
GAGACGTGTGAATGCATTAG+GGG - chr2.4:3378645-3378664 None:intergenic 45.0%
GAGAGACGTGTGAATGCATT+AGG - chr2.4:3378647-3378666 None:intergenic 45.0%
GCTGTACGATAATGCACATC+TGG - chr2.4:3378987-3379006 None:intergenic 45.0%
GTGCATTATCGTACAGCTTG+TGG + chr2.4:3378990-3379009 MS.gene85140:CDS 45.0%
TCTAATGACCCTCCCTCTAT+AGG + chr2.4:3378776-3378795 MS.gene85140:CDS 45.0%
TCTTTCTCTTTGTCAGTGCG+AGG - chr2.4:3379343-3379362 None:intergenic 45.0%
TGGGTGAAGCAGATTCTACA+GGG + chr2.4:3379571-3379590 MS.gene85140:CDS 45.0%
TTGTTAAATTGTGGAGGGGG+TGG + chr2.4:3379159-3379178 MS.gene85140:CDS 45.0%
! TAGTCTGTGTTGCTACCAGA+TGG + chr2.4:3378957-3378976 MS.gene85140:intron 45.0%
!! TAGGGGTTAGTTTGAGTTGG+AGG - chr2.4:3378628-3378647 None:intergenic 45.0%
!!! AGTGCCGACTGCTCTAATTT+TGG - chr2.4:3378720-3378739 None:intergenic 45.0%
GGGTGAAGCAGATTCTACAG+GGG + chr2.4:3379572-3379591 MS.gene85140:CDS 50.0%
GTGGGTGAAGCAGATTCTAC+AGG + chr2.4:3379570-3379589 MS.gene85140:CDS 50.0%
TGAAGCAGATTCTACAGGGG+TGG + chr2.4:3379575-3379594 MS.gene85140:CDS 50.0%
TGCACATCTGGTGTTCCATC+TGG - chr2.4:3378975-3378994 None:intergenic 50.0%
!! CTTGTGGTGGACAGAAGCTT+AGG + chr2.4:3379006-3379025 MS.gene85140:CDS 50.0%
CGGCACTGTCCCTGAAAAGA+AGG + chr2.4:3378733-3378752 MS.gene85140:CDS 55.0%


Chromosome Type Strat End Strand Name
chr2.4 gene 3378617 3379808 3378617 ID=MS.gene85140
chr2.4 mRNA 3378617 3379808 3378617 ID=MS.gene85140.t1;Parent=MS.gene85140
chr2.4 exon 3378617 3378814 3378617 ID=MS.gene85140.t1.exon1;Parent=MS.gene85140.t1
chr2.4 CDS 3378617 3378814 3378617 ID=cds.MS.gene85140.t1;Parent=MS.gene85140.t1
chr2.4 exon 3378960 3379070 3378960 ID=MS.gene85140.t1.exon2;Parent=MS.gene85140.t1
chr2.4 CDS 3378960 3379070 3378960 ID=cds.MS.gene85140.t1;Parent=MS.gene85140.t1
chr2.4 exon 3379150 3379206 3379150 ID=MS.gene85140.t1.exon3;Parent=MS.gene85140.t1
chr2.4 CDS 3379150 3379206 3379150 ID=cds.MS.gene85140.t1;Parent=MS.gene85140.t1
chr2.4 exon 3379313 3379375 3379313 ID=MS.gene85140.t1.exon4;Parent=MS.gene85140.t1
chr2.4 CDS 3379313 3379375 3379313 ID=cds.MS.gene85140.t1;Parent=MS.gene85140.t1
chr2.4 exon 3379534 3379596 3379534 ID=MS.gene85140.t1.exon5;Parent=MS.gene85140.t1
chr2.4 CDS 3379534 3379596 3379534 ID=cds.MS.gene85140.t1;Parent=MS.gene85140.t1
chr2.4 exon 3379725 3379808 3379725 ID=MS.gene85140.t1.exon6;Parent=MS.gene85140.t1
chr2.4 CDS 3379725 3379808 3379725 ID=cds.MS.gene85140.t1;Parent=MS.gene85140.t1
Gene Sequence

>MS.gene85140

ATGTCACTCCTCCAACTCAAACTAACCCCTAATGCATTCACACGTCTCTCTTCTTCCTCACATAAAAAATTCAGACCAAACACAACACTCTTTACAAGAACCAAAATTAGAGCAGTCGGCACTGTCCCTGAAAAGAAGGATTCAGAGACCACTAGTGACTCTAATGACCCTCCCTCTATAGGTTTTGCATTTGTCAGTGTAAGTTCAAATTCTTAATACTATACTAAATGTACATACATGTAACATAACATAACATTGTAACTAATTAATTCTACTTATATCTAGTTGGTTTTACATTTATTATTAAATTTATGAAATTAATCTCTAATGTTTTGTGGATTAGTCTGTGTTGCTACCAGATGGAACACCAGATGTGCATTATCGTACAGCTTGTGGTGGACAGAAGCTTAGGAACATAATGTTGGATTCTAACATTGAACTCTATGGACCTTATGTAATTATCTCACTAACTTAAATTATTTTATTTTTAAGCAATAATTGGATGATAATTATTTTGTTGTTGATTTTTCCAGGGTAGAATTTTGTTAAATTGTGGAGGGGGTGGAACTTGTGTTACATGTATGGTAGAGGTGAGCTATAATAATCTTATATAATTTTCTAGCAAAAAATGCACATTTTATTGGGTAGTATATAGTTATATAGTACTTATTGTATTTTTTTTTAACTTGCTATTAGGTTCTTGAAGGCAAGGAGCTTCTGAGTCCTCGCACTGACAAAGAGAAAGAAAAACTTAAGAGGGTAAATGATTAAATCTTAACTTGATTAATGTTATTTTTTAATAAGAACTTAATTGTCATATTGAAAGAAAGAACAAACTTTTAGCATAAGTATATGTGAAATGTGAACTCTTGTGGTAAGAAAGATTACAATTATGATATCTTGTGTTTTCTTTATAGAAACCAAAGAATTGGAGATTAGCATGTCAAACAACTGTGGGTGAAGCAGATTCTACAGGGGTGGTTAGTACTACTAATTTTTTGGGTTAATTAATATACAGATTAGAAATTAATAAAATGGCTGTATTTATTATTTATGCTTAATTTATGTTGAGCAATATATTGGTACATTTTCATTCCATGTGATGTAGGTTGTGATTCAACAATTACCAGAGTGGAAAGGACATGAATGGAAATATGAAAAGGATGATGATGACTCAGCAGACTCTTTGTGA

Protein sequence

>MS.gene85140.t1

MSLLQLKLTPNAFTRLSSSSHKKFRPNTTLFTRTKIRAVGTVPEKKDSETTSDSNDPPSIGFAFVSSVLLPDGTPDVHYRTACGGQKLRNIMLDSNIELYGPYGRILLNCGGGGTCVTCMVEVLEGKELLSPRTDKEKEKLKRKPKNWRLACQTTVGEADSTGVVVIQQLPEWKGHEWKYEKDDDDSADSL