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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATGGGTTACAAAAACCCTATTCTTTTGCTTCATCCGTTAGGTGGGTTTACAAAGGCTGATGATGTTCCTTTAGATTGGAGGATGAAGCAACACGAGAAGgtaaaaaaagttattgattgttgtgtgtctcttgagtgtgagtgtgtgtatcttgaaatgctaaatgtgtttatgaatgtaaaacag

Basic information

species Arabidopsis thaliana
transcript AT3G22890.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G22890.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: LOC_Os03g53230.1 (Oryza sativa), 5'ss of exon 2
GATGGGTTACAAAAACCCTATTCTTTTGCTTCATCCGTTAGGTGGGTTTACAAAGGCTGATGATGTTCCTTTAGATTGGAGGATGAAGCAACACGAGAAGgta-------aaaaaagttattg-attgttgtgtgtctcttgagtgtgagtgtgtgtatcttgaaat-gctaaatgtgttta---tgaatgtaaaacag----------------------------------------------
||||||||||||||| ||| ||||| |||||||||| || || || || ||||| || |||||||| ||| |   |||||| |||||||| || || ||||||       | |  ||  || | | |||    | | | | |    ||  |||  ||  ||||   | | | ||    |||    | | |  |  || |                                              
GATGGGTTACAAAAATCCTGTTCTTCTGCTTCATCCATTGGGAGGATTCACAAAAGCAGATGATGTGCCTCTTAGTTGGAGAATGAAGCAGCATGAAAAGgtacgctttaagagtagcaatcgtactgtcaaatctttttagcaaatgcatgttggtgccttgttgttgatgaaaccatttgatttaattacactactgtaaggcccaattcatgcacaattttgatgcgtgtttattttggtag

upper sequence: AT3G22890.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GRMZM2G051270_T02 (Zea mays), 5'ss of exon 3
GATGGGTTACAAAAACCCTATTCTTTTGCTTCATCCGTTAGGTGGGTTTACAAAGGCTGATGATGTTCCTTTAGATTGGAGGATGAAGCAACACGAGAAGgtaaaaaaagttattgattgttgtgtgtctcttgagtgtgagt-----gtgtgtatcttgaaatgct------aaatgtgtttatgaatgtaaaacag--
||||||||| ||||||||| ||||| |||| |||||  | || || || ||||| || |||||||| ||| |   |||||| ||||||||||| |||||||||   | |     | ||| |  | |  |  || |     | |      |   |  ||| |  |  |      |   |    ||||  | | ||  |   
GATGGGTTATAAAAACCCTGTTCTTCTGCTCCATCCACTGGGAGGATTCACAAAAGCAGATGATGTGCCTCTTAGTTGGAGAATGAAGCAACATGAGAAGgtatttagatgctataattatactctcccctttcatctcaaattctcaataattggcttcatgttttctccgcagtagcagctatgtctctgaactaaac

upper sequence: AT3G22890.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GRMZM2G149952_T01 (Zea mays), 5'ss of exon 2
GATGGGTTACAAAAACCCTATTCTTTTGCTTCATCCGTTAGGTGGGTTTACAAAGGCTGATGATGTTCCTTTAGATTGGAGGATGAAGCAACACGAGAAGgta---aaaaaagttattg-attgttgtgtgtctcttgagtgtgagtgtgt---gtatcttgaaatgctaaatgtgtt-tatgaatgtaaaacag-------
||||||||| ||||||||| ||||| |||| |||||  | || || || ||||| || |||||||| ||| |   |||||| ||||||||||| |||||||||   |      |  ||  | | ||   | ||   | ||  | | || ||    | || |  ||  |||||  | || | |  |||  |            
GATGGGTTATAAAAACCCTGTTCTTCTGCTCCATCCACTGGGAGGATTCACAAAAGCAGATGATGTGCCTCTTAGTTGGAGAATGAAGCAACATGAGAAGgtatccagctggatagttctactcttccctttcatctcagaataattgggttccatgtccttgaa--ctaaacatcttgttttgatgggatctgctatgtca

upper sequence: AT3G22890.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: Vv05s0020g04210.t01 (Vitis vinifera), 5'ss of exon 2
GATGGGTTACAAAAACCCTATTCTTTTGCTTCATCCGTTAGGTGGGTTTACAAAGGCTGATGATGTTCCTTTAGATTGGAGGATGAAGCAACACGAGAAGgtaaaaaaagttattgattgttgtgtgtctc---ttgagtgtgagt-gtgtgtat-cttgaaatgctaaatgtgtttatgaatgtaaaacag-----------------------------------
|||||| ||||| |||||| | || || |||||||| ||||| || | ||||||||| |||||||||||  | | |||||| ||||||||||| ||||||||  |  || | ||    || ||| |  |||   ||||   | |||  |   | | |  |||  |   | | |||   ||  |      |||                                   
GATGGGCTACAAGAACCCTGTCCTCTTACTTCATCCATTAGGAGGCTATACAAAGGCAGATGATGTTCCGCTTGGTTGGAGAATGAAGCAACATGAGAAGgttcatgaactgatcctatgatgtattgctcaatttgaaaatcagttatccctctgccagaagggtccattatgtaattgccttaccttcagttctaattctgattaatattgaaaatgttcctcag

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|125245014|gb|EL259099.1|EL259099
EST:     CAAAGGCTGATGATGTTCCTTTAGATTGGAGGATGAAGCAACACGAGAAG                         GTTCTAGAGGATGGTGTT
genomic: CAAAGGCTGATGATGTTCCTTTAGATTGGAGGATGAAGCAACACGAGAAGgtaaaaaaag ... tgtaaaacagGTTCTAGAGGATGGTGTT
EST: gi|125230995|gb|EL245080.1|EL245080
EST:     GATTGGAGGATGAAGCAACACGAGAAG                         GTTCTAGAGGATGGTGTTCTCGATCCGGAGACTACAGTGGTTTCGA
genomic: GATTGGAGGATGAAGCAACACGAGAAGgtaaaaaaag ... tgtaaaacagGTTCTAGAGGATGGTGTTCTCGATCCGGAGACTACAGTGGTTTCGA
EST: gi|116447940|gb|EG490532.1|EG490532
EST:     CAAAGGCTGATGATGTTCCTTTAGATTGGAGGATGAAGCAACACGAGAAG                         GTTCTAGAGGATGGTGTTCTCGATCCGGAGACTACAGTGGTTTCGATATTC
genomic: CAAAGGCTGATGATGTTCCTTTAGATTGGAGGATGAAGCAACACGAGAAGgtaaaaaaag ... tgtaaaacagGTTCTAGAGGATGGTGTTCTCGATCCGGAGACTACAGTGGTTTCGATATTC
EST: gi|116460581|gb|EG503173.1|EG503173
EST:     CAAAGGCTGATGATGTTCCTTTAGATTGGAGGATGAAGCAACACGAGAAG                         GTTCTAGAGGATGGTGTTCTCGATCCGGAGACTACAGTGGTTTCGATATTC
genomic: CAAAGGCTGATGATGTTCCTTTAGATTGGAGGATGAAGCAACACGAGAAGgtaaaaaaag ... tgtaaaacagGTTCTAGAGGATGGTGTTCTCGATCCGGAGACTACAGTGGTTTCGATATTC
EST: gi|116460580|gb|EG503172.1|EG503172
EST:     CAAAGGCTGATGATGTTCCTTTAGATTGGAGGATGAAGCAACACGAGAAG                         GTTCTAGAGGATGGTGTTCTCGATCCGGAGACTACAGTGGTTTCGATATTC
genomic: CAAAGGCTGATGATGTTCCTTTAGATTGGAGGATGAAGCAACACGAGAAGgtaaaaaaag ... tgtaaaacagGTTCTAGAGGATGGTGTTCTCGATCCGGAGACTACAGTGGTTTCGATATTC
EST: gi|301501831|gb|HO207371.1|HO207371
EST:     CAAAGGCTGATGATGTTCCTTTAGATTGGAGGATGAAGCAACACGAGAAG                         GTTCTAGAGGATGGTGTTCTCGATCCGGAGACTACAGTGGTTTCGATATTC
genomic: CAAAGGCTGATGATGTTCCTTTAGATTGGAGGATGAAGCAACACGAGAAGgtaaaaaaag ... tgtaaaacagGTTCTAGAGGATGGTGTTCTCGATCCGGAGACTACAGTGGTTTCGATATTC
EST: gi|124859552|gb|EH943989.1|EH943989
EST:     CAAAGGCTGATGATGTTCCTTTAGATTGGAGGATGAAGCAACACGAGAAG                         GTTCTAGAGGATGGTGTTCTCGATCCGGAGACTACAGTGGTTTCGATATTC
genomic: CAAAGGCTGATGATGTTCCTTTAGATTGGAGGATGAAGCAACACGAGAAGgtaaaaaaag ... tgtaaaacagGTTCTAGAGGATGGTGTTCTCGATCCGGAGACTACAGTGGTTTCGATATTC
EST: gi|124923809|gb|EL001961.1|EL001961
EST:     ATTGGAGGATGAAGCAACACGAGAAG                         GTTCTAGAGGATGGTGTTCTCGATCCGGAGACTACAGTGGTTTCGA
genomic: ATTGGAGGATGAAGCAACACGAGAAGgtaaaaaaag ... tgtaaaacagGTTCTAGAGGATGGTGTTCTCGATCCGGAGACTACAGTGGTTTCGA
EST: gi|125103175|gb|EL157674.1|EL157674
EST:     CAAAGGCTGATGATGTTCCTTTAGATTGGAGGATGAAGCAACACGAGAAG                         GTTCTAGAGGATGGTGTTCTCGATCC
genomic: CAAAGGCTGATGATGTTCCTTTAGATTGGAGGATGAAGCAACACGAGAAGgtaaaaaaag ... tgtaaaacagGTTCTAGAGGATGGTGTTCTCGATCC
EST: gi|116453692|gb|EG496284.1|EG496284
EST:     CAAAGGCTGATGATGTTCCTTTAGATTGGAGGATGAAGCAACACGAGAAG                         GTTCTAGAGGATGGTGTTCTCGATCCGGAGACTACAGTGGTTTCGATATTC
genomic: CAAAGGCTGATGATGTTCCTTTAGATTGGAGGATGAAGCAACACGAGAAGgtaaaaaaag ... tgtaaaacagGTTCTAGAGGATGGTGTTCTCGATCCGGAGACTACAGTGGTTTCGATATTC
EST: gi|125252837|gb|EL266922.1|EL266922
EST:     CAAAGGCTGATGATGTTCCTTTAGATTGGAGGATGAAGCAACACGAGAAG                         GTTCTAGAGGATGGTGTTCTCGATCCGGAGACTACAGTGGTTTCGATATTC
genomic: CAAAGGCTGATGATGTTCCTTTAGATTGGAGGATGAAGCAACACGAGAAGgtaaaaaaag ... tgtaaaacagGTTCTAGAGGATGGTGTTCTCGATCCGGAGACTACAGTGGTTTCGATATTC
EST: gi|116447947|gb|EG490539.1|EG490539
EST:     CAAAGGCTGATGATGTTCCTTTAGATTGGAGGATGAAGCAACACGAGAAG                         GTTCTAGAGGATGGTGTTCTCGATCCGGAGACTACAGTGGTTTCGATATTC
genomic: CAAAGGCTGATGATGTTCCTTTAGATTGGAGGATGAAGCAACACGAGAAGgtaaaaaaag ... tgtaaaacagGTTCTAGAGGATGGTGTTCTCGATCCGGAGACTACAGTGGTTTCGATATTC
EST: gi|125064965|gb|EL132381.1|EL132381
EST:     GGAGGATGAAGCAACACGAGAAG                         GTTCTAGAGGATGGTGTTCTCGATCCGGAGACTACAGTGGTTTCGATATTC
genomic: GGAGGATGAAGCAACACGAGAAGgtaaaaaaag ... tgtaaaacagGTTCTAGAGGATGGTGTTCTCGATCCGGAGACTACAGTGGTTTCGATATTC
EST: gi|125208677|gb|EL223631.1|EL223631
EST:     CAAAGGCTGATGATGTTCCTTTAGATTGGAGGATGAAGCAACACGAGAAG                         GTTCTAGAGGATGGTGTT
genomic: CAAAGGCTGATGATGTTCCTTTAGATTGGAGGATGAAGCAACACGAGAAGgtaaaaaaag ... tgtaaaacagGTTCTAGAGGATGGTGTT
EST: gi|124732049|gb|EH823451.1|EH823451
EST:     CAAAGGCTGATGATGTTCCTTTAGATTGGAGGATGAAGCAACACGAGAAG                         GTTCTAGAGGATGGTGTTCTC
genomic: CAAAGGCTGATGATGTTCCTTTAGATTGGAGGATGAAGCAACACGAGAAGgtaaaaaaag ... tgtaaaacagGTTCTAGAGGATGGTGTTCTC
EST: gi|124916793|gb|EH990667.1|EH990667
EST:     CAAAGGCTGATGATGTTCCTTTAGATTGGAGGATGAAGCAACACGAGAAG                         GTTCTAGAGGATGGTGTT
genomic: CAAAGGCTGATGATGTTCCTTTAGATTGGAGGATGAAGCAACACGAGAAGgtaaaaaaag ... tgtaaaacagGTTCTAGAGGATGGTGTT
EST: gi|116420530|gb|EG463122.1|EG463122
EST:     CAAAGGCTGATGATGTTCCTTTAGATTGGAGGATGAAGCAACACGAGAAG                         GTTCTAGAGGATGGTGTTCTCGATCCGGAGACTACAGTGGTTTCGATATTC
genomic: CAAAGGCTGATGATGTTCCTTTAGATTGGAGGATGAAGCAACACGAGAAGgtaaaaaaag ... tgtaaaacagGTTCTAGAGGATGGTGTTCTCGATCCGGAGACTACAGTGGTTTCGATATTC

Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GATGGGTTACAAAAACCCTATTCTTTTGCTTCATCCGTTAGGTGGGTTTACAAAGGCTGATGATGTTCCTTTAGATTGGAGGATGAAGCAACACGAGAAGgtaaaaaaagttattgattgttgtgtgtctcttgagtgtgagtgtgtgtatcttgaaatgctaaatgtgtttatgaatgtaaaacag

- - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA