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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGGAATGAAACTGATCTTGTCTTTGTGCTTAGCTGAAGGGTTTGACACGTTTCCTACACTGCTTTGTGCTGATGGATGTTCCATGATTGATCGAAGAATGgtattaaaagcaatctttgatcgaaactgattgttgtttcttgttttgtttggctattaagattgatttcttttttttcctgtatttgaag

Basic information

species Arabidopsis thaliana
transcript AT1G35580.3
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G35580.3 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GRMZM2G007277_T01 (Zea mays), 5'ss of exon 3
GGGAATGAAACTGATCTTGTCTTTGTGCTTAGCTGAAGGGTTTGACACGTTTCCTACACTGCTTTGTGCTGATGGATGTTCCATGATTGATCGAAGAATGgtattaaaagcaatctttgatcgaaactgattgttgtttcttgttttgtttggctatta---agattgatttcttttttttcctg--tatttgaag-----
| | ||||  |||||  ||  | | |||||| ||||||| ||||| || ||||| || ||||||||  | ||||| ||||| |||||||||||  ||||||||  |  |     | |||||| ||      | | | | | | |   ||     ||  |   ||  | ||||  ||  | |||||   |  ||||      
GTGCATGAGGCTGATACTGAATCTCTGCTTATCTGAAGGATTTGATACTTTTCCAACTCTGCTTTGCACAGATGGCTGTTCAATGATTGATCGTCGAATGgtaggaccatttcaccttgatctaattcatatttagatgcatatcc-gtagaagtagcacatagcctcattttgttagtgtcctgatcaggtgaaagttca

upper sequence: AT1G35580.3 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA20G31730.2 (Glycine max), 5'ss of exon 3
GGGAATGAAACTGATCTTGTCTTTGTGCTTAGCTGAAGGGTTTGACACGTTTCCTACACTGCTTTGTGCTGATGGATGTTCCATGATTGATCGAAGAATGgtattaaaa-----gcaatctttgatcgaaactgattgttgtttcttgttttgtttggctattaagattgatttcttttttttcctgtatttgaag-------
|||||||||||| ||  || || | |||||  | || |||||||| || ||||| ||  ||||||||||||||||||||| |||| |||||||||||||||||  | |      |      ||  || ||  ||||  || || ||||||   | ||||||| |||| |||||| |  |   | |  |  || | |       
GGGAATGAAACTTATACTGACTCTATGCTTGTCAGAGGGGTTTGATACATTTCCAACTTTGCTTTGTGCTGATGGATGTTGCATGGTTGATCGAAGAATGgtaagatatagtttgtggctgtttctctaagatgatcattattgcttgtt--atctggctat-aagaatgatttttggtgcattccattgtttatgaacaaag

upper sequence: AT1G35580.3 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA10G35890.2 (Glycine max), 5'ss of exon 3
GGGAATGAAACTGATCTTGTCTTTGTGCTTAGCTGAAGGGTTTGACACGTTTCCTACACTGCTTTGTGCTGATGGATGTTCCATGATTGATCGAAGAATGgta-----ttaaaagcaatctttgatcgaaactgattgttgtttcttgttttgtttggctattaagattgatttcttttttttcctgtatttgaag------
|||||||||||| ||  || || | |||||  | || || ||||| || ||||| ||  ||||||||||||||||||||| |||| |||||||||||||||||     | |   ||     ||  || ||  | |||  | || ||||||   | ||||||| || ||   |||  ||   ||||  |  ||          
GGGAATGAAACTTATACTGACTCTATGCTTGTCAGAGGGTTTTGATACATTTCCAACTTTGCTTTGTGCTGATGGATGTTGCATGGTTGATCGAAGAATGgtaagacataatttgcggctgtttgtctaagataattaatattgcttgtt--atctggctataaaaatgatttttgttgcattccattggttatgatttata

upper sequence: AT1G35580.3 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: Vv18s0072g01040.t01 (Vitis vinifera), 5'ss of exon 3
GGGAATGAAACTGATCTTGTCTTTGTGCTTAGCTGAAGGGTTTGACACGTTTCCTACACTGCTTTGTGCTGATGGATGTTCCATGATTGATCGAAGAATGgta----ttaaaagcaatctttgatcgaaactg--attgttgtttcttgttttgttt---ggctat-taagat-tgatttcttttttttcctgt-atttgaag
||||||||| || || ||| |||| ||| |  | || |||||||| || ||||| || |||||||||||||||||||| || ||| |||| ||||||||||||    ||    ||||  ||   |  |   ||  | ||    ||   |||  |||    | || | || ||| ||| | | |    || || | || ||   
GGGAATGAAGCTTATATTGACTTTATGCCTCTCGGAGGGGTTTGATACATTTCCAACTCTGCTTTGTGCTGATGGATGCTCTATGGTTGACCGAAGAATGgtaagatttccttgcaaatttaattttaccatgctactgcaagttacggttcagttgcaagcctgtgtaggatatgagtgcatgcagttgctttcatatg---

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|125269597|gb|EL283682.1|EL283682
EST:     ATCGAAGAATG                         GGTGTTTATGGGTATCCCATTGAGATCCAAGCGTTGTTCTTCATGGCTTTG
genomic: ATCGAAGAATGgtattaaaag ... gtatttgaagGGTGTTTATGGGTATCCCATTGAGATCCAAGCGTTGTTCTTCATGGCTTTG
EST: gi|124715854|gb|EH807256.1|EH807256
EST:     TGATCGAAGAATG                         GGTGTTTATGGGTATCCCATTGAGATCCAAGCGTTGTTCTTCATGGCTTTG
genomic: TGATCGAAGAATGgtattaaaag ... gtatttgaagGGTGTTTATGGGTATCCCATTGAGATCCAAGCGTTGTTCTTCATGGCTTTG
EST: gi|125200030|gb|EL214984.1|EL214984
EST:     ATGATTGATCGAAGAATG                         GGTGTTTATGGGTATCCCATTGAGATCCAAGCGTTGTTCTTCATGGCTTTG
genomic: ATGATTGATCGAAGAATGgtattaaaag ... gtatttgaagGGTGTTTATGGGTATCCCATTGAGATCCAAGCGTTGTTCTTCATGGCTTTG
EST: gi|125282465|gb|EL296550.1|EL296550
EST:     TTCCTACACTGCTTTGTGCTGATGGATGTTCCATGATTGATCGAAGAATG                         GGTGTTTATGGGTACCCCATTGAGATCCAAGCGTTG
genomic: TTCCTACACTGCTTTGTGCTGATGGATGTTCCATGATTGATCGAAGAATGgtattaaaag ... gtatttgaagGGTGTTTATGGGTATCCCATTGAGATCCAAGCGTTG
EST: gi|124969683|gb|EL043571.1|EL043571
EST:     TTCCTACACTGCTTTGTGCTGATGGATGTTCCATGATTGATCGAAGAATG                         GGTGTTTATGGGTATCCCA
genomic: TTCCTACACTGCTTTGTGCTGATGGATGTTCCATGATTGATCGAAGAATGgtattaaaag ... gtatttgaagGGTGTTTATGGGTATCCCA
EST: gi|125045668|gb|EL117937.1|EL117937
EST:     TTCCTACACTGCTTTGTGCTGATGGATGTTCCATGATTGATCGAAGAATG                         GGTGTTTATGGGT
genomic: TTCCTACACTGCTTTGTGCTGATGGATGTTCCATGATTGATCGAAGAATGgtattaaaag ... gtatttgaagGGTGTTTATGGGT
EST: gi|125229419|gb|EL243504.1|EL243504
EST:     TTCCTACACTGCTTTGTGCTGATGGATGTTCCATGATTGATCGAAGAATG                         GGTGTTTATGGGTATCCCATTGAGATCCAAGCGTTGTTCTTCA
genomic: TTCCTACACTGCTTTGTGCTGATGGATGTTCCATGATTGATCGAAGAATGgtattaaaag ... gtatttgaagGGTGTTTATGGGTATCCCATTGAGATCCAAGCGTTGTTCTTCA
EST: gi|125120870|gb|EL168361.1|EL168361
EST:     CCTACACTGCTTTGTGCTGATGGATGTTCCATGATTGATCGAAGAATG                         GGTGTTTATGGGTATCCCATTGAGATCCAAGCGTTGTTCTTCATGG
genomic: CCTACACTGCTTTGTGCTGATGGATGTTCCATGATTGATCGAAGAATGgtattaaaag ... gtatttgaagGGTGTTTATGGGTATCCCATTGAGATCCAAGCGTTGTTCTTCATGG
EST: gi|124981900|gb|EL054741.1|EL054741
EST:     CTTTGTGCTGATGGATGTTCCATGATTGATCGAAGAATG                         GGTGTTTATGGGTATCCCATTGAGATCCAAGCGTTGTTCTTCATGGCTTTG
genomic: CTTTGTGCTGATGGATGTTCCATGATTGATCGAAGAATGgtattaaaag ... gtatttgaagGGTGTTTATGGGTATCCCATTGAGATCCAAGCGTTGTTCTTCATGGCTTTG
EST: gi|125041687|gb|EL113956.1|EL113956
EST:     TTCCTACACTGCTTTGTGCTGATGGATGTTCCATGATTGATCGAAGAATG                         GGTGTTTATGGGTATCCCATTGAGATCCAAG
genomic: TTCCTACACTGCTTTGTGCTGATGGATGTTCCATGATTGATCGAAGAATGgtattaaaag ... gtatttgaagGGTGTTTATGGGTATCCCATTGAGATCCAAG
EST: gi|164221126|gb|EL992897.1|EL992897
EST:     GATCGAAGAATG                         GGTGTTTATGGGTATCCCATTGAGATCCAAGCGTTGTTCTTCATGGCTTTG
genomic: GATCGAAGAATGgtattaaaag ... gtatttgaagGGTGTTTATGGGTATCCCATTGAGATCCAAGCGTTGTTCTTCATGGCTTTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGGAATGAAACTGATCTTGTCTTTGTGCTTAGCTGAAGGGTTTGACACGTTTCCTACACTGCTTTGTGCTGATGGATGTTCCATGATTGATCGAAGAATGgtattaaaagcaatctttgatcgaaactgattgttgtttcttgttttgtttggctattaagattgatttcttttttttcctgtatttgaag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CGAAGA