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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGACACAGAAGTAAAAGTAACAGCAACGTGTATACGTGTTCCAGTTATGCGTGCTCATGCAGAGAGTGTGAATCTTCAGTTTGAGAATCCTCTTGATGAGgtaataacacacgtcgaacccgatttctactgattctgtgttgttgtgttaccttatgatttcactcactgatatgacaatttgaatcataatttgaagt...

Basic information

species Arabidopsis thaliana
transcript AT1G14810.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G14810.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: LOC_Os03g55280.1 (Oryza sativa), 5'ss of exon 5
TGACACAGAAGTAAAAGTAACAGCAACGTGTATACGTGTTCCAGTTATGCGTGCTCATGCAGAGAGTGTGAATCTTCAGTTTGAGAATCCTCTTGATGAGgta---ataacacacgtc--gaacccgatttctactgattctgtgttgttgtgttaccttatgatt-tcactcactgatatgacaatttgaatcataatttgaagt
||| | ||| || || ||||| ||||| || ||||| ||||| || |||||||| ||||| || ||||||||||| |||||||| || || |||||||||||    |||| | |  ||   |     | ||||  | |   ||     |  | |   ||| || |  ||    ||   | |      ||   |  |||| ||    
TGATAAAGATGTGAAGGTAACTGCAACCTGCATACGAGTTCCTGTGATGCGTGCACATGCTGAAAGTGTGAATCTACAGTTTGAAAAGCCACTTGATGAGgttagcataaaatatttcttaatgataaattctggttagcatgaagaatcctttctgcttgtggtaatcctatacccttcttttg--ttaggtattaatatg----

upper sequence: AT1G14810.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GRMZM2G076885_T01 (Zea mays), 5'ss of exon 5
TGACACAGAAGTAAAAGTAACAGCAACGTGTATACGTGTTCCAGTTATGCGTGCTCATGCAGAGAGTGTGAATCTTCAGTTTGAGAATCCTCTTGATGAGgt-aataacacacgtcgaacccgatttctactgattctgtgttgttgtgttaccttatg-atttcactcactgata-tgacaatttgaatcataatttgaagt
|||||  || || |||||||| || || || ||||| ||||| || ||||| || ||||| || ||||| ||||| |||||||| || || |||||||||||   ||     | |   |   | |  |||    |   |  ||  |||     |  ||   ||||  ||  | ||| |  |   ||   ||   ||| |    
TGACAAGGAGGTGAAAGTAACTGCGACTTGCATACGGGTTCCTGTGATGCGCGCACATGCTGAAAGTGTCAATCTACAGTTTGAAAAGCCACTTGATGAGgttggtattctgcatattatgtgctaactagcattagagcttttctgtacgtgcgaatatgtttctttccttcatactatcctcttttgtctctattagt---

upper sequence: AT1G14810.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GLYMA08G05250.1 (Glycine max), 5'ss of exon 5
TGACACAGAAGTAAAAGTAACAGCAACGTGTATACGTGTTCCAGTTATGCGTGCTCATGCAGAGAGTGTGAATCTTCAGTTTGAGAATCCTCTTGATGAGgtaataacacacgtcgaacccgatttctactgattctgtgttgttgtgttaccttatgattt-cactcactgatatgacaat-ttgaat-cataatttgaagt------
| | |  || || |||||||| || || || ||||| ||||| || ||||| |||||||| ||||||||||||||||| ||||| |  || |||||||||||| |        ||   |  |  | ||  ||  | | ||   |||    | || ||  ||  || |   | |  |  |||   ||||| || ||||| ||        
TAATAAGGACGTTAAAGTAACTGCCACATGCATACGAGTTCCTGTCATGCGAGCTCATGCTGAGAGTGTGAATCTTCAATTTGAAACACCCCTTGATGAGgtact--------tcatgctggcatgctg-tgtctttatgccattgccaaaactcatagttgacattgctttacgtcccaaaactgaatacagaattttaacctagacc

upper sequence: AT1G14810.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GLYMA05G34420.1 (Glycine max), 5'ss of exon 5
TGACACAGAAGTAAAAGTAACAGCAACGTGTATACGTGTTCCAGTTATGCGTGCTCATGCAGAGAGTGTGAATCTTCAGTTTGAGAATCCTCTTGATGAGgtaataacacacgtcgaacccgatttc--tactgattctgtgttgttg-tgttaccttatgatttcactcactgatatgacaatttgaatcataatttgaagt
|||||  || || |||||||| || || || ||||| |||||  | ||||| |||||||| ||||||||||||||||| ||||| |  || |||||||||||| |       |||       ||  |  | |  |  ||   | ||||   || | ||| |     |   |||||    | ||||| ||||   |  |     
TGACAAGGATGTTAAAGTAACTGCCACATGCATACGAGTTCCCATCATGCGAGCTCATGCTGAGAGTGTGAATCTTCAATTTGAAAGACCCCTTGATGAGgtacttcatgttgtcatgtgttatgccattgccaaaact-catagttgacattgctttacgtcccaaa--actgaatacagaattttaatccagacctagtac

upper sequence: AT1G14810.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: Vv01s0011g05860.t01 (Vitis vinifera), 5'ss of exon 5
TGACACAGAAGTAAAAGTAACAGCAACGTGTATACGTGTTCCAGTTATGCGTGCTCATGCAGAGAGTGTGAATCTTCAGTTTGAGAATCCTCTTGATGAGgtaataacacacgtcgaacccgatttctactgattctgtgttgttgtgttaccttatgatttcactcactgatatgacaatttgaatcataatttgaagt---
|||||   | || ||||| || || || || ||||| || || ||||||||||| ||||| |||||||| ||||| |||||||||||||| ||||||||||||  ||      |   |    |  | || || || |      | |||     |||    ||     | ||||||    |   ||||  |  |||        
TGACATGAATGTTAAAGTGACTGCCACATGCATACGGGTCCCTGTTATGCGTGCGCATGCTGAGAGTGTTAATCTCCAGTTTGAGAATCCCCTTGATGAGgta-caatgatgatgctataaaagatatattgcttataaaacttggtgcacaattagatgttggtctattgatattcataaaagaatttt--tttagcacaag

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|116453473|gb|EG496065.1|EG496065
EST:     GTGCTCATGCAGAGAGTGTGAATCTTCAGTTTGAGAATCCTCTTGATGAG                         AACACAGCAAGGGAGATACTGAAGAAAGCACCTGGAGTTTATATAATAGAT
genomic: GTGCTCATGCAGAGAGTGTGAATCTTCAGTTTGAGAATCCTCTTGATGAGgtaataacac ... atcataacagAACACAGCAAGGGAGATACTGAAGAAAGCACCTGGAGTTTATATAATAGAT
EST: gi|125051193|gb|EL123462.1|EL123462
EST:     GTGCTCATGCAGAGAGTGTGAATCTTCAGTTTGAGAATCCTCTTGATGAG                         AACACAGCAAGGGAGATA
genomic: GTGCTCATGCAGAGAGTGTGAATCTTCAGTTTGAGAATCCTCTTGATGAGgtaataacac ... atcataacagAACACAGCAAGGGAGATA
EST: gi|116396484|gb|EG439076.1|EG439076
EST:     GTGCTCATGCAGAGAGTGTGAATCTTCAGTTTGAGAATCCTCTTGATGAG                         AACACAGCAAGGGAGATACTGAAGAAAGCACCTGGAGTTTATATAATAGAT
genomic: GTGCTCATGCAGAGAGTGTGAATCTTCAGTTTGAGAATCCTCTTGATGAGgtaataacac ... atcataacagAACACAGCAAGGGAGATACTGAAGAAAGCACCTGGAGTTTATATAATAGAT
EST: gi|116453474|gb|EG496066.1|EG496066
EST:     GTGCTCATGCAGAGAGTGTGAATCTTCAGTTTGAGAATCCTCTTGATGAG                         AACACAGCAAGGGAGATACTGAAGAAAGCACCTGGAGTTTATATAATAGAT
genomic: GTGCTCATGCAGAGAGTGTGAATCTTCAGTTTGAGAATCCTCTTGATGAGgtaataacac ... atcataacagAACACAGCAAGGGAGATACTGAAGAAAGCACCTGGAGTTTATATAATAGAT
EST: gi|86083642|gb|DR379401.1|DR379401
EST:     GTGCTCATGCAGAGAGTGTGAATCTTCAGTTTGAGAATCCTCTTGATGAG                         AACACAGCAAGGGAGATACTGAAGAAAGCACCTGGAGTTTATATAATAGAT
genomic: GTGCTCATGCAGAGAGTGTGAATCTTCAGTTTGAGAATCCTCTTGATGAGgtaataacac ... atcataacagAACACAGCAAGGGAGATACTGAAGAAAGCACCTGGAGTTTATATAATAGAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGACACAGAAGTAAAAGTAACAGCAACGTGTATACGTGTTCCAGTTATGCGTGCTCATGCAGAGAGTGTGAATCTTCAGTTTGAGAATCCTCTTGATGAGgtaataacacacgtcgaacccgatttctactgattctgtgttgttgtgttaccttatgatttcactcactgatatgacaatttgaatcataatttgaagt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tttcactc