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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAAAATTGTTGCCGTTGGAACTGATGCCAAAGGAAACATTAACATCGAAGAGTTGAGGAACGCCGCCGAAGCCAACAAGGACAACTTGGCTGCTCTTATGgtatgtatttacttctttcatcactatagatgaaacaatgtcacttttgggtcaatccactttctaattctacaacttctgtttgaatattag

Basic information

species Arabidopsis thaliana
transcript AT2G26080.1
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G26080.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: LOC_Os06g40940.1 (Oryza sativa), 5'ss of exon 7
GAAAATTGTTGCCGTTGGAACTGATGCCAAAGGAAACATTAACATCGAAGAGTTGAGGAACGCCGCCGAAGCCAACAAGGACAACTTGGCTGCTCTTATGgtatgtatttacttctttcatcactatagatgaaacaatgtcacttttgggtcaatccactttctaattctacaacttctgtttgaatattag---------
||| |||||||| |||||||||||| ||||||| |||||||||||||| ||||||||||| || || ||||| ||||||||||||||||||||||||||||||    | |  ||  |   | | | |      |   || |    ||  |||    |       |   | |      |||| |  | ||||           
GAAGATTGTTGCTGTTGGAACTGATTCCAAAGGTAACATTAACATCGAGGAGTTGAGGAAAGCTGCTGAAGCAAACAAGGACAACTTGGCTGCTCTTATGgtactgttctttttgctctgtaaatgttatc--atttatctggtcttctggtagtactgtggaatgcctatggtctctctggtcaactattcactgttaaat

upper sequence: AT2G26080.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: LOC_Os01g51410.2 (Oryza sativa), 5'ss of exon 6
GAAAATTGTTGCCGTTGGAACTGATGCCAAAGGAAACATTAACATCGAAGAGTTGAGGAACGCCGCCGAAGCCAACAAGGACAACTTGGCTGCTCTTATGgtatgtatttacttctttcatcactatagatgaaacaatgtcacttttgggtcaatccactttctaattctacaacttctgtttgaatattag---------
||| || ||||| |||||||||||| ||||||| |||||||||||||| ||||||||||| || || ||||| ||||||||||||||||||||||||||||||    |    ||  |   | | | |      |   ||      ||  |||            |   | |     ||||| |  | ||||           
GAAGATCGTTGCTGTTGGAACTGATTCCAAAGGTAACATTAACATCGAGGAGTTGAGGAAAGCTGCTGAAGCAAACAAGGACAACTTGGCTGCTCTTATGgtactgttccttttgctctgtaaatgttatc--atttatcaggtcttcaggtagtaatgtggaatgcctatggtctttctggtcaactattcactgttaaat

upper sequence: AT2G26080.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: GRMZM2G104310_T03 (Zea mays), 5'ss of exon 7
GAAAATTGTTGCCGTTGGAACTGATGCCAAAGGAAACATTAACATCGAAGAGTTGAGGAACGCCGCCGAAGCCAACAAGGACAACTTGGCTGCTCTTATGgta----tgtatttacttctttcatc-actatagatgaaacaatgtcacttttgggtcaatccactttctaattctacaacttctgtttgaatattag---
||| |||||||| ||||||||||||||||| || ||||| |||||||| || |||||||| || || ||||| ||||||||||||||||||||||| ||||||    ||   ||     ||| ||| |  ||   |   |  || | || |   | |       |     | || |  ||      | |||   |||    
GAAGATTGTTGCTGTTGGAACTGATGCCAAGGGTAACATAAACATCGAGGAATTGAGGAAAGCTGCAGAAGCAAACAAGGACAACTTGGCTGCTCTGATGgtactcttgctcttggacatttaatctatcatttctatgagtatat-acctggcgattctcttgcccgtgactttttgaaaaaaaatctgacctttatgta

upper sequence: AT2G26080.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: GLYMA06G05470.1 (Glycine max), 5'ss of exon 8
GAAAATTGTTGCCGTTGGAACTGATGCCAAAGGAAACATTAACATCGAAGAGTTGAGGAACGCCGCCGAAGCCAACAAGGACAACTTGGCTGCTCTTATGgtatgtatt----tacttc-----------tttcatcactatagatgaaacaatgtcacttttgggtcaatc---cactttctaattctacaacttctgtttgaatattag----------------------------
|||||||||  | ||||||||||||||||| |||||||| || || |||||||||||||| || || ||| |  | ||||||||| | |||||||||||||||    ||    | ||||           ||| |     ||   |   | ||  |    |||||   ||        || | | ||   ||  || | ||| ||||||                              
GAAAATTGTATCTGTTGGAACTGATGCCAAGGGAAACATCAATATTGAAGAGTTGAGGAAGGCTGCTGAAACACATAAGGACAACCTAGCTGCTCTTATGgtacaacttgcgttgcttcctatattcgaattttacttgcattatttggataacctggaatttggaggaaaggggtgtttccgacttggccattttttttttaaatattcatttttggtggttttgatttaaattatag

upper sequence: AT2G26080.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: GLYMA14G10820.1 (Glycine max), 5'ss of exon 7
GAAAATTGTTGCCGTTGGAACTGATGCCAAAGGAAACATTAACATCGAAGAGTTGAGGAACGCCGCCGAAGCCAACAAGGACAACTTGGCTGCTCTTATGgtatgtatttacttctttcatcactatagatgaaacaatgtcact-tttgggtcaatccac----tttctaattctacaacttctgtttgaata--ttag-----------------
|||||||||  | ||||||||||||||||| ||||||||||| || |||||| ||||||| || || ||| |  ||||||| |||||  |||| |||||||||   | || |||| |  |  | | ||     |  |  | |  | |       |||  |     ||   ||  |||    || ||||  ||||  || |                 
GAAAATTGTCTCTGTTGGAACTGATGCCAAGGGAAACATTAATATAGAAGAGCTGAGGAAGGCTGCTGAAACACACAAGGATAACTTATCTGCACTTATGgtaca-acttgcttcctatagaattctactcatattacagactttataccaactaattgagagtattgtcaaacctaggcattttgttacaatagcttggtttcgattaaattgcag

upper sequence: AT2G26080.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: GLYMA04G05420.2 (Glycine max), 5'ss of exon 7
GAAAATTGTTGCCGTTGGAACTGATGCCAAAGGAAACATTAACATCGAAGAGTTGAGGAACGCCGCCGAAGCCAACAAGGACAACTTGGCTGCTCTTATGgtatg---------------tatttacttctttcatcactatagatgaaacaa--tgtcacttttgggtcaa--------tccacttt--ctaattctacaacttctgtttgaatattag-------------------------------
|||||||||  | ||||||||||||||||| |||||||| || || || ||||||||||| || || ||| |  | ||||||||| | |||||||| ||||||                 ||| | ||  ||| |  |  ||   |   | ||  ||  | ||| | |  ||        ||||  ||  |||||| |    ||| | ||| ||||||                                 
GAAAATTGTATCTGTTGGAACTGATGCCAAGGGAAACATCAATATTGATGAGTTGAGGAAGGCTGCTGAAACACATAAGGACAACCTAGCTGCTCTCATGgtacaacttgcgttgcttcctatattctaattttactagcattatttggataacctgggaatttggaggaaaggggtgtttccaacttggctaattttttt-cttttttttaaatattcatttgttgtggtggttttgatttaaattatag

upper sequence: AT2G26080.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: GLYMA17G34690.1 (Glycine max), 5'ss of exon 7
GAAAATTGTTGCCGTTGGAACTGATGCCAAAGGAAACATTAACATCGAAGAGTTGAGGAACGCCGCCGAAGCCAACAAGGACAACTTGGCTGCTCTTATGgtatg----------tat------ttacttctttcatc-actatagatgaaacaat----gtcacttttgggtcaatccactttctaattcta---caacttctgtttgaatattag
|||||||||  | ||||||||||| ||||| || |||||||| || ||||| ||||| || || |||||| |  | |||||||||||  |||| |||||||||            |||      |||||  | | ||  ||| || |  | | |||    |  | | |     | |  || ||| | |   ||       ||   ||| |||   ||
GAAAATTGTCTCTGTTGGAACTGACGCCAAGGGTAACATTAATATAGAAGAATTGAGAAAGGCTGCCGAAACACATAAGGACAACTTATCTGCACTTATGgtacaacttgcttcctatagaatcttactcatattatttactctataccagataattgagggtattgtcaaacctaggcatttttttacattagtttggttttaatttaaattgcag

upper sequence: AT2G26080.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: Vv04s0008g01300.t01 (Vitis vinifera), 5'ss of exon 7
GAAAATTGTTGCCGTTGGAACTGATGCCAAAGGAAACATTAACATCGAAGAGTTGAGGAACGCCGCCGAAGCCAACAAGGACAACTTGGCTGCTCTTATGgtatgtatttacttctttcatcactatagatgaaacaatgtcacttttgggtcaatccactttctaattctacaacttctgtttgaatattag
|||||||||||| ||||||||||||||||| |||||||| ||||| |||||||| ||||| || || ||||| || ||||| ||| |  ||||||||||||||||||  |       |      ||  | ||     |  |||    |  |  |   ||  |  | |||     | ||   ||||||| | ||
GAAAATTGTTGCTGTTGGAACTGATGCCAAGGGAAACATCAACATTGAAGAGTTAAGGAAGGCTGCTGAAGCAAATAAGGAAAACCTATCTGCTCTTATGgtatgtaggt-------tggagggtagggttggtgtgagatcatgcctatgaaatatcaagtgttcatt----gattttgatttgaatttcag

upper sequence: AT2G26080.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: Vv11s0016g02280.t01 (Vitis vinifera), 5'ss of exon 8
GAAAATTGTTGCCGTTGGAACTGATGCCAAAGGAAACATTAACATCGAAGAGTTGAGGAACGCCGCCGAAGCCAACAAGGACAACTTGGCTGCTCTTATGgtatgtatttact---tctttcatcactatagatgaaacaatgtcactttt---gggtcaatccacttt---ctaattctacaacttctgtttga-atattag----------------------------
|||||||||||| |||||||||||||||||||| ||||| |||||| | ||||| || || || || ||||| || | ||||||  |  |||||||||||||||| || |  |   |  || ||  |||  | |||    || | | |      |||  ||   ||      || | | |   |  || |||  |  ||| |                             
GAAAATTGTTGCTGTTGGAACTGATGCCAAAGGCAACATCAACATCAAGGAGTTAAGAAAGGCAGCTGAAGCAAATAGGGACAATCTATCTGCTCTTATGgtatggatatcttgaatgcttaattgctagtggtgatttcatttgattagaaaagggagaaataacaagaaactcactatggcagatcagttaaatgtataattattgaaaaattctgactccatggccag

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|47829567|gb|CK119251.1|CK119251
EST:     AGTTGAGGAACGCCGCCGAAGCCAACAAGGACAACTTGGCTGCTCTTATG                         GTTACATACCCTTCCACCCATGGAGTCTACGAAGAGGGTATCGACGAGATC
genomic: AGTTGAGGAACGCCGCCGAAGCCAACAAGGACAACTTGGCTGCTCTTATGgtatgtattt ... tgaatattagGTTACATACCCTTCCACCCATGGAGTCTACGAAGAGGGTATCGACGAGATC
EST: gi|47831551|gb|CK121235.1|CK121235
EST:     AGTTGAGGAACGCCGCCGAAGCCAACAAGGACAACTTGGCTGCTCTTATG                         GTTACATACCCTTCCACCCATGGAGTCTACGAAGAGGGTATCGACGAGATC
genomic: AGTTGAGGAACGCCGCCGAAGCCAACAAGGACAACTTGGCTGCTCTTATGgtatgtattt ... tgaatattagGTTACATACCCTTCCACCCATGGAGTCTACGAAGAGGGTATCGACGAGATC
EST: gi|116423224|gb|EG465816.1|EG465816
EST:     GTTGAGGAACGCCGCCGAAAGCCAACAAGGACAACTTGGCTGCTCTTATG                         GTTACATACCCTTTCCACCCATGGAGTCTACGAAGAGGGTATCGACGAGAT
genomic: GTTGAGGAACGCCGCCG-AAGCCAACAAGGACAACTTGGCTGCTCTTATGgtatgtattt ... tgaatattagGTTACATACCC-TTCCACCCATGGAGTCTACGAAGAGGGTATCGACGAGAT
EST: gi|116423223|gb|EG465815.1|EG465815
EST:     AGTTGAGGAACGCCGCCGAAGCCAACAAGGACAACTTGGCTGCTCTTATG                         GTTACATACCCTTCCACCCATGGAGTCTACGAAGAGGGTATCGACGAGATC
genomic: AGTTGAGGAACGCCGCCGAAGCCAACAAGGACAACTTGGCTGCTCTTATGgtatgtattt ... tgaatattagGTTACATACCCTTCCACCCATGGAGTCTACGAAGAGGGTATCGACGAGATC
EST: gi|47830981|gb|CK120665.1|CK120665
EST:     AGTTGAGGAACGCCGCCGAAGCCAACAAGGACAACTTGGCTGCTCTTATG                         GTTACATACCCTTCCACCCATGGAGTCTACGAAGAGGGTATCGACGAGATC
genomic: AGTTGAGGAACGCCGCCGAAGCCAACAAGGACAACTTGGCTGCTCTTATGgtatgtattt ... tgaatattagGTTACATACCCTTCCACCCATGGAGTCTACGAAGAGGGTATCGACGAGATC
EST: gi|125327461|gb|EL341541.1|EL341541
EST:     CGAAGCCAACAAGGACAACTTGGCTGCTTCTTATG                         GTTACATACCCTTCCACCCANGGAGTCTACGAAGAGGGTATCGACGAGAT
genomic: CGAAGCCAACAAGGACAACTTGGCTGC-TCTTATGgtatgtattt ... tgaatattagGTTACATACCCTTCCACCCATGGAGTCTACGAAGAGGGTATCGACGAGAT
EST: gi|164037941|gb|EL972029.1|EL972029
EST:     GACAACTTGGCTGCTCTTATG                         GTTACATACCCTTCCACCCATGGAGTCTACGAAGAGGGTATCGACGAGATC
genomic: GACAACTTGGCTGCTCTTATGgtatgtattt ... tgaatattagGTTACATACCCTTCCACCCATGGAGTCTACGAAGAGGGTATCGACGAGATC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAAAATTGTTGCCGTTGGAACTGATGCCAAAGGAAACATTAACATCGAAGAGTTGAGGAACGCCGCCGAAGCCAACAAGGACAACTTGGCTGCTCTTATGgtatgtatttacttctttcatcactatagatgaaacaatgtcacttttgggtcaatccactttctaattctacaacttctgtttgaatattag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT