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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTACACAGAAGACATGGAACTTGACGATGCCATTCACACAGCGATACTGACATTGAAAGAAGGgtaagtacaaatctacattattattagaaagtagttcgcctgataatcagagttcacttcatattcatagatcacactctcagtgtgactgatagattac...

Basic information

species Arabidopsis thaliana
transcript AT1G16470.2
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G16470.1 (Arabidopsis thaliana), 5'ss of exon 10
lower sequence: LOC_Os03g26970.1 (Oryza sativa), 5'ss of exon 9
GTACACAGAAGACATGGAACTTGACGATGCCATTCACACAGCGATACTGACATTGAAAGAAGGgtaagtacaaatctacattattattagaaagtagttcgcctgataatcagagttcacttcatattcatagatcacactctcagtgtgactgatagattac--
 ||||||||||| ||||| ||||||||||||||||| || || ||  | ||  |||||||||||||         |  || |||||||      |  || |  |   |        |   ||| | || | | |  ||    |   || || |   |  || |  
ATACACAGAAGATATGGAGCTTGACGATGCCATTCATACTGCTATTTTAACTCTGAAAGAAGGgta---------cctcactattattgtgtgttgatttgtttacca-------cttctttcctttttaaaaacaac----ttgatg-gattacaaacttgcag

upper sequence: AT1G16470.1 (Arabidopsis thaliana), 5'ss of exon 10
lower sequence: LOC_Os02g42320.1 (Oryza sativa), 5'ss of exon 8
GTACACAGAAGACATGGAACTTGACGATGCCATTCACACAGCGATACTGACATTGAAAGAAGGgtaagtacaaatctacattattattagaaagtagttcgcctgataatcagagttcacttcatattcatagatcacactctcagtgtgactgatagattac
 ||||||||||||||||| ||||| |||||||| || || || ||  ||||  ||||||||||||| || |   |      |  | ||   |  |      | |  | |   |||||     |  ||||   | |  ||                        
ATACACAGAAGACATGGAGCTTGATGATGCCATCCATACTGCCATTTTGACTCTGAAAGAAGGgtatgt-cttgtaggtgcttctgtttctatttccggaacatccttact-gagttactgactgattcgggggttgcag-----------------------

upper sequence: AT1G16470.1 (Arabidopsis thaliana), 5'ss of exon 10
lower sequence: GRMZM5G850355_T02 (Zea mays), 5'ss of exon 10
GTACACAGAAGACATGGAACTTGACGATGCCATTCACACAGCGATACTGACATTGAAAGAAGGgtaagtacaaatctacattattattagaaagtagttcgcctgataatcagagttcacttcatattcatagatcacactctcagtgtgactgatagattac
 |||||||| || ||||||||||| |||||||| ||||| || ||  |||| ||||||||||||||  |   || | || || |  ||    |||      | |  |||  ||     | ||  | |    |  |   |||  |||                 
ATACACAGAGGATATGGAACTTGATGATGCCATCCACACTGCAATTTTGACTTTGAAAGAAGGgta--ttgcaacccac-ttgtagttgcttagtttaaaacatcctaaatagttactaattggt-tctgcatcttggacttgcag-----------------

upper sequence: AT1G16470.1 (Arabidopsis thaliana), 5'ss of exon 10
lower sequence: GRMZM5G850355_T04 (Zea mays), 5'ss of exon 9
GTACACAGAAGACATGGAACTTGACGATGCCATTCACACAGCGATACTGACATTGAAAGAAGGgtaagtacaaatctacattattattagaaagtagttcgcctgataatcagagttcacttcatattcatagatcacactctcag-tgtgactgatagattac---
 |||||||| || ||||||||||| |||||||| ||||| || ||  |||| ||||||||||||||  |   || | || || |  ||    |||      | |  |||  ||     | ||  | |    |  |   |||  ||| | |||  |  | ||| |   
ATACACAGAGGATATGGAACTTGATGATGCCATCCACACTGCAATTTTGACTTTGAAAGAAGGgta--ttgcaacccac-ttgtagttgcttagtttaaaacatcctaaatagttactaattggt-tctgcatcttggacttgcagatatgaggggcaaatttcctc

upper sequence: AT1G16470.1 (Arabidopsis thaliana), 5'ss of exon 10
lower sequence: GRMZM5G824831_T03 (Zea mays), 5'ss of exon 10
GTACACAGAAGACATGGAACTTGACGATGCCATTCACACAGCGATACTGACATTGAAAGAAGGgtaa-gtacaaatctacattattattagaaagtagttcgcctgataatcagagttcacttcatattcatagatcacactctcagtgtgactgatagattac
 ||||||||||| ||||| ||||| |||||||| ||||| || ||  |||| ||||||||||||||  |  |  |||    || |  ||    |||  || |    |||  |  | |  | || ||| |  | | ||    |||  |  |  | |         
ATACACAGAAGATATGGAGCTTGATGATGCCATCCACACTGCAATTTTGACTTTGAAAGAAGGgtatcgctcgcatccctgttgtacttgcttagt--ttaga--aatatcctaaat--agttaataat--tggttccggatcttggacttgcag---------

upper sequence: AT1G16470.1 (Arabidopsis thaliana), 5'ss of exon 10
lower sequence: GRMZM2G382240_T01 (Zea mays), 5'ss of exon 11
GTACACAGAAGACATGGAACTTGACGATGCCATTCACACAGCGATACTGACATTGAAAGAAGGgtaagtacaaatctacattattattagaaagtagttcgcctgataatcagagttcacttcatattcatagatcacactctcagtgtgactgatagattac
 |||||||| || ||||| ||||| |||||||| ||||| || ||  |||| ||||||||||||||  |   || | || || |  ||    |||      | |  |||  ||     | ||  | |    |  |   |||  |||                 
ATACACAGAGGATATGGAGCTTGATGATGCCATCCACACTGCAATTTTGACTTTGAAAGAAGGgta--ttgcaacccac-ttgtagttgcttagtttaaaacatcctaaatagttactaattggt-tctgcatcttggacttgcag-----------------

upper sequence: AT1G16470.1 (Arabidopsis thaliana), 5'ss of exon 10
lower sequence: PP1S61_202V6.1 (Physcomitrella patens), 5'ss of exon 9
GTACACAGAAGACATGGAACTTGACGATGCCATTCACACAGCGATACTGACATTGAAAGAAGGgtaagtacaaatctacattattattagaaagtagttcgcctgataatcagagttcacttcatattcatagatcacactct-cagtgtgactgatagattac-------------------------------------------------
||| || || ||||||||||| || || || |||||||||||||| || || ||||| |||||||||||  |    ||  |     ||   | || |     ||| | |   |  ||||     |  ||   ||||| | | | || | |||  | |||||  |                                                 
GTATACCGATGACATGGAACTCGAAGACGCTATTCACACAGCGATTCTTACCTTGAAGGAAGGgtaagtttagcgttatgtc----ttgagaggtggaaatactggtcacatgctttcaacatgtgctc---gatcatatttttcaatctga--gctagatccctaccacatgtactggtcagtttcgaatatctaacagttggacatgacag

upper sequence: AT1G16470.1 (Arabidopsis thaliana), 5'ss of exon 10
lower sequence: PP1S2_595V6.1 (Physcomitrella patens), 5'ss of exon 9
GTACACAGAAGACATGGAACTTGACGATGCCATTCACACAGCGATACTGACATTGAAAGAAGGgtaagtacaaatctacattattattagaaagtagttcgcctgataatcagagttcacttcatattcatagatcacactctcagtgtgactgata--gattac------------------------------
|||  | || ||||||||||| || ||||| |||||||| ||||| ||||| ||||| ||||||||||| |  || | ||      ||  |  |  | |  | || |   |   ||  | |  ||  |   | || |   ||| ||| ||| |  |   | | |                               
GTATTCTGATGACATGGAACTCGAAGATGCTATTCACACTGCGATTCTGACCTTGAAGGAAGGgtaagt-cgtatgttcagag--gttgaattgctgattacatg-tctccgacgtatattctatcatggaaaataa--ttctgagtttgatttgtgcgggtcaatttcaaatttctaacacttacacgtgacag

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|86075658|gb|DR371415.1|DR371415
EST:     ATGGAACTTGACGATGCCATTCACACAGCGATACTGACATTGAAAGAAGG                         CTTTGAGGGAGAGATCTCAAGCAAAAATATTGAAATTGGCAAAATCGGTGC
genomic: ATGGAACTTGACGATGCCATTCACACAGCGATACTGACATTGAAAGAAGGgtaagtacaa ... tttgtgatagCTTTGAGGGAGAGATCTCAAGCAAAAATATTGAAATTGGCAAAATCGGTGC
EST: gi|125142131|gb|EL179632.1|EL179632
EST:     ATGGAACTTGACGATGCCATTCACACAGCGATACTGACATTGAAAGAAGG                         CTTTGAGGGAGAGATCTCAAG
genomic: ATGGAACTTGACGATGCCATTCACACAGCGATACTGACATTGAAAGAAGGgtaagtacaa ... tttgtgatagCTTTGAGGGAGAGATCTCAAG
EST: gi|86082335|gb|DR378094.1|DR378094
EST:     ATGGAACTTGACGATGCCATTCACACAGCGATACTGACATTGAAAGAAGG                         CTTTGAGGGAGAGATCTCAAGCAAAAATATTGAAATTGGCAAAATCGGTGC
genomic: ATGGAACTTGACGATGCCATTCACACAGCGATACTGACATTGAAAGAAGGgtaagtacaa ... tttgtgatagCTTTGAGGGAGAGATCTCAAGCAAAAATATTGAAATTGGCAAAATCGGTGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTACACAGAAGACATGGAACTTGACGATGCCATTCACACAGCGATACTGACATTGAAAGAAGGgtaagtacaaatctacattattattagaaagtagttcgcctgataatcagagttcacttcatattcatagatcacactctcagtgtgactgatagattac

- - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG