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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagttgtttctcttctcccttctgaaaggacgggatgattatagctctatcagctttctaaagctcttggaatttttcagGTAGCAAAGGAGGCATCTGACTTGGTGTTGGCAGATGATAATTTCAGCACCATTGTTGCAGCTGTTGGTGAAGGCAGGTCCATCTATAACAACATGAAGG

Basic information

species Arabidopsis thaliana
transcript AT1G07670.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G07670.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os05g02940.1 (Oryza sativa), 3'ss of exon 1
-------------gtagttgtttctcttctcccttctgaaaggacgggatgattatagc------tctatcagctttctaaagctcttggaatttttcagGTAGCAAAGGAGGCATCTGACTTGGTGTTGGCAGATGATAATTTCAGCACCATTGTTGCAGCTGTTGGTGAAGGCAGGTCCATCTATAACAACATGAAGG
             | | || |   |||| |    ||  ||| |    |||   | |  |      |  ||  |  |   |    | ||    || ||||||| ||||| ||||| |||||| ||||  | || ||||| ||||| || ||||||||||| || ||||||||||| ||||| || || ||||||||||| |
ttagagataacatgaatttataggtcttttattgtcccaaaagtactgatatctgtgacataatttgaattggtatctcacttatttttcttttgttcagGTTGCAAAAGAGGCCTCTGACATGGTTCTTGCTGATGACAATTTTAGTACCATTGTTGCGGCAGTTGGTGAAGGAAGGTCTATTTACAACAACATGAAAG

upper sequence: AT1G07670.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os03g17310.1 (Oryza sativa), 3'ss of exon 5
---------------gtagttgtttctcttctcccttctgaaaggacgggatga-ttatagctctatcagctttctaaagctcttgga--atttt--tcagGTAGCAAAGGAGGCATCTGACTTGGTGTTGGCAGATGATAATTTCAGCACCATTGTTGCAGCTGTTGGTGAAGGCAGGTCCATCTATAACAACATGAAGG
               || |||| | || | ||   |||| |    | |  || |   | |   ||  |  | || |    ||  || |  |||||  | |||| ||||| || || || ||  ||||  | ||||||||||| ||||| || || || ||||||||||||||||| ||||| |||||  |||| |||||||
cagtcctgaaagcatgtggttggtgctgtactta-ttctcagtaaatgtaataaaccagaatcctgacctcgtttttttccttatgtataatttttgttagGTTGCAAAAGAAGCTTCAGATATGGTTCTTGCAGATGATAACTTCAGTACAATAGTCGCAGCTGTTGGTGAAGGGAGGTCAATCTACGACAATATGAAGG

upper sequence: AT1G07670.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G056014_T01 (Zea mays), 3'ss of exon 5
------------------------------------------------------------------------gtagttgtttctcttctcccttctgaaaggacgggatgattatagctctatcagctttctaaagctcttggaatttttcagGTAGCAAAGGAGGCATCTGACTTGGTGTTGGCAGATGATAATTTCAGCACCATTGTTGCAGCTGTTGGTGAAGGCAGGTCCATCTATAACAACATGAAGG
                                                                        ||| |  | ||      |  || | | |    |    | || |   | | | |       ||||||||   ||| |||||||| || || ||||| |||||| |||||||||| || || ||||| |||||||| ||| | || || |||||||| || || ||||| ||||||||||| |
gtaaattcctaccttctttctagttacctggaattcaatgcccacgactgcttttattgaaaggggtgtattgtattgttctccacctgcttttttcataatttgaagcgtttctttttttctaaaac----aaagctct---aatgtttcagGTTGCCAAAGAGGCGTCTGACATGGTGTTGGCTGACGACAATTTTAGCACCATAGTTTCTGCAGTCGGTGAAGGAAGATCGATCTACAACAACATGAAAG

upper sequence: AT1G07670.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G141704_T01 (Zea mays), 3'ss of exon 1
gtagttgtttctcttctcccttctgaaaggacgggatgattatagctctatcagctttctaaagctcttggaatttttcagGTAGCAAAGGAGGCATCTGACTTGGTGTTGGCAGATGATAATTTCAGCACCATTGTTGCAGCTGTTGGTGAAGGCAGGTCCATCTATAACAACATGAAGG
||| | | || |        |  |||          |  |  |||   |  | |    |     || |     | | |||||| || || || || || ||  ||||  | ||||||||||| ||||| || || || ||||| ||||||||||| ||||| || || |||||||||||||
gta-tggcttattgcactattgttgattttttcacgttttgttagaagtgcctgacgccatgtcctatgaacttgtgtcagGTTGCTAAAGAAGCTTCAGATATGGTACTTGCAGATGATAACTTCAGTACTATAGTCGCAGCAGTTGGTGAAGGGAGGTCTATTTACAACAACATGAAGG

upper sequence: AT1G07670.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA03G33240.1 (Glycine max), 3'ss of exon 5
----gtagttgtttctcttctcccttctgaaaggacgggatgat--tatagctctat-----------cagctttctaaagctcttggaattt--ttcagGTAGCAAAGGAGGCATCTGACTTGGTGTTGGCAGATGATAATTTCAGCACCATTGTTGCAGCTGTTGGTGAAGGCAGGTCCATCTATAACAACATGAAGG
     |  ||||  ||  |      |   | |  ||    | ||  | |   | |||           || || | | |   | |   ||| |  |  |||| |||||||| || || ||  |||||||||||||||||||||| ||  | |||||||| ||||||||||| || || || ||||| || || |||||||
actgattattgtaactagttatagattaaagaacactaattaatattgttattttattcttggcaactcatctcttttatcttatgctaatctaatgtagGTGGCAAAGGAAGCTTCAGATATGGTGTTGGCAGATGATAATTTTAGTTCAATTGTTGCTGCTGTTGGTGAGGGTAGATCTATCTACAATAATATGAAGG

upper sequence: AT1G07670.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA19G35960.1 (Glycine max), 3'ss of exon 5
------------gtagttgtttctcttctcccttctgaaaggacgggatgattatagctctatcagct----ttctaaagctcttggaattt---ttcagGTAGCAAAGGAGGCATCTGACTTGGTGTTGGCAGATGATAATTTCAGCACCATTGTTGCAGCTGTTGGTGAAGGCAGGTCCATCTATAACAACATGAAGG
            ||| ||  ||   ||          ||   |     | ||| |   | |  || ||    |  |  | ||  ||  |||    |  |||| |||||||| || || ||  |||||||||||||||||||||| ||  | |||||||| ||||||||||| || || || ||||| || || |||||||
tgactgattattgtaattagttagattaaaggacactaattaatattgttattttgtttttggcaactcatctcttttatcttatgctattccaatgtagGTGGCAAAGGAAGCTTCAGATATGGTGTTGGCAGATGATAATTTTAGTTCAATTGTTGCTGCTGTTGGTGAGGGTAGATCTATCTACAATAATATGAAGG

upper sequence: AT1G07670.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv06s0004g03900.t01 (Vitis vinifera), 3'ss of exon 5
------------gtagttgtttctcttctcccttctgaaaggacgggatgattatagctc------tatcagctttctaaagctcttggaattt--ttcagGTAGCAAAGGAGGCATCTGACTTGGTGTTGGCAGATGATAATTTCAGCACCATTGTTGCAGCTGTTGGTGAAGGCAGGTCCATCTATAACAACATGAAGG
                ||| |    |       |   |||  |     |  |  |||  |      |||| | |||||||  |   ||     |  || |||| |||||||| || |||||| |||| ||||||||||||||||| | ||| || ||||| ||||||||||||||||| ||||| || ||||| |||||||
aatctagtccccaattttggtatgatgaagttattcaaaactatattcttttcttagtccattgtttatc-gttttctaacccctatgtgcactgatttagGTTGCAAAGGAAGCCTCTGACATGGTCTTGGCAGATGATAATTTTAACACAATAGTTGCTGCTGTTGGTGAAGGCAGATCCATTTACAACAATATGAAGG

upper sequence: AT1G07670.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv08s0040g02830.t01 (Vitis vinifera), 3'ss of exon 5
------------------------gtagttgtttctcttctcccttctgaaaggacgggatgattatagctctatcagctttctaaagctcttggaatttttcagGTAGCAAAGGAGGCATCTGACTTGGTGTTGGCAGATGATAATTTCAGCACCATTGTTGCAGCTGTTGGTGAAGGCAGGTCCATCTATAACAACATGAAGG
                          |||||||||| | |||   | | |          || |||||  |  |  |   ||  | | ||  |    |||||||||| || || || || |||||  ||||||||||||| |||||||| || || || ||||| |||||||| |||||  | || ||||| ||||| |||||||
aaattatgttgctttctttacatttgagttgtttctgtcctcatatttaatgtcttactgtgtttatacattaa--aatatttaatatcttct---ctttttcagGTTGCTAAAGAAGCCTCTGATATGGTGTTGGCAGACGATAATTTTAGTACAATAGTTGCTGCTGTTGGGGAAGGGCGATCTATCTACAACAATATGAAGG

upper sequence: AT1G07670.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: PP1S248_28V6.1 (Physcomitrella patens), 3'ss of exon 5
------------------------------------------------------------------------------------------gtagttgtttctcttctcccttctgaaaggacg------ggatgattatagct-ctatcagctttctaaagctc----ttggaat----ttttcagGTAGCAAAGGAGGCATCTGACTTGGTGTTGGCAGATGATAATTTCAGCACCATTGTTGCAGCTGTTGGTGAAGGCAGGTCCATCTATAACAACATGAAGG
                                                                                            || | |    |     | |  ||  || |        |  | |||  ||   |||||  |    | ||  |     ||||  |     ||  |||| || ||||||||| | ||| ||||| | |||||||| ||||| ||||| ||||| ||||| ||||| |||||  | || || || |||||||||||||
gtacatcaataaatacctgcggtggtgcttgcatttttcacttttatgagtcttgttgttctctcaaagtacaagcttccaaagtttctctaagctttgaagcggaggcttcgtggtagaatatatattgcttaatttcagtcactatcccccgaatgaacataatggttgggctgtgacttgtagGTGGCCAAGGAGGCAGCCGACATGGTGCTTGCAGATGACAATTTTAGCACTATTGTGGCAGCCGTTGGAGAAGGTCGTTCTATATACAACAACATGAAGG

upper sequence: AT1G07670.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: PP1S78_99V6.2 (Physcomitrella patens), 3'ss of exon 7
----gtagttgtttctc-------ttctcccttctgaaaggacgggatgattatagctctatcagctt-------tctaaagct-cttggaatttttcagGTAGCAAAGGAGGCATCTGACTTGGTGTTGGCAGATGATAATTTCAGCACCATTGTTGCAGCTGTTGGTGAAGGCAGGTCCATCTATAACAACATGAAGG
     ||   |||||         |  ||     |||     | |  |||||  |  |  |   |          | | ||| | | ||    | | ||||| || ||||||||| | ||| ||||| | |||||||||||||| ||||| ||||| ||||||||||| |||||  | || || || || || |||||||
atttttaaacgtttcagagaaaagtcttcgaggttgagtatgctgagtgatttcactttcacgtgtgcgaaataatttgaagttgcatgatgatatgcagGTGGCGAAGGAGGCAGCAGACATGGTGCTTGCAGATGATAATTTTAGCACGATTGTGGCAGCTGTTGGAGAAGGTCGTTCGATATACAATAATATGAAGG

upper sequence: AT1G07670.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: EFJ35276 (Selaginella moellendorffii), 3'ss of exon 5
gtagttgtttctcttctcccttctgaaaggacgggatgattatagctctatcagctttctaaagctcttggaattttt-cagGTAGCAAAGGAGGCATCTGACTTGGTGTTGGCAGATGATAATTTCAGCACCATTGTTGCAGCTGTTGGTGAAGGCAGGTCCATCTATAACAACATGAAGG
                            | ||   |  || ||      | | | | | |  |     || |||     ||||||||||| || ||  | ||| ||||||||||||| ||||| |||||||| |||||  |||| ||||  |||||  | || ||||| ||||||||||| |
----------------------------gtacaaaaaaatcattatcggaac-gttctatgtactgactgcaatccacacagGTAGCAAAAGAAGCTGCAGACATGGTGTTGGCAGACGATAACTTCAGCACGATTGTATCAGCCGTTGCAGAAGGTCGTTCAATCTACAACAACATGAAAG

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|125194772|gb|EL209726.1|EL209726
EST:     CCCTGAAGTTGGCTGATATTGGTGTGGCTATGGGCATTTCCGGGACAGAG                         GTAGCAAAGGAGGCATCTGACTTGGTGTTGG
genomic: CCCTGAAGTTGGCTGATATTGGTGTGGCTATGGGCATTTCCGGGACAGAGgtagttgttt ... aatttttcagGTAGCAAAGGAGGCATCTGACTTGGTGTTGG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaggacgggatgattatagctctatcagctttctaaagctcttggaatttttcagGTAGCAAAGGAGGCATCTGACTTGGTGTTGGCAGATGATAATTTCAGCACCATTGTTGCAGCTGTTGGTGAAGGCAGGTCCATCTATAACAACATGAAGG
                              ttctaaa  putative branch site (score: 2)
                                               tttttc  putative PPT
         atgattata  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagttgtttctcttctcccttctgaaaggacgggatgattatagctctatcagctttctaaagctcttggaatttttcagGTAGCAAAGGAGGCATCTGACTTGGTGTTGGCAGATGATAATTTCAGCACCATTGTTGCAGCTGTTGGTGAAGGCAGGTCCATCTATAACAACATGAAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT