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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaatttctctcctatttttgctttagacttgttattacaacttcaaattgttggaagttagaaataatcctgtgactaacgggtacagATCAGAGAGGGGCTACACTACAATCCTTATTTCCCTGGTGGAGCAATCGCTATGCCAAAAATGCTCAACGATGAAGCTGTGGAATATGAAGATGGAACTC

Basic information

species Arabidopsis thaliana
transcript AT5G40810.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G40810.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os05g23620.1 (Oryza sativa), 3'ss of exon 6
-gtaaatttct--ctcctattttt------gctttagacttgttattacaacttcaaattgttggaagttagaaataatcctgtgactaacgggtac---agATCAGAGAGGGGCTACACTACAATCCTTATTTCCCTGGTGGAGCAATCGCTATGCCAAAAATGCTCAACGATGAAGCTGTGGAATATGAAGATGGAACTC
  ||  |||||  ||   ||||||      | ||  |   |||||||     |    | |||   |  |||| ||  |  || ||  | |   |||    ||||| | |||||  | || |||||||| || ||||||||||| || || |||||||| || ||||| |  |||| |||||| |||||||||||||| ||||
gttatttttctagctgtaatttttcaagctggttgtgttctgttatttgctttctgcagtgtgcaacattagtaa--actctctggttgatttgtattctagATCCGTGAGGGTTTGCATTACAATCCCTACTTCCCTGGTGGTGCCATAGCTATGCCCAAGATGCTTATAGATGGAGCTGTTGAATATGAAGATGGTACTC

upper sequence: AT5G40810.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G032367_T01 (Zea mays), 3'ss of exon 5
------gtaaatt-tctctcctatt-tttgctttagacttgttattacaacttcaaattgttggaagtta-gaaataatcctgtgactaacgggtac---agATCAGAGAGGGGCTACACTACAATCCTTATTTCCCTGGTGGAGCAATCGCTATGCCAAAAATGCTCAACGATGAAGCTGTGGAATATGAAGATGGAACTC
       |  ||| ||| || || | ||| | ||    ||||  || |  ||| |   | ||  |||| | || | ||  |  ||  | |   |||    ||||  | ||||| || |||||||| || || ||||||||||| || || || ||||| || |||||||| |||| |||||| || ||||| ||||| ||||
ttaaggatgtattatctttcatactcttttccttttttttgtgtttgc--ctttactatcttacaagtaacgataaaaaacattggttgatctgtatcctagATTCGTGAGGGTCTGCACTACAACCCCTACTTCCCTGGTGGTGCCATAGCCATGCCCAAGATGCTCAATGATGGAGCTGTTGAGTATGAGGATGGTACTC

upper sequence: AT5G40810.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G158479_T04 (Zea mays), 3'ss of exon 5
----gtaaatttctctcctatttttgctttagactt-gttattacaacttcaaattgttggaagttaga--aataatcctgtgactaacgggtac---agATCAGAGAGGGGCTACACTACAATCCTTATTTCCCTGGTGGAGCAATCGCTATGCCAAAAATGCTCAACGATGAAGCTGTGGAATATGAAGATGGAACTC
       ||  || |     |||    | | | ||| |  |  |   ||     |   | | | | | |  |  ||  || ||  | |   | |    ||||  | ||||| || ||||||||||| || ||||||||||| || || || ||||| || ||||| || |||| |||||| || ||||| ||||| || |
gcataccaaggtcaccttggtttgccttgtcgcctttgaaaccatggctcttgttatctcgtaatcaaaccataaaaactttggtttatttgcatcctagATTCGTGAGGGTCTGCACTACAATCCCTACTTCCCTGGTGGTGCCATAGCCATGCCGAAGATGCTTAATGATGGAGCTGTTGAGTATGAGGATGGTACAC

upper sequence: AT5G40810.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA16G06700.2 (Glycine max), 3'ss of exon 5
-------gtaaatttctctcctatttttgctttagacttgttattacaacttcaaattgttggaagttagaaataatcctgtgactaacg----ggtacagATCAGAGAGGGGCTACACTACAATCCTTATTTCCCTGGTGGAGCAATCGCTATGCCAAAAATGCTCAACGATGAAGCTGTGGAATATGAAGATGGAACTC
          | ||  | |   |||||  |  || ||  | | |    |  |    || ||  |  ||      |   || ||   ||        |  |||| |||||||| || || || |||||||| || |||||||||||||| || ||||| |||||||| || ||||  |||||||||||||||||||| ||||
atttagtactagttcatatatcattttgtccctatacc-gatgtactgatattgtgttcttaaacctttttttcatggctatgttcaaaataataatgtagATAAGAGAGGGACTTCATTATAATCCTTACTTTCCTGGTGGAGCAATTGCCATGCCTAAAATGCTTAATGATGGTGCTGTGGAATATGAAGATGGTACTC

upper sequence: AT5G40810.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA19G24620.2 (Glycine max), 3'ss of exon 5
--------gtaaatttctctcctatttttgctttagacttgttattacaacttcaaattgttggaagt-tagaaataatcctgtgactaacg--ggtacagATCAGAGAGGGGCTACACTACAATCCTTATTTCCCTGGTGGAGCAATCGCTATGCCAAAAATGCTCAACGATGAAGCTGTGGAATATGAAGATGGAACTC
           | ||  | |   |||||  |  || ||  | | |    |  |    || ||  |  | |    || |   |||    ||      |  |||| |||||||| || || || |||||||| || |||||||||||||| || ||||| |||||||| || ||||  |||||||||||||||||||| || |
tatatggtactagttcatatatcattttgtccctatacc-gatgtactgatattgtgttcttaaacttcttttcatgactatgttcaaaataataatgtagATAAGAGAGGGACTTCATTATAATCCTTACTTTCCTGGTGGAGCAATTGCCATGCCTAAAATGCTTAATGATGGTGCTGTGGAATATGAAGATGGTACCC

upper sequence: AT5G40810.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA19G22530.2 (Glycine max), 3'ss of exon 5
--------gtaaatttctctcctatttttgctttagacttgttattacaacttcaaattg--ttggaagttagaaataatcctgtgactaacgggtacagATCAGAGAGGGGCTACACTACAATCCTTATTTCCCTGGTGGAGCAATCGCTATGCCAAAAATGCTCAACGATGAAGCTGTGGAATATGAAGATGGAACTC
         || | ||        || |   | |  ||   |    | |  ||  | ||    || || ||   | |  |  | |    ||    |  |||| ||||| || || ||||| ||||||||||| |||||||| || || |||||||| |||||||| || ||||  ||||| |||||||||||||| || |
gaacttaattatactttctcaactttctaattctcaacaaatctaaatatattgcacttaaagtgaaaatttcgattgtttttttttaaaaaaaatgtagATTAGAGAAGGACTGCACTATAATCCTTATTTTCCTGGTGGGGCTATTGCTATGCCTAAAATGCTTAATGATGGCGCTGTTGAATATGAAGATGGTACCC

upper sequence: AT5G40810.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA05G07020.1 (Glycine max), 3'ss of exon 5
-------gtaaatttctctcctatttttgctttagacttgttattacaacttcaaatt---gttggaagttagaa-ataatcctgtgactaacgggtacagATCAGAGAGGGGCTACACTACAATCCTTATTTCCCTGGTGGAGCAATCGCTATGCCAAAAATGCTCAACGATGAAGCTGTGGAATATGAAGATGGAACTC
        || | ||        || | | | |  ||   |    | |  ||  | ||   ||   || || ||  ||  | || | | |||    |  |||| ||||| || || ||||| ||||||||||| ||||| || || || |||||||| |||||||| || ||||  ||||| |||||||||||||| || |
aacttaattatactttctcaactttctagttctcaacaaatctaaatatattgcacttaaagtgaaaattttgattatggttctctaaataataa-tgtagATTAGAGAAGGACTGCACTATAATCCTTATTTTCCTGGCGGGGCTATTGCTATGCCTAAAATGCTTAATGATGGTGCTGTTGAATATGAAGATGGTACCC

upper sequence: AT5G40810.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv09s0002g05950.t01 (Vitis vinifera), 3'ss of exon 4
------gtaaatttctctcctatttttgctttagac--ttgttattacaacttcaaattgttggaagttagaaa-taatcctgt-gactaacgggtacagATCAGAGAGGGGCTACACTACAATCCTTATTTCCCTGGTGGAGCAATCGCTATGCCAAAAATGCTCAACGATGAAGCTGTGGAATATGAAGATGGAACTC
       | |  ||  ||    ||||  | | |     ||| | || |  | |    ||  || | |||  |   | ||    | ||        |  ||||  |||| ||||| ||||| |||||||||||||||||||| ||||| |||||||| |||||||||| |||||  ||||| || ||||||||||| || |
ccgataatcatcttgacttgggttttgtcatcatttgattgctctttctgcattcttttaatgaatgttccatcctgatgtcattgaactctttctgtagATTCGAGACGGGCTGCACTATAATCCTTATTTCCCTGGTGGGGCAATAGCTATGCCCAAAATGCTCATCGATGGTGCTGTTGAGTATGAAGATGGTACCC

upper sequence: AT5G40810.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv14s0171g00330.t01 (Vitis vinifera), 3'ss of exon 5
--gtaaatttctctcctatttt-tgctt-tagacttgttattacaacttcaaattgttggaagttagaaataatcctgtgactaacgggtac------agATCAGAGAGGGGCTACACTACAATCCTTATTTCCCTGGTGGAGCAATCGCTATGCCAAAAATGCTCAACGATGAAGCTGTGGAATATGAAGATGGAACTC
   | | ||| | |  | |||| || || | ||| | || |    |     |  | ||         ||  ||||  ||   | ||   ||       ||||| |||| ||| | |||||||||||||| |||||||| || ||||| |||||||| ||||||||||  ||||  ||  | || ||||||||||| || |
tgctgatttttttttattttttatgtttatggacatattctgttcatgatgacctattcctctacctaatcaatcaagttgttcacaaatatttttgtagATCCGAGAAGGGTTGCACTACAATCCTTACTTCCCTGGGGGTGCAATTGCTATGCCTAAAATGCTCATTGATGGTGCACTTGAGTATGAAGATGGTACGC

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|116466135|gb|EG508727.1|EG508727
EST:     ATGTCTTTGCTCTGTTGACTGGTTATCGTGATCCTCCTGCTGGAATTTCG                         ATCAGAGAGGGGCTACACTACAATCCTTATTTCCCTGGTGGAGCAATCGCT
genomic: ATGTCTTTGCTCTGTTGACTGGTTATCGTGATCCTCCTGCTGGAATTTCGgtaaatttct ... acgggtacagATCAGAGAGGGGCTACACTACAATCCTTATTTCCCTGGTGGAGCAATCGCT
EST: gi|125007689|gb|EL079958.1|EL079958
EST:     CGTGAT-CTCCTGCTGGAATTTCG                         T
genomic: CGTGATCCTCCTGCTGGAATTTCGgtaaatttct ... acgggtacag-
EST: gi|125007689|gb|EL079958.1|EL079958
EST:     CGTGAT-CTCCTGCTGGAATTTCG                         T
genomic: CGTGATCCTCCTGCTGGAATTTCGgtaaatttct ... acgggtacag-
EST: gi|86078839|gb|DR374596.1|DR374596
EST:     ATGTCTTTGCTCTGTTGACTGGTTATCGTGATCCTCCTGCTGGAATTTCA                         ATCAGAGAGGGGCTACACTACAATCCTTATTTCCCTGGTGGAGCAATCGCT
genomic: ATGTCTTTGCTCTGTTGACTGGTTATCGTGATCCTCCTGCTGGAATTTCGgtaaatttct ... acgggtacagATCAGAGAGGGGCTACACTACAATCCTTATTTCCCTGGTGGAGCAATCGCT
EST: gi|86083864|gb|DR379623.1|DR379623
EST:     GTCCTTTGCTCTGTTGACTGGTTATCGGTGATCCTCCTGCTGGAATTTCA                         ATCAGAGAGGGGCTACACTACAATCCTTATTTCCCTGGTGGAGCAAATCGC
genomic: GT-CTTTGCTCTGTTGACTGGTTATC-GTGATCCTCCTGCTGGAATTTCGgtaaatttct ... acgggtacagATCAGAGAGGGGCTACACTACAATCCTTATTTCCCTGGTGGAGC-AATCGC
EST: gi|86080213|gb|DR375970.1|DR375970
EST:     ATGTCTTTGCTCTGTTGACTGGTTATCGTGATCCTCCTGCTGGAATTTCA                         ATCAGAGAGGGGCTACACTACAATCCTTATTTCCCTGGTGGAGCAATCGCT
genomic: ATGTCTTTGCTCTGTTGACTGGTTATCGTGATCCTCCTGCTGGAATTTCGgtaaatttct ... acgggtacagATCAGAGAGGGGCTACACTACAATCCTTATTTCCCTGGTGGAGCAATCGCT
EST: gi|124989417|gb|EL061736.1|EL061736
EST:     GTTGACTGGTTATCGTGATCCTCCTGCTTTGGAATTTCG                         ATCAGAGAGGGGCTACACTACAATCCTTATTTCCCTGGTGGAGCAATCGCT
genomic: GTTGACTGGTTATCGTGATCCTCCTGC--TGGAATTTCGgtaaatttct ... acgggtacagATCAGAGAGGGGCTACACTACAATCCTTATTTCCCTGGTGGAGCAATCGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attacaacttcaaattgttggaagttagaaataatcctgtgactaacgggtacagATCAGAGAGGGGCTACACTACAATCCTTATTTCCCTGGTGGAGCAATCGCTATGCCAAAAATGCTCAACGATGAAGCTGTGGAATATGAAGATGGAACTC
                                        gactaac  putative branch site (score: 1)
                     aagttagaaataat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaatttctctcctatttttgctttagacttgttattacaacttcaaattgttggaagttagaaataatcctgtgactaacgggtacagATCAGAGAGGGGCTACACTACAATCCTTATTTCCCTGGTGGAGCAATCGCTATGCCAAAAATGCTCAACGATGAAGCTGTGGAATATGAAGATGGAACTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA