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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtttgggttttgttctacccttgtaatttatatgaatgatatgaagatgtcttggatttctcattgtttttattattcttcattagCTGGAAAGTCCTCAGTTTTGATTGATATCAAACCGTGGGATGATGAGACTGACATGAAGAAGCTTGAGGAAGCTGTGAAGTCCATTCAGATGGAAGGTTT

Basic information

species Arabidopsis thaliana
transcript AT1G30230.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G30230.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os07g42300.2 (Oryza sativa), 3'ss of exon 5
-----------------------------------------------gtaagtttgggttttgttctaccct----------tgtaatttata--tgaatgat--------atgaagatgtcttggatttctcattgttttt--attattcttcatt-agCTGGAAAGTCCTCAGTTTTGATTGATATCAAACCGTGGGATGATGAGACTGACATGAAGAAGCTTGAGGAAGCTGTGAAGTCCATTCAGATGGAAGGTTT
                                                 || | |   |||| || ||  ||          ||||| |||      ||| ||        || |  |||    |   | ||  |   || |  |    | || ||| |||||| ||||||||||| ||| ||||| ||||||| ||||| ||||||||||||||||  ||  | || |||||||||| |    || ||||||||||  |
gtatgccatcctgcattatactataccatttttatgcaatgaataatacaattattcattttattttattctcatctgtagctgtaaattaagaccaaatcatcactattcattataatgcaaagtgctacttctaacttgtcaacacctttttattcagCTGGGAAGTCCTCAGTGTTGCTTGATGTCAAACCATGGGACGATGAGACTGACATGACCAAATTGGAAGAAGCTGTGAGGAATGTTAAGATGGAAGGCCT

upper sequence: AT1G30230.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G031545_T03 (Zea mays), 3'ss of exon 5
------------------------------------------------------------------------------gtaagtttgggtt-ttgttctacccttgtaatttatatgaatgatatgaagatgtcttggatttc-tcattgtttttattattcttcattagCTGGAAAGTCCTCAGTTTTGATTGATATCAAACCGTGGGATGATGAGACTGACATGAAGAAGCTTGAGGAAGCTGTGAAGTCCATTCAGATGGAAGGTTT
                                                                                |   ||||     | |       ||  ||  | | |   ||||||  | |    |  |||||| ||| | || ||   || | |  | |||||| ||||| ||||||||  ||||| | || || ||||| |||||||||||||||   ||||| ||||||||||| | |    | |||||||||||  |
gtatgtcagtgtgcatattttttctgtttcattctctcatcacactgtgttgacatgtgctgacactaatctataatgacacccttggaccactatatcgttttttgaagctctgtt--tgatatccaaaaacttgtgatttcatcaatcttctttccatacattgtcagCTGGGAAGTCATCAGTTTTACTTGATGTGAAGCCATGGGACGATGAGACTGACATGGCCAAGCTCGAGGAAGCTGTTAGGAGTGTCCAGATGGAAGGGCT

upper sequence: AT1G30230.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA09G07350.1 (Glycine max), 3'ss of exon 4
-------------------------------------------------------------------------------------------------------gtaagtttgggttttgttctacccttgtaat--ttatatgaatgatatgaagatgtcttggatttctcattgtttttattattcttcattagCTGGAAAGTCCTCAGTTTTGATTGATATCAAACCGTGGGATGATGAGACTGACATGAAGAAGCTTGAGGAAGCTGTGAAGTCCATTCAGATGGAAGGTTT
                                                                                                        |   ||||   ||| | || ||| |    |   ||||   |  |  |   || | | | |||||     || ||  |||     |||  |||||||||||| || ||| || | ||| | ||||| ||||||||||| ||||||||||||||||| |||||||| || |  || ||| |||||||||| ||
gtattttcccaatgataaaatgtggttgattaatttcttgtttccttttcacattatgtgccttaactcatggttggttcatctttgtcatttactcattgtattgtctttgaactttatactgcccctcccctgactatacataccactttgtgagggcattgattttgtgctgattccatt----ctcaacagCTGGAAAGTCATCTGTTATGTTGGATGTGAAACCTTGGGATGATGAAACTGACATGAAGAAGCTCGAGGAAGCAGTAAGATCTATTGAGATGGAAGGGTT

upper sequence: AT1G30230.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA04G37120.2 (Glycine max), 3'ss of exon 5
-----------------------gtaagtttgggttttgttctacccttgtaatttatatgaatgatatgaagatgtcttggatttctcattgtttttattattcttcattagCTGGAAAGTCCTCAGTTTTGATTGATATCAAACCGTGGGATGATGAGACTGACATGAAGAAGCTTGAGGAAGCTGTGAAGTCCATTCAGATGGAAGGTTT
                        ||  ||||   ||| | ||||||   |  |  || |  |  |  |   |||| | | |||||     || ||        | |  | |||||| || || || ||| || | ||| | ||||| ||||||||||| |||||||||||||||||||| ||| | ||||  ||  ||||||||||||| ||
gtgagtttctttcttgtcactagttatctttgaactttatcctaccccc-tcctccat-tataccactttgtgatggcattgattttctgctgattc-------ccttttcagCTGGGAAATCATCTGTTCTGTTGGATGTAAAACCATGGGATGATGAAACTGACATGAAGAAGCTTGAAGAATCAGTGAGATCTGTTCAGATGGAAGGGTT

upper sequence: AT1G30230.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA06G17930.4 (Glycine max), 3'ss of exon 5
gtaagtttgggttttgtt-----ctacccttgtaatttatatgaa----tgatatgaagatgtcttggatttctcattg--tttttatta--ttcttcattagCTGGAAAGTCCTCAGTTTTGATTGATATCAAACCGTGGGATGATGAGACTGACATGAAGAAGCTTGAGGAAGCTGTGAAGTCCATTCAGATGGAAGGTTT
||||||||   | ||||       || | ||| | |||||         |  |    | |   ||| |   |  |||||  | | | ||   | | |  | |||||| || || || ||| || | ||| | ||||| ||||| ||||| ||||||||||||||||| || ||||| ||||  ||  ||||||||||||| ||
gtaagtttctttcttgtcactaattatctttgaactttatcctgtgctcttctccatataccactttgcaatggcattgattctctgttgattcccttttcagCTGGGAAATCATCTGTTCTGTTGGATGTGAAACCATGGGACGATGAAACTGACATGAAGAAGCTCGAAGAAGCAGTGAGATCTGTTCAGATGGAAGGGTT

upper sequence: AT1G30230.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv17s0000g01540.t01 (Vitis vinifera), 3'ss of exon 5
gtaagtttgg-gttttgttctacccttgtaatttatatgaatgatatgaagatgtc-----ttggatttctc---attgtttttat-tattcttcattagCTGGAAAGTCCTCAGTTTTGATTGATATCAAACCGTGGGATGATGAGACTGACATGAAGAAGCTTGAGGAAGCTGTGAAGTCCATTCAGATGGAAGGTTT
 | | |  |  ||      |||   || |  |  |||||  |  | |     | ||     || |  |  ||   ||| | ||| | | ||  |  | |||||| ||||| ||||||||| | ||| | ||||| ||||||||||||||||||||||| |||||||||||||| ||      |||| | |||||||| ||
attattgagatgtacctgcctatatttcttttaaatatgggtcctctcctactttccctttttagcataatctgaattttatttgtgtgtttattctcagCTGGCAAGTCTTCAGTTTTGTTGGATGTGAAACCATGGGATGATGAGACTGACATGAAAAAGCTTGAGGAAGCAGTACGTAGCATTAAAATGGAAGGGTT

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|164075239|gb|ES036585.1|ES036585
EST:     GTCAAGGCATCTACAAAGAAGAAGGAAT                         CTGGAAAGTCCTCAGTTTTGATTGATATCAAACCGTGGGATGATGAGACTG
genomic: GTCAAGGCATCTACAAAGAAGAAGGAATgtaagtttgg ... tcttcattagCTGGAAAGTCCTCAGTTTTGATTGATATCAAACCGTGGGATGATGAGACTG
EST: gi|124825612|gb|EH910478.1|EH910478
EST:     AGAGCAGCTTCTGTCAAGGCATCTACAAAGAAGAAGGAAT                         CTGGAAAGTCCTCAGTTTTGATTGATAT
genomic: AGAGCAGCTTCTGTCAAGGCATCTACAAAGAAGAAGGAATgtaagtttgg ... tcttcattagCTGGAAAGTCCTCAGTTTTGATTGATAT
EST: gi|116453709|gb|EG496301.1|EG496301
EST:     TGCTGAAGAGAGAGCAGCTTCTGTCAAGGCATCTACAAAGAAGAAGGAAT                         CTGGAAAGTCCTCAGTTTTGATTGATATCAAACCGTGGGATGATGAGACTG
genomic: TGCTGAAGAGAGAGCAGCTTCTGTCAAGGCATCTACAAAGAAGAAGGAATgtaagtttgg ... tcttcattagCTGGAAAGTCCTCAGTTTTGATTGATATCAAACCGTGGGATGATGAGACTG
EST: gi|47831915|gb|CK121599.1|CK121599
EST:     TGCTGAAGAGAGAGCAGCTTCTGTCAAGGCATCTACAAAGAAGAAGGAAT                         CTGGAAAGTCCTCAGTTTTGATTGATATCAAACCGTGGGATGATGAGACTG
genomic: TGCTGAAGAGAGAGCAGCTTCTGTCAAGGCATCTACAAAGAAGAAGGAATgtaagtttgg ... tcttcattagCTGGAAAGTCCTCAGTTTTGATTGATATCAAACCGTGGGATGATGAGACTG
EST: gi|164221737|gb|ES048529.1|ES048529
EST:     CAAGGCATCTACAAAGAAGAAGGAAT                         CTGGAAAGTCCTCAGTTTTGATTGATATCAAACCGTGGGATGATGAGACTG
genomic: CAAGGCATCTACAAAGAAGAAGGAATgtaagtttgg ... tcttcattagCTGGAAAGTCCTCAGTTTTGATTGATATCAAACCGTGGGATGATGAGACTG
EST: gi|164075517|gb|ES165380.1|ES165380
EST:     TGCTGAAGAGAGAGCAGCTTCTGTCAAGGCATCTACAAAGAATAAGGAAT                         CTGGAAAGTCC
genomic: TGCTGAAGAGAGAGCAGCTTCTGTCAAGGCATCTACAAAGAAGAAGGAATgtaagtttgg ... tcttcattagCTGGAAAGTCC
EST: gi|125125799|gb|EL171234.1|EL171234
EST:     AGAGCAGCTTCTGTCAAGGCATCTACAAAGAAGAAGGAAT                         CTGGAAAGTCCTCAGTTTTGATTGATATCAAACCGTGGGATGA
genomic: AGAGCAGCTTCTGTCAAGGCATCTACAAAGAAGAAGGAATgtaagtttgg ... tcttcattagCTGGAAAGTCCTCAGTTTTGATTGATATCAAACCGTGGGATGA
EST: gi|116453708|gb|EG496300.1|EG496300
EST:     TGCTGAAGAGAGAGCAGCTTCTGTCAAGGCATCTACAAAGAAGAAGGAAT                         CTGGAAAGTCCTCAGTTTTGATTGATATCAAACCGTGGGATGATGAGACTG
genomic: TGCTGAAGAGAGAGCAGCTTCTGTCAAGGCATCTACAAAGAAGAAGGAATgtaagtttgg ... tcttcattagCTGGAAAGTCCTCAGTTTTGATTGATATCAAACCGTGGGATGATGAGACTG
EST: gi|86085521|gb|DR381280.1|DR381280
EST:     TGCTGAAGAGAGAGCAGCTTCTGTCAAGGCATCTACAAAGAAGAAGGAAT                         CTGGAAAGTCCTCAGTTTTGATTGATATCAAMCCGTGGGATGATGAGACTG
genomic: TGCTGAAGAGAGAGCAGCTTCTGTCAAGGCATCTACAAAGAAGAAGGAATgtaagtttgg ... tcttcattagCTGGAAAGTCCTCAGTTTTGATTGATATCAAACCGTGGGATGATGAGACTG
EST: gi|125119250|gb|EL167563.1|EL167563
EST:     TGCTGAAGAGAGAGCAGCTTCTGTCAAGGCATCTACAAAGAAGAAGGAAT                         CTGGAAAGTCCTCAGTTTTGATTGATATCAAACCGTGGGA
genomic: TGCTGAAGAGAGAGCAGCTTCTGTCAAGGCATCTACAAAGAAGAAGGAATgtaagtttgg ... tcttcattagCTGGAAAGTCCTCAGTTTTGATTGATATCAAACCGTGGGA
EST: gi|125120930|gb|EL168394.1|EL168394
EST:     GCTGAAGAGAGAGCAGCTTCTGTCAAGGCATCTAACAAAGAAGAAGGAAT                         CTGGAAAGTCCTCAGTT
genomic: GCTGAAGAGAGAGCAGCTTCTGTCAAGGCATCTA-CAAAGAAGAAGGAATgtaagtttgg ... tcttcattagCTGGAAAGTCCTCAGTT
EST: gi|164132777|gb|ES030810.1|ES030810
EST:     CTGTCAAGGCATCTACAAAGAAGAAGGAAT                         CTGGAAAGTCCTCAGTTTTGATTGATATCAAACCGTGGGATGATGAGACTG
genomic: CTGTCAAGGCATCTACAAAGAAGAAGGAATgtaagtttgg ... tcttcattagCTGGAAAGTCCTCAGTTTTGATTGATATCAAACCGTGGGATGATGAGACTG
EST: gi|152037744|gb|BP796307.2|BP796307
EST:     TGCTGAAGAGAGAGCAGCTTCTGTCAAGGCATCTACAAAGAAGAAGGAAT                         CTGGAAAGTCCTCAGTTTTGATTGATATCAAACCGTGGGATGATGAGACTG
genomic: TGCTGAAGAGAGAGCAGCTTCTGTCAAGGCATCTACAAAGAAGAAGGAATgtaagtttgg ... tcttcattagCTGGAAAGTCCTCAGTTTTGATTGATATCAAACCGTGGGATGATGAGACTG
EST: gi|116416034|gb|EG458626.1|EG458626
EST:     TGCTGAAGAGAGAGCAGCTTCTGTCAAGGCATCTACAAAGAAGAAGGAAT                         CTGGAAAGTCCTCAGTTTTGATTGATATCAAACCGTGGGATGATGAGACTG
genomic: TGCTGAAGAGAGAGCAGCTTCTGTCAAGGCATCTACAAAGAAGAAGGAATgtaagtttgg ... tcttcattagCTGGAAAGTCCTCAGTTTTGATTGATATCAAACCGTGGGATGATGAGACTG
EST: gi|152037721|gb|BP796075.2|BP796075
EST:     TGCTGAAGAGAGAGCAGCTTCTGTCAAGGCATCTACAAAGAAGAAGGAAT                         CTGGAAAGTCCTCAGTTTTGATTGATATCAAACCGTGGGATGATGAGACTG
genomic: TGCTGAAGAGAGAGCAGCTTCTGTCAAGGCATCTACAAAGAAGAAGGAATgtaagtttgg ... tcttcattagCTGGAAAGTCCTCAGTTTTGATTGATATCAAACCGTGGGATGATGAGACTG
EST: gi|164040360|gb|ES134265.1|ES134265
EST:     TGCTGAAGAGAGAGCAGCTTCTGTCAAGGCATCTACAAAGAAGAAGGAAT                         CTGGAAAGTCCTCAGTTTTGATTGATATCAAACCGTGGGA
genomic: TGCTGAAGAGAGAGCAGCTTCTGTCAAGGCATCTACAAAGAAGAAGGAATgtaagtttgg ... tcttcattagCTGGAAAGTCCTCAGTTTTGATTGATATCAAACCGTGGGA
EST: gi|124747665|gb|EH837795.1|EH837795
EST:     AGAGAGCAGCTTCTGTCAAGGCATCTACAAAGAAGAAGGAAT                         CTGGAAAGTCCTCAGTTTTGATTGATATCAAACCGTGGGATGAT
genomic: AGAGAGCAGCTTCTGTCAAGGCATCTACAAAGAAGAAGGAATgtaagtttgg ... tcttcattagCTGGAAAGTCCTCAGTTTTGATTGATATCAAACCGTGGGATGAT
EST: gi|125275348|gb|EL289433.1|EL289433
EST:     TCTACAAAGAAGAAGGAAT                         CTGGAAAGTCCTCAGTTTTGATTGATATCAAACCGTGGGATGATGAGACTG
genomic: TCTACAAAGAAGAAGGAATgtaagtttgg ... tcttcattagCTGGAAAGTCCTCAGTTTTGATTGATATCAAACCGTGGGATGATGAGACTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgaatgatatgaagatgtcttggatttctcattgtttttattattcttcattagCTGGAAAGTCCTCAGTTTTGATTGATATCAAACCGTGGGATGATGAGACTGACATGAAGAAGCTTGAGGAAGCTGTGAAGTCCATTCAGATGGAAGGTTT
                                   tttttattattcttc  CT-rich tract
                               attgtttttattattc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtttgggttttgttctacccttgtaatttatatgaatgatatgaagatgtcttggatttctcattgtttttattattcttcattagCTGGAAAGTCCTCAGTTTTGATTGATATCAAACCGTGGGATGATGAGACTGACATGAAGAAGCTTGAGGAAGCTGTGAAGTCCATTCAGATGGAAGGTTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG