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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttaaactattttcataaacctgatctataacccattgataatggttatctgattacttgttgtttgaaagaacagGTATGACGCTCACTCAGGAGGTGAACGTGAGATCCAAAGAACTATGTTGGAACTTCTGAACCAGCTTGATGGATTTGATTCAAGAGGAGATGTTAAGGTC

Basic information

species Arabidopsis thaliana
transcript AT4G29040.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G29040.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os03g18690.1 (Oryza sativa), 3'ss of exon 3
-----------------------------------------------------gtaagttaaactattttcataaacctgatctataacccattgataatggttatctgatta--cttgttgtttgaaagaacagGTATGACGCTCACTCAGGAGGTGAACGTGAGATCCAAAGAACTATGTTGGAACTTCTGAACCAGCTTGATGGATTTGATTCAAGAGGAGATGTTAAGGTC
                                                     ||   |   |  |  ||  |  | ||   |   ||    || ||| ||  ||| |||| |   || || |||      | |||||||| ||||| || || || || ||||| || || ||||| ||||||||  | || || ||||| ||||| ||||||||||| ||||||||||| || 
gtagagtagtgcatacttcaaatgggaagtcttctatatgatgaatgttgtttgtgtatagtaaaagattggtggaacttcccatgaaatagtttata-tgagtat-tgatgaacttttttttttctccttatagGTATGATGCTCATTCGGGTGGAGAGCGTGAAATTCAGAGAACCATGTTGGAGTTGCTTAATCAGCTGGATGGTTTTGATTCAAGGGGAGATGTTAAAGTT

upper sequence: AT4G29040.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G104373_T01 (Zea mays), 3'ss of exon 3
-------------gtaagttaaactattttcataaacctgat-ctataac--ccattgataatggttatctga--ttacttgttgtttgaa--agaacagGTATGACGCTCACTCAGGAGGTGAACGTGAGATCCAAAGAACTATGTTGGAACTTCTGAACCAGCTTGATGGATTTGATTCAAGAGGAGATGTTAAGGTC
                  | | | | || | | |||  || | ||  | |  | | ||| |    | || |||  ||   ||||  | |         |||||||| ||||| || || ||||| |||||||| || ||||| ||||||||  |  | || ||||| ||||| ||||||||||||||||||||||| || 
ggtctttcccttcccggctgagatttttatgaaaaaaatgttgctgaagcttctagtgaaaggattaatatgagttttgctgtttctcgccctgttgtagGTATGATGCTCATTCTGGTGGTGAGCGTGAGATTCAGAGAACCATGTTGGAGTTGTTAAATCAGCTGGATGGTTTTGATTCAAGAGGAGATGTTAAAGTT

upper sequence: AT4G29040.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA13G19280.1 (Glycine max), 3'ss of exon 3
-----------------------------------------------gtaagttaaactattttcataaacctg-----atctataacccattgataatggttatctgattacttgttgtt-tgaaagaacagGTATGACGCTCACTCAGGAGGTGAACGTGAGATCCAAAGAACTATGTTGGAACTTCTGAACCAGCTTGATGGATTTGATTCAAGAGGAGATGTTAAGGTC
                                               | |||    |    ||  || |  ||         ||  |  | ||    |   | ||  | |||||  |   | || |   |||||||||| |||||||||||||| |||||||| || ||||| || ||| | ||  | ||||||||| | ||||| |||||||||||||||||||| || || 
gtaattttaacctccaactttagtattcatgaaggtagggtggggttggaagagtgatgtcttgtatcactctatgagctcttaggattcttttcctacattcatgagcttactaataaatatgtatttacagGTATGATGCTCACTCAGGAGGAGAACGTGAAATTCAAAGGACCATGCTAGAGTTGCTGAACCAGTTAGATGGTTTTGATTCAAGAGGAGATGTGAAAGTG

upper sequence: AT4G29040.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA10G04920.1 (Glycine max), 3'ss of exon 3
---------------------------------------------gtaagttaaactattttcataaacct--gatctat---aacccattgataatggttatctgattacttgttg-tttgaaagaacagGTATGACGCTCACTCAGGAGGTGAACGTGAGATCCAAAGAACTATGTTGGAACTTCTGAACCAGCTTGATGGATTTGATTCAAGAGGAGATGTTAAGGTC
                                             | |||    |    ||  || |  ||  || || |    |  | ||    |   | ||  | ||||  ||   | || |   |||||||||| ||||||||||| || ||||||||||| ||||| || ||||| ||  | ||||||||| | ||||| |||||||| ||||||||||| || || 
gtaattttaacccccaactttagctgtcatgaaggtaccggggatggaagagtgatgccttgtatcactctatgagctcttgggattcttttcctacattcatgagcttaccagtaaatatgtatttacagGTATGATGCTCACTCAGGTGGAGAACGTGAGATTCAAAGGACCATGTTAGAGTTGCTGAACCAGTTAGATGGTTTTGATTCTAGAGGAGATGTAAAAGTG

upper sequence: AT4G29040.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA19G35510.1 (Glycine max), 3'ss of exon 3
----------------------------------------------------------------------------------gtaagttaaactattttcataaacctgatctataacccat-tgataatggttatctgattacttgttgtttgaaag---aacagGTATGACGCTCACTCAGGAGGTGAACGTGAGATCCAAAGAACTATGTTGGAACTTCTGAACCAGCTTGATGGATTTGATTCAAGAGGAGATGTTAAGGTC
                                                                                  |  ||  |  |       | |   ||| |  |  |   || | || |      ||| ||||  |||   ||  | |     ||||||||| || |||||||| || |||||||| || || || |||||||||||  | ||||||||| | ||||| || ||||||||||| |||||||| || 
gtaagttatcgagtatcagcttctggagtcactgttttaagacattttctatcctctttttccggatgtagttttttgttttgggagg-aggcagggggtacaggactggtagaagagtgatatcatgagtcaattcttattatatgtctcttatatgctttgcagGTATGATGCCCACTCAGGTGGAGAACGTGAAATTCAGAGGACTATGTTGGAGTTGCTGAACCAGTTAGATGGTTTCGATTCAAGAGGTGATGTTAAAGTG

upper sequence: AT4G29040.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA03G32800.1 (Glycine max), 3'ss of exon 3
-----------------------------------------------------------------------------gtaagttaaactattttcataaacctgatctataacccattgataatggtta--tctgattacttgttgtttgaaagaa---cagGTATGACGCTCACTCAGGAGGTGAACGTGAGATCCAAAGAACTATGTTGGAACTTCTGAACCAGCTTGATGGATTTGATTCAAGAGGAGATGTTAAGGTC
                                                                             |  ||     |             ||| | ||||      |   |  | | |  ||| | ||  |||   ||  | | |   ||||||||| || ||||| || || |||||||| || || || |||||||||||  | ||||||||| | ||||| ||||||||||||||||| || || || 
gtaagttattgaacatcagctttaggagtcactgtgtcaagacattttctatcttcttttttctgatttttttttccgggagg-gggcaggggatgcgggactggt-tatagagtgatatcatggatcaattcttagtatatgtctcttttatgcattgcagGTATGATGCCCACTCTGGTGGAGAACGTGAAATTCAGAGGACTATGTTGGAGTTGCTGAACCAGTTAGATGGTTTTGATTCAAGAGGAGACGTAAAAGTT

upper sequence: AT4G29040.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA11G27200.1 (Glycine max), 3'ss of exon 3
--------------------------------------------------------------------------------gtaagttaaactattttcataaacctgatctataacccat-tgataatggttatctgattacttgttgtttgaaaga---acagGTATGACGCTCACTCAGGAGGTGAACGTGAGATCCAAAGAACTATGTTGGAACTTCTGAACCAGCTTGATGGATTTGATTCAAGAGGAGATGTTAAGGTC
                                                                                 |  |    | ||     | ||  ||  |  |  |   || | || |      ||| ||||  |||   ||  | |     ||||||||| || |||||| | || |||||||| || || || |||||| ||||  | ||||||||| | ||||| || ||||||||||| |||||||| || 
gtaagttatcaagtatcagcttctagagtcactgttttaagacattttctatcctctttttccggatgtagtttttttgttttgggaggagtaggggtacaagactagtagaagagtgatatcatgagtcaattcttattatatgtctcttatatgctttgcagGTATGATGCCCACTCAAGTGGAGAACGTGAAATTCAGAGGACTATGATGGAGTTGCTGAACCAGTTAGATGGTTTCGATTCAAGAGGTGATGTTAAAGTG

upper sequence: AT4G29040.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv07s0005g05160.t01 (Vitis vinifera), 3'ss of exon 3
gtaagttaaactattttcataaacctgatctataacccattgataatggttatctgattacttgttgtttgaaagaacagGTATGACGCTCACTCAGGAGGTGAACGTGAGATCCAAAGAACTATGTTGGAACTTCTGAACCAGCTTGATGGATTTGATTCAAGAGGAGATGTTAAGGTC
|| |||  |   |  ||  | |     |   |||         |  |  || | |  | | |      |        ||||||||| ||||||||||| ||||||||||| ||||| || || ||||||||||| || |||||| | || || ||||||||||| |||||||| || || 
gtgagtcgatgaacattagtgatgaaaaatcatatttttcaagttcttttttttttttaattatcaaatattccttgcagGTATGATGCTCACTCAGGTGGTGAACGTGAAATCCAGAGGACCATGTTGGAACTGCTAAACCAGTTAGACGGTTTTGATTCAAGGGGAGATGTCAAAGTG

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|125030658|gb|EL102927.1|EL102927
EST:     TCACCATCAATCGTCTTCATAGATGAGATTGATGCTGTTGGTACCAAGCG                         GTATGACGCTC
genomic: TCACCATCAATCGTCTTCATAGATGAGATTGATGCTGTTGGTACCAAGCGgtaagttaaa ... gaaagaacagGTATGACGCTC
EST: gi|86082474|gb|DR378233.1|DR378233
EST:     TCATAGATGAGATTGATGCTGTTGGTACCAAGCG                         GTATGACGCTCACTCAGGAGGTGAACGTGAGATCCAAAGAACTATGTTGGA
genomic: TCATAGATGAGATTGATGCTGTTGGTACCAAGCGgtaagttaaa ... gaaagaacagGTATGACGCTCACTCAGGAGGTGAACGTGAGATCCAAAGAACTATGTTGGA
EST: gi|164146034|gb|ES197659.1|ES197659
EST:     GCTGTTGGTACCAAGCG                         GTATGACGCTCACTCAGGAGGTGAACGTGAGATCCAAAGAACTATGTTGGA
genomic: GCTGTTGGTACCAAGCGgtaagttaaa ... gaaagaacagGTATGACGCTCACTCAGGAGGTGAACGTGAGATCCAAAGAACTATGTTGGA
EST: gi|125243947|gb|EL258032.1|EL258032
EST:     TCACCATCAATCGTCTTCATAGATGAGATTGATGCTGTTGGTACCAAGCG                         GTATGACGCTCACTCAGGAGGTG
genomic: TCACCATCAATCGTCTTCATAGATGAGATTGATGCTGTTGGTACCAAGCGgtaagttaaa ... gaaagaacagGTATGACGCTCACTCAGGAGGTG
EST: gi|125063705|gb|EL131590.1|EL131590
EST:     TCACCATCAATCGTCTTCATAGATGAGATTGATGCTGTTGGTACCAAGCG                         GTATGACGCTCAC
genomic: TCACCATCAATCGTCTTCATAGATGAGATTGATGCTGTTGGTACCAAGCGgtaagttaaa ... gaaagaacagGTATGACGCTCAC
EST: gi|125280251|gb|EL294336.1|EL294336
EST:     TCACCATCAATCGTCTTCATAGATGAGATTGATGCTGTTGGTACCAAGCG                         GTATGACGCTCACTCAGGAGGTGAACGTGAGATCCAAA
genomic: TCACCATCAATCGTCTTCATAGATGAGATTGATGCTGTTGGTACCAAGCGgtaagttaaa ... gaaagaacagGTATGACGCTCACTCAGGAGGTGAACGTGAGATCCAAA
EST: gi|125193051|gb|EL208005.1|EL208005
EST:     TCACCATCAATCGTCTTCATAGATGAGATTGATGCTGTTGGTACCAAGCG                         GTATGACGCTCACTCAGGAGGTGAA
genomic: TCACCATCAATCGTCTTCATAGATGAGATTGATGCTGTTGGTACCAAGCGgtaagttaaa ... gaaagaacagGTATGACGCTCACTCAGGAGGTGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgatctataacccattgataatggttatctgattacttgttgtttgaaagaacagGTATGACGCTCACTCAGGAGGTGAACGTGAGATCCAAAGAACTATGTTGGAACTTCTGAACCAGCTTGATGGATTTGATTCAAGAGGAGATGTTAAGGTC
             attgataat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagttaaactattttcataaacctgatctataacccattgataatggttatctgattacttgttgtttgaaagaacagGTATGACGCTCACTCAGGAGGTGAACGTGAGATCCAAAGAACTATGTTGGAACTTCTGAACCAGCTTGATGGATTTGATTCAAGAGGAGATGTTAAGGTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG