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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttcgtgtgaatatagatatattctcatatcaccttcatataatcagaatcgttagttactgatctaatatgtttatgcagACAATCAAGACCAATGTGATTGGTACACTCAACATGCTCGGTCTTGCCAAGCGTGTTGGAGCAAG

Basic information

species Arabidopsis thaliana
transcript AT5G59290.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G59290.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA12G06990.1 (Glycine max), 3'ss of exon 5
------------------gtt-cgtgtga-atatagatatattctcatatcaccttcatataatcagaatcgttagttactgatctaatatgtttatgcagACAATCAAGACCAATGTGATTGGTACACTCAACATGCTCGGTCTTGCCAAGCGTGTTGGAGCAAG
                  ||   |||| | || | || |  |     | ||| |||    |    | | |   || |   |     ||||  ||| | |||||||| ||||| ||||||||||||||||| |||||||| || ||||||||||| ||||| |||||
tatatttattctacttctgtcatgtgtcatatcttgaaagttctgtttttcagcttatccttgagacactatctaatatgttgggaaata-atttttacagACAATAAAGACAAATGTGATTGGTACACTGAACATGCTTGGGCTTGCCAAGCGAGTTGGGGCAAG

upper sequence: AT5G59290.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA12G06980.2 (Glycine max), 3'ss of exon 4
---------------gttcgtgtgaat-atagatatattc-tcatatcaccttcatataatcagaatcgttagttactgatctaa--tatgtttatgcagACAATCAAGACCAATGTGATTGGTACACTCAACATGCTCGGTCTTGCCAAGCGTGTTGGAGCAAG
               | | || |  || |   |   |||  |    || |  |  |  | |  ||    |||  ||    |  ||   |    | | |||||||| ||||| ||||||||||| ||||| |||||||| |||||||| |||||||| ||||||||
atgcctagtaattcagattgtatttatgacctactcattagttgattctctctagtgaatttcgagaaattatctaacagttaaagtaaaacctttacagACAATAAAGACAAATGTGATTGGAACACTGAACATGCTTGGTCTTGCTAAGCGTGTGGGAGCAAG

upper sequence: AT5G59290.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA11G15010.1 (Glycine max), 3'ss of exon 5
-----------gttcgtgtgaat-atagatatattctcatatcaccttcatataatcagaatcg-----ttagttactgatctaa--tatgtttatgcagACAATCAAGACCAATGTGATTGGTACACTCAACATGCTCGGTCTTGCCAAGCGTGTTGGAGCAAG
           | | ||||  || |   |   |||     ||   ||  || || | |   |||     |||  ||    |  ||   |    | | |||||||| ||||| ||||||||||| ||||| |||||||| || ||||| |||||||| ||||||||
ccagtaattcagattgtgtttatgacctactcattggtcgattctctctatctagtgaatttcgagaaattatctaacagttaaagtaaaacctttacagACAATAAAGACAAATGTGATTGGAACACTGAACATGCTTGGGCTTGCTAAGCGTGTGGGAGCAAG

upper sequence: AT5G59290.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA13G40960.1 (Glycine max), 3'ss of exon 6
-----------------gttcgtgtgaatatagatatattct-catatcaccttcatataatcagaatcgttagttactgatctaata-tgtttatgcagACAATCAAGACCAATGTGATTGGTACACTCAACATGCTCGGTCTTGCCAAGCGTGTTGGAGCAAG
                 |      |||    |  |    ||| | ||||        | |  |   ||   || ||  | ||  | || |   | | |||||||| ||||| ||||||||||| ||||| |||||||| || ||||| ||||| || ||||||||
tgtctacctcctgtcatgcatcattgatcgaaagttctctctgcttatctgtccttgaaagactatatatctaatttgtaatggagtaattactttacagACAATAAAGACAAATGTGATTGGCACACTGAACATGCTTGGGCTTGCAAAGCGAGTAGGAGCAAG

upper sequence: AT5G59290.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA15G04500.2 (Glycine max), 3'ss of exon 6
-------------gttcgtgtgaatatagatatattctcatatcaccttcatataatc-----agaatcgttagttactgatctaata-tgtttatgcagACAATCAAGACCAATGTGATTGGTACACTCAACATGCTCGGTCTTGCCAAGCGTGTTGGAGCAAG
             | |  ||  | |||   |      | |  |||  || || | | |     ||| |   || ||  | ||  || | |   | | |||||||| ||||| ||||||||||| ||||| |||||||| || || || ||||| || ||||||||
atagttatgtctagctactgctagtatcattggtcaataagttcatgtttatctgaccctgaaagactatctaatttataatgaaacaattactttacagACAATAAAGACAAATGTGATTGGCACACTGAACATGCTTGGGCTCGCTAAGCGAGTAGGAGCAAG

upper sequence: AT5G59290.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA11G15020.1 (Glycine max), 3'ss of exon 5
--gttcgtgtgaatatag--atatattctcatatca----ccttcatataatcagaatcgttagttactgatctaatatgtt------------tatgcagACAATCAAGACCAATGTGATTGGTACACTCAACATGCTCGGTCTTGCCAAGCGTGTTGGAGCAAG
   ||  |   | |   |  || | || |    | |     ||   | | | | ||  | | ||  ||| ||||||||||||            | | |||||||| ||||| ||||||||||| ||||| |||||||| || ||||| || || ||||| |||||
atattaattctacttctgtcatgtgttattgcttgaaagttctgtttttcagctgatccttgagacact-atctaatatgttaggaaaataatttttacagACAATAAAGACAAATGTGATTGGCACACTGAACATGCTTGGGCTTGCAAAACGAGTTGGGGCAAG

upper sequence: AT5G59290.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: PP1S189_118V6.1 (Physcomitrella patens), 3'ss of exon 5
-------------------------gttcgtgtgaatatagatatattctcatatcaccttcatataatcagaatcgttagttactgatctaatatgtttatgcagACAATCAAGACCAATGTGATTGGTACACTCAACATGCTCGGTCTTGCCAAGCGTGTTGGAGCAAG
                         ||| ||  || |  ||| ||||   | | |||  |||| ||       |   || |||  |||   ||  |  || ||||||| |||||||| |||||||||||||| ||||||||||| || || || || || ||||| |||||
tatatatatataagaatccttgagcgtttgta-gagtgaagagatatgtgcgtttcagtttcagattggtttgaaatttggtt--tga---aacttcattttgcagACCATCAAGACAAATGTGATTGGTACGCTCAACATGCTTGGACTCGCTAAACGAGTTGGTGCAAG

upper sequence: AT5G59290.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: EFJ17446 (Selaginella moellendorffii), 3'ss of exon 4
gttcgtgtgaatatagatatattctcatatcaccttcatataatcagaatcgttagttactgatct-aatat--gtttatgcagACAATCAAGACCAATGTGATTGGTACACTCAACATGCTCGGTCTTGCCAAGCGTGTTGGAGCAAG
                                     |  |  | | || |  || |   | |||  |||    | || | ||||| ||||| || |||||||| || ||||| || ||||| || |||||||||||||||||||| ||
-------------------------------gtgagtagctgtttaaaaacactactagttcatcccaatgctggcttttccagACCATCAAAACGAATGTGATGGGCACACTAAATATGCTGGGCCTTGCCAAGCGTGTTGGAGCCAG

upper sequence: AT5G59290.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: EFJ35029 (Selaginella moellendorffii), 3'ss of exon 4
gttcgtgtgaatatagatatattctcatatcaccttcatataatcagaatcgttagttactgatct-aatat--gtttatgcagACAATCAAGACCAATGTGATTGGTACACTCAACATGCTCGGTCTTGCCAAGCGTGTTGGAGCAAG
                                     |  |  | | || |  || |   | |||| |||    | || | ||||| ||||| || |||||||| || ||||| || ||||| || |||||||||||||||||||| ||
-------------------------------gtgagtagctgtttaaaaacactactagttcatctcaatgctggcttttccagACCATCAAAACGAATGTGATGGGCACACTAAATATGCTGGGCCTTGCCAAGCGTGTTGGAGCCAG

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|125256603|gb|EL270688.1|EL270688
EST:     CAAATACAACCCTGTTAAG                         GCAATCAAGACCAATGTGATTGGTACACTCAACATGCTCGGTCTTGCCAAG
genomic: CAAATACAACCCTGTTAAGgttcgtgtga ... gtttatgcagACAATCAAGACCAATGTGATTGGTACACTCAACATGCTCGGTCTTGCCAAG
EST: gi|86047698|gb|DR343453.1|DR343453
EST:     ATCTTGCTTGTCCTGCCTCTCCTATCTTCTACAAATACAACCCTGTTAAG                         ACAATCAAGACCAATGTGATTGGTACACTCAACATGCTC
genomic: ATCTTGCTTGTCCTGCCTCTCCTATCTTCTACAAATACAACCCTGTTAAGgttcgtgtga ... gtttatgcagACAATCAAGACCAATGTGATTGGTACACTCAACATGCTC
EST: gi|124884979|gb|EH963881.1|EH963881
EST:     TCTTGCTTGTCCTGCCTCTCCTATCGTTCTACAAATACAACCCTGTTAAG                         ACAATCAAGACCAATGTGAATTGGTACACTCAACATGCTCGGTCTTGCCAA
genomic: TCTTGCTTGTCCTGCCTCTCCTATC-TTCTACAAATACAACCCTGTTAAGgttcgtgtga ... gtttatgcagACAATCAAGACCAATGTGA-TTGGTACACTCAACATGCTCGGTCTTGCCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atatcaccttcatataatcagaatcgttagttactgatctaatatgtttatgcagACAATCAAGACCAATGTGATTGGTACACTCAACATGCTCGGTCTTGCCAAGCGTGTTGGAGCAAG
                                    atctaatatgtttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttcgtgtgaatatagatatattctcatatcaccttcatataatcagaatcgttagttactgatctaatatgtttatgcagACAATCAAGACCAATGTGATTGGTACACTCAACATGCTCGGTCTTGCCAAGCGTGTTGGAGCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG