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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcgttagattagttatctgtcgcaaaatgaaactttatgttgattattgccttctcaattgccagGTTCTGTCAATGGAGGCAACAGTGCAGAGCTTGCCAAAGAAGAAGACATTGATGGATTTCTTGTTGGTGGTGCCTCCTTGAAG

Basic information

species Arabidopsis thaliana
transcript AT2G21170.2
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G21170.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os09g36450.1 (Oryza sativa), 3'ss of exon 7
------------------------gtgcgttag-attagttatctgtcg--caaaatgaaactttatg-----ttgattattgccttctcaattgc-cagGTTCTGTCAATGGAGGCAACAGTGCAGAGCTTGCCAAAGAAGAAGACATTGATGGATTTCTTGTTGGTGGTGCCTCCTTGAAG
                         |||   |  |||| ||   || |    |  |||   |  ||||      ||||| |    |||    | |  |||||||||| |||| || |||  |||| ||||| || ||  ||||||| ||||| || || ||||||||||||||||| ||||||
aaggcttgtgacttcagagaatatttgcaccattattaatttgatgccagctaggatgtggcaatatgcctcactgattttatgattcgttctggtacagGTTCTGTAAATGCAGCCAATTGTGCCGAGCTAGCAAAGAAAGAAGATATTGACGGCTTCCTTGTTGGTGGTGCCTCTTTGAAG

upper sequence: AT2G21170.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G002807_T01 (Zea mays), 3'ss of exon 7
----------------------------------gtgcgttagat-tagttatctgtcgcaaaatgaaactttatgttgattattgccttctcaattgccagGTTCTGTCAATGGAGGCAACAGTGCAGAGCTTGCCAAAGAAGAAGACATTGATGGATTTCTTGTTGGTGGTGCCTCCTTGAAG
                                  | | |||  |  || |||      || |  |||  |    ||   ||  |    | ||    |  |||||||||| |||| || |||| |||| ||||| || ||  ||||||| |||||||| |||||||||||||||||||| ||||||
atgttctgttaaattttatttcagtgttgttgtggggtgtttaacgtacttactgactgcgatgtga--ccaactgaccatcctcctttgcttgtgttgcagGTTCTGTGAATGCAGCCAACTGTGCGGAGCTAGCAAAGAAAGAAGATATTGATGGTTTTCTTGTTGGTGGTGCCTCTTTGAAG

upper sequence: AT2G21170.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM5G852968_T03 (Zea mays), 3'ss of exon 7
------------------------------------------------------------------------------------------------------------------------gtgcgttagattagttatctgtcgcaaaatgaaactttatgttgattattgccttctcaattgc----cagGTTCTGTCAATGGAGGCAACAGTGCAGAGCTTGCCAAAGAAGAAGACATTGATGGATTTCTTGTTGGTGGTGCCTCCTTGAAG
                                                                                                                         || |    |   |||     | ||   |||   || |    |||  ||   | | |    ||     |||||||||| |||| || |||| |||||||||| || ||  |||| || || ||||| |||||||||||||||||||||||||||
gttggtttctcgtttcacataagctgtcaggataacgtgtttcgcgtgtttctttttccattaaatttgaaaatggaaagattgaacttggaaccgtggtttgcagtttgctaaattactatgaggataacgtgtttaacatggcttgatggccctgtgatgtgaccatcttcatttgctctgtgttgcagGTTCTGTGAATGCAGCCAACTGTGCAGAGCTAGCAAAGAAAGAGGATATCGATGGTTTTCTTGTTGGTGGTGCCTCCTTGAAG

upper sequence: AT2G21170.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM5G852968_T02 (Zea mays), 3'ss of exon 8
gtgcgttagattagttatctgtcgcaaaatgaaactttatgttgattattgccttctcaattgccagGTTCTGTCAATGGAGGCAACAGTGCAGAGCTTGCCAAAGAAGAAGACATTGATGGATTTCTTGTTGGTGGTGCCTCCTTGAAG
                                                                                                      ||  |||| || || ||||| |||||||||||||||||||||||||||
------------------------------------------------------------------------------------------------------aAGAAAGAGGATATCGATGGTTTTCTTGTTGGTGGTGCCTCCTTGAAG

upper sequence: AT2G21170.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA13G20930.1 (Glycine max), 3'ss of exon 7
-------------------gtgcgttagattagttatctgtcgcaaaat-----gaaactttatgtt-gattattgccttctcaat--------tgccagGTTCTGTCAATGGAGGCAACAGTGCAGAGCTTGCCAAAGAAGAAGACATTGATGGATTTCTTGTTGGTGGTGCCTCCTTGAAG
                    |   | |   || || | | |  || |||     | | |   ||  | || || |  | ||  | |        |  |||| ||||| |||| | |||||||||| |||||||| ||  ||||||| |||||||||||||||||||||||||| || || |||
accatctcagaattggttcttatttgaatgtaattttttttttcagaatacagtgcagcagcattctagaatactaacatcaaagtaatctgtctttcagGATCTGTAAATGCAAGCAACAGTGCTGAGCTTGCAAAGCAAGAAGATATTGATGGATTTCTTGTTGGTGGTGCTTCATTAAAG

upper sequence: AT2G21170.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA10G06740.1 (Glycine max), 3'ss of exon 7
--------------------------gtgcgttagattagttatc----tgtcgcaaaatgaaact--ttatgttgattattgccttctcaattgc-cagGTTCTGTCAATGGAGGCAACAGTGCAGAGCTTGCCAAAGAAGAAGACATTGATGGATTTCTTGTTGGTGGTGCCTCCTTGAAG
                            |  ||  || ||  |       |  |||  ||   | |   |||| | |   |    |  ||  |    |||| ||||| ||||   |||||||||| ||||| || ||  ||||||| |||||||||||||||||||||||||| || || |||
tcagaatttaatttttcttcaaatgaaagattttaatcagccagtacagcgcagcagcattgtagtagatatgctaacattgaagtaatctgtccttcagGGTCTGTAAATGCGAGCAACAGTGCTGAGCTCGCGAAGCAAGAAGATATTGATGGATTTCTTGTTGGTGGTGCTTCATTAAAG

upper sequence: AT2G21170.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA19G36990.2 (Glycine max), 3'ss of exon 7
--------------------------------gtgcgttagattagttatctgtcgcaaaatgaaactt-tatgttgattattgccttctcaattgccagGTTCTGTCAATGGAGGCAACAGTGCAGAGCTTGCCAAAGAAGAAGACATTGATGGATTTCTTGTTGGTGGTGCCTCCTTGAAG-----------------
                                     |||  | | || | |    ||     | |    ||     |   |    || ||  ||  |||| ||||| |||||||| |||||||| ||||| || ||  ||||||| |||||||||||||| ||||| ||||| || || |||                 
cagtatatttgaccacttgagattataagtctcatttttatgtaaattttttccatcacggcaacatcgatacccaaacattaaatttatctgttttcagGGTCTGTAAATGGAGGGAACAGTGCTGAGCTAGCAAAGCAAGAAGATATTGATGGATTTCTCGTTGGAGGTGCTTCATTAAAGGTACATGGTTTCTTCAA

upper sequence: AT2G21170.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA03G34300.1 (Glycine max), 3'ss of exon 7
-----------------------------gtgcgttagattagttatctgtcgcaaaat---gaaacttta-tgttgattattgccttctcaattgccagGTTCTGTCAATGGAGGCAACAGTGCAGAGCTTGCCAAAGAAGAAGACATTGATGGATTTCTTGTTGGTGGTGCCTCCTTGAAG
                             |   || | |||  |        |||  ||   || ||  ||   || | |    | || |   ||  |||| ||||| ||||||||||||||||| || || || ||  ||||||| |||||||||||||| ||||| ||||| || || |||
cttgagaaatgagaaaatagttctcatttgaaggtaaaatttttccagcaaagcagcatccggatacagtaacattaaattcatcttttttttttttcagGGTCTGTAAATGGAGGCAACAGTGCTGAACTGGCAAAGCAAGAAGATATTGATGGATTTCTCGTTGGAGGTGCTTCATTAAAG

upper sequence: AT2G21170.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA19G36990.1 (Glycine max), 3'ss of exon 7
--------------------------------gtgcgttagattagttatctgtcgcaaaatgaaactt-tatgttgattattgccttctcaattgccagGTTCTGTCAATGGAGGCAACAGTGCAGAGCTTGCCAAAGAAGAAGACATTGATGGATTTCTTGTTGGTGGTGCCTCCTTGAAG
                                     |||  | | || | |    ||     | |    ||     |   |    || ||  ||  |||| ||||| |||||||| |||||||| ||||| || ||  ||||||| |||||||||||||| ||||| ||||| || || |||
cagtatatttgaccacttgagattataagtctcatttttatgtaaattttttccatcacggcaacatcgatacccaaacattaaatttatctgttttcagGGTCTGTAAATGGAGGGAACAGTGCTGAGCTAGCAAAGCAAGAAGATATTGATGGATTTCTCGTTGGAGGTGCTTCATTAAAG

upper sequence: AT2G21170.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv03s0038g01780.t01 (Vitis vinifera), 3'ss of exon 7
--------------------------gtgcgttagattagt-tatctgtcgcaaaatgaaactt----tatgttgattattgcc---ttctcaattgccagGTTCTGTCAATGGAGGCAACAGTGCAGAGCTTGCCAAAGAAGAAGACATTGATGGATTTCTTGTTGGTGGTGCCTCCTTGAAG
                           || ||  || |  | |   | ||   | |||           ||| ||  | |   |    ||||  |||| |||||| || |||||  ||||  || ||||||| |||||| |||| || |||||||||||||||||||| ||||| ||||| |||
ttggatgtcaaatgtagttttatactctgtgtctgaatgttctggttttctggagatgctgtccagtgcatgctgcatctgatcaaactctcttttgc-agGTTCAGTGAATGGGAGCAATTGTTCAGAGCTCGCCAAACAAGAGGATATTGATGGATTTCTTGTTGGCGGTGCTTCCTTAAAG

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|116400904|gb|EG443496.1|EG443496
EST:     GAAGAATGTGTCTGAGGAAGTTGCTTCCAAAACGAGAATCATATATGGAG                         GTTCTGTCAATGGAGGCAACAGTGCAGAGCTTGCCAAAGAAGGAGACATTG
genomic: GAAGAATGTCTCTGAGGAAGTTGCTTCCAAAACGAGAATCATATATGGAGgtgcgttaga ... caattgccagGTTCTGTCAATGGAGGCAACAGTGCAGAGCTTGCCAAAGAAGAAGACATTG
EST: gi|47828644|gb|CK118328.1|CK118328
EST:     GAAGAATGTCTCTGAGGAAGTTGCTTCCAAAACGAGAATCATATATGGAG                         GTTCTGTCAATGGAGGCAACAGTGCAGAGCTTGCCAAAGAAGAAGACATTG
genomic: GAAGAATGTCTCTGAGGAAGTTGCTTCCAAAACGAGAATCATATATGGAGgtgcgttaga ... caattgccagGTTCTGTCAATGGAGGCAACAGTGCAGAGCTTGCCAAAGAAGAAGACATTG
EST: gi|125014412|gb|EL086681.1|EL086681
EST:     TCTGAGGAAGTTGCTTCCAAAACGAGAATCATATATGGAG                         GTTCTGTCAATGGAGGCAACAGTGCAGAGCTTGCCAAAGAAGAAGACATTG
genomic: TCTGAGGAAGTTGCTTCCAAAACGAGAATCATATATGGAGgtgcgttaga ... caattgccagGTTCTGTCAATGGAGGCAACAGTGCAGAGCTTGCCAAAGAAGAAGACATTG
EST: gi|124762342|gb|EH852472.1|EH852472
EST:     CAAAACGAGAATCATATATGGAG                         GTTCTGTCAATGGAGGCAACAGTGCAGAGCTTGCCAAAGAAGAAGACATTG
genomic: CAAAACGAGAATCATATATGGAGgtgcgttaga ... caattgccagGTTCTGTCAATGGAGGCAACAGTGCAGAGCTTGCCAAAGAAGAAGACATTG
EST: gi|47831761|gb|CK121445.1|CK121445
EST:     GAAGAATGTCTCTGAGGAAGTTGCTTCCAAAACGAGAATCATATATGGAG                         GTTCTGTCAATGGAGGCAACAGTGCAGAGCTTGCCA
genomic: GAAGAATGTCTCTGAGGAAGTTGCTTCCAAAACGAGAATCATATATGGAGgtgcgttaga ... caattgccagGTTCTGTCAATGGAGGCAACAGTGCAGAGCTTGCCA
EST: gi|125248364|gb|EL262449.1|EL262449
EST:     GAAGAATGTCTCTGAGGAAGTTGCTTCCAAAACGAGAATCATATATGGAG                         TTTCTGTCAATGGAGGCAACAG
genomic: GAAGAATGTCTCTGAGGAAGTTGCTTCCAAAACGAGAATCATATATGGAGgtgcgttaga ... caattgccagGTTCTGTCAATGGAGGCAACAG
EST: gi|116463095|gb|EG505687.1|EG505687
EST:     GAAGAATGTTTTTGAGGAAGTTGCTTCCAAAACGAGAATCATATATGGAG                         GTTCTGTCAATGGAGGCAACAGTGCAGAGCTTGCCAAAGAAGAAGACATTG
genomic: GAAGAATGTCTCTGAGGAAGTTGCTTCCAAAACGAGAATCATATATGGAGgtgcgttaga ... caattgccagGTTCTGTCAATGGAGGCAACAGTGCAGAGCTTGCCAAAGAAGAAGACATTG
EST: gi|116454376|gb|EG496968.1|EG496968
EST:     GAAGAATGTCTCTGAGGAAGTTGCTTCCAAAACGAGAATCATATATGGAG                         GTTCTGTCAATGGAGGCAACAGTGCAGAGCTTGCCAAAGAAGAAGACATTG
genomic: GAAGAATGTCTCTGAGGAAGTTGCTTCCAAAACGAGAATCATATATGGAGgtgcgttaga ... caattgccagGTTCTGTCAATGGAGGCAACAGTGCAGAGCTTGCCAAAGAAGAAGACATTG
EST: gi|124773586|gb|EH863715.1|EH863715
EST:     TTCCAAAACGAGAATCATATATGGAG                         GTTCTGTCAATGGAGGCAACAGTGCAGAG
genomic: TTCCAAAACGAGAATCATATATGGAGgtgcgttaga ... caattgccagGTTCTGTCAATGGAGGCAACAGTGCAGAG
EST: gi|163973824|gb|ES054038.1|ES054038
EST:     GAAGAATGTCTCTGAGGAAGTTGCTTCCAAAACGAGAATCATATATGGAG                         GTTCTGTCAATGGAGGCAACAGTGCAGAGCTTACCAAAGAAGAAGA
genomic: GAAGAATGTCTCTGAGGAAGTTGCTTCCAAAACGAGAATCATATATGGAGgtgcgttaga ... caattgccagGTTCTGTCAATGGAGGCAACAGTGCAGAGCTTGCCAAAGAAGAAGA
EST: gi|125111311|gb|EL162841.1|EL162841
EST:     GGAAGTTGCTTCCAAAACGAGAATCATATATGGAG                         GTTCTGTCAATGGAGGCAACAGTGCAGAGCTTGCCAAAGAAGAAGACATTG
genomic: GGAAGTTGCTTCCAAAACGAGAATCATATATGGAGgtgcgttaga ... caattgccagGTTCTGTCAATGGAGGCAACAGTGCAGAGCTTGCCAAAGAAGAAGACATTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agttatctgtcgcaaaatgaaactttatgttgattattgccttctcaattgccagGTTCTGTCAATGGAGGCAACAGTGCAGAGCTTGCCAAAGAAGAAGACATTGATGGATTTCTTGTTGGTGGTGCCTCCTTGAAG
                           tgttgat  putative branch site (score: 4)
                                    ttgccttctc  putative PPT
             aaaatgaaactttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgcgttagattagttatctgtcgcaaaatgaaactttatgttgattattgccttctcaattgccagGTTCTGTCAATGGAGGCAACAGTGCAGAGCTTGCCAAAGAAGAAGACATTGATGGATTTCTTGTTGGTGGTGCCTCCTTGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG