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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attggtcttctactaaacgctgtgcaaatcctttccttatatgcaattcattcattgtcttacatatcattacatcgtttttgtttcttcgcattggcagGTGGGCAATTGTATACATTGCGCAGATGAACCCTCTCATTGTCCCTATCTTAAGCGAGGTGGAGTAGAAACCATTCTACTCAAACTAGGAAACCAATGCA

Basic information

species Arabidopsis thaliana
transcript AT4G26710.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G26710.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv00s0187g00310.t01 (Vitis vinifera), 3'ss of exon 3
attggtcttctactaaacgctgtgcaaatcctttccttatatgcaattcattcat---tgtcttacatatcattacatcgtttttgtttcttcgcattggcagGTGGGCAATTGTATACATTGCGCAGATGAACCCTCTCATTGTCCCTATCTTAAGCGAGGTGGAGTAGAAACCATTCTACTCAAACTAGGAAACCAATGCA-
     | || |  | |    | |    | | |      |   | |||    | ||   | | ||| ||     |  |      |   |||| | | |||  |||||||||||||||||  | || ||||||||||| ||||||||||| ||| | |  || ||||||| || |  |||||||  | | |        ||     
--gcattttatttttatttttatagtgaacttgaatgcagtaggaatatcattatgcatattttatatggtgatttactaaaatcccttctccac-ttgttagGTGGGCAATTGTATATCTGGCACAGATGAACCCACTCATTGTCCCAATCCTCAATGAAGTGGAGT-GAGATGATTCTACAAAGAGTGCATGCGGAAGATTG
















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|125123059|gb|EL169508.1|EL169508
EST:     TTACATCTTACATTGGTCATCACCGCAACTGTCTGCTGTTGGATGAT                         GTGGGCAATTGTATACATTGCGCAGATGAACCCTCTC
genomic: TTACATCTTACATTGGTCATCACCGCAACTGTCTGCTGTTGGATGATgtaagtttat ... gcattggcagGTGGGCAATTGTATACATTGCGCAGATGAACCCTCTC
EST: gi|86053715|gb|DR349472.1|DR349472
EST:     GTTACATCTTACATTGGTCATCACCGCAACTGTCTGCTGTTGGATGAT                         GTGGGCAATTGTATACATTGCGCAGATGAACCCTCTCATTGTCCCTATCTT
genomic: GTTACATCTTACATTGGTCATCACCGCAACTGTCTGCTGTTGGATGATgtaagtttat ... gcattggcagGTGGGCAATTGTATACATTGCGCAGATGAACCCTCTCATTGTCCCTATCTT
EST: gi|124987647|gb|EL060091.1|EL060091
EST:     GTCATCACCGCAACTGTCTGCTGTTGGATGAT                         GTGGGCAATTGTATACAATTGCGCAGATGAACCCTCTCAT
genomic: GTCATCACCGCAACTGTCTGCTGTTGGATGATgtaagtttat ... gcattggcagGTGGGCAATTGTATACA-TTGCGCAGATGAACCCTCTCAT
EST: gi|125227395|gb|EL241480.1|EL241480
EST:     TGCTGTTGGATGAT                         GTGGGCAATTGTATACATTGCGCAGATGAACCCTCTCATTGTCCCTATCTT
genomic: TGCTGTTGGATGATgtaagtttat ... gcattggcagGTGGGCAATTGTATACATTGCGCAGATGAACCCTCTCATTGTCCCTATCTT
EST: gi|124865561|gb|EH949998.1|EH949998
EST:     TCTGCTGTTGGATGAT                         GTGGGCAATTGTATACATTGCGCAGATGAACCCTCTCATTGTCCCTATCTT
genomic: TCTGCTGTTGGATGATgtaagtttat ... gcattggcagGTGGGCAATTGTATACATTGCGCAGATGAACCCTCTCATTGTCCCTATCTT
EST: gi|125230437|gb|EL244522.1|EL244522
EST:     GTTACATCTTACATTGGTCATCACCGCAACTGTCTGCTGTTGGATGAT                         GTGGGCAATTGTATACATTGCG
genomic: GTTACATCTTACATTGGTCATCACCGCAACTGTCTGCTGTTGGATGATgtaagtttat ... gcattggcagGTGGGCAATTGTATACATTGCG
EST: gi|125039042|gb|EL111311.1|EL111311
EST:     TCTTACATTGGTCATCACCGCAACTGTCTGCTGTTGGATGAT                         GTGGGCAATTGTATACATTGCGCAGATGAACCCTCTCATTG
genomic: TCTTACATTGGTCATCACCGCAACTGTCTGCTGTTGGATGATgtaagtttat ... gcattggcagGTGGGCAATTGTATACATTGCGCAGATGAACCCTCTCATTG
EST: gi|86083717|gb|DR379476.1|DR379476
EST:     GTTACATCTTACATTGGTCATCACCGCAACTGTCTGCTGTTGGATGAT                         GTGGGCAATTGTATACATTGCGCAGATGAACCCTCTCATTGTCCCTATCTT
genomic: GTTACATCTTACATTGGTCATCACCGCAACTGTCTGCTGTTGGATGATgtaagtttat ... gcattggcagGTGGGCAATTGTATACATTGCGCAGATGAACCCTCTCATTGTCCCTATCTT
EST: gi|124719957|gb|EH811359.1|EH811359
EST:     CACCGCAACTGTCTGCTGTTGGATGAT                         GTGGGCAATTGTATACATTGCGCAGATGAACCCTCTCATTGTCCCTATCTT
genomic: CACCGCAACTGTCTGCTGTTGGATGATgtaagtttat ... gcattggcagGTGGGCAATTGTATACATTGCGCAGATGAACCCTCTCATTGTCCCTATCTT
EST: gi|124835371|gb|EH919810.1|EH919810
EST:     TCACCGCAACTGTCTGCTGTTGGATGAT                         GTGGGCAATTGTATACATTGCGCAGATGAACCCTACTCATTGTCCCTATCT
genomic: TCACCGCAACTGTCTGCTGTTGGATGATgtaagtttat ... gcattggcagGTGGGCAATTGTATACATTGCGCAGATGAACCCT-CTCATTGTCCCTATCT
EST: gi|86053714|gb|DR349471.1|DR349471
EST:     GTTACATCTTACATTGGTCATCACCGCAACTGTCTGCTGTTGGATGAT                         GTGGGCAATTGTATACATTGCGCAGATGAACCCTCTCATTGTCCCTATCTT
genomic: GTTACATCTTACATTGGTCATCACCGCAACTGTCTGCTGTTGGATGATgtaagtttat ... gcattggcagGTGGGCAATTGTATACATTGCGCAGATGAACCCTCTCATTGTCCCTATCTT
EST: gi|86079112|gb|DR374869.1|DR374869
EST:     GTTACATCTTACATTGGTCATCACCGCAACTGTCTGCTGTTGGATGAT                         GTGGGCAATTGTATACATTGCGCAGATGWWCCCTCTCATTGTCCCTATCTT
genomic: GTTACATCTTACATTGGTCATCACCGCAACTGTCTGCTGTTGGATGATgtaagtttat ... gcattggcagGTGGGCAATTGTATACATTGCGCAGATGAACCCTCTCATTGTCCCTATCTT
EST: gi|125197391|gb|EL212345.1|EL212345
EST:     CAACTGTCTGCTGTTGGATGAT                         GTGGGCAATTGTATACATTGCGCAGATGAACCCTCTCATTGTCCCTATCTT
genomic: CAACTGTCTGCTGTTGGATGATgtaagtttat ... gcattggcagGTGGGCAATTGTATACATTGCGCAGATGAACCCTCTCATTGTCCCTATCTT
EST: gi|124858847|gb|EH943284.1|EH943284
EST:     CTGTTACATCTTACATTGGTCATCACCGCAACTGTCTGCTGTTGGATGAT                         GTGGGCAATTGTATACATTGCGCAGATGAACCC
genomic: CTGTTACATCTTACATTGGTCATCACCGCAACTGTCTGCTGTTGGATGATgtaagtttat ... gcattggcagGTGGGCAATTGTATACATTGCGCAGATGAACCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attcattcattgtcttacatatcattacatcgtttttgtttcttcgcattggcagGTGGGCAATTGTATACATTGCGCAGATGAACCCTCTCATTGTCCCTATCTTAAGCGAGGTGGAGTAGAAACCATTCTACTCAAACTAGGAAACCAATGCA
           gtcttac  putative branch site (score: 3)
                                tttttgtttcttcgc  putative PPT
                  atatcatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attggtcttctactaaacgctgtgcaaatcctttccttatatgcaattcattcattgtcttacatatcattacatcgtttttgtttcttcgcattggcagGTGGGCAATTGTATACATTGCGCAGATGAACCCTCTCATTGTCCCTATCTTAAGCGAGGTGGAGTAGAAACCATTCTACTCAAACTAGGAAACCAATGCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - -actaaac
- - - - - - - - - - - - caaatcc
- - - - - - - - - - - - - - - - - - - - - -caattca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - cttacat