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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattgtctagaatctgtataaccctacattgcaagatagagaatgattttgatcattgttatgtttgtttggtttagGGAACACGAATACATTGGCGGGTAATGTACCACCGAAGGCGAATCTCGGTGATTTGAGGGGTTTAGCCGGCGGATTAAACGGTTTAAACAGCTCAGCTAT

Basic information

species Arabidopsis thaliana
transcript AT4G27440.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G27440.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA12G35050.2 (Glycine max), 3'ss of exon 3
-------------gtattgtctagaatctgtataaccctacattgcaagat-agagaatgattttgatcattgttatgtttgtttggtttagGGAACACGAATACATTGGCGGGTAATGTACCACCGAAGGCGAATCTCGGTGATTTGAGGGGTTTAGCCGGCGGATTAAACGGTTTAAACAGCTCAGCTAT
             | || || ||   |  ||   |      ||  ||  || ||       || | ||  |  || ||| | ||      ||||||||| || |||||||| ||||||||||| || ||||| || || ||||| ||||||||  |    || || || || ||  ||||||||||||| ||
gtctagttcattagcat-gtttattgtgagttccagttcttatcacaccattaggttgcatttcttatgctgattgtgtgtattcaac--agGGAACACAAACACATTGGCTGGTAATGTACCTCCCAAGGCTAACCTTGGTGACTTGAGGGGACTTCAGGGTGGTTTGAATGGGCTAAACAGCTCAGCCAT
















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|116443986|gb|EG486578.1|EG486578
EST:     TTCTTCATCATCTTTCAAGGACTCGAGTCTTTTTGGTGCCTCCATTACCGACCAAATCAAATCCGAACATGGATCTTCCTCGTTAAGATTCAAG
genomic: TTCTTCATCATCTTTCAAGGACTCGAGTCTTTTTGGTGCCTCCATTACCGACCAAATCAAATCCGAACATGGATCTTCCTCGTTAAGATTCAAG
EST: gi|124832077|gb|EH916516.1|EH916516
EST:     GAAATCTGATTACCCTTCAAAGCGTCTCATCATCGTCGGATCCATTACCG                         GGAACACGAATACATTGGCGGGT
genomic: GAAATCTGATTACCCTTCAAAGCGTCTCATCATCGTCGGATCCATTACCGgtattgtcta ... tttggtttagGGAACACGAATACATTGGCGGGT
EST: gi|163967998|gb|ES159343.1|ES159343
EST:     TCAAAGCGTCTCATCATCGTCGGATCCATTACCG                         GGAACACGAATACATTGGCGGGTAATGTACCACCGAAGGCGAATCTCGGTG
genomic: TCAAAGCGTCTCATCATCGTCGGATCCATTACCGgtattgtcta ... tttggtttagGGAACACGAATACATTGGCGGGTAATGTACCACCGAAGGCGAATCTCGGTG
EST: gi|125200768|gb|EL215722.1|EL215722
EST:     TTACCCTTCAAAGCGTCTCATCATCGTCGGATCCATTACCG                         GGAACACGAATACATTGGCGGGTAATGTACCACCGAAGGCGAATCTCGGTG
genomic: TTACCCTTCAAAGCGTCTCATCATCGTCGGATCCATTACCGgtattgtcta ... tttggtttagGGAACACGAATACATTGGCGGGTAATGTACCACCGAAGGCGAATCTCGGTG
EST: gi|164132971|gb|EL975709.1|EL975709
EST:     AAATCTGATTACCCTTNAAAAGCGTCTCATCATCGTCGGATCCATTACCG                         GGAACACGAATACATTGGCGGGTAATGTACCACCGAAGGCGAATCTCGGTG
genomic: AAATCTGATTACCCTT-CAAAGCGTCTCATCATCGTCGGATCCATTACCGgtattgtcta ... tttggtttagGGAACACGAATACATTGGCGGGTAATGTACCACCGAAGGCGAATCTCGGTG
EST: gi|125246297|gb|EL260382.1|EL260382
EST:     CGGATCCATTACCG                         GGAACACGAATACATTGGCGGGTAATGTACCACCGAAGGCGAATCTCGGTG
genomic: CGGATCCATTACCGgtattgtcta ... tttggtttagGGAACACGAATACATTGGCGGGTAATGTACCACCGAAGGCGAATCTCGGTG
EST: gi|125099875|gb|EL155525.1|EL155525
EST:     CCCTTCAAAGCGTCTCATCATCGTCGGATCCATTACCG                         GGAACACGAATACATTGGCGGGTAATGTACCACCGAAGGCGAATCTCGGTG
genomic: CCCTTCAAAGCGTCTCATCATCGTCGGATCCATTACCGgtattgtcta ... tttggtttagGGAACACGAATACATTGGCGGGTAATGTACCACCGAAGGCGAATCTCGGTG
EST: gi|116440576|gb|EG483168.1|EG483168
EST:     TTCTTCATCATCTTTCAAGGACTCGAGTCTTTTTGGTGCCTCCATTACCGACCAAATCAAATCCGAACATGGATCTTCCTCGTTAAGATTCAAG
genomic: TTCTTCATCATCTTTCAAGGACTCGAGTCTTTTTGGTGCCTCCATTACCGACCAAATCAAATCCGAACATGGATCTTCCTCGTTAAGATTCAAG
EST: gi|163968154|gb|EL979108.1|EL979108
EST:     TCATCATCGTCGGATCCATTACCG                         GGAACACGAATACATTGGCGGGTAATGTACCACCGAAGGCGAATCTCGGTG
genomic: TCATCATCGTCGGATCCATTACCGgtattgtcta ... tttggtttagGGAACACGAATACATTGGCGGGTAATGTACCACCGAAGGCGAATCTCGGTG
EST: gi|124820449|gb|EH905315.1|EH905315
EST:     GAAATCTGATTACCCTTCAAAGCGTCTCATCATCGTCGGATCCATTACCG                         GGAACACGAAT
genomic: GAAATCTGATTACCCTTCAAAGCGTCTCATCATCGTCGGATCCATTACCGgtattgtcta ... tttggtttagGGAACACGAAT
EST: gi|124846382|gb|EH930819.1|EH930819
EST:     TCATCGTCGGATCCATTACCG                         GGAACACGAATACATTGGCGGGTAATGTACCACCGAAGGCGAATCTCGGTG
genomic: TCATCGTCGGATCCATTACCGgtattgtcta ... tttggtttagGGAACACGAATACATTGGCGGGTAATGTACCACCGAAGGCGAATCTCGGTG
EST: gi|164183400|gb|ES120762.1|ES120762
EST:     TCGTCGGATCCATTACCG                         GGAACACGAATACATTGGCGGGTAATGTACCACCGAAGGCGAATCTCGGTG
genomic: TCGTCGGATCCATTACCGgtattgtcta ... tttggtttagGGAACACGAATACATTGGCGGGTAATGTACCACCGAAGGCGAATCTCGGTG
EST: gi|124825962|gb|EH910828.1|EH910828
EST:     CCCTTCAAAGCGTCTCATCATCGTCGGATCCATTACCG                         GGAACACGAATACATTGGCGGGTAATGTACCACCGAAGGCGAATCTCGGTG
genomic: CCCTTCAAAGCGTCTCATCATCGTCGGATCCATTACCGgtattgtcta ... tttggtttagGGAACACGAATACATTGGCGGGTAATGTACCACCGAAGGCGAATCTCGGTG
EST: gi|125026886|gb|EL099155.1|EL099155
EST:     GAAATCTGATTACCCTTCAAAGCGTCTCATCATCGTCGGATCCATTACCG                         GGAACACGAATACATTGGCGGGTAA
genomic: GAAATCTGATTACCCTTCAAAGCGTCTCATCATCGTCGGATCCATTACCGgtattgtcta ... tttggtttagGGAACACGAATACATTGGCGGGTAA
EST: gi|116416037|gb|EG458629.1|EG458629
EST:     GAAATCTGATTACCCTTCAAAGCGTCTCATCATCGTCGGATCCATTACCG                         GGAACACGAATACATTGGCGGGTAATGTACCACCGAAGGCGAATCTCGGTG
genomic: GAAATCTGATTACCCTTCAAAGCGTCTCATCATCGTCGGATCCATTACCGgtattgtcta ... tttggtttagGGAACACGAATACATTGGCGGGTAATGTACCACCGAAGGCGAATCTCGGTG
EST: gi|125010684|gb|EL082953.1|EL082953
EST:     GAAATCTGATTACCCTTCAAAGCGTCTCATCATCGTCGGATCCATTACCG                         GGAACACGAATA
genomic: GAAATCTGATTACCCTTCAAAGCGTCTCATCATCGTCGGATCCATTACCGgtattgtcta ... tttggtttagGGAACACGAATA
EST: gi|125060883|gb|EL129560.1|EL129560
EST:     CCCTTCAAAGCGTCTCATCATCGTCGGATCCATTACCG                         GGAACACGAATACATTGGCGGGTAATGTACCACCGAAGGCGAATCTCGGTG
genomic: CCCTTCAAAGCGTCTCATCATCGTCGGATCCATTACCGgtattgtcta ... tttggtttagGGAACACGAATACATTGGCGGGTAATGTACCACCGAAGGCGAATCTCGGTG
EST: gi|116440655|gb|EG483247.1|EG483247
EST:     CTTTTTGGTGCCTCCATTACCGACCAAATCAAATCCGAACATGGATCTTCCTCGTTAAGATTCAAG
genomic: CTTTTTGGTGCCTCCATTACCGACCAAATCAAATCCGAACATGGATCTTCCTCGTTAAGATTCAAG
EST: gi|86058735|gb|DR354492.1|DR354492
EST:     GAAATCTGATTACCCTTCAAAGCGTCTCATCATCGTCGGATCCATTACCG                         GGAACACGAATACATTGGCGGGTAATGTACCACCGAAGGCGAATCTCGGTG
genomic: GAAATCTGATTACCCTTCAAAGCGTCTCATCATCGTCGGATCCATTACCGgtattgtcta ... tttggtttagGGAACACGAATACATTGGCGGGTAATGTACCACCGAAGGCGAATCTCGGTG
EST: gi|124839274|gb|EH923713.1|EH923713
EST:     AATCTGATTTACCCTTCAAAGCGTCTCATACATCGTCGGATCCATTACCG                         GGAACACGAATA
genomic: AATCTGATT-ACCCTTCAAAGCGTCTCAT-CATCGTCGGATCCATTACCGgtattgtcta ... tttggtttagGGAACACGAATA
EST: gi|124836571|gb|EH921010.1|EH921010
EST:     GAAATCTGATTACCCTTCAAAGCGTCTCATCATCGTCGGATCCATTACCG                         GGAACACGAATACATTGG
genomic: GAAATCTGATTACCCTTCAAAGCGTCTCATCATCGTCGGATCCATTACCGgtattgtcta ... tttggtttagGGAACACGAATACATTGG
EST: gi|124807191|gb|EH893606.1|EH893606
EST:     CCCTTCAAAGCGTCTCATCATCGTCGGATCCATTACCG                         GGAACACGAATACATTGGCGGGTAATGTACCACCGAAGGCGAATCTCGGTG
genomic: CCCTTCAAAGCGTCTCATCATCGTCGGATCCATTACCGgtattgtcta ... tttggtttagGGAACACGAATACATTGGCGGGTAATGTACCACCGAAGGCGAATCTCGGTG
EST: gi|124937288|gb|EL014075.1|EL014075
EST:     GAAATCTGATTACCCTTCAAAGCGTCTCATCATCGTCGGATCCATTACCG                         GGAACACGAATACATTGGCGGGTAATGTACCACCGAAGGCGAA
genomic: GAAATCTGATTACCCTTCAAAGCGTCTCATCATCGTCGGATCCATTACCGgtattgtcta ... tttggtttagGGAACACGAATACATTGGCGGGTAATGTACCACCGAAGGCGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cctacattgcaagatagagaatgattttgatcattgttatgtttgtttggtttagGGAACACGAATACATTGGCGGGTAATGTACCACCGAAGGCGAATCTCGGTGATTTGAGGGGTTTAGCCGGCGGATTAAACGGTTTAAACAGCTCAGCTAT
                        ttttgat  putative branch site (score: 4)
                                         tttgttt  putative PPT
                   aatgatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattgtctagaatctgtataaccctacattgcaagatagagaatgattttgatcattgttatgtttgtttggtttagGGAACACGAATACATTGGCGGGTAATGTACCACCGAAGGCGAATCTCGGTGATTTGAGGGGTTTAGCCGGCGGATTAAACGGTTTAAACAGCTCAGCTAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT