Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagaatatcattcttggagctcttagattagaaaggcatctgttcattaaaaactttccctgtttattgactgaatttttcatatggtatggtgttgtgcagGTTGACCTGTTCTTTTACAGGGAACCTGAGGAGACTAAGCCAGAGGATGAAGATGAAGCTGGCCCTCAGGCAGAATATGGTGCACTTCCTGCTCCAGAAT

Basic information

species Arabidopsis thaliana
transcript AT1G72370.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G72370.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: PP1S209_48V6.1 (Physcomitrella patens), 3'ss of exon 3
gtaagaatatcattcttggagctcttagattagaaaggcatctgttcattaaaaactttccctgtttattgactgaatttttcatatggtatggtgtt--gtgcagGTTGACCTGTTCTTTTACAGGGAACCTGAGGAGACTAAG---CCAGAGGATGAAGATGAAGCTGGCCCTCAGGCAGAATATGGTGCACTTCCTGCTCCAGAAT
    ||||    |    ||| |    ||    |   ||     |||  |    |         | | ||||   || ||        |||  |||||   |||||||||||||||||||| |||||||| || || ||    |||   |  ||||| || || | ||  |   || ||   |     | || |    | || ||     
--gggaat----tgggaggaacggagagcggggctgggtgatagttggtggcgaggggagggggctgattgtgcgagttggggggggggtcgggtgtgcggtgcagGTTGACCTGTTCTTCTACAGGGAGCCCGATGAAGGCAAGGACCGCGAGGAAGAGGAGGGAGGAGCAGCTGAGTTCGCCGCAGTTGAATACGCGGCGCCGA---

upper sequence: AT1G72370.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: PP1S173_16V6.1 (Physcomitrella patens), 3'ss of exon 3
---------------------------------gtaagaatatcattcttggagctcttagattagaaaggc----atctgtt-cattaaaaactttccctgtttattgac-tgaatttttcatatggtatggtgttgtgcagGTTGACCTGTTCTTTTACAGGGAACCTGAGGAGACTAAG---CCAGAGGATGAAGATGAAGCTGGCCCTCAGGCAGAATATGGTGCACTTC-CTGCTCCAGAAT
                                 ||  |||  | | | | || |       |   |    ||    || || | | |     |     |  | ||   ||     |   | |   ||     |  | |||||||| |||||||||||||||||||| || || ||    |||   |  ||||| || || | |||  ||  |   |        |||  | | | |||| ||||   
gtaagtgcgggagtaagtgcgacagggagtgcggtttgaagttgaatgtgggtgtgggggaagctgtggtgcttgaatgtgatgcctgggggatggggcggggttgcggaggctgaccgtccgcttgtggacggatggtgcagGTGGACCTGTTCTTTTACAGGGAGCCCGACGAAGGCAAGGACCGCGAGGACGAGGAGGGAGC-AGCAGTGGAGTTCGCGGCGGTAGAGTACGCTGCGCCAG---
















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|164034087|gb|ES174739.1|ES174739
EST:     TCCTTCAGGTGCGTGGAACCATTGCTGCTGGACAGAAGTGGGATGTCATG                         GTTGACCTGTTCTTTTACAGGGAACCTGA
genomic: TCCTTCAGATGCGTGGAACCATTGCTGCTGGACAGAAGTGGGATGTCATGgtaagaatat ... tgttgtgcagGTTGACCTGTTCTTTTACAGGGAACCTGA
EST: gi|116467170|gb|EG509762.1|EG509762
EST:     TCCTTCAGATGCGTGGAACCATTGCTGCTGGACAGAAGTGGGATGTCATG                         GTTGACCTGTTCTTTTACAGGGAACCTGAGGAGACTAAGCCAGAGGATGAA
genomic: TCCTTCAGATGCGTGGAACCATTGCTGCTGGACAGAAGTGGGATGTCATGgtaagaatat ... tgttgtgcagGTTGACCTGTTCTTTTACAGGGAACCTGAGGAGACTAAGCCAGAGGATGAA
EST: gi|125162675|gb|EL189445.1|EL189445
EST:     AACCATTGCTGCTGGACAGAAGTGGGTATGTCATG                         GTTGACCTGTTCTTTTACAGGGAACCTGAGGAGACTAAGCCAGAGGATGA
genomic: AACCATTGCTGCTGGACAGAAGTGGG-ATGTCATGgtaagaatat ... tgttgtgcagGTTGACCTGTTCTTTTACAGGGAACCTGAGGAGACTAAGCCAGAGGATGA
EST: gi|125314216|gb|EL328301.1|EL328301
EST:     ACAGAAGTGGGTATGTCATG                         GTTGACCTGTTCTTTTACAGGGAACCTGAGGAGACTAAGCCAGAGGA
genomic: ACAGAAGTGGG-ATGTCATGgtaagaatat ... tgttgtgcagGTTGACCTGTTCTTTTACAGGGAACCTGAGGAGACTAAGCCAGAGGA
EST: gi|124915562|gb|EH989436.1|EH989436
EST:     TCCTTCAGATGCGTGGAACCATTGCTGCTGGACAGAAGTGGGATGTCATG                         GTTGACCTGTTCTTTTACAGGGAA
genomic: TCCTTCAGATGCGTGGAACCATTGCTGCTGGACAGAAGTGGGATGTCATGgtaagaatat ... tgttgtgcagGTTGACCTGTTCTTTTACAGGGAA
EST: gi|124840518|gb|EH924957.1|EH924957
EST:     GCTGGACAGAAGTGGGATGTCATG                         GTTGACCTGTTCTTTTACAGGGAACCTGAGGAGACTAAGCCAGAGGATGAA
genomic: GCTGGACAGAAGTGGGATGTCATGgtaagaatat ... tgttgtgcagGTTGACCTGTTCTTTTACAGGGAACCTGAGGAGACTAAGCCAGAGGATGAA
EST: gi|116470236|gb|EG512828.1|EG512828
EST:     TCCTTCAGATGCGTGGAACCATTGCTGCTGGACAGAAGTGGGATGTCATG                         GTTGACCTGTTCTTTTACAGGGAACCTGAGGAGACTAAGCCAGAGGATGAA
genomic: TCCTTCAGATGCGTGGAACCATTGCTGCTGGACAGAAGTGGGATGTCATGgtaagaatat ... tgttgtgcagGTTGACCTGTTCTTTTACAGGGAACCTGAGGAGACTAAGCCAGAGGATGAA
EST: gi|124865338|gb|EH949775.1|EH949775
EST:     CTGCTGGACAGAAGTGGGATGTCATG                         GTTGACCTGTTCTTTTACAGGGAACCTGAGGAGACTAAGCCAGAGGATGAA
genomic: CTGCTGGACAGAAGTGGGATGTCATGgtaagaatat ... tgttgtgcagGTTGACCTGTTCTTTTACAGGGAACCTGAGGAGACTAAGCCAGAGGATGAA
EST: gi|124861550|gb|EH945987.1|EH945987
EST:     TGCTGCTGGACAGAAGTGGGATGTCATG                         GTTGACCTGTTCTTTTACAGGGAACCTGAGGAG
genomic: TGCTGCTGGACAGAAGTGGGATGTCATGgtaagaatat ... tgttgtgcagGTTGACCTGTTCTTTTACAGGGAACCTGAGGAG
EST: gi|125141967|gb|EL179468.1|EL179468
EST:     TCCTTCAGATGCGTGGAACCATTGCTGCTGGACAGAAGTGGGATGTCATG                         GTTGACCTGTTCTTTTACAGG
genomic: TCCTTCAGATGCGTGGAACCATTGCTGCTGGACAGAAGTGGGATGTCATGgtaagaatat ... tgttgtgcagGTTGACCTGTTCTTTTACAGG
EST: gi|163996607|gb|ES050657.1|ES050657
EST:     TGCGTGGAACCATTGCTGCTGGACAGAAGTGGGATGTCATG                         GTTGACCTGTTCTTTTACAGGGAACCTGAGGAGACTAAGCCAGAGGATGAA
genomic: TGCGTGGAACCATTGCTGCTGGACAGAAGTGGGATGTCATGgtaagaatat ... tgttgtgcagGTTGACCTGTTCTTTTACAGGGAACCTGAGGAGACTAAGCCAGAGGATGAA
EST: gi|125233356|gb|EL247441.1|EL247441
EST:     GGAACCGATTGCTGCTGGACAGAAGTGGGATGTCATG                         GTTGACCTGTTCTTTTACAGGGAACCTGAGGAGACTAAGCCAGAGG
genomic: GGAACC-ATTGCTGCTGGACAGAAGTGGGATGTCATGgtaagaatat ... tgttgtgcagGTTGACCTGTTCTTTTACAGGGAACCTGAGGAGACTAAGCCAGAGG
EST: gi|125069335|gb|EL135148.1|EL135148
EST:     GATGCGTGGAACCATTGCTGCTGGACAGAAGTGGGATGTCATG                         GTTGACCTGTTCTTTTACAGGGAACCTGAGGAGACTAAGCCAGAGGATGAA
genomic: GATGCGTGGAACCATTGCTGCTGGACAGAAGTGGGATGTCATGgtaagaatat ... tgttgtgcagGTTGACCTGTTCTTTTACAGGGAACCTGAGGAGACTAAGCCAGAGGATGAA
EST: gi|164188535|gb|EL992079.1|EL992079
EST:     AGAAGTGGGATGTCATG                         GTTGACCTGTTCTTTTACAGGGAACCTGAGGAGACTAAGCCAAGAGGATGA
genomic: AGAAGTGGGATGTCATGgtaagaatat ... tgttgtgcagGTTGACCTGTTCTTTTACAGGGAACCTGAGGAGACTAAGCCA-GAGGATGA
EST: gi|164109033|gb|ES161256.1|ES161256
EST:     TCCTTCAGATGCGTGGAACCATTGCTGCTGGACAGAAGTGGGATGTCATG                         GTTGACCTGTTCTTTTACAGGGAACCTGAGGAGACTAAGCCAG
genomic: TCCTTCAGATGCGTGGAACCATTGCTGCTGGACAGAAGTGGGATGTCATGgtaagaatat ... tgttgtgcagGTTGACCTGTTCTTTTACAGGGAACCTGAGGAGACTAAGCCAG
EST: gi|125136668|gb|EL176698.1|EL176698
EST:     TCCTTCAGATGCGTGGAACCATTGCTGCTGGACAGAAGTGGGATGTCATG                         GTTGACCTGTTCTTTTACAGGGAA
genomic: TCCTTCAGATGCGTGGAACCATTGCTGCTGGACAGAAGTGGGATGTCATGgtaagaatat ... tgttgtgcagGTTGACCTGTTCTTTTACAGGGAA
EST: gi|125022124|gb|EL094393.1|EL094393
EST:     AACCATTGCTGCTGGACAGAAGTGGGATGTCATG                         GTTGACCTGTTCTTTTACAGGGAACCTGAGGAGACTAA
genomic: AACCATTGCTGCTGGACAGAAGTGGGATGTCATGgtaagaatat ... tgttgtgcagGTTGACCTGTTCTTTTACAGGGAACCTGAGGAGACTAA
EST: gi|125193660|gb|EL208614.1|EL208614
EST:     AGTGGGATGTCATG                         GTTGACCTGTTCTTTTACAGGGAACCTGAGGAGACTAAGCCAGAGGATGAA
genomic: AGTGGGATGTCATGgtaagaatat ... tgttgtgcagGTTGACCTGTTCTTTTACAGGGAACCTGAGGAGACTAAGCCAGAGGATGAA
EST: gi|47830956|gb|CK120640.1|CK120640
EST:     TCCTTCAGATGCGTGGAACCATTGCTGCTGGACAGAAGTGGGATGTCATG                         GTTGACCTGTTCTTTTACAGGGAACCTGAGGAGACTAAGCCAGAGGATGAA
genomic: TCCTTCAGATGCGTGGAACCATTGCTGCTGGACAGAAGTGGGATGTCATGgtaagaatat ... tgttgtgcagGTTGACCTGTTCTTTTACAGGGAACCTGAGGAGACTAAGCCAGAGGATGAA
EST: gi|125312531|gb|EL326616.1|EL326616
EST:     CTTCAGATGCGTGGAACCATTGCTGCTGGACAGAAGTGGGATGTCATG                         GTTGACCTGTTCTTTTACAGGGAACCTGAGGAGACTAAGCCAGAGGA
genomic: CTTCAGATGCGTGGAACCATTGCTGCTGGACAGAAGTGGGATGTCATGgtaagaatat ... tgttgtgcagGTTGACCTGTTCTTTTACAGGGAACCTGAGGAGACTAAGCCAGAGGA
EST: gi|124930470|gb|EL007916.1|EL007916
EST:     TCCTTCAGATGCGTGGAACCATTGCTGCTGGACAGAAGTGGGATGTCATG                         GTTGACCTGTTCTTTTACAGGGAACCTGAGGAGACT
genomic: TCCTTCAGATGCGTGGAACCATTGCTGCTGGACAGAAGTGGGATGTCATGgtaagaatat ... tgttgtgcagGTTGACCTGTTCTTTTACAGGGAACCTGAGGAGACT
EST: gi|164161625|gb|ES128643.1|ES128643
EST:     TGGGATGTCATG                         GTTGACCTGTTCTTTTACAGGGAACCTGAGGAGACTAAGCCAGAGGATGAA
genomic: TGGGATGTCATGgtaagaatat ... tgttgtgcagGTTGACCTGTTCTTTTACAGGGAACCTGAGGAGACTAAGCCAGAGGATGAA
EST: gi|124815715|gb|EH900581.1|EH900581
EST:     TCCTTCAGATGCGTGGAACCATTGCTGCTGGACAGAAGTGGGATGTCATG                         GTTGACCTGTTCTTTTACAGGGAACCTGAGG
genomic: TCCTTCAGATGCGTGGAACCATTGCTGCTGGACAGAAGTGGGATGTCATGgtaagaatat ... tgttgtgcagGTTGACCTGTTCTTTTACAGGGAACCTGAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taaaaactttccctgtttattgactgaatttttcatatggtatggtgttgtgcagGTTGACCTGTTCTTTTACAGGGAACCTGAGGAGACTAAGCCAGAGGATGAAGATGAAGCTGGCCCTCAGGCAGAATATGGTGCACTTCCTGCTCCAGAAT
                 tattgac  putative branch site (score: 2)
                        tgaatttttcatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagaatatcattcttggagctcttagattagaaaggcatctgttcattaaaaactttccctgtttattgactgaatttttcatatggtatggtgttgtgcagGTTGACCTGTTCTTTTACAGGGAACCTGAGGAGACTAAGCCAGAGGATGAAGATGAAGCTGGCCCTCAGGCAGAATATGGTGCACTTCCTGCTCCAGAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG