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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtccttttaccctttcattttcattttttttcagtttccttcatttatacttacaagtagctacagtctctgaaactttgattcttccttcttgatcagGGTCTTGAGGCTGCAGGCTGGACACAAATACTGTCTGTTGGGTCGCCTTTCTTCTGAAGTCGGGTGGAACCACTACGACACCATCAAG

Basic information

species Arabidopsis thaliana
transcript AT3G07110.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G07110.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv05s0029g00020.t01 (Vitis vinifera), 3'ss of exon 2
gtttgtccttttaccctttcattttcattttttttcagtt-tccttcatttatacttacaagtagctacagtctctgaaactttgattcttcc--ttcttg-----atcagGGTCTTGAGGCTGCAGGCTGGACACAAATACTGTCTGTTGGGTCGCCTTTCTTCTGAAGTCGGGTGGAACCACTACGACACCATCAAG
    ||   ||     ||| | ||| ||||||| |   || |  || |||||  | || || |   |   |  | ||| ||||| || |||    || |||     |||||||| |||||||| || ||||| ||||| |||||  |||||||  | ||||| || || || || ||||||||||| || |||||||||
----gtgagttctgtatttgagttttattttttattttttattttttatttaggcctataaattcttgttgg-tttgagactttaatgcttgagatttttgggaaaatcagGGTTTTGAGGCTTCAAGCTGGGCACAAGTACTGCTTGTTGGGCAGGCTTTCATCAGAGGTGGGATGGAACCACTATGAAACCATCAAG

upper sequence: AT3G07110.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: PP1S165_40V6.1 (Physcomitrella patens), 3'ss of exon 3
gtttgtccttttaccctttcattttcattttttttcagtttccttcat-ttatacttacaa-gtagctacagtctctgaaactttgattcttcc-ttcttgatcagGGTCTTGAGGCTGCAGGCTGGACACAAATACTGTCTGTTGGGTCGCCTTTCTTCTGAAGTCGGGTGGAACCACTACGACACCATCAAG
 |      | | |   ||  ||| | | |||| ||   || | | |   || |  | ||||  |  |  ||    ||||  | |  || || |   ||    ||||||| |||||||||||| |||| ||||||| |||| ||||||| ||| | ||    || ||||| ||| | || |||||||||||||||
-tccacattatgatgatt--attattacttttatt--attacttccgcgttgtggtcacaatatcacagcacgtgctgat-cctgaatactacggctccacttcagGGTGTTGAGGCTGCAGCCTGGCCACAAATTCTGTTTGTTGGGACGCTTGTCAGAGGAGGTCGGATGGCATCATTACGACACCATCAAG
















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|47832259|gb|CK121943.1|CK121943
EST:     CCTACTCCATATGACAAGATCAAGAGGATGGTCGTTCCTGATGCTCTCAA                         GGTCTTGAGGCTGCAGGCTGGACACAAATACTGTCTGTTGGGTCGCCTTTC
genomic: CCTACTCCATATGACAAGATCAAGAGGATGGTCGTTCCTGATGCTCTCAAgtttgtcctt ... tcttgatcagGGTCTTGAGGCTGCAGGCTGGACACAAATACTGTCTGTTGGGTCGCCTTTC
EST: gi|116476045|gb|EG518637.1|EG518637
EST:     CCTACTCCATATGACAAGATCAAGAGGATGGTCGTTCCTGATGCTCTCAA                         GGTCTTGAGGCTGCAGGCTGGACACAAATACTGTCTGTTGGGTCGCCTTTC
genomic: CCTACTCCATATGACAAGATCAAGAGGATGGTCGTTCCTGATGCTCTCAAgtttgtcctt ... tcttgatcagGGTCTTGAGGCTGCAGGCTGGACACAAATACTGTCTGTTGGGTCGCCTTTC
EST: gi|116476043|gb|EG518635.1|EG518635
EST:     CCTACTCCATATGACAAGATCAAGAGGATGGTCGTTCCTGATGCTCTCAA                         GGTCTTGAGGCTGCAGGCTGGACACAAATACTGTCTGTTGGGTCGCCTTTC
genomic: CCTACTCCATATGACAAGATCAAGAGGATGGTCGTTCCTGATGCTCTCAAgtttgtcctt ... tcttgatcagGGTCTTGAGGCTGCAGGCTGGACACAAATACTGTCTGTTGGGTCGCCTTTC
EST: gi|47828023|gb|CK117707.1|CK117707
EST:     CCTACTCCATATGACAAGATCAAGAGGATGGTCGTTCCTGATGCTCTCAA                         GGTCTTGAGGCTGCAGGCTGGACACAAATACTGTCTGTTGGGTCGCCTTTC
genomic: CCTACTCCATATGACAAGATCAAGAGGATGGTCGTTCCTGATGCTCTCAAgtttgtcctt ... tcttgatcagGGTCTTGAGGCTGCAGGCTGGACACAAATACTGTCTGTTGGGTCGCCTTTC
EST: gi|124998364|gb|EL070633.1|EL070633
EST:     CTACTCCATATGACAAGATCTAAGAGGATGGTCGTTCCTGATGCTCTCAA                         GGTCTTGAGGCTGCAGGCTGGACACAAATACTGT
genomic: CTACTCCATATGACAAGATC-AAGAGGATGGTCGTTCCTGATGCTCTCAAgtttgtcctt ... tcttgatcagGGTCTTGAGGCTGCAGGCTGGACACAAATACTGT
EST: gi|164237726|gb|ES111608.1|ES111608
EST:     CTACCTCCATATGACAAGATCAAGAGGATGGTCGTTCCTGATGCTCTCAA                         GGTCTTGAGGCTGCAGGCTGGAC
genomic: CTA-CTCCATATGACAAGATCAAGAGGATGGTCGTTCCTGATGCTCTCAAgtttgtcctt ... tcttgatcagGGTCTTGAGGCTGCAGGCTGGAC
EST: gi|164028574|gb|ES114297.1|ES114297
EST:     GGATGGT-GTTCCTGATGCTCTCAA                         GGTCTTGAGGCTGCAGGCTGGACACAAATACTGTCTGTTGGGTCGCCTTTC
genomic: GGATGGTCGTTCCTGATGCTCTCAAgtttgtcctt ... tcttgatcagGGTCTTGAGGCTGCAGGCTGGACACAAATACTGTCTGTTGGGTCGCCTTTC
EST: gi|124991924|gb|EL064193.1|EL064193
EST:     CCTACTCCATATGACAAGATCAAGAGGATGGTCGTTCCTGATGCTCTCAA                         GGTCTTGAGGCTGCAGGCTGGACACAAATACTGT
genomic: CCTACTCCATATGACAAGATCAAGAGGATGGTCGTTCCTGATGCTCTCAAgtttgtcctt ... tcttgatcagGGTCTTGAGGCTGCAGGCTGGACACAAATACTGT
EST: gi|164126500|gb|ES025351.1|ES025351
EST:     AAGAGGATGGTCGTTCCTGATGCTCTCAA                         GGTCTTGAGGCTGCAGGCTGGACACAAATACTGTCTGTTGGGTCGCCTTTC
genomic: AAGAGGATGGTCGTTCCTGATGCTCTCAAgtttgtcctt ... tcttgatcagGGTCTTGAGGCTGCAGGCTGGACACAAATACTGTCTGTTGGGTCGCCTTTC
EST: gi|164125823|gb|ES167477.1|ES167477
EST:     GATCAAGAGGATGGTCGTTCCTGATGCTCTCAA                         GGTCTTGAGGCTGCAGGCTGGACACAAATACTGTCTGTTGGGTCGTCCTTT
genomic: GATCAAGAGGATGGTCGTTCCTGATGCTCTCAAgtttgtcctt ... tcttgatcagGGTCTTGAGGCTGCAGGCTGGACACAAATACTGTCTGTTGGGTCG-CCTTT
EST: gi|116476053|gb|EG518645.1|EG518645
EST:     CCTACTCCATATGACAAGATCAAGAGGATGGTCGTTCCTGATGCTCTCAA                         GGTCTTGAGGCTGCAGGCTGGACACAAATACTGTCTGTTGGGTCGCCTTTT
genomic: CCTACTCCATATGACAAGATCAAGAGGATGGTCGTTCCTGATGCTCTCAAgtttgtcctt ... tcttgatcagGGTCTTGAGGCTGCAGGCTGGACACAAATACTGTCTGTTGGGTCGCCTTTC
EST: gi|124918200|gb|EH992062.1|EH992062
EST:     CCTACTCCATATGACAAGATCAAGAGGATGGTCGTTCCTGATGCTCTCAA                         GGTCTTGAGGCTGCAGGCTGGACACAAA
genomic: CCTACTCCATATGACAAGATCAAGAGGATGGTCGTTCCTGATGCTCTCAAgtttgtcctt ... tcttgatcagGGTCTTGAGGCTGCAGGCTGGACACAAA
EST: gi|116476052|gb|EG518644.1|EG518644
EST:     CCTACTCCATATGACAAGATCAAGAGGATGGTCGTTCCTGATGCTCTCAA                         GGTCTTGAGGCTGCAGGCTGGACACAAATACTGTCTGTTGGGTCGCCTTTC
genomic: CCTACTCCATATGACAAGATCAAGAGGATGGTCGTTCCTGATGCTCTCAAgtttgtcctt ... tcttgatcagGGTCTTGAGGCTGCAGGCTGGACACAAATACTGTCTGTTGGGTCGCCTTTC
EST: gi|86071402|gb|DR367159.1|DR367159
EST:     CCTACTCCATATGACAAGATCAAGAGGATGGTCGTTCCTGATGCTCTCAA                         GGTCTTGAGGCTGCAGGCTGGACACAAATACTGTCTGTTGGGTCGCCTTTC
genomic: CCTACTCCATATGACAAGATCAAGAGGATGGTCGTTCCTGATGCTCTCAAgtttgtcctt ... tcttgatcagGGTCTTGAGGCTGCAGGCTGGACACAAATACTGTCTGTTGGGTCGCCTTTC
EST: gi|125070425|gb|EL135839.1|EL135839
EST:     CCATATGACAAGATCAAGAGGATGGTCGTTCCTGATGCTCTCAA                         GGTCTTGAGGCTGCAGGCTGGACACAAATACTGTCTGTTGGGTCG
genomic: CCATATGACAAGATCAAGAGGATGGTCGTTCCTGATGCTCTCAAgtttgtcctt ... tcttgatcagGGTCTTGAGGCTGCAGGCTGGACACAAATACTGTCTGTTGGGTCG
EST: gi|164004429|gb|ES139760.1|ES139760
EST:     CCTACTCCATATGACAAGATCAAGAGGATGGTCGTTCCTGATGCTCTCAA                         GGTTCTTGAGGCTGCAGGCTGGACACAAA
genomic: CCTACTCCATATGACAAGATCAAGAGGATGGTCGTTCCTGATGCTCTCAAgtttgtcctt ... tcttgatcagGGT-CTTGAGGCTGCAGGCTGGACACAAA
EST: gi|47828463|gb|CK118147.1|CK118147
EST:     CCTACTCCATATGACAAGATCAAGAGGATGGTCGTTCCTGATGCTCTCAA                         GGTCTTGAGGCTGCAGGCTGGACACAAATACTGTCTGTTGGGTCGCCTTTC
genomic: CCTACTCCATATGACAAGATCAAGAGGATGGTCGTTCCTGATGCTCTCAAgtttgtcctt ... tcttgatcagGGTCTTGAGGCTGCAGGCTGGACACAAATACTGTCTGTTGGGTCGCCTTTC
EST: gi|164090559|gb|ES204970.1|ES204970
EST:     CCTACTCCATATGACAAGATCAAGAGGATGGTCGTTCCTGATGCTCTCAA                         GGTCTTGAGGCTGCAGGCTGG
genomic: CCTACTCCATATGACAAGATCAAGAGGATGGTCGTTCCTGATGCTCTCAAgtttgtcctt ... tcttgatcagGGTCTTGAGGCTGCAGGCTGG
EST: gi|86071400|gb|DR367157.1|DR367157
EST:     CCTACTCCATATGACAAGATCAAGAGGATGGTCGTTCCTGATGCTCTCAA                         GGTCTTGAGGCTGCAGGCTGGACACAAATACTGTCTGTTGGGTCGCCTTTC
genomic: CCTACTCCATATGACAAGATCAAGAGGATGGTCGTTCCTGATGCTCTCAAgtttgtcctt ... tcttgatcagGGTCTTGAGGCTGCAGGCTGGACACAAATACTGTCTGTTGGGTCGCCTTTC
EST: gi|124855338|gb|EH939775.1|EH939775
EST:     CCATATGACAAGATCAAGAGGATGGTCGTTCCTGATGCTCTCAA                         GGTCTTGAGGCTGCAGGCTGGACACAAATACTGTCTGTTGGGTCGCCTTT
genomic: CCATATGACAAGATCAAGAGGATGGTCGTTCCTGATGCTCTCAAgtttgtcctt ... tcttgatcagGGTCTTGAGGCTGCAGGCTGGACACAAATACTGTCTGTTGGGTCGCCTTT
EST: gi|163966499|gb|ES185804.1|ES185804
EST:     CCTACTCCATATGACAAGATCAAGAGGATGGTCGTTCCTGATGCTCTCAA                         GGTCTTGAGGCTGCAGG
genomic: CCTACTCCATATGACAAGATCAAGAGGATGGTCGTTCCTGATGCTCTCAAgtttgtcctt ... tcttgatcagGGTCTTGAGGCTGCAGG
EST: gi|86071403|gb|DR367160.1|DR367160
EST:     CCTACTCCATATGACAAGATCAAGAGGATGGTCGTTCCTGATGCTCTCAA                         GGTCTTGAGGCTGCAGGCTGGACACAAATACTGTCTGTTGGGTCGCCTTTC
genomic: CCTACTCCATATGACAAGATCAAGAGGATGGTCGTTCCTGATGCTCTCAAgtttgtcctt ... tcttgatcagGGTCTTGAGGCTGCAGGCTGGACACAAATACTGTCTGTTGGGTCGCCTTTC
EST: gi|125000163|gb|EL072432.1|EL072432
EST:     CCTACTCCATATGACAAGATCAAGAGGATGGTCGTTCCTGATGCTCTCAA                         GGTCTTGAGGCTGCAGGCTGGACACAAATA
genomic: CCTACTCCATATGACAAGATCAAGAGGATGGTCGTTCCTGATGCTCTCAAgtttgtcctt ... tcttgatcagGGTCTTGAGGCTGCAGGCTGGACACAAATA
EST: gi|47832308|gb|CK121992.1|CK121992
EST:     CCTACTCCATATGACAAGATCAAGAGGATGGTCGTTCCTGATGCTCTCAA                         GGTCTTGAGGCTGCAGGCTGGACACAAATACTGTCTGTTGGGTCGCCTTTC
genomic: CCTACTCCATATGACAAGATCAAGAGGATGGTCGTTCCTGATGCTCTCAAgtttgtcctt ... tcttgatcagGGTCTTGAGGCTGCAGGCTGGACACAAATACTGTCTGTTGGGTCGCCTTTC
EST: gi|47830930|gb|CK120614.1|CK120614
EST:     CCTACTCCATATGACAAGATCAAGAGGATGGTCGTTCCTGATGCTCTCAA                         GGTCTTGAGGCTGCAGGCTGGACACAAATACTGTCTGTTGGGTCGCCTTTC
genomic: CCTACTCCATATGACAAGATCAAGAGGATGGTCGTTCCTGATGCTCTCAAgtttgtcctt ... tcttgatcagGGTCTTGAGGCTGCAGGCTGGACACAAATACTGTCTGTTGGGTCGCCTTTC
EST: gi|124858960|gb|EH943397.1|EH943397
EST:     TATGACAAGATCAAGAGGATGGTCGTTCCTGATGCTCTCAA                         GGTCTTGAGGCTGCAGGCTGGACACAAATACTGTCTGTTGGGTCG
genomic: TATGACAAGATCAAGAGGATGGTCGTTCCTGATGCTCTCAAgtttgtcctt ... tcttgatcagGGTCTTGAGGCTGCAGGCTGGACACAAATACTGTCTGTTGGGTCG
EST: gi|116447425|gb|EG490017.1|EG490017
EST:     CCTACTCCATATGACAAGATCAAGAGGATGGTCGTTCCTGATGCTCTCAA                         GGTCTTGAGGCTGCAGGCTGGACACAAA
genomic: CCTACTCCATATGACAAGATCAAGAGGATGGTCGTTCCTGATGCTCTCAAgtttgtcctt ... tcttgatcagGGTCTTGAGGCTGCAGGCTGGACACAAA
EST: gi|116476054|gb|EG518646.1|EG518646
EST:     CCTACTCCATATGACAAGATCAAGAGGATGGTCGTTCCTGATGCTCTCAA                         GGTCTTGAGGCTGCAGGCTGGACACAAATACTGTCTGTTGGGTCGCCTTTC
genomic: CCTACTCCATATGACAAGATCAAGAGGATGGTCGTTCCTGATGCTCTCAAgtttgtcctt ... tcttgatcagGGTCTTGAGGCTGCAGGCTGGACACAAATACTGTCTGTTGGGTCGCCTTTC
EST: gi|124836536|gb|EH920975.1|EH920975
EST:     CCTACTCCATATGACAAGATCAAGAGGATGGTCGTTCCTGATGCTCTCAA                         GGTCTTGAGGCTGCAGGCTGGACACAAATACTGTCTG
genomic: CCTACTCCATATGACAAGATCAAGAGGATGGTCGTTCCTGATGCTCTCAAgtttgtcctt ... tcttgatcagGGTCTTGAGGCTGCAGGCTGGACACAAATACTGTCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttatacttacaagtagctacagtctctgaaactttgattcttccttcttgatcagGGTCTTGAGGCTGCAGGCTGGACACAAATACTGTCTGTTGGGTCGCCTTTCTTCTGAAGTCGGGTGGAACCACTACGACACCATCAAG
                               ctttgattcttccttc  CT-rich tract
                            aaacttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgtccttttaccctttcattttcattttttttcagtttccttcatttatacttacaagtagctacagtctctgaaactttgattcttccttcttgatcagGGTCTTGAGGCTGCAGGCTGGACACAAATACTGTCTGTTGGGTCGCCTTTCTTCTGAAGTCGGGTGGAACCACTACGACACCATCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA