Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtttgtttaagtaaagttgttaacacacttcccttattcggtacttgagctgatgatgatccatgtcacgactcttacagGAACTGGATAGACAAGTTCCACTGATGGATGAAATCGACACAAAG

Basic information

species Arabidopsis thaliana
transcript AT3G09740.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G09740.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os05g48020.1 (Oryza sativa), 3'ss of exon 5
gtgagtttgtttaagtaaagttgt-taacacacttccct--tattcggtacttgagctgatgatgat--ccatgtcacgactctta-------cagGAACTGGATAGACAAGTTCCACTGATGGATGAAATCGACACAAAG
||  |||  | |   | |  |||  | | ||| | |  |   || |  |  ||      |  ||  |  |||||   | | | ||        |||||||||||||| ||||||||  ||||||||||||| |||   |||
gttggttgctgtgcttcatcttgagttatacaatactatacgatgcaatggttatatgaaacatagttaccatgct-caatttttgtgatcatcagGAACTGGATAGGCAAGTTCCCTTGATGGATGAAATGGACGAGAAG

upper sequence: AT3G09740.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA19G36410.1 (Glycine max), 3'ss of exon 5
gtgagtttgtttaagtaaagttgttaacacacttcccttattcggtacttgagctgatgatgatccatgtcacgactcttacagGAACTGGATAGACAAGTTCCACTGATGGATGAAATCGACACAAAG
|| || ||  |   |||    | ||       ||   |  ||   | |      | | | | ||   |       |   ||||||||||||||||||||||||||||||||||||| ||||| || |||
gtcagattcctgttgtatttgtctttctttctttttgtgtttattttcccacatttaagttcattatttatgtaccaaatacagGAACTGGATAGACAAGTTCCACTGATGGATGAGATCGATACTAAG

upper sequence: AT3G09740.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA10G05870.1 (Glycine max), 3'ss of exon 6
-------gtgagtttgtttaagtaaagttgttaacacacttcccttattcg-gtacttgagctgatgatgatccatgtcacgactctt---------acagGAACTGGATAGACAAGTTCCACTGATGGATGAAATCGACACAAAG
          |  || || |  |||  |||||   |  |||||||| | || ||   ||   | ||  |     |  | |  | |  |         |||||||||||||||||||||||||||||||||||| || ||||| |||
tgtcggaaccaaatttttaatttaaccttgtttttat-cttcccttgtgcgtgtgtatgttttaatcctttctaagtttattatttatgtgttgaatacagGAACTGGATAGACAAGTTCCACTGATGGATGAGATTGACACTAAG

upper sequence: AT3G09740.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA03G33680.1 (Glycine max), 3'ss of exon 5
gtgagtttgtttaagtaaa-gttgttaacacacttcccttattcggtacttgagctga--tgatgatccatgtcacgactcttacagGAACTGGATAGACAAGTTCCACTGATGGATGAAATCGACACAAAG
|| || ||  |   ||    ||  ||  |   |||    | | |    |   |  | |  | || ||  ||||  | | |   ||||||||||||||||||||||||||||||||| || || || || |||
gtcagattcctgttgtgtttgtctttctctttctttttgtgtccccccccacatttaagttcattatttatgtaccaaat---acagGAACTGGATAGACAAGTTCCACTGATGGACGAGATTGATACTAAG

upper sequence: AT3G09740.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA13G20220.1 (Glycine max), 3'ss of exon 5
---gtgagtttgtttaagtaaagttgttaacacacttcccttattcg---gtacttgagct--gatgatgatccatgtcacgactctt---------acagGAACTGGATAGACAAGTTCCACTGATGGATGAAATCGACACAAAG
      |  || || |  |||  |||||   |  |||||||| |  |   || | || | |   ||  |  |  |  |||  | |  |         ||||||||||||||||||||||||||| ||||| || || ||||| |||
agaaccaaatttttaatttaaccttgtttttat-cttcccttgtgtgcgcgtgcgtgtgttttaatcctttttaagttcattatttatgtgttgaatacagGAACTGGATAGACAAGTTCCACTTATGGACGAGATTGACACTAAG

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|86081762|gb|DR377521.1|DR377521
EST:     TCTCCGAAGGGTTAGATGCTTTGAAGAACATGGCTTCTGATATGAACGAG                         GAACTGGATAGACAAGTTCCACTGATGGATGAAATCGACACAAAG
genomic: TCTCCGAAGGGTTAGATGCTTTGAAGAACATGGCTTCTGATATGAACGAGgtgagtttgt ... actcttacagGAACTGGATAGACAAGTTCCACTGATGGATGAAATCGACACAAAG
EST: gi|164234219|gb|EL981032.1|EL981032
EST:     GGGTTAGATGCTTTGAAGAACATGGCTTCTGATATGAACGAG                         GAACTGGATAGACAAGTTCCACTGATGGATGAAATCGACACAAAGGTGGAC
genomic: GGGTTAGATGCTTTGAAGAACATGGCTTCTGATATGAACGAGgtgagtttgt ... actcttacagGAACTGGATAGACAAGTTCCACTGATGGATGAAATCGACACAAAGGTGGAC
EST: gi|116431994|gb|EG474586.1|EG474586
EST:     TCTCCGAAGGGTTAGATGCTTTGAAGAACATGGCTTCTGATATGAACGAG                         GAACTGGATAGACAAGTTCCACTGATGGATGAAATCGACACAAAG
genomic: TCTCCGAAGGGTTAGATGCTTTGAAGAACATGGCTTCTGATATGAACGAGgtgagtttgt ... actcttacagGAACTGGATAGACAAGTTCCACTGATGGATGAAATCGACACAAAG
EST: gi|125318072|gb|EL332157.1|EL332157
EST:     TCTCCGAAGGGTTAGATGCTTTGAAGAACATGGCTTCTGATATGAACGAG                         GAACTGGATAGACAAGTTCCACTGATGGATGAAATC
genomic: TCTCCGAAGGGTTAGATGCTTTGAAGAACATGGCTTCTGATATGAACGAGgtgagtttgt ... actcttacagGAACTGGATAGACAAGTTCCACTGATGGATGAAATC
EST: gi|86084593|gb|DR380352.1|DR380352
EST:     TCTCCGAAGGGTTAGATGCTTTGAAGAACATGGCTTCTGATATGAACGAG                         GAACTGGATAGACAAGTTCCACTGATGGATGAAATCGACACAAAG
genomic: TCTCCGAAGGGTTAGATGCTTTGAAGAACATGGCTTCTGATATGAACGAGgtgagtttgt ... actcttacagGAACTGGATAGACAAGTTCCACTGATGGATGAAATCGACACAAAG
EST: gi|125080705|gb|EL142210.1|EL142210
EST:     ATGGCTTCTGATATGAACGAG                         GAACTGGATAGACAAGTTCCACTGATGGATGAAATCGACACAAAG
genomic: ATGGCTTCTGATATGAACGAGgtgagtttgt ... actcttacagGAACTGGATAGACAAGTTCCACTGATGGATGAAATCGACACAAAG
EST: gi|125295292|gb|EL309377.1|EL309377
EST:     GATATGAACGAG                         GAACTGGATAGACAAGTTCCACTGATGGATGAAATCGACACAAAGGTGGA
genomic: GATATGAACGAGgtgagtttgt ... actcttacagGAACTGGATAGACAAGTTCCACTGATGGATGAAATCGACACAAAGGTGGA
EST: gi|116435937|gb|EG478529.1|EG478529
EST:     TCTCCGAAGGGTTAGATGCTTTGAAGAACATGGCTTCTGATATGAACGAG                         GAACTGGATAGACAAGTTCCACTGATGGATGAAATCGACACAAAG
genomic: TCTCCGAAGGGTTAGATGCTTTGAAGAACATGGCTTCTGATATGAACGAGgtgagtttgt ... actcttacagGAACTGGATAGACAAGTTCCACTGATGGATGAAATCGACACAAAG
EST: gi|125004744|gb|EL077013.1|EL077013
EST:     GATATGAACGAG                         GAACTGGATAGACAAGTTCCACTGATGGATGAAATCGACACAAAG
genomic: GATATGAACGAGgtgagtttgt ... actcttacagGAACTGGATAGACAAGTTCCACTGATGGATGAAATCGACACAAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cacttcccttattcggtacttgagctgatgatgatccatgtcacgactcttacagGAACTGGATAGACAAGTTCCACTGATGGATGAAATCGACACAAAG
                      agctgat  putative branch site (score: 4)
                                              ctcttac  putative PPT
        ttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtttgtttaagtaaagttgttaacacacttcccttattcggtacttgagctgatgatgatccatgtcacgactcttacagGAACTGGATAGACAAGTTCCACTGATGGATGAAATCGACACAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA