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'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttcatttgtgctggttattgttgtctacttgtcttcatgcaaagcttttctaaagaatacatgtacacttcgggtagttggcagtgttagtggcctgacaagtcatctaattgtttttcagGAAGCAACTGAACTAGGTAAAAAGGCAAGAGATCTAAAGAAAGCAGCTGATGCACTTCACCAGGAAGAACGAAGTGGTGCTAAGGGAAGGAAGTGGAGGA

Basic information

species Arabidopsis thaliana
transcript AT5G01460.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G01460.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os06g03760.2 (Oryza sativa), 3'ss of exon 5
--------gttcatttgtgctggttattg-ttgtctacttgtcttcatgcaaagcttttctaaagaatacatgta-cacttcgggtagttggcagtgttagtggcctgacaagtcatctaattgtttttcagGAAGCAACTGAACTAGGTAAAAAGGCAAGAGATCTAAAGAAAGCAGCTGATGCACTTCACCAGGAAGAACGAAGTGGTGCTAAGGGAAGGAAGTGGAGGA
         |||     | ||  || |   || |   | |   ||    | |   |||||||    ||| |  || ||||| |   | ||  || |||   | |   |||    |||   ||| || | ||||||||||||||||||||||| |||||  | ||  | |||||||||||||| || |||||||| |||||   ||||||    ||||| || || ||| | |
gtgcctatattctcacatacttcttttcaattatgagcattcattagaaccatatttttctactacatataattatcactttga--aattttcaatgtggattga--gactgaacat---att-ttctgcagGAAGCAACTGAACTAGGTAAGAAGGCTCGGGAATTGAAGAAAGCAGCTGAAGCCCTTCACCAAGAAGAGAAAAGTGGGAAGAAGGGCAGAAAATGGCGCA

upper sequence: AT5G01460.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os06g03760.3 (Oryza sativa), 3'ss of exon 3
gttcatttgtgctggttattgttgtctacttgtcttcatgcaaagcttttctaaagaatacatgta-cacttcgggtagttggcagtgttagtggcctgacaagtcatctaattgtttttcagGAAGCAACTGAACTAGGTAAAAAGGCAAGAGATCTAAAGAAAGCAGCTGATGCACTTCACCAGGAAGAACGAAGTGGTGCTAAGGGAAGGAAGTGGAGGA
               ||    || |   | |   ||    | |   |||||||    ||| |  || ||||| |   | ||  || |||   | |   |||    |||   ||| || | ||||||||||||||||||||||| |||||  | ||  | |||||||||||||| || |||||||| |||||   ||||||    ||||| || || ||| | |
---------------tttcaattatgagcattcattagaaccatatttttctactacatataattatcactttga--aattttcaatgtggattga--gactgaacat---att-ttctgcagGAAGCAACTGAACTAGGTAAGAAGGCTCGGGAATTGAAGAAAGCAGCTGAAGCCCTTCACCAAGAAGAGAAAAGTGGGAAGAAGGGCAGAAAATGGCGCA

upper sequence: AT5G01460.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA03G07890.1 (Glycine max), 3'ss of exon 5
gttcatttgtgctggttattgttgtctacttgtcttcatgcaaagcttttctaaagaatacatgtacacttcgggtagttggcagtgttagtggcctgacaagtcatctaattgtttttcagGAAGCAACTGAACTAGGTAAAAAGGCAAGAGATCTAAAGAAAGCAGCTGATGCACTTCACCAGGAAGAACGAAGTGGTGCTAAGGGAAGGAAGTGGAGGA
                   || | | | ||| | |  |     ||   | ||||| | |   || | |    |  |  |    | |||  ||||  || |  || ||    |||     ||||||||||||||||| |||||||| |||| ||| || ||||||||||||||  ||||||| ||||||||| |||||||| | ||||| ||||| |   | |
------------------gtgctatatgcttttat--agcaggagacatactaaatattgattgaatatgctgtattatatttattgt--gtggt-tggctggttat--ggttg-----cagGAAGCAACTGAACTGGGTAAAAAAGCAAAAGAACTGAAGAAAGCAGCTGAATCACTTCATCAGGAAGAAAGAAGTGGTTCGAAGGGTAGGAAATTTCGTA

upper sequence: AT5G01460.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA01G30400.1 (Glycine max), 3'ss of exon 5
gttcatttgtgctggttattgttgt-ctacttgtcttcat-gcaaagcttttctaaagaatacatgtacacttcgggtagttggcagtgttagtggcctgacaagtcatctaattgtttttcagGAAGCAACTGAACTAGGTAAAAAGGCAAGAGATCTAAAGAAAGCAGCTGATGCACTTCACCAGGAAGAACGAAGTGGTGCTAAGGGAAGGAAGTGGAGGA
                       || |||  ||  || || || |||   | |||||   |   || | |      | |||   |  | ||  |||  ||    ||    || | ||| |  |||||||||| ||||| |||||||| |||| ||| || ||||||||||||||  ||||||| ||||||||| |||||||| | ||||||||||| |   | |
-----------------------gtgctatatgcttttatagcgaagacgtactaaatgttgattgaatat-----gcagt--actatatttatggtgtggttggttggtta-tggttgt--agGAAGCAACCGAACTGGGTAAAAAAGCAAAAGAACTGAAGAAAGCAGCTGAGTCACTTCATCAGGAAGAAAGAAGTGGTTCGAAGGGAAGGAAATTTCGTA

upper sequence: AT5G01460.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA07G18160.1 (Glycine max), 3'ss of exon 5
gttcatttgtgctggttattgttgtctacttgtcttcatgcaaagcttttctaaagaatacatgtacacttcgggtagttggca-gtgttagtggcctgacaagtcatctaattgttt--ttcagGAAGCAACTGAACTAGGTAAAAAGGCAAGAGATCTAAAGAAAGCAGCTGATGCACTTCACCAGGAAGAACGAAGTGGTGCTAAGGGAAGGAAGTGGAGGA
        |||||   |||||||    |      |  ||   ||  | ||     || ||  |||  | || || ||  ||  | |   || |    | |     |  ||   || ||  |  ||||||| |||||||| |||||||| |||||||| ||||| ||||||||||| ||||| || ||||||||| |||||||| | ||||| || ||||   | |
--------gtgcta--tattgttactgaaggagat--atattaaattgtt-----gattatgtgtgtattt-ggttacatgatatgccatactatatttatggtgctcctggctggttactgtagGAAGCCACTGAACTGGGTAAAAAAGCAAGAGAACTAAAAAAAGCAGCTGAGGCACTACATCAGGAAGAAAGAAGTGGTTCAAAGGGTAGAAAGTTTCGTA

upper sequence: AT5G01460.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA18G43020.1 (Glycine max), 3'ss of exon 5
gttcatttgtgctggttattgttgtctacttgtcttcatgcaaagcttttcta-aagaatacatgtacacttcgggtagttggcagtgttagtggcctgacaagtcatctaattgtttttcagGAAGCAACTGAACTAGGTAAAAAGGCAAGAGATCTAAAGAAAGCAGCTGATGCACTTCACCAGGAAGAACGAAGTGGTGCTAAGGGAAGGAAGTGGAGGA
        |||||   |||||||    |      |  ||  || | ||   ||   |  ||  ||   |  |    |      |  | ||  |||  || |  |    ||  ||  | |  ||||||| |||||||| |||||||| || ||||| ||||||||||||||||| ||||| || ||||||||| |||||||| | ||||| || ||||   | |
--------gtgcta--tattgttactgaaggagatatattaaatggttgattatgtgtgtatttggttatatgatatgccatactatatttatggtgtggctgg----ctggttactgt--agGAAGCCACTGAACTGGGTAAAAAAGCTAGAGAACTAAAGAAAGCAGCTGAGGCACTCCATCAGGAAGAAAGAAGTGGTTCAAAGGGTAGAAAGTTTCGTA

upper sequence: AT5G01460.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA16G19230.1 (Glycine max), 3'ss of exon 4
gttcatttgtgctggttattgttgtctacttgtcttcatgcaaagcttttctaaagaatacatgtacacttcgggtagttggca-gtgttagtggcctgacaagtcatctaattgttt--ttcagGAAGCAACTGAACTAGGTAAAAAGGCAAGAGATCTAAAGAAAGCAGCTGATGCACTTCACCAGGAAGAACGAAGTGGTGCTAAGGGAAGGAAGTGGAGGA
        ||||||  |||||||    |      |  ||   ||  | ||     || ||  |||  | || || ||  ||  | |   || |    | |        ||   || ||  |  ||||||| |||||||| |||||||| |||||||| ||||| ||||||||||| ||||| || ||||||||| ||| |||| | ||||| || ||||   | |
--------gtgctg--tattgttactgaaggagat--atattaaattgtt-----gattatgtgtgtattt-ggttacatgatatgccatactatatttatggtgttcctggctggttactgtagGAAGCCACTGAACTGGGTAAAAAAGCAAGAGAACTAAAAAAAGCAGCTGAGGCACTACATCAGGAAGAAAGAACTGGTTCAAAGGGTAGAAAGTTTCGTA

upper sequence: AT5G01460.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv08s0007g02270.t01 (Vitis vinifera), 3'ss of exon 5
---gttcatttgtgctggttattgttgtctacttgtcttcatgcaaagcttttctaaagaatacatgtac---acttcgggtagttggcagtgttagtggcctgacaa--gtcatc-taattgtttttcagGAAGCAACTGAACTAGGTAAAAAGGCAAGAGATCTAAAGAAAGCAGCTGATGCACTTCACCAGGAAGAACGAAGTGGTGCTAAGGGAAGGAAGTGGAGGA
    | | ||| | ||  ||| |  ||  | | ||| | |||   ||  | |   ||    |     ||    |    || || |||   || | | |  | |    |  ||  || |   | |  |  ||||||| ||||||||||||||||||||||||||  | |||||||| |||||||| || || ||||||||| |||||||| | ||||| || |||||| | |
gtgctgctttttttctttttaatagtgcat-cgtgtatccatttgaaattatctaaatatttttggttatgtgatgatggatatttgcatgtttcaatcacttatggatggttgtcattgatatcctgtagGAAGCCACTGAACTAGGTAAAAAGGCAAGAGACTTGAAGAAAGCGGCTGATGCGCTCCATCAGGAAGAAAGAAGTGGTTCCAAGGGTAGAAAGTGGCGTA

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|164219494|gb|ES058672.1|ES058672
EST:     CATTCATCAGGCGACCAAAGGCTGTTATCACTCGGTCACAGTATATAAAG                         GAAGCAACTGAACTAGGTAAA
genomic: CATTCATCAGGCGACCAAAGGCTGTTATCACTCGGTCACAGTATATAAAGgttcatttgt ... tgtttttcagGAAGCAACTGAACTAGGTAAA
EST: gi|164220496|gb|ES039604.1|ES039604
EST:     CATTCATCAGGCGACCAAAGGCTGTTATCACTCGGTCACAGTATATAAAG                         GAAGCAACTGAACTAGGTAAA
genomic: CATTCATCAGGCGACCAAAGGCTGTTATCACTCGGTCACAGTATATAAAGgttcatttgt ... tgtttttcagGAAGCAACTGAACTAGGTAAA
EST: gi|125125560|gb|EL170995.1|EL170995
EST:     CATTCATCAGGCGACCAAAGGCTGTTATCACTCGGTCACAGTATATAAAG                         GAAGCAACTGAACT
genomic: CATTCATCAGGCGACCAAAGGCTGTTATCACTCGGTCACAGTATATAAAGgttcatttgt ... tgtttttcagGAAGCAACTGAACT
EST: gi|125207286|gb|EL222240.1|EL222240
EST:     ATTCATCAGGCGAACCAAAGGCTGTTATCACTCGGTCACAGTATATAAAG                         GAAGCAACTGAACTACGGTAAAAAGG
genomic: ATTCATCAGGCG-ACCAAAGGCTGTTATCACTCGGTCACAGTATATAAAGgttcatttgt ... tgtttttcagGAAGCAACTGAACTA-GGTAAAAAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acttcgggtagttggcagtgttagtggcctgacaagtcatctaattgtttttcagGAAGCAACTGAACTAGGTAAAAAGGCAAGAGATCTAAAGAAAGCAGCTGATGCACTTCACCAGGAAGAACGAAGTGGTGCTAAGGGAAGGAAGTGGAGGA
                                      atctaat  putative branch site (score: 3)
                                            ttgtttttc  CT-rich tract
                                      atctaattgttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttcatttgtgctggttattgttgtctacttgtcttcatgcaaagcttttctaaagaatacatgtacacttcgggtagttggcagtgttagtggcctgacaagtcatctaattgtttttcagGAAGCAACTGAACTAGGTAAAAAGGCAAGAGATCTAAAGAAAGCAGCTGATGCACTTCACCAGGAAGAACGAAGTGGTGCTAAGGGAAGGAAGTGGAGGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA