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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atattattagtcaatgatatgccctccattgttaaacccatatcacctgatcatggtggtatcttctacaatattctgaatttttgtttgttatttgcagCTGAGTTTTGTGGATCTTGCTGGTTCTGAGAGAGTTAAAAAGTCGGGCTCAGCTGGTTGTCAACTCAAAGAAGCTCAAAGTATCAACAAATCACTTTCTG

Basic information

species Arabidopsis thaliana
transcript AT5G65930.2
intron # 19
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G65930.2 (Arabidopsis thaliana), 3'ss of exon 19
lower sequence: LOC_Os04g57140.2 (Oryza sativa), 3'ss of exon 21
atattattagtcaatgatatgccctccattgttaaacccatatcacctgatcatggtggtatcttctacaatattctgaatttttg---tttgttatttg--cagCTGAGTTTTGTGGATCTTGCTGGTTCTGAGAGAGTTAAAAAGTCGGGCTCAGCTGGTTGTCAACTCAAAGAAGCTCAAAGTATCAACAAATCACTTTCTG
   | |||| | ||  |||      |   ||   |   || |  |  || | | | | |  | |   |   |||||| |  | |     |||    | ||  ||||| ||||| ||||| ||||||||||||||||| || |||||||| |||||||| ||    ||||| |||||||||||||| ||||| || || |||||||
---taattaattaagaataaataaact-ctgcacagaacacactatatg-ttaagctaggctgtgagatgctattctaagctgtcaaaattttccgtgtgaacagCTAAGTTTCGTGGACCTTGCTGGTTCTGAGAGGGTGAAAAAGTCCGGCTCAGCAGGAAAACAACTGAAAGAAGCTCAAAGCATCAATAAGTCTCTTTCTG

upper sequence: AT5G65930.2 (Arabidopsis thaliana), 3'ss of exon 19
lower sequence: GRMZM2G423861_T02 (Zea mays), 3'ss of exon 20
----atattattagtcaatgatatgccct----ccattgttaaacccatatcacctgatcatggtggtatcttctacaatattctgaatttttgtttgttatttgcagCTGAGTTTTGTGGATCTTGCTGGTTCTGAGAGAGTTAAAAAGTCGGGCTCAGCTGGTTGTCAACTCAAAGAAGCTCAAAGTATCAACAAATCACTTTCTG
    | | ||||      | |   | |||    |  ||||  |     | |||| | |   |   ||          |  |||   | | ||  | |||| |   ||||| ||||||||||| ||||||||||||||||| || ||||| || || || || ||    ||||| |||||||| |||||||| |||||||| |||||||
tgtgaaactattgcatcctaaacagtccttgggcttttgtagagtttgtttcacattacacttacgggga-------agaattgacagtgttcctctgtt-tgaacagCTAAGTTTTGTGGACCTTGCTGGTTCTGAGAGGGTGAAAAAATCTGGTTCCGCAGGAAAGCAACTGAAAGAAGCACAAAGTATAAACAAATCTCTTTCTG

upper sequence: AT5G65930.2 (Arabidopsis thaliana), 3'ss of exon 19
lower sequence: GRMZM2G070273_T01 (Zea mays), 3'ss of exon 20
atattattagtc-aatgatatgccctccattgttaaacccatatcacctgatcatggtggtatcttctacaata-ttctgaatttttgtttgttatttgcagCTGAGTTTTGTGGATCTTGCTGGTTCTGAGAGAGTTAAAAAGTCGGGCTCAGCTGGTTGTCAACTCAAAGAAGCTCAAAGTATCAACAAATCACTTTCTG
|||||  |  |  ||  | |  || |    ||||  |   | ||  ||   |     |  |||       || | ||   | | ||| | |||| |   ||||| ||||||||||| ||||||||||||||||| || ||||| || || ||||| ||    ||| | |||||||| |||||||| || ||||| |||||||
atatttctgctggaactaaagtccttgagctgttgcaatta-atgtccaagtttgtttcatattaaagggaagaattgacagtgtttctctgtt-tgaacagCTAAGTTTTGTGGACCTTGCTGGTTCTGAGAGGGTGAAAAAATCAGGTTCAGCAGGAAAGCAATTGAAAGAAGCGCAAAGTATAAATAAATCTCTTTCTG

upper sequence: AT5G65930.2 (Arabidopsis thaliana), 3'ss of exon 19
lower sequence: GRMZM2G109420_T01 (Zea mays), 3'ss of exon 6
----atattattagtcaatgatatgccct--ccattgttaaacccatatcacctgatcatggtggtatcttc-tacaatattctgaatttttgtttgttatttgcagCTGAGTTTTGTGGATCTTGCTGGTTCTGAGAGAGTTAAAAAGTCGGGCTCAGCTGGTTGTCAACTCAAAGAAGCTCAAAGTATCAACAAATCACTTTCTG
       ||    | || ||  | |||    | |   ||   || ||  |      |    |   ||||| | ||| | |||   | | ||| | |||| |   ||||| ||||||||||| ||||||||||||||||| || ||||| || || ||||| ||    ||| | |||||||| |||                      
gtacgcgttgcgcgccactg-cacgccgaggcgaagctttcgccgatggcgatgactagctggcctatctacgtacga-attgacagTGTTTCTCTGTT-TGAACAGCTAAGTTTTGTGGACCTTGCTGGTTCTGAGAGGGTGAAAAAATCTGGTTCAGCAGGAAAGCAATTGAAAGAAGCGCAAG---------------------

upper sequence: AT5G65930.2 (Arabidopsis thaliana), 3'ss of exon 19
lower sequence: GLYMA01G35950.1 (Glycine max), 3'ss of exon 22
----------------------------------------------atattattagtcaatgatatgccctc---------cattgttaaaccca--tatcacctgatcatg----gtggtatcttctacaatattctgaatttttgtttgttatttg-----cagCTGAGTTTTGTGGATCTTGCTGGTTCTGAGAGAGTTAAAAAGTCGGGCTCAGCTGGTTGTCAACTCAAAGAAGCTCAAAGTATCAACAAATCACTTTCTG
                                              || ||| ||  | ||  | | || |          || | | |||| ||  |||    ||| |  |     | | |  || |  ||  || | |   |   ||||| |||||     ||| | |||||||||||||||||||| || || ||||| ||||||||||||||  | ||| ||||||| ||||||||||||||||||||||||||| | || |
gtattggtgtacattacttcaattttacctttgaatatcagtatgaatgttaatataccatattcttcctttattttgtggcaatttgaaacacaagtattttatgacctcgaggcattgcagtttttttaacttttttatgctggatttgtcatttgtcatacagTTAAGTTTTGTGGATCTTGCTGGCTCAGAAAGAGTAAAAAAGTCGGGCTCTTCAGGTAGTCAACTTAAAGAAGCTCAAAGTATCAACAAATCATTATCAG

upper sequence: AT5G65930.2 (Arabidopsis thaliana), 3'ss of exon 19
lower sequence: GLYMA11G09480.1 (Glycine max), 3'ss of exon 22
-----------------------------------------------------------atattattagtcaatgatatgcc--ctccattgttaaac-ccatatcacct--gatcatggtggtatcttctacaatattctgaattt-ttgtttgttatttgcagCTGAGTTTTGTGGATCTTGCTGGTTCTGAGAGAGTTAAAAAGTCGGGCTCAGCTGGTTGTCAACTCAAAGAAGCTCAAAGTATCAACAAATCACTTTCTG
                                                           ||||| ||  |  || || |  |   || |    |||      ||| ||||     ||  ||||  | |       |||  || |||| |  ||||| ||   ||| | |||||||||||||||||||| || || ||||| |||||||| || ||  | ||| ||||||| ||||||||||||||||||||||||||| | || |
gtattattgtacattacttgtattttacctttgaatatcagtatgaatgttagtataccatattcttcctttattatgtagcaattcgaaacataagtattgtatgacctcgaggcaatgtggattttaactttttatgttggatttgtcatttgtcat--acagTTAAGTTTTGTGGATCTTGCTGGCTCAGAAAGAGTAAAAAAGTCTGGTTCTTCAGGTAGTCAACTTAAAGAAGCTCAAAGTATCAACAAATCATTATCAG

upper sequence: AT5G65930.2 (Arabidopsis thaliana), 3'ss of exon 19
lower sequence: GLYMA09G32740.1 (Glycine max), 3'ss of exon 22
---atattattagtcaatgatatgccctccattgttaaacccat-atcacctgatcatggtggtatcttctacaatattctgaatttttgtttgttatttgcagCTGAGTTTTGTGGATCTTGCTGGTTCTGAGAGAGTTAAAAAGTCGGGCTCAGCTGGTTGTCAACTCAAAGAAGCTCAAAGTATCAACAAATCACTTTCTG
   | ||  ||  ||| || || ||       ||  | | | ||  |  | ||| | ||  || || | ||    |||| |    | |||  |   || ||||||||||||||||||||||||||||||| || ||||| |||||||| || ||  ||||  |||| || || ||||||||||| || ||||| ||| | || |
ggaaaatgtttcttcattgttaagcaacaatatggaacatcaattgtttcttgagcttga-ggcatgtgcttacttatttta---tgttggattcaatatgcagCTGAGTTTTGTGGATCTTGCTGGTTCAGAAAGAGTGAAAAAGTCAGGTTCTACTGGGAGTCAGCTTAAGGAAGCTCAAAGCATTAACAAGTCATTATCAG

upper sequence: AT5G65930.2 (Arabidopsis thaliana), 3'ss of exon 19
lower sequence: GLYMA16G21340.1 (Glycine max), 3'ss of exon 25
atattattagtcaatgatatgccctccattgttaaac--ccatatcac---ctgatcatggtggtatcttctacaatattctgaatttttgtttgtt---atttgcagCTGAGTTTTGTGGATCTTGCTGGTTCTGAGAGAGTTAAAAAGTCGGGCTCAGCTGGTTGTCAACTCAAAGAAGCTCAAAGTATCAACAAATCACTTTCTG
        ||  ||  || |   || ||||||||| |  | || |       ||||  |      | ||  |      | || | ||| | || | |   || ||||||| ||||||||||||||||||||||| || ||||| |||||||| || ||  | ||  |||| || || |||||||| || || ||||| ||| | || |
-------cagggaaaaatgt-ttcttcattgttaagcaacaatgtggaacattgattgtttcttgagctcgtggtgcgtgcttattttatcttggattcaatatgcagCTAAGTTTTGTGGATCTTGCTGGTTCAGAAAGAGTGAAAAAGTCAGGTTCTACCGGGAGTCAGCTTAAGGAAGCTCAGAGCATTAACAAGTCATTATCAG

upper sequence: AT5G65930.2 (Arabidopsis thaliana), 3'ss of exon 19
lower sequence: Vv04s0044g02020.t01 (Vitis vinifera), 3'ss of exon 21
-atat-tattagtcaatgatatgccctccattgttaaacccatatcacc-tgatcatggtggtatcttctacaatattctgaatttttgtttgttatttgcagCTGAGTTTTGTGGATCTTGCTGGTTCTGAGAGAGTTAAAAAGTCGGGCTCAGCTGGTTGTCAACTCAAAGAAGCTCAAAGTATCAACAAATCACTTTCTG
 || | | |||        | ||   |   |||||    |    | |   |||| ||| |  | | |  |   ||      ||||||       ||| ||||||| ||||||||||||||||||||||| || || || || || || |||||  | |||  |||||| || ||||||||||| |||||||| |||||||| |
aatctgtgttaacatggagtgtgagatgtcttgttggggcttacttattgtgataatgtttatttgtctttacatgac---aattttaaaactctatctgcagCTAAGTTTTGTGGATCTTGCTGGTTCAGAAAGGGTGAAGAAATCAGGCTCTTCAGGTAATCAACTTAAGGAAGCTCAAAGCATCAACAAGTCACTTTCAG

upper sequence: AT5G65930.2 (Arabidopsis thaliana), 3'ss of exon 19
lower sequence: PP1S199_47V6.1 (Physcomitrella patens), 3'ss of exon 23
atattattagtcaatgatatgccctccattgttaaacccatatcac--ctgatcatggtggtatcttcta-caatattctgaatttttgtttg---ttatttg--cagCTGAGTTTTGTGGATCTTGCTGGTTCTGAGAGAGTTAAAAAGTCGGGCTCAGCTGGTTGTCAACTCAAAGAAGCTCAAAGTATCAACAAATCACTTTCTG
            |||| | |||| |      ||   | ||| |      |    || |   ||| |  |    |  |||||||||||  ||||   || | ||  ||||||||||||||||||||||| || ||||| ||||| || || || || ||   ||||   ||||| ||||| || ||||| || || |||||  | || |
--------caagaatggtgtgccttgttagtttcgtcacattttgtaattagcaattgcactatttcttggtgaatttctgaattttattttggacttctctgagcagCTGAGTTTTGTGGATCTTGCGGGCTCTGAAAGAGTGAAGAAATCTGGATCCAGTGGTGAACAACTGAAAGAGGCCCAAAGCATTAATAAATCTTTGTCAG

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|125159594|gb|EL187604.1|EL187604
EST:     TGCTGCGAGGGGCAAG                         CTGAGTTTTGTGGATCTTGCTGGTTCTGAGAGAGTTAAAAAGTCGGGCTCA
genomic: TGCTGCGAGGGGCAAGgtgacaaaat ... ttatttgcagCTGAGTTTTGTGGATCTTGCTGGTTCTGAGAGAGTTAAAAAGTCGGGCTCA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cctgatcatggtggtatcttctacaatattctgaatttttgtttgttatttgcagCTGAGTTTTGTGGATCTTGCTGGTTCTGAGAGAGTTAAAAAGTCGGGCTCAGCTGGTTGTCAACTCAAAGAAGCTCAAAGTATCAACAAATCACTTTCTG
 acctgat  putative branch site (score: 4)
                        aatattctgaattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atattattagtcaatgatatgccctccattgttaaacccatatcacctgatcatggtggtatcttctacaatattctgaatttttgtttgttatttgcagCTGAGTTTTGTGGATCTTGCTGGTTCTGAGAGAGTTAAAAAGTCGGGCTCAGCTGGTTGTCAACTCAAAGAAGCTCAAAGTATCAACAAATCACTTTCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA
- - - - - - - - - - -ccctcca
- - - - - - - - - - - - - - - - -aaaccca
- - - - - - - - - - - - - - - - - - - - - - - ctgatca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cttctac