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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagactttatttcttgtccattaccagcattgcagaaaagctttgtttatgtaagttttacttgtcaacttttttagcctgagcttaacttgttattatgtttttgtgatttcagTTGTATGCCAATTACGCTATTGGAAAGGACGTGCAGGCCATGAAAGCCGTGGTTGGAGAAGAAGCTCTTTCTTCCGAGGATCTG

Basic information

species Arabidopsis thaliana
transcript AT4G38510.4
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G38510.4 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: LOC_Os06g37180.1 (Oryza sativa), 3'ss of exon 13
gtaagactttatttcttgtccattaccagcattgcagaaaagctttgtttatgtaagttttacttgtcaacttttttagcctgagcttaacttgttattatgtttttgtgatttcagTTGTATGCCAATTACGCTATTGGAAAGGACGTGCAGGCCATGAAAGCCGTGGTTGGAGAAGAAGCTCTTTCTTCCGAGGATCTG
                     |  |   | | | || | |     | || || |||| | |    | ||| |  ||      ||||| |     ||||  |||||   || || ||| | |||||||| || || ||||| ||||| || ||||||||||||||||| || ||||| || || || ||||| |||||||||
------------------gtaaacatttggactccatacatttgat-ttcatttaagctat----ggcaaatacttacagtggagctcat----ttatgctgtttc-atg-ttacagCTTTATGCCAACTATGCAATTGGGAAGGATGTCCAGGCCATGAAAGCCGTTGTGGGAGAGGAGGCGCTCTCTTCTGAGGATCTG

upper sequence: AT4G38510.4 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: GRMZM2G181151_T01 (Zea mays), 3'ss of exon 13
gtaagactttatttcttgtccattaccagcattgcagaaaagctttgtttatgtaagttttacttgtcaacttttttagcctgagcttaacttgttattatgtttttgtgatttcagTTGTATGCCAATTACGCTATTGGAAAGGACGTGCAGGCCATGAAAGCCGTGGTTGGAGAAGAAGCTCTTTCTTCCGAGGATCTG
    |    || |    ||||||    |   |||   |     |   |    ||   |  |||   |||    |  | |    || | || |||  ||    | |||    |||||| | |||||||| ||||| ||||||||||| || ||||||||||| || || |||||||| || || || || || |||||||||
----gtacatactatgagtccat-gttatttttgataagggagtccata---gtctttgctacccttcagacatgat-gtgcaagatgaa-ttgacatctgctgttttctctttcagCTTTATGCCAACTACGCAATTGGAAAGGATGTTCAGGCCATGAAGGCAGTCGTTGGAGAGGAGGCACTCTCGTCTGAGGATCTG

upper sequence: AT4G38510.4 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: GRMZM2G094497_T02 (Zea mays), 3'ss of exon 12
gtaagactttatttcttgtccattaccagcattgcagaaaagctttgtttatgtaagttttacttgtcaacttttttagcctgagcttaacttgttattatgtttttgtgatttcagTTGTATGCCAATTACGCTATTGGAAAGGACGTGCAGGCCATGAAAGCCGTGGTTGGAGAAGAAGCTCTTTCTTCCGAGGATCTG
                                     |     | ||  |   || | |||  ||    || |  |  |  | || | || |      ||   |||| ||  ||||| | |||||||| || |||||||||||||| || ||||||||||| || || |||||||| || || || || || |||||||||
-----------------------------------gtacctattatgagtccataggctttgttttcagacatgat--gtgtaagatgaattgacatctactgttttctg--ttcagCTTTATGCCAACTATGCTATTGGAAAGGATGTTCAGGCCATGAAGGCTGTCGTTGGAGAGGAGGCACTCTCGTCTGAGGATCTG

upper sequence: AT4G38510.4 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: GLYMA20G24070.1 (Glycine max), 3'ss of exon 14
gtaagactttatttcttgtccattaccagcattgcagaa-aagctttgtttatgtaagttttacttgtcaacttttttagcctgagcttaacttgtt-attatgtttttgtgattt-cagTTGTATGCCAATTACGCTATTGGAAAGGACGTGCAGGCCATGAAAGCCGTGGTTGGAGAAGAAGCTCTTTCTTCCGAGGATCTG
                               |  | ||  | | |||||| ||   ||||  | || ||   || |    |   ||  || ||  || ||  | ||||| |  ||| ||| | ||||| ||||| |||||||||||||| || ||||| |||||||| ||||||||||||||||| ||||| || ||||| |||
------------------------------gtctctgatcatgttttgttcatcacagtt--atttttctgtttatcacac---agactatctcattcatgttatttttatttttttcagCTCTATGCAAATTATGCTATTGGAAAGGATGTCCAGGCAATGAAAGCAGTGGTTGGAGAAGAAGCACTTTCATCTGAGGACCTG

upper sequence: AT4G38510.4 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: GLYMA10G42940.3 (Glycine max), 3'ss of exon 13
gtaagactttatttcttgtccattaccagcattgcagaaaa-gctttgtttatgtaagttttacttgtcaacttttttagcctgagcttaacttgtt-attatgtttttgtgattt-cagTTGTATGCCAATTACGCTATTGGAAAGGACGTGCAGGCCATGAAAGCCGTGGTTGGAGAAGAAGCTCTTTCTTCCGAGGATCTG
                               |  | ||    | |||||| ||   |   ||| || ||   ||  | |    ||   || ||  || ||  | ||||| |  ||| ||| | || || ||||| ||||| |||||||| |||||||| |||||||| ||||||||||||||||| ||||| || ||||| |||
------------------------------gtctctgatcttgttttgttcatcacatagttatttttctg-ttcatcacatagactatatctcattcatgttatttttatttttttcagCTCTACGCAAATTATGCTATCGGAAAGGATGTGCAGGCAATGAAAGCAGTGGTTGGAGAAGAAGCACTTTCATCTGAGGACCTG

upper sequence: AT4G38510.4 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: GLYMA18G48280.1 (Glycine max), 3'ss of exon 13
gtaagactttatttcttgtccattaccagcattgcagaaaagctttgtttatgtaagttttacttgtcaacttttttagcctgagcttaacttgttattatgtttttgtgatttcagTTGTATGCCAATTACGCTATTGGAAAGGACGTGCAGGCCATGAAAGCCGTGGTTGGAGAAGAAGCTCTTTCTTCCGAGGATCTG-
                         |  |  ||||       |    ||  | |   || |  || | |||  | | |   ||         ||||||| ||||| |    ||| || | ||||| ||||| || ||||||||||| || ||||| |||||||||||||| ||||||||||| ||||| || ||||| ||| 
------------------------tctggttttgcctgcttaccacattgctattttttctgtttataaaccatctca--ttgg--------tgttattttgtttct----tttaagcTCTATGCAAATTATGCCATTGGAAAGGATGTCCAGGCAATGAAAGCCGTGGTCGGAGAAGAAGCACTTTCATCTGAGGACCTGG

upper sequence: AT4G38510.4 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: GLYMA09G38110.1 (Glycine max), 3'ss of exon 13
gtaagactttatttcttgtccattaccagcattgcagaaaagctttgtttatgtaagttttacttgtcaacttttttagcctgagcttaacttgttattatgtttttgtgatttcagTTGTATGCCAATTACGCTATTGGAAAGGACGTGCAGGCCATGAAAGCCGTGGTTGGAGAAGAAGCTCTTTCTTCCGAGGATCTG
                                    |    | |||| || | ||    |   |||  |  |||| |      |    | ||| ||  | | || || |  |||||| | ||||| ||||| || ||||||||||| || ||||| |||||||| ||||| ||||||||||| ||||| || ||||| |||
------------------------------------gtctggttttgcttgttta---ctacattgctattttttctgtttataagccatcttattggtgttttgtt-tcttttcagCTCTATGCAAATTATGCCATTGGAAAGGATGTCCAGGCAATGAAAGCTGTGGTCGGAGAAGAAGCACTTTCATCTGAGGACCTG

upper sequence: AT4G38510.4 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: Vv03s0038g02760.t01 (Vitis vinifera), 3'ss of exon 13
gtaagactttatttcttgtccattaccagcattgcagaaaagctttgtttatgtaagttttacttgtcaacttttttagcctgagcttaacttgttattatgtttttgtgatttcagTTGTATGCCAATTACGCTATTGGAAAGGACGTGCAGGCCATGAAAGCCGTGGTTGGAGAAGAAGCTCTTTCTTCCGAGGATCTG
                                        ||  ||   | |    | |    |   |  || ||| |||  |  |  ||||    ||    || || |  |||||| | ||||| ||||| || ||||| ||||| || || || |||||||| ||||||||||||||||| |||||||| |||||||||
--------------------------------------gtagtatttgatgttcgggctgcgttcaccttctctttgagcacgt-cccaacta---atgcgattcttcttctttcagCTCTATGCAAATTATGCAATTGGGAAGGATGTTCAAGCAATGAAAGCTGTGGTTGGAGAAGAAGCACTTTCTTCTGAGGATCTG

upper sequence: AT4G38510.4 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: PP1S100_117V6.1 (Physcomitrella patens), 3'ss of exon 13
gtaagactttatttcttgtccattaccagcattgcagaaaagctttgtttatgtaagttttacttgtcaacttttttagcctgagctta-acttgttattatgtttttgtgatttcagTTGTATGCCAATTACGCTATTGGAAAGGACGTGCAGGCCATGAAAGCCGTGGTTGGAGAAGAAGCTCTTTCTTCCGAGGATCTG
       ||| | | |    |||   || | |  ||         ||  |||       | |    |  |      |||   || |||| || |   || ||||||   || |  ||||||||||| ||||| || ||||||||||| || || || ||||| || || |||||||| |||||| | ||||| || ||||||
-------tttttgtttcaagcat--gcaacttctcaagtgcctaatgcctattacgaaatcaggaatgga------tagg--gaacttacacctaacatcatgtttgcctg-tcccagTTGTATGCTAATTATGCCATTGGAAAGGATGTTCAAGCAATGAAGGCTGTCGTTGGAGAGGAAGCTTTGTCTTCAGAAGATCTG

upper sequence: AT4G38510.4 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: PP1S425_12V6.1 (Physcomitrella patens), 3'ss of exon 12
-gtaagactttatttcttgtccattaccagcattgcagaaaagctttgtttatgtaagttttacttgtcaacttttttagcctgagcttaacttgttattatgtttttgtgatttcagTTGTATGCCAATTACGCTATTGGAAAGGACGTGCAGGCCATGAAAGCCGTGGTTGGAGAAGAAGCTCTTTCTTCCGAGGATCTG
   | ||    ||   ||||     | || | |  |        |||  | ||| |   |      |||||   |||      | | ||||| || | |       |    ||| |||||||| || || || || ||||||||||| || || |||||||| || ||||| |||||||||||  | ||||| |||||||||
cacatgagagcatcatttgtg-gccatcaacttcccca-----tttttctgatgaagtctgcttgagtcaagacttt------gggtttaacatggtgtc------tacccattgcagTTGTACGCAAACTATGCGATTGGAAAGGATGTACAAGCCATGAAGGCTGTGGTGGGAGAAGAAGCCTTGTCTTCAGAGGATCTG

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|124824155|gb|EH909021.1|EH909021
EST:     CTCGCAGGGACCACTCTGATGTTTCTAATCAA                         TTGTATGCCAATTACGCTATTGGAAAGGACGTGCAGGCCATGAAAGCCGT
genomic: CTCGCAGGGACCACTCTGATGTTTCTAATCAAgtaagacttt ... gtgatttcagTTGTATGCCAATTACGCTATTGGAAAGGACGTGCAGGCCATGAAAGCCGT
EST: gi|125318034|gb|EL332119.1|EL332119
EST:     TGTTTCTAATCAA                         TTGTATGCCAATTACGCTATTGGAAAGGACGTGCAGGCCATGAAAGCCGTG
genomic: TGTTTCTAATCAAgtaagacttt ... gtgatttcagTTGTATGCCAATTACGCTATTGGAAAGGACGTGCAGGCCATGAAAGCCGTG
EST: gi|164031420|gb|EL996362.1|EL996362
EST:     CCATTGGTGAGGGTATGACTCGCAGGGACCACTCTGATGTTTCTAATCAA                         TTGTATGCCAATTACGCTATT
genomic: CCATTGGTGAGGGTATGACTCGCAGGGACCACTCTGATGTTTCTAATCAAgtaagacttt ... gtgatttcagTTGTATGCCAATTACGCTATT
EST: gi|124772760|gb|EH862889.1|EH862889
EST:     TTGGTGAGGGTATGACTCGCAGGGACCACTCTGATGTTTCTAATCAA                         TTGTATGCCAATTACGCTATTGGAAAGGACGTGCAGGCCATGAAAGCCGTG
genomic: TTGGTGAGGGTATGACTCGCAGGGACCACTCTGATGTTTCTAATCAAgtaagacttt ... gtgatttcagTTGTATGCCAATTACGCTATTGGAAAGGACGTGCAGGCCATGAAAGCCGTG
EST: gi|125166086|gb|EL192050.1|EL192050
EST:     ACCACTCTGATGTTTCTAATCAA                         TTGTATGCCAATTACGCTATTGGAAAGGACGTGCAGGCCATGAAAGCCGT
genomic: ACCACTCTGATGTTTCTAATCAAgtaagacttt ... gtgatttcagTTGTATGCCAATTACGCTATTGGAAAGGACGTGCAGGCCATGAAAGCCGT
EST: gi|116476764|gb|EG519356.1|EG519356
EST:     CCATTGGTGAGGGTATGACTCGCAGGGACCACTCTGATGTTTCTAATCAA                         TTGTATGCCAATTACGCTATTGGAAAGGACGTGCAGGCCATGAAAGCCGTG
genomic: CCATTGGTGAGGGTATGACTCGCAGGGACCACTCTGATGTTTCTAATCAAgtaagacttt ... gtgatttcagTTGTATGCCAATTACGCTATTGGAAAGGACGTGCAGGCCATGAAAGCCGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttgtcaacttttttagcctgagcttaacttgttattatgtttttgtgatttcagTTGTATGCCAATTACGCTATTGGAAAGGACGTGCAGGCCATGAAAGCCGTGGTTGGAGAAGAAGCTCTTTCTTCCGAGGATCTG
                      gcttaac  putative branch site (score: 3)
                                        tttttgt  putative PPT
                        ttaacttgttattatg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagactttatttcttgtccattaccagcattgcagaaaagctttgtttatgtaagttttacttgtcaacttttttagcctgagcttaacttgttattatgtttttgtgatttcagTTGTATGCCAATTACGCTATTGGAAAGGACGTGCAGGCCATGAAAGCCGTGGTTGGAGAAGAAGCTCTTTCTTCCGAGGATCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT