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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaattacatgtttttaaaaaaaatcttaatatgttacttttaatctcatgtgatggttttaatctcaatatgtgtgttaatagGATTTTGAATTTGAAGAGTTTGATGAAGTTCTGAAATACTACCCTCATGGTTATCATGGTGTTGATAAAGAAGGAAGGCCTGTTTACATTGAAAGATTAG

Basic information

species Arabidopsis thaliana
transcript AT1G75370.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G75370.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os02g04020.1 (Oryza sativa), 3'ss of exon 4
----gtgaa-ttacatgtttttaaaaaaaatcttaatatgttacttttaatctcatgtgatggttttaatctcaatatgtgtgttaatagGATTTTGAATTTGAAGAGTTTGATGAAGTTCTGAAATACTACCCTCATGGTTATCATGGTGTTGATAAAGAAGGAAGGCCTGTTTACATTGAAAGATTAG
    |||   || | |||   || |||| |  ||      ||   |||      |  | |||  | |||      ||  | | |   ||||||||||| |   | ||||| || |  |||||| |||| || ||||| ||||||||||| ||||| ||||| || || |||||||| ||||||||  | |
gttagtgttcttgcttgtgcctataaaacaatttgg---attttgtttggctataaataatgcctgtaac-----tacatttctctgtagGATTTTGATTACAATGAGTTAGACGCTGTTCTGCAATATTATCCTCACGGTTATCATGGAGTTGACAAAGACGGGAGACCTGTTTATATTGAAAGGCTTG

upper sequence: AT1G75370.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G073571_T03 (Zea mays), 3'ss of exon 3
--------gtgaa-ttacatgtttttaaaaaaaatcttaat-atgttacttttaatctcatgtgatggttttaatctcaatatgtgtgttaatagGATTTTGAATTTGAAGAGTTTGATGAAGTTCTGAAATACTACCCTCATGGTTATCATGGTGTTGATAAAGAAGGAAGGCCTGTTTACATTGAAAGATTAG
         |||  |||     ||||  |     | | | | || |  ||  |    | |    |||     |||     ||||||| |  |||||| || ||||     |||||       ||| || |||| || ||||||||||||||||| ||||| ||||| || || |||||||||||||||||  | |
gttattggctgagcttattcagtttttcactttgtttgatttatatggctcctgtcttaaaacaatgaccggaattattttatgtgt-tccatagGACTTCGAATACACTGAGTTGAGCACCGTTTTGCAATATTATCCTCATGGTTATCATGGAGTTGACAAAGAGGGGAGACCTGTTTACATTGAAAGGCTTG

upper sequence: AT1G75370.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G171354_T03 (Zea mays), 3'ss of exon 4
--------------gtgaattacatgtttttaaaaaaaatcttaat-atgttacttttaatctcatgtgatggttttaatctcaatatgtgtgtta-atagGATTTTGAATTTGAAGAGTTTGATGAAGTTCTGAAATACTACCCTCATGGTTATCATGGTGTTGATAAAGAAGGAAGGCCTGTTTACATTGAAAGATTAG
               | | | | |  ||||| ||     | |   | || |  ||  |    | |    ||  | | ||  ||| | ||||| ||  |||||| || ||||     ||||| || |  ||| || |||| || ||||||||||||||||| ||||| ||||| || || || ||||| ||||||||  | |
gtcagtgtctgagctttagtcagacattttttaagtttgtttggcttatatggctcctgtcttaaaacaataatctgaaa-tcattttgtgtttttcatagGACTTCGAATACACTGAGTTGGACGCTGTTTTGCAATATTATCCTCATGGTTATCATGGAGTTGACAAAGAGGGGAGACCCGTTTATATTGAAAGGCTTG

upper sequence: AT1G75370.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA06G03300.1 (Glycine max), 3'ss of exon 3
------------gtgaatta-catgtttttaaa--aaaaatcttaatat--gttacttttaatctcatgtgat---ggtttta-----atctcaatatgtgtgtta----atagGATTTTGAATTTGAAGAGTTTGATGAAGTTCTGAAATACTACCCTCATGGTTATCATGGTGTTGATAAAGAAGGAAGGCCTGTTTACATTGAAAGATTAG
             |  ||||  || | |||||    | ||||| || ||   ||  |||   |||   |  ||   || || |     ||  || | ||  |  ||    |||||||||||||||  | |||||  ||||||| ||||| |||||||| ||||||||||||||||| ||||  |||||||| |||||||| ||||| ||  |||
gtgatccatcttatacattaatatatgtttaatttgataatctgaacattgatttttttctttctttcggaatttggggttcatgtatattacactgtggtttctactctatagGATTTTGAATTCAAGGAGTTGAATGAAGTCCTGAAGTACTACCCGCATGGTTATCATGGTGTAGATAGGGAAGGAAGACCTGTTTATATTGAGAGGCTAG

upper sequence: AT1G75370.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA04G03230.1 (Glycine max), 3'ss of exon 2
------------------gtgaattacatgtttttaaaaaaaatcttaatatgttacttttaatctcatgt--gatg-gttttaatctcaatatgtgtgttaatagGATTTTGAATTTGAAGAGTTTGATGAAGTTCTGAAATACTACCCTCATGGTTATCATGGTGTTGATAAAGAAGGAAGGCCTGTTTACATTGAAAGATTAG
                   | ||||  ||    | || |   || ||| | | ||  |||  |  |   ||   |||  |  || ||||    |     |  |||||||||||||||  | |||||  ||||||| || || |||||||| |||||| |||||||||| ||||  ||||||||||||||||| ||||| ||  |||
gtgatccatctaatacaatttaatttgataacctgaacattgat-ttattttatttttttcgaatttgggtttcatgtatactactctctggtttctactctatagGATTTTGAATTCAAGGAGTTGAATGAAGTCCTAAAGTACTACCCGCATGGTAATCATGGTGTAGATAGGGAAGGAAGGCCTGTTTATATTGAGAGGCTAG

upper sequence: AT1G75370.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA14G07850.1 (Glycine max), 3'ss of exon 3
----------------------------------------gtgaattacatgtttttaaaaaaa--atcttaatatgttacttttaat-ctcatgtgatggt--tttaatctcaatatgtgtgttaatagGATTTTGAATTTGAAGAGTTTGATGAAGTTCTGAAATACTACCCTCATGGTTATCATGGTGTTGATAAAGAAGGAAGGCCTGTTTACATTGAAAGATTAG
                                        ||  ||    | || ||  |  ||   |  |  | | ||    |   |  |||||  ||  |  |||  | ||  | | | | |   |||||||||||||| |  |||||  ||||||| ||| | ||||| || ||||||||||||||||| ||||| |||||||| |||||||| ||||| || ||||
gtgagttatccgatttgaaaaatataatcaacttattttggttgatcctgttttatttgatcaactgtactgtttttttgaaatcgttgttcatgctatactactttggtttcc-tgtctttctctttagGATTTTGAATTCGGTGAGTTGAATGAAGTCCTGCAGTACTATCCACATGGTTATCATGGTGTGGATAAGGAAGGAAGACCTGTTTATATTGAGAGGTTAG

upper sequence: AT1G75370.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA17G37150.1 (Glycine max), 3'ss of exon 3
--------------------------------------------gtgaattacatgtttttaaaaaaaat---cttaatatgttacttttaatc-----tcatgtgatggt--tttaatctcaatatgtgtgttaatagGATTTTGAATTTGAAGAGTTTGATGAAGTTCTGAAATACTACCCTCATGGTTATCATGGTGTTGATAAAGAAGGAAGGCCTGTTTACATTGAAAGATTAG
                                            ||  ||    | || ||  |  || |   |||  |  |||  ||  ||||     |||||  ||  |  |||  | ||  | | | | |   |||||||||||||| |  |||||  ||||||| ||| | | ||| || ||||| ||||||||||| ||||| |||||||| ||| |||| ||||| || ||||
gtgagtcatctgatttgaaaaatatatttcaacttcttattttggttgatcctgttttgtttgattaactgtacttttttagttttttgaaatcattgttcatgatatactactttggtttcc-tgtctttctctttagGATTTTGAATTCGGTGAGTTGAATGAAGTCCTGCAGTGCTATCCACATGGCTATCATGGTGTGGATAAGGAAGGAAGACCTATTTATATTGAGAGGTTAG

upper sequence: AT1G75370.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: PP1S307_16V6.1 (Physcomitrella patens), 3'ss of exon 4
-----------------gtgaattacatgtttttaaaaaaaatcttaatatgttacttttaatctcatgtgatggttttaatct-caatatgtgtgttaatagGATTTTGAATTTGAAGAGTTTGATGAAGTTCTGAAATACTACCCTCATGGTTATCATGGTGTTGATAAAGAAGGAAGGCCTGTTTACATTGAAAGATTAG
                 ||  || ||   ||| |   |     | ||   |||  ||||  ||| |   |  |  |   ||  |   ||  ||  |||   |||| ||  |||||  |||  ||||  ||||   ||| ||||| ||||| || |||||||| || ||||||||||| |||||||| |||||||||||| | |
tacgtgcttcgacaccagtacat-actgatttatgtgagggggcatatattgtctctttatatcacgattcttattcgcaagttgtgattcgttcgtt--cagGACTTCAAATTTACAGAAATTGACAAAGTGAGGAATTACTATCCTCAAGGGTATCATGGGGTGGATAAAGAAGGCAGGCCTGTGTACATTGAAAGAATTG

upper sequence: AT1G75370.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: PP1S47_303V6.1 (Physcomitrella patens), 3'ss of exon 2
-------------------------------gtgaattacatgtttttaaaaaaaatcttaatatgttacttttaatctcatgtgatggttttaa---tctcaatatgtgtgttaatagGATTTTGAATTTGAAGAGTTTGATGAAGTTCTGAAATACTACCCTCATGGTTATCATGGTGTTGATAAAGAAGGAAGGCCTGTTTACATTGAAAGATTAG
                                |   | |  |  |||||| |    |    ||     |  ||||     || ||  | |  | |   ||    ||||    | || |||| ||  | ||    || || |||  |||||  |||||||| ||||| ||  | ||||||||||| ||||||||||| |||||||| |||||     |||
gttttggatcctggtgccatgatttagcatcttttgtaatttacttttaagattcctacacatgaacaaaatttacaggaatttgcggatactgaggctcctgttatgatgttgaacagGACTTCCAGTTCACCGAATTGGATTCAGTTCGAAAATACTATCCTCAAGGACACCATGGTGTTGACAAAGAAGGAAGACCTGTTTATATTGAGCAGATAG

upper sequence: AT1G75370.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: PP1S88_63V6.1 (Physcomitrella patens), 3'ss of exon 3
---------gtg-aattacatgtttttaaaaaaaatctta------atatgttacttttaatctcatgtgatggttttaatctcaat-atgtgtgttaatagGATTTTGAATTTGAAGAGTTTGATGAAGTTCTGAAATACTACCCTCATGGTTATCATGGTGTTGATAAAGAAGGAAGGCCTGTTTACATTGAAAGATTAG
         |||  | |  ||  ||  |    || | ||       ||||| |    ||  | | || | |    | |  | | | |  | ||  |    ||||||||   |||  |||| ||||   |||   || ||  || || || ||  |||| || || ||||||||||| ||||||||||||||||||||| | |
ggaattcctgtgcgactgtatccttcaatgtgaattattgtccgacatatgctgaactt--ttttatatcacaactcttttgttatttgtttgcctgctcagGATTTTCTTTTTACAGAGATTGACACAGTAAGGAGATTTTATCCACAAGGGCATCACGGGGTGGATAAAGAAGGCAGGCCTGTTTACATTGAAAGAATTG

upper sequence: AT1G75370.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: EFJ37207 (Selaginella moellendorffii), 3'ss of exon 2
gtgaattacatgtttttaaaaaaaatcttaatatgtt-acttttaatctcatgtgatggttttaatctcaatatgtgtgttaatagGATTTTGAATTTGAAGAGTTTGATGAAGTTCTGAAATACTACCCTCATGGTTATCATGGTGTTGATAAAGAAGGAAGGCCTGTTTACATTGAAAGATTAG
                               |||| | |  |||  || |  ||   |    |||  |  |  |   | ||   ||  ||||| ||| || ||  | || || ||   ||| || ||||| |||||| |||| || || || ||||||||||||||||||||||| ||  |  | |
------------------------------gtatgctgaagttttgtccctcgttccg----taaaatgtaggtccttttttgcagTCTTTTGCATTCGAGGAACTAGAAGAGGTGAAGAAGTATTACCCCCATGGTAATCACGGCGTGGACAAAGAAGGAAGGCCTGTTTACATCGAGCGTCTTG

upper sequence: AT1G75370.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: EFJ27737 (Selaginella moellendorffii), 3'ss of exon 2
gtgaattacatgtttttaaaaaaaatcttaatatgtt-acttttaatctcatgtgatggttttaatctcaatatgtgtgttaatagGATTTTGAATTTGAAGAGTTTGATGAAGTTCTGAAATACTACCCTCATGGTTATCATGGTGTTGATAAAGAAGGAAGGCCTGTTTACATTGAAAGATTAG
                               |||| | |  |||  || |  ||   |    |||  |  |  |   | ||   ||  ||||| ||| || ||  | || || ||   ||| || ||||| |||||| |||| || || || ||||||||||||||||||||||| ||  |  | |
------------------------------gtatgctgaagttttgtccctcgtttcg----taaaatgtaggtccttttttgcagTCTTTTGCATTCGAGGAACTAGAAGAGGTGAAGAAGTATTACCCCCATGGTAATCACGGCGTGGACAAAGAAGGAAGGCCTGTTTACATCGAGCGTCTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atatgttacttttaatctcatgtgatggttttaatctcaatatgtgtgttaatagGATTTTGAATTTGAAGAGTTTGATGAAGTTCTGAAATACTACCCTCATGGTTATCATGGTGTTGATAAAGAAGGAAGGCCTGTTTACATTGAAAGATTAG
                            ttttaat  putative branch site (score: 3)
                            ttttaatctcaatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgaattacatgtttttaaaaaaaatcttaatatgttacttttaatctcatgtgatggttttaatctcaatatgtgtgttaatagGATTTTGAATTTGAAGAGTTTGATGAAGTTCTGAAATACTACCCTCATGGTTATCATGGTGTTGATAAAGAAGGAAGGCCTGTTTACATTGAAAGATTAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA