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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcctaaacattttaagatcatcttctttttcttctcctttaattaaagtctgatcctttttacttcttctttcaaaagGACTTTGATTTCAAGGAGATTGATGAAGTCCTCAAGTACTACCCTCAAGGTTACCATGGTGTTGACAAAGATGGAAGGCCTGTTTACATTGAGAGGCTAG

Basic information

species Arabidopsis thaliana
transcript AT2G21540.3
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G21540.3 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os02g24430.2 (Oryza sativa), 3'ss of exon 4
------------gtcctaaacat-tttaagatcatcttctttttctt------ctcctttaattaaagtc---tgatcctttttacttc--ttctttcaaaagGACTTTGATTTCAAGGAGATTGATGAAGTCCTCAAGTACTACCCTCAAGGTTACCATGGTGTTGACAAAGATGGAAGGCCTGTTTACATTGAGAGGCTAG
            |    ||| || |||    | ||| |  | |  ||        || ||  ||| |  |   |||  | |||| ||||   || |     |||| ||||| ||  | ||   |||  | ||     | | ||| ||||||||||||||||| ||||| || || ||||||||||| ||||||||  | || |
gtaattgcttaagattaaaatatatttggactaatccttctatggttgacacatacccttgtttataagcagttgacacatttttcttcaaatcctatctcagGATTTTGAATTTGAAGAAGCTGACAAGGTGGCAGAATGCTATCCTCAAGGTTACCATGGGGTTGATAAGGAAGGAAGGCCTGTCTACATTGAACGTCTTG

upper sequence: AT2G21540.3 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os10g03400.2 (Oryza sativa), 3'ss of exon 3
--------------------------gtcctaaacat-tttaagatcatcttctttttctt------ctcctttaattaaagtc---tgatcctttttacttcttctttcaa--aagGACTTTGATTTCAAGGAGATTGATGAAGTCCTCAAGTACTACCCTCAAGGTTACCATGGTGTTGACAAAGATGGAAGGCCTGTTTACATTGAGAGGCTAG
                          |    ||  || |||    | ||| | || |  ||        |||||  ||| |  |   |||  | |||| | ||   ||  |    |||| ||||| ||  | ||   ||   | ||     | | ||| ||||||||||| ||||| ||||| || || ||||||||||| ||||||||  | || |
gtaattgcatctatcaaataggttaaggttaaactatatttggactaatccttttatggttgatacatacctttgtttataagcagttgacacatttttcatcaaattctatctcagGATTTTGAATTTGAAGAAGCTGGCAAGGTGGCAGAATGCTATCCTCAAGGTTATCATGGGGTTGATAAGGAAGGAAGGCCTGTCTACATTGAACGACTTG

upper sequence: AT2G21540.3 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G162461_T01 (Zea mays), 3'ss of exon 4
----------------gtcctaaacattttaag--atcatcttctttttcttctcctttaa----ttaaagtctgatcctttttacttcttctttcaaaagGACTTTGATTTCAAGGAGATTGATGAAGTCCTCAAGTACTACCCTCAAGGTTACCATGGTGTTGACAAAGATGGAAGGCCTGTTTACATTGAGAGGCTAG
                     || || | | ||  || || | |    | ||      |||    ||  |  ||  |||||||  ||  | |  ||  | | | || || ||| | ||   |||| | ||     | | ||||||||||||||||||||| ||||| || || || |||||||| ||| ||||  |||| |
atacatatacacaaaaaagagaagcaatcttaggaattatttacaggctattagttcataaacttttgtaaccttttccttttctctaatgcaatcttagGAA-TTCGAATTCGAAGAAGCTGATAAGGTGGCAGAATGCTACCCTCAAGGTTACCATGGGGTTGATAAGGAAGGCAGGCCTGTCTACTTTGAACGGCTTG

upper sequence: AT2G21540.3 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: PP1S47_303V6.1 (Physcomitrella patens), 3'ss of exon 2
---------------------gtcctaaacattttaagatcatcttctttttcttctcctt-taattaaagtct-------------gatcct-----ttttacttcttctttcaaaagGACTTTGATTTCAAGGAGATTGATGAAGTCCTCAAGTACTACCCTCAAGGTTACCATGGTGTTGACAAAGATGGAAGGCCTGTTTACATTGAGAGGCTAG
                      |     |  ||||   ||   ||| |     | || |   | |  ||| | |             ||| ||     |  |  |      || || |||||||  | ||||  ||  | |||  ||| |  || ||||| ||||||||  ||||||||||||||||||| ||||| |||||||| ||||||  | |||
gttttggatcctggtgccatgatttagcatcttttgtaatttacttttaagattcctacacatgaacaaaatttacaggaatttgcggatactgaggctcctgttatgatgttgaacagGACTTCCAGTTCACCGAATTGGATTCAGTTCGAAAATACTATCCTCAAGGACACCATGGTGTTGACAAAGAAGGAAGACCTGTTTATATTGAGCAGATAG

upper sequence: AT2G21540.3 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: EFJ21359 (Selaginella moellendorffii), 3'ss of exon 2
gtcctaaacattttaagatcatcttctttttcttctcctttaattaaagtctgatcctttttacttcttctttcaaaagGACTTTGATTTCAAGGAGATTGATGAAGTCCTCAAGTACTACCCTCAAGGTTACCATGGTGTTGACAAAGATGGAAGGCCTGTTTACATTGAGAGGCTAG
               | || || |    ||   | || |||  | |  ||  |         ||||| | | |  | |||| || || ||    ||||| || |||||    || ||||| ||||||||| ||||||| ||||||||||| || |||||  ||||||| ||| |  | |
-------------gtaaatgatatctcattgtatatctttttgtcactgtgagga-----aaacttcgtttgtgtacagGATTTCGAGTTTGGTGAGATCGAGGAAGTGAAAAAATACTATCCTCAAGGTCACCATGGGGTTGACAAAGAAGGGAGGCCCATTTACATCGAGCGCTTGG

upper sequence: AT2G21540.3 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: EFJ23906 (Selaginella moellendorffii), 3'ss of exon 2
gtcctaaacattttaagatcatcttctttttcttctcctttaattaaagtctgatcctttttacttcttctttcaaaagGACTTTGATTTCAAGGAGATTGATGAAGTCCTCAAGTACTACCCTCAAGGTTACCATGGTGTTGACAAAGATGGAAGGCCTGTTTACATTGAGAGGCTAG
               | || || |    ||   | || |||  |||  ||  |         ||||| | | |  | |||| || || ||    ||||| || |||||    || ||||| ||||||||| ||||||| ||||||||||| || |||||  ||||||| ||| |  | |
-------------gtaaatgatatctcattgtatatctttttgttactgtgagga-----aaacttcgtttgtgtacagGATTTCGAGTTTGGTGAGATCGAGGAAGTGAAAAAATACTATCCTCAAGGTCACCATGGGGTTGACAAAGAAGGGAGGCCCATTTACATCGAGCGCTTGG

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|125046341|gb|EL118610.1|EL118610
EST:     TTGACACAATCATGGAG                         GACTTTGATTTCAAGGAGATTGATGAAGTCCTCAAGTACTACCCTCAAGGT
genomic: TTGACACAATCATGGAGgtcctaaaca ... ctttcaaaagGACTTTGATTTCAAGGAGATTGATGAAGTCCTCAAGTACTACCCTCAAGGT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctttttcttctcctttaattaaagtctgatcctttttacttcttctttcaaaagGACTTTGATTTCAAGGAGATTGATGAAGTCCTCAAGTACTACCCTCAAGGTTACCATGGTGTTGACAAAGATGGAAGGCCTGTTTACATTGAGAGGCTAG
                        gtctgat  putative branch site (score: 4)
                         tctgatcctttttact  CT-rich tract
              tttaattaaagtct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcctaaacattttaagatcatcttctttttcttctcctttaattaaagtctgatcctttttacttcttctttcaaaagGACTTTGATTTCAAGGAGATTGATGAAGTCCTCAAGTACTACCCTCAAGGTTACCATGGTGTTGACAAAGATGGAAGGCCTGTTTACATTGAGAGGCTAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG