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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaacaaacataagacccatcaattcttttttttacttactgtctattagagaaataaactaacataccaaattctctcagGATGAGAGTGTGAAGGAAACAGCACAGCTCATGTACCAGACAGCTTTGATCGAGAGTGGATTCATACTCACCGACCCAAAAGACTTTGCTGCCCGTATTT

Basic information

species Arabidopsis thaliana
transcript AT4G24190.1
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G24190.1 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: GLYMA14G40320.4 (Glycine max), 3'ss of exon 14
------gtaaaacaaacataagacccatcaattcttttttttacttactgtctattagagaaataaactaacataccaaattct----ctcagGATGAGAGTGTGAAGGAAACAGCACAGCTCATGTACCAGACAGCTTTGATCGAGAGTGGATTCATACTCACCGACCCAAAAGACTTTGCTGCCCGTATTT
         | |  |  | || |       |  | | | ||| || |      ||  |    ||    ||||| |      | |     |||||||||| |||||||| | ||||||||||| ||||||||||| ||  |  | || || || ||| | ||    || || || || |||||| |||| ||||
gtacattctagattattagaacattttctgaggcatctctttcctcaactcaaatggggtttatctgttaacacaatctgctttacttttcagGATGAGGGTGTGAAGCATACAGCACAGCTGATGTACCAGACTGCACTCTTTGAAAGCGGCTTCCTGCTTGATGATCCCAAGGATTTTGCTTCCCGGATTT

upper sequence: AT4G24190.1 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: Vv18s0001g14500.t01 (Vitis vinifera), 3'ss of exon 14
--------------------gtaaaacaaacataagacccatcaattcttttttttacttactgtctattagagaaataaactaacataccaaattctctcagGATGAGAGTGTGAAGGAAACAGCACAGCTCATGTACCAGACAGCTTTGATCGAGAGTGGATTCATACTCACCGACCCAAAAGACTTTGCTGCCCGTATTT
                    | |  ||  | | || ||  || ||   |    | ||  |   ||||  ||   | |   | | || | ||   | |  |||||||||| | || ||| |||||||||||||||||||||| |||||  | || |||||||| ||| | ||||  ||||| ||  | |||||  |   ||| |
tgtatagcagagtcctatatgcattactta-aaaaaactaattaaacatgcaatatatctttagtctgctactcacaacgatttacttgcc--ttcccttcagGATGAGGGCGTAAAGAAAACAGCACAGCTCATGTACCAAACAGCACTCATGGAGAGTGGTTTCCTGCTCAGTGACCCCAAGCATTTTGCCTCTAATATCT
















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|47830337|gb|CK120021.1|CK120021
EST:     GACACCCTATCATCAAAGAACTCAAGGATAGAATTGCAAGTGACCCAGAG                         GATGAGAGTGTGAAGGAAACAGCACAGCTCATGTACCAGACAGCTTTGATC
genomic: GACACCCTATCATCAAAGAACTCAAGGATAGAATTGCAAGTGACCCAGAGgtaaaacaaa ... attctctcagGATGAGAGTGTGAAGGAAACAGCACAGCTCATGTACCAGACAGCTTTGATC
EST: gi|47829028|gb|CK118712.1|CK118712
EST:     GACACCCTATCATCAAAGAACTCAAGGATAGAATTGCAAGTGACCCAGAG                         GATGAGAGTGTGAAGGAAACAGCACAGCTCATGTACCAGACAGCTTTGATC
genomic: GACACCCTATCATCAAAGAACTCAAGGATAGAATTGCAAGTGACCCAGAGgtaaaacaaa ... attctctcagGATGAGAGTGTGAAGGAAACAGCACAGCTCATGTACCAGACAGCTTTGATC
EST: gi|47829573|gb|CK119257.1|CK119257
EST:     GACACCCTATCATCAAAGAACTCAAGGATAGAATTGCAAGTGACCCAGAG                         GATGAGAGTGTGAAGGAAACAGCACAGCTCATGTACCAGACAGCTTTGATC
genomic: GACACCCTATCATCAAAGAACTCAAGGATAGAATTGCAAGTGACCCAGAGgtaaaacaaa ... attctctcagGATGAGAGTGTGAAGGAAACAGCACAGCTCATGTACCAGACAGCTTTGATC
EST: gi|164231689|gb|EL998568.1|EL998568
EST:     GGATAGAATTGCAAGTGACCCAGAG                         GATGAGAGTGTGAAGGAAACAGCACAGCTCATGTACCAGACAGCTTTGATC
genomic: GGATAGAATTGCAAGTGACCCAGAGgtaaaacaaa ... attctctcagGATGAGAGTGTGAAGGAAACAGCACAGCTCATGTACCAGACAGCTTTGATC
EST: gi|164151723|gb|ES048230.1|ES048230
EST:     GAATTGCAAGTGACCCAGAG                         GATGAGAGTGTGAAGGAAACAGCACAGCTCATAGTACCAGAC
genomic: GAATTGCAAGTGACCCAGAGgtaaaacaaa ... attctctcagGATGAGAGTGTGAAGGAAACAGCACAGCTCAT-GTACCAGAC
EST: gi|164003243|gb|ES077970.1|ES077970
EST:     ACACCCTATCATCAAAGAACTCAAGGATAGAATTGCAAGTGACCCCAGAG                         GATGAGAGTGTGAAGGAAACAGCACAGCTCA
genomic: ACACCCTATCATCAAAGAACTCAAGGATAGAATTGCAAGTGACCC-AGAGgtaaaacaaa ... attctctcagGATGAGAGTGTGAAGGAAACAGCACAGCTCA
EST: gi|124771672|gb|EH861802.1|EH861802
EST:     TAGAATTGCAAGTGACCCAGAG                         GATGAGAGTGTGAAGGAAACAGCACAGCTCATGTACCAGACAGCTTTGATC
genomic: TAGAATTGCAAGTGACCCAGAGgtaaaacaaa ... attctctcagGATGAGAGTGTGAAGGAAACAGCACAGCTCATGTACCAGACAGCTTTGATC
EST: gi|86058796|gb|DR354553.1|DR354553
EST:     GACACCCTATCATCAAAGAACTCAAGGATAGAATTGCAAGTGACCCAGAG                         GATGAGAGTGTGAAGGAAACAGCACAGCTCATGTACCAGACAGCTTTGATC
genomic: GACACCCTATCATCAAAGAACTCAAGGATAGAATTGCAAGTGACCCAGAGgtaaaacaaa ... attctctcagGATGAGAGTGTGAAGGAAACAGCACAGCTCATGTACCAGACAGCTTTGATC
EST: gi|125230391|gb|EL244476.1|EL244476
EST:     GAACTACAAGGATAGAATTGCAAGTGACCCAGAG                         GATGAGAGTGTGAAGGAAACAGCACAGCTCATGTACCA
genomic: GAACT-CAAGGATAGAATTGCAAGTGACCCAGAGgtaaaacaaa ... attctctcagGATGAGAGTGTGAAGGAAACAGCACAGCTCATGTACCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttttttacttactgtctattagagaaataaactaacataccaaattctctcagGATGAGAGTGTGAAGGAAACAGCACAGCTCATGTACCAGACAGCTTTGATCGAGAGTGGATTCATACTCACCGACCCAAAAGACTTTGCTGCCCGTATTT
                               aactaac  putative branch site (score: 1)
                                              ttctctc  putative PPT
                  tattagagaaataaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaaacaaacataagacccatcaattcttttttttacttactgtctattagagaaataaactaacataccaaattctctcagGATGAGAGTGTGAAGGAAACAGCACAGCTCATGTACCAGACAGCTTTGATCGAGAGTGGATTCATACTCACCGACCCAAAAGACTTTGCTGCCCGTATTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC