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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactaaatcacaaccaaaagctcttcttcattgaaattgaaacaacacagaactaatagagtacttgtatcagGTACCATGTAATGCAGGCTGCAAAGACGCTGGTGAACAAAGGGTATGATCCAGAGGTTATCGACATAAGGTCGTTGAAGCCGTTTGATCTCTACACAATT

Basic information

species Arabidopsis thaliana
transcript AT2G34590.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G34590.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G088565_T03 (Zea mays), 3'ss of exon 1
------------------------------------------------------------gtactaaatc-acaaccaaaagctcttcttcat--tgaaattgaaacaacacagaacta--atagagtactt--gtatcagGTACCATGTAATGCAGGCTGCAAAGACGCTGGTGAACAAAGGGTATGATCCAGAGGTTATCGACATAAGGTCGTTGAAGCCGTTTGATCTCTACACAATT
                                                            | | || |||  |  ||   ||         ||  ||          | |||   || |   |   |||||   | || |||||||| || ||||||||||| ||||||||||||||||| ||||| || || ||||| |                                         
ccccgtggtgctgtttgagcacgtcctcttgtacaacctgaaggagaaaatccccgacgaggagtacatctgctgcctggaggaggcggagatggtgcggCCAGGTGAGCACGTGACCATCCTCACGTACTCCCGCATGAGGTACCACGTGATGCAGGCTGCCAAGACGCTGGTGAACAAGGGGTACGACCCCGAGGTCA-----------------------------------------

upper sequence: AT2G34590.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: PP1S101_170V6.3 (Physcomitrella patens), 3'ss of exon 2
-------------------------------------gtactaaatcacaaccaaaagctcttcttcattgaaattgaaac----aacacagaactaatagagtacttgtatcagGTACCATG--TAATGCAGGCTGCAAAGACGCTGGTGAACAAAGGGTATGATCCAGAGGTTATCGACATAAGGTCGTTGAAGCCGTTTGATCTCTACACAATT----------------
                                     |||  | |   |     |   |     ||    |        |     |||   |  | ||| | |      | |  |    |  |  |  |||||||||||||||| |||||| ||| |||||| || |||||| | |||||||| |||||  ||||||| || ||| | ||||||||                 
gtgatgctgggatcctaaaccctccttggaattctatgtagcatactgcttttgaggacgggcttttggagttgcaaggattgtaaacgtgggccgaatggggatggcatgtttgtgggcggggttggtgcagGCTGCAAAGACCCTGGTGGACAGAGGGTACGACCCAGAGATCATCGACATCAGGTCTCTGAAGCCATTCGATATGTACACAATCGGGGAGTCCGTGAAGA
















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|125144721|gb|EL180241.1|EL180241
EST:     ATGGTCAGACCCGGTGAACACATCACGATACTGACGTATTCAAGGATGAG                         GTACCATGTAATGCAGGCTGCAA
genomic: ATGGTCAGACCCGGTGAACACATCACGATACTGACGTATTCAAGGATGAGgtactaaatc ... cttgtatcagGTACCATGTAATGCAGGCTGCAA
EST: gi|164028417|gb|ES207772.1|ES207772
EST:     GAACACATCACGATACTGACGTA-TCAAGGATGAG                         GTACCATGTAATGCAGGCTGCAAAGACGCTGGTGAACAAAGGGTATGATCC
genomic: GAACACATCACGATACTGACGTATTCAAGGATGAGgtactaaatc ... cttgtatcagGTACCATGTAATGCAGGCTGCAAAGACGCTGGTGAACAAAGGGTATGATCC
EST: gi|125029528|gb|EL101797.1|EL101797
EST:     TGAACACATCACGATACTGACGTATTCAAGGATGAG                         GTACCATGTAATGCAGGCTGCAAAGACGCTGGTGAACAAAGGGTATGATCC
genomic: TGAACACATCACGATACTGACGTATTCAAGGATGAGgtactaaatc ... cttgtatcagGTACCATGTAATGCAGGCTGCAAAGACGCTGGTGAACAAAGGGTATGATCC
EST: gi|124983503|gb|EL056230.1|EL056230
EST:     ATGGTCAGACCCGGTGAACACATCACGATACTGACGTATTCAAGGATGAG                         GTACCATGTAATGCAGGCTGCA
genomic: ATGGTCAGACCCGGTGAACACATCACGATACTGACGTATTCAAGGATGAGgtactaaatc ... cttgtatcagGTACCATGTAATGCAGGCTGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agctcttcttcattgaaattgaaacaacacagaactaatagagtacttgtatcagGTACCATGTAATGCAGGCTGCAAAGACGCTGGTGAACAAAGGGTATGATCCAGAGGTTATCGACATAAGGTCGTTGAAGCCGTTTGATCTCTACACAATT
                                aactaat  putative branch site (score: 2)
           attgaaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtactaaatcacaaccaaaagctcttcttcattgaaattgaaacaacacagaactaatagagtacttgtatcagGTACCATGTAATGCAGGCTGCAAAGACGCTGGTGAACAAAGGGTATGATCCAGAGGTTATCGACATAAGGTCGTTGAAGCCGTTTGATCTCTACACAATT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC