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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatataagtctacgttgatgaaacattagtcctgtttcattctagtttttttttttttttttaattctatcttagtttatctggagttataactcaggatgattttacccccatgatttcatttgcaacagATTCTAACTCTATGGTATAGAGCTCCGGAAGTTCTTCTTGGAGCAACCCATTACTCTACTGGAGTGGATATGTGGTCTGTTGGCTGTATTTTTG

Basic information

species Arabidopsis thaliana
transcript AT1G20930.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G20930.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv18s0122g00550.t01 (Vitis vinifera), 3'ss of exon 4
gtatataagtctacgttgatgaaacattagtcctgtttcattctagtttttttttttttttttaattctatcttagtttatctggagttataactcaggatgattttacccccatgatttcatttgcaacagATTCTAACTCTATGGTATAGAGCTCCGGAAGTTCTTCTTGGAGCAACCCATTACTCTACTGGAGTGGATATGTGGTCTGTTGGCTGTATTTTTG
                                             ||      || |||  | ||    |  ||||    ||         || | |  |  | | || |    ||||     |||   ||||| || ||| | ||||||||||| || ||||| ||| | ||  | ||||||||||| |||| ||| ||||||||||| ||||||||||| ||||
---------------------------------------------gtacaggcttatttgctcaacatcaaattagaagttcctatcaggcaattaataa--aatgtatc----tgatca---ttgttccagATACTGACTTTGTGGTATAGAGCCCCTGAAGTACTTTTGGGGTCTACCCATTACTCAACTGCAGTAGATATGTGGTCAGTTGGCTGTATATTTG

upper sequence: AT1G20930.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: PP1S127_92V6.1 (Physcomitrella patens), 3'ss of exon 4
gtatataagtctacgttgatgaaacattagtcctgtttcattctagtttttttttttttttttaattctatcttagtttatctggagttataactcaggatgattttacccccatgatttcatttgcaacagATTCTAACTCTATGGTATAGAGCTCCGGAAGTTCTTCTTGGAGCAACCCATTACTCTACTGGAGTGGATATGTGGTCTGTTGGCTGTATTTTTG
                                  ||    ||   |  ||  ||        ||| |    |||     | |   | |    | | | | |  || | ||   |||   |         |||||| | |||||||||||  ||||||| ||||||||||||||||| ||||| ||||||      |||||||| ||||||||||| || || || |
----------------------------------gtactctttccgcattcgttgacgcccgtaactaatccttg---caacc--aatctccatttatggtacttatgccgt-atgcggtggaccttttcagATTGTTACTCTATGGTACCGAGCTCCTGAAGTTCTTCTTGGAGCGACCCACTACTCTCTACCTGTGGATATCTGGTCTGTTGGGTGCATCTTCG

upper sequence: AT1G20930.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: PP1S214_1V6.1 (Physcomitrella patens), 3'ss of exon 4
gtatataagtctacgttgatgaaacattagtcctgtttcattctagtttttttttttttttttaattctatcttagtttatctggagttataactcaggatgatt--ttaccccca-tgatttcatttgcaacagATTCTAACTCTATGGTATAGAGCTCCGGAAGTTCTTCTTGGAGCAACCCATTACTCTACTGGAGTGGATATGTGGTCTGTTGGCTGTATTTTTG
                                           ||  |     || |  |  |    |    ||| | || | | | ||    |||   ||  ||  | ||  |   |||||   |      |||||  | || || |||||  ||||||| ||||||||||| ||||||||||| |||||   |   || ||||| ||||||||||| |||||||| |
------------------------------------------gtacgtacagcttgtcatggttgcgcagaattattctaacagaaatttctcctctctattcttgctcacatctggtgattcggtgcctggcagATCGTCACACTGTGGTACCGAGCTCCCGAAGTTCTTCTCGGAGCAACCCACTACTCCCTTCCTGTTGATATTTGGTCTGTTGGATGTATTTTCG

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|86083531|gb|DR379290.1|DR379290
EST:     TCACTCTCCCAATGAAAAAGTATACACATGAG                         ATTCTAACTCTATGGTATAGAGCTCCGGAAGTTCTTCTTGGAGCAACCCAT
genomic: TCACTCTCCCAATGAAAAAGTATACACATGAGgtatataagt ... tttgcaacagATTCTAACTCTATGGTATAGAGCTCCGGAAGTTCTTCTTGGAGCAACCCAT
EST: gi|19877265|gb|AU238096.1|AU238096
EST:     TTGGATTAGCCAGAGCCTTCACTCTCCCAATGAAAAAGTNTACACATGAG                         ATTCTACCTCTATGGTATAGAGCTCCG
genomic: TTGGATTAGCCAGAGCCTTCACTCTCCCAATGAAAAAGTATACACATGAGgtatataagt ... tttgcaacagATTCTAACTCTATGGTATAGAGCTCCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttatctggagttataactcaggatgattttacccccatgatttcatttgcaacagATTCTAACTCTATGGTATAGAGCTCCGGAAGTTCTTCTTGGAGCAACCCATTACTCTACTGGAGTGGATATGTGGTCTGTTGGCTGTATTTTTG
          ttataac  putative branch site (score: 2)
                                        tttcattt  putative PPT
                      atgatttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatataagtctacgttgatgaaacattagtcctgtttcattctagtttttttttttttttttaattctatcttagtttatctggagttataactcaggatgattttacccccatgatttcatttgcaacagATTCTAACTCTATGGTATAGAGCTCCGGAAGTTCTTCTTGGAGCAACCCATTACTCTACTGGAGTGGATATGTGGTCTGTTGGCTGTATTTTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA