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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttggtgttaatggtagtaatctgcaaatttttatgtcacacaaacacttgactatagaaaatgtcgtactttcattataaccatataacatggagtcttctttactaattttgtgcttgttgtaaattggtagGAACGTCTTATACTCAGCAATCTTACAAAGTCAGCGACTCTTTTCCTTTCAAGTGGATAAACAAGAAATGGAAAGAAGATTTCCATGTAACCTCCATGAC

Basic information

species Arabidopsis thaliana
transcript AT5G18190.1
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G18190.1 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: LOC_Os03g57940.1 (Oryza sativa), 3'ss of exon 14
gttggtgttaatggtagtaatctgcaaatttttatgtcacacaaacacttgactatagaaaatgtcgtactttcattataaccatataacatggagtcttctttactaattttgtgcttgttgtaaattggtagGAACGTCTTATACTCAGCAATCTTACAAAGTCAGCGACTCTTTTCCTTTCAAGTGGATAAACAAGAAATGGAAAGAAGATTTCCATGTAACCTCCATGAC
                             || ||      ||   |  | ||||  |     |   ||    |  |  |  || |  |  | |      || ||   ||    |    | |  | | |    ||||||  | || || ||||| || ||||||||||| || || ||||||| ||||||||| ||||| || |||||||||| ||||||||| || || ||| |
-----------------------------ttctactctcaactgtc--tggactccaatttttcctgtgagcttctggtgtccttccatta-gatactatcgttctaaaccaggcatgtatcatcatt--acagGAACTCCATACACACAGCAGTCATACAAAGTCAGTGAATCCTTTCCTTACAAGTGGATTAACAAAAAGTGGAAAGAAGGTTTCCATGTGACATCTATGGC

upper sequence: AT5G18190.1 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: LOC_Os01g56580.1 (Oryza sativa), 3'ss of exon 14
gttggtgttaatggtagtaatctgcaaatttttatgtcacacaaacacttgactatagaaaatgtcgtactttcattataaccatataacatggagtcttctttactaattttgtgcttgttgtaaattggtagGAACGTCTTATACTCAGCAATCTTACAAAGTCAGCGACTCTTTTCCTTTCAAGTGGATAAACAAGAAATGGAAAGAAGATTTCCATGTAACCTCCATGAC
                ||| | |    | ||  ||||  ||||  |||||          | |||  | ||||  ||       ||| ||||| |      |   || |  | ||| ||        ||   ||||||  |||| ||||| || ||||||||||| || || || ||||| ||||| ||||| |||||||||||||||||||  || ||||| || || |||||
----------------gta-tatattgacttgcatgttccaca--cactt----------agtgt--ttcttttgtttatgtattatgacatgaatggggttagtctgacatggtgatttactc---tttccagGAACTCCTTACACTCAACAGTCTTACAAAGTTAGTGAATCGTTTCCCTTCAAATGGATCAACAAGAAATGGAAAGAAGGATTTCATGTTACATCAATGAC

upper sequence: AT5G18190.1 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: GRMZM2G116086_T01 (Zea mays), 3'ss of exon 14
gttggtgttaatggtagtaatctgcaaatttttatg-tcacacaaacacttgactatagaaaatgtcgtactttcattataaccatataacatggagtcttctttactaattttgtgcttgttgtaaattggtagGAACGTCTTATACTCAGCAATCTTACAAAGTCAGCGACTCTTTTCCTTTCAAGTGGATAAACAAGAAATGGAAAGAAGATTTCCATGTAACCTCCATGAC
                            ||| |  | |   | | |   ||| |         |  |   |||||| | |  |       ||| || |  ||| | |     ||   | | ||     || | ||||||  |||| |||||||| ||||||||||| || || || || || | ||||||||| ||||||||||||||||||| ||| ||||| || || |||||
----------------------------tttctgcgattctatagatgtttggcctgtctctgtacc---ctttcactttgccttgtctgcatcgatttatctgtgca----ttaaacctttttactttttgcagGAACTCCTTACACTCAGCAGTCTTACAAAGTTAGTGAATCATTCCCCTACAAGTGGATCAACAAGAAATGGAAAGAAGGTTTTCATGTTACATCAATGAC

upper sequence: AT5G18190.1 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: GRMZM2G164265_T02 (Zea mays), 3'ss of exon 14
gttggtgttaatggtagtaatctgcaaatttttatgtcacacaaacacttgactatagaaaatgtcgtactttcattataaccatataacatggagtcttctttactaattttgtgcttgttgtaaattggtagGAACGTCTTATACTCAGCAATCTTACAAAGTCAGCGACTCTTTTCCTTTCAAGTGGATAAACAAGAAATGGAAAGAAGATTTCCATGTAACCTCCATGAC
                             |  ||||  |     |   || |     |      |||  | || ||||| |   | |   |||   |  | |    |||| |  |  |   |        | ||||||  |||| || |||||||| ||||| || ||||| || || |||| ||||||||| || || || ||||||||||  ||||||||||| || ||| |
---------------------------tgtcctatgcaatttccat-tttaagccccgtttgcatcgctcattaattatcatggtctgctatgatataatttggggtaatat-attttcactact-----gcagGAACTCCTTACACACAGCAATCATACAAGGTTAGCGAATCGTTCCCTTACAAGTGGATCAATAAAAAGTGGAAAGAAGGGTTCCATGTAACATCTATGGC

upper sequence: AT5G18190.1 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: GLYMA16G04580.1 (Glycine max), 3'ss of exon 14
gttggtgttaatggtagtaatctgcaaatttttatgtcacacaaacacttgactatagaaaatgtcgtactttcattataaccatataacatggagtcttctttactaattttgtgcttgttgtaaattggtagGAACGTCTTATACTCAGCAATCTTACAAAGTCAGCGACTCTTTTCCTTTCAAGTGGATAAACAAGAAATGGAAAGAAGATTTCCATGTAACCTCCATGAC
                             |||||  ||    ||   ||    |  |   ||  ||     ||| | | ||   ||| || |    | |   | |     ||||      ||     ||  |||||||  |||| || ||||| || |||||||| || || || ||||||||||| |||||||||||||| ||||||||||  |||||||| ||||| |||||
---------------------------tattttagctcgtttaacttctgtgatgaaaggaacatcaactgttcttcagaatt-tatgactttatatttatctcatg---tttgaatcctttac---tttatagGAACTCCTTACACGCAGCAGTCCTACAAAGTGAGTGAATCATTTCCTTTCAAATGGATAAACAAGAAGTGGAAAGAAGGATTCCATGTTACCTCAATGAC

upper sequence: AT5G18190.1 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: PP1S131_16V6.1 (Physcomitrella patens), 3'ss of exon 13
gttggtgttaatggtagtaatctgcaaatttttatgtcacacaaacacttgactatagaaaatgtcgtactttcattataaccatataacatggagtcttctttactaattttgtgcttgttgtaaattggtagGAACGTCTTATACTCAGCAATCTTACAAAGTCAGCGACTCTTTTCCTTTCAAGTGGATAAACAAGAAATGGAAAGAAGATTTCCATGTAACCTCCATGAC
                                   |||| |       || | | |||  | | |   | ||| | | |     |||      || ||||| ||     |  | | |   || |   ||   |||||| || ||||| ||||| || |||||||| || ||||||||||| || |||||||| || |||||||||  |||||  ||| | || || || ||| |
----------------------------------cgtcatagtcctttttaattttagttattttttaatttttagttttgagttattcgtatgaatcttcgttgtagctcatctcccgattttgtgttaacagGAACATCATATACACAGCAGTCATACAAAGTGAGTGACTCTTTTCCATTTAAGTGGATCAATAAGAAATGGCGAGAAGGCTTCTACGTTACATCTATGGC

upper sequence: AT5G18190.1 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: PP1S66_174V6.1 (Physcomitrella patens), 3'ss of exon 13
---------------------gttggtgttaatggtagtaatctgcaaa-----tttttatgtcacacaaacacttgactatagaaaatgtcgtactttcattataaccatataacatggagtcttctttactaattttgtgct------tgttgtaaattg--gtagGAACGTCTTATACTCAGCAATCTTACAAAGTCAGCGACTCTTTTCCTTTCAAGTGGATAAACAAGAAATGGAAAGAAGATTTCCATGTAACCTCCATGAC
                      ||| |||  || | |   || | || |     | |  | |       |  | ||     || ||  |||| |      |   |       |    |||    |  ||||||  ||   || |       | |||  |||   ||||||||||| || || ||||| ||||||||||| |||||||||||||| || |||||||| || |||||||||  |||||  ||  | || || || ||| |
gtattttattggatagtatcctttgatgtatattgaatctattttcagagttgatctcaagggtgtttgatgatttattcttataatttgtcatttggagacctttttgtggttttctggctcttgttttacttgttgcatgatgtctcacggtgtttatttctgtagGAACGTCGTACACGCAGCAGTCTTACAAAGTGAGCGACTCTTTTCCATTTAAGTGGATCAATAAGAAATGGCGAGAAGGCTTTTACGTGACTTCAATGGC

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|86087382|gb|DR383141.1|DR383141
EST:     CGGGAACTCATTAGTGGTTATGTCAAAAG                         AAACGTCTTATACTCAGCAATCTTACAAAGTCAGCGACTCTTTTACTTTCA
genomic: CGGGAACTCATTAGTTGTTATGTCAAAAGgttggtgtta ... aaattggtagGAACGTCTTATACTCAGCAATCTTACAAAGTCAGCGACTCTTTTCCTTTCA
EST: gi|19875875|gb|AU236706.1|AU236706
EST:     TTCCATAGCTGGTTCAGATAACGGGAACTCATTAGTTGTTATGTCAAAAG                         GAACGTCTTATACTCAGCAATCTTACAAAGTCAGCGACTCTTTTCCTTTCA
genomic: TTCCATAGCTGGTTCAGATAACGGGAACTCATTAGTTGTTATGTCAAAAGgttggtgtta ... aaattggtagGAACGTCTTATACTCAGCAATCTTACAAAGTCAGCGACTCTTTTCCTTTCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaccatataacatggagtcttctttactaattttgtgcttgttgtaaattggtagGAACGTCTTATACTCAGCAATCTTACAAAGTCAGCGACTCTTTTCCTTTCAAGTGGATAAACAAGAAATGGAAAGAAGATTTCCATGTAACCTCCATGAC
                        tactaat  putative branch site (score: 1)
                   ttctttactaatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttggtgttaatggtagtaatctgcaaatttttatgtcacacaaacacttgactatagaaaatgtcgtactttcattataaccatataacatggagtcttctttactaattttgtgcttgttgtaaattggtagGAACGTCTTATACTCAGCAATCTTACAAAGTCAGCGACTCTTTTCCTTTCAAGTGGATAAACAAGAAATGGAAAGAAGATTTCCATGTAACCTCCATGAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG