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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttggcattttggttagtcaattcaaattttcttggcatggtatctgttgtatgattgaaagttattgatgtaaatgtaatgtctcttgtctttgagcagGTCAAAATTTGGTGTACAAATCAGGAAGCTAGTGTTCTAAATATAGACATGAAAGCAAACATATGCTGTGTCAAATATAATCCTGGATCTGGCAATTATA

Basic information

species Glycine max
transcript GLYMA14G05430.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA14G05430.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G104920_T02 (Zea mays), 3'ss of exon 8
tttggcattttggttagtcaattcaa----attttcttggcatggtatctgttgtatgattgaaagttattgatgtaaatgtaatgtctcttgtctttgagcagGTCAAAATTTGGTGTACAAATCAGGAAGCTAGTGTTCTAAATATAGACATGAAAGCAAACATATGCTGTGTCAAATATAATCCTGGATCTGGCAATTATA
  ||    ||  |||  | ||  |||    |  || ||||  |      | |    | |    ||   |  || | ||   | | | || |||| | || |||||| ||| | ||||| |||||||| ||||| |||||  | ||||| || ||||||||||| || ||||  || |||||||||||||||||  ||   ||  
-atgaatattaagttcatgaacacaacaacagatttttggtgtatgcattttcaagtaaggacaaaaaa--gaagaaataattacggctgttgtttatg-gcagGTGAAAGTGTGGTGCACAAATCAAGAAGCAAGTGTGATCAATATTGATATGAAAGCAAATATTTGCTCGGTTAAATATAATCCTGGATCAAGCTTCTACG

upper sequence: GLYMA14G05430.1 (Glycine max), 3'ss of exon 9
lower sequence: AT2G32950.1 (Arabidopsis thaliana), 3'ss of exon 9
--tttggcattttggt--tagtcaattcaaattttcttggcatggtatctgttgtatgattgaaagttattgatgtaaatgtaatgtctcttgtctttgagc-agGTCAAAATTTGGTGTACAAATCAGGAAGCTAGTGTTCTAAATATAGACATGAAAGCAAACATATGCTGTGTCAAATATAATCCTGGATCTGGCAATTATA
  |  | || ||   |  |||| ||| |  |          || | |||||||  || ||     ||     |  | ||   | |||    ||| ||||| | |||| ||| ||||||| || |  |||||||| |||||  | ||||| || ||||||||||||||||| |||||||| || |||||||| ||  |||| || |
tttaagtcaattcactactagttaatcctcaaccatgcattattgcatctgttaaatcat-----gtctcatagattaaccaattgtgctgtgtgtttgatccagGTTAAAGTTTGGTGCACGAGGCAGGAAGCAAGTGTGATTAATATTGATATGAAAGCAAACATATGTTGTGTCAAGTACAATCCTGGCTCAAGCAACTACA

upper sequence: GLYMA14G05430.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv12s0059g01420.t01 (Vitis vinifera), 3'ss of exon 9
-----tttggcattttggt--tagtcaattcaaattttcttggcatggtatctgttgtatgattgaaagttattgatgtaaatgtaatgtctcttgtctttgagcagGTCAAAATTTGGTGTACAAATCAGGAAGCTAGTGTTCTAAATATAGACATGAAAGCAAACATATGCTGTGTCAAATATAATCCTGGATCTGGCAATTATA
      ||   ||   |||  | |  | | || |||   ||| |||| ||        ||  ||    ||   || | | ||  |||||| | |      | | ||||||||| ||||||| ||||| ||||| ||||| ||||| || || |||||||||||||| ||||| |||||||| ||||||||||||||| ||| |||||
agttcattataatcagggtactggggactccatattggtttgacatgctaaactaaccatagttt---gtatctgttatgaacttaatgtatgtaa----taaacagGTCAAAGTTTGGTGCACAAACCAGGAGGCTAGCGTTCTTAACATTGACATGAAAGCAAATATATGTTGTGTCAAGTATAATCCTGGATCTAGCATTTATA

upper sequence: GLYMA14G05430.1 (Glycine max), 3'ss of exon 9
lower sequence: PP1S25_325V6.1 (Physcomitrella patens), 3'ss of exon 9
tttggcattttggttagtcaatt-caaattttcttggcatggtatctgttgtatgattgaaagtta---ttgatgtaaatgtaatgtctcttgtctttgagcagGTCAAAATTTGGTGTACAAATCAGGAAGCTAGTGTTCTAAATATAGACATGAAAGCAAACATATGCTGTGTCAAATATAATCCTGGATCTGGCAATTATA
       ||||||||   | ||| |         |  ||  |  | | | || |||||   | | |     |  || ||    |  |     |  |||  |||||| ||  ||||||| || |||||||| ||||||||| | | |||||||||||| || ||||| ||||| || || || |||||||| ||  ||||  |||
-cccatgttttggttgcacgattacgggggaatataacagagactgtctcgt-tgattcttactcaagtcagccgttaaaagcagatggggggatttt--gcagGTTAAGCTTTGGTGCACTAATCAGGAGGCTAGTGTTTTTAGTATAGACATGAAGGCCAACATCTGCTGCGTTAAGTACAATCCTGGTTCAAGCAACCATA

upper sequence: GLYMA14G05430.1 (Glycine max), 3'ss of exon 9
lower sequence: PP1S135_17V6.1 (Physcomitrella patens), 3'ss of exon 9
---------------------------------------tttg--gcattttggttagtcaa-----ttcaaattttcttggcatggtatctgttgtatgattgaaagttattgatgtaaatgtaatgtctct-tgtctttga--gcagGTCAAAATTTGGTGTACAAATCAGGAAGCTAGTGTTCTAAATATAGACATGAAAGCAAACATATGCTGTGTCAAATATAATCCTGGATCTGGCAATTATA
                                        |||  ||  ||  |||  ||||     |||||| |    |    |||  | |   | || ||    | |    | |  |   | ||||| | | |||   ||   |||||| || || ||||| || |  || ||  | || ||  |||||||||||||||| ||||| || |||||||| || ||||||||||||||  |||  ||| 
gtaacctgttgaaatctggtgaacttaatcactcttgtacttgatgcggttctgtttttcaagctttttcaaactcaggttatttggagttttccgcatcatgtttaatatgcggttgatccgaaatgtttttatgttactgtttgcagGTGAAGATATGGTGCACGAGGCAAGAGTCAAGCGTGATAAATATAGACATGAAGGCAAATATTTGCTGTGTGAAGTATAATCCTGGATCAAGCAGCTATG

upper sequence: GLYMA14G05430.1 (Glycine max), 3'ss of exon 9
lower sequence: EFJ20512 (Selaginella moellendorffii), 3'ss of exon 9
tttggcattttggttagtcaattcaaattttcttggcatggtatctgttgtatgattgaaagttattgatgtaaatgtaatgtctcttgtctttga---gcagGTCAAAATTTGGTGTACAAATCAGGAAGCTAGTGTTCTAAATATAGACATGAAAGCAAACATATGCTGTGTCAAATATAATCCTGGATCTGGCAATTATA
                                                ||| | |||   | |||   |    |||    ||| | | || |||||    ||||||||  | ||||| || |  |||||  | ||||| || || || |||||||| |||||||| |||||||||||||| ||||| |||||| |||||| | 
-----------------------------------------------gtgttttattattacttacacacccgaattccctgtttgt-gtttttgacgcacagGTCAAGCTGTGGTGCACCAGGCAGGAGACAAGTGTCCTGAACATTGACATGAAGGCAAACATTTGCTGTGTCAAATACAATCCCGGATCTAGCAATTTTG

upper sequence: GLYMA14G05430.1 (Glycine max), 3'ss of exon 9
lower sequence: EFJ28584 (Selaginella moellendorffii), 3'ss of exon 9
tttggcattttggttagtcaattcaaattttcttggcatggtatctgttgtatgattgaaagttattgatgtaaatgtaatgtctcttgtctttga---gcagGTCAAAATTTGGTGTACAAATCAGGAAGCTAGTGTTCTAAATATAGACATGAAAGCAAACATATGCTGTGTCAAATATAATCCTGGATCTGGCAATTATA
                                             |  ||| | |||   | |||   |    |||  | ||| | | || |||||    ||||||||  | ||||| || |  |||||  | ||||| || || || |||||||| |||||||| |||||||||||||| ||||| |||||| |||||| | 
--------------------------------------------gtagtgttttattattacttacacacccgaattcactgtttgt-gtttttgacgcacagGTCAAGCTGTGGTGCACCAGGCAGGAGACAAGTGTCCTGAACATTGACATGAAGGCAAACATTTGCTGTGTCAAATACAATCCCGGATCTAGCAATTTTG

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|105633923|gb|DW247286.1|DW247286
EST:     TTTCAAGAACAGACCCCTCTATGCTTGTATCTGGTAGCGATGACTGTAAG                         GTCAAAATTTGGTGT
genomic: TTTCAAGAACAGACCCCTCTATGCTTGTATCTGGTAGCGATGACTGTAAGgtacttgaaa ... ctttgagcagGTCAAAATTTGGTGT
EST: gi|193629154|gb|FK578102.1|FK578102
EST:     TTTCAAGAACAGACCCCTCTATGCTTGTATCTGGTAGCGATGACTGTAAG                         GTCAAAATTTGGTGTACAAATCAGGAAGCTAGTGTTCTAAATA
genomic: TTTCAAGAACAGACCCCTCTATGCTTGTATCTGGTAGCGATGACTGTAAGgtacttgaaa ... ctttgagcagGTCAAAATTTGGTGTACAAATCAGGAAGCTAGTGTTCTAAATA
EST: gi|7042199|gb|AW472102.1|AW472102
EST:     TTTCAAGAACAGACCCCTCTATGCTTGTATCTGGTAGCGATGACTGTAAG                         GTCAAAATTTGGTGTACAAATCATGAAGCTAGTGTTCTAAATATAGACATG
genomic: TTTCAAGAACAGACCCCTCTATGCTTGTATCTGGTAGCGATGACTGTAAGgtacttgaaa ... ctttgagcagGTCAAAATTTGGTGTACAAATCAGGAAGCTAGTGTTCTAAATATAGACATG
EST: gi|151403867|gb|EV273677.1|EV273677
EST:     TTTCAAGAACAGACCCCTCTATGCTTGTATCTGGTAGCGATGACTGTAAG                         GTCAAAATTTGGTGTACAAATCAGGAAGCTAGTGTTCTAAATATAGACATG
genomic: TTTCAAGAACAGACCCCTCTATGCTTGTATCTGGTAGCGATGACTGTAAGgtacttgaaa ... ctttgagcagGTCAAAATTTGGTGTACAAATCAGGAAGCTAGTGTTCTAAATATAGACATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttgtatgattgaaagttattgatgtaaatgtaatgtctcttgtctttgagcagGTCAAAATTTGGTGTACAAATCAGGAAGCTAGTGTTCTAAATATAGACATGAAAGCAAACATATGCTGTGTCAAATATAATCCTGGATCTGGCAATTATA
                  tattgat  putative branch site (score: 3)
                                   tgtctcttgtcttt  putative PPT
                 ttattgatgtaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttggcattttggttagtcaattcaaattttcttggcatggtatctgttgtatgattgaaagttattgatgtaaatgtaatgtctcttgtctttgagcagGTCAAAATTTGGTGTACAAATCAGGAAGCTAGTGTTCTAAATATAGACATGAAAGCAAACATATGCTGTGTCAAATATAATCCTGGATCTGGCAATTATA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG