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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcaccaaaaatatcgtgcatgtgaaagtgtatctatgatttagtaaattatacttttaaaaccaggcctcataactttgttattgtcttcaacgttgcagGATCCTTCAAAGCATGTTTTTCACCTTGTTACCGATAAACTAAATTTTGGAGCCATGAACATGTGGTTTCTTTTAAACCCTCCTGAAAAAGCTACAATCC

Basic information

species Glycine max
transcript GLYMA07G08910.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G08910.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os09g36180.1 (Oryza sativa), 3'ss of exon 8
gcaccaaaaatatcgtgcatgtgaaagtgtatctatgatttagtaaattatacttttaaaaccaggcctcataactttgttattgtcttcaacgttgcagGATCCTTCAAAGCATGTTTTTCACCTTGTTACCGATAAACTAAATTTTGGAGCCATGAACATGTGGTTTCTTTTAAACCCTCCTGAAAAAGCTACAATCC
                    ||      || |   |  || |  || |   |  | | | |   |  || | | || | |   || | | | | || ||||| |||   ||||||||||| || ||||| || |||||  | || |||||||||||||||||||||||| |  | ||||||||||  || || || ||||
--------------------gtagtttcgtcttcctttttaatcaagtgcaaagtgtgataattgttctaacagctatcta--tggcataatcttttcagGAGCCTGAGAAGCATGTTTTCCATCTTGTGACTGATAAGTTGAACTTTGGAGCCATGAACATGTGGTTTTTGCTGAACCCTCCTGGGAAGGCCACCATCC

upper sequence: GLYMA07G08910.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os09g36190.1 (Oryza sativa), 3'ss of exon 7
gcaccaaaaatatcgtgcatgtgaaagtgtatctatgatttagt--aaattat-acttttaaaaccaggcctcataactttgttattgtcttcaacgttgcagGATCCTTCAAAGCATGTTTTTCACCTTGTTACCGATAAACTAAATTTTGGAGCCATGAACATGTGGTTTCTTTTAAACCCTCCTGAAAAAGCTACAATCC
            | ||   |||     |   ||| | ||  | |  ||| | | |    | | |   |  || | |||| |||   || | | | | || ||||| |||   ||||||||||| || ||||| || |||||  | || |||||||||||||||||||||||| |  | ||||| ||||  || || || ||||
-----------gtagtttctgtc----ttcctctttaatcaaatgcaaactgtgataagtgataagtgttctgacaactatgta--tggcataaccttttcagGAGCCTGAGAAGCATGTTTTCCATCTTGTGACTGATAAGTTGAACTTTGGAGCCATGAACATGTGGTTTTTGCTGAACCCACCTGGGAAGGCCACCATCC

upper sequence: GLYMA07G08910.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G076276_T03 (Zea mays), 3'ss of exon 7
----gcaccaaaaatatcgtgcatgtgaaagtgtatctatgatttagtaaattatacttttaaaaccaggcctcataac---tttg--ttattgtcttcaacgttgcagGATCCTTCAAAGCATGTTTTTCACCTTGTTACCGATAAACTAAATTTTGGAGCCATGAACATGTGGTTTCTTTTAAACCCTCCTGAAAAAGCTACAATCC
    |    |     ||| || |  || |||||||       || | ||  |    | || ||   |       ||| |   ||||  ||  | |||  ||  || ||||| |||  ||| ||||| |||||||||||||| || ||||| || ||||| |||||||||||||||||| |  | || || ||||   | || ||||| |
gttagtgtaatccccatcttgaaactggaagtgtaatctc--ttcattatgtctaccattgaatgacccattatatagcacttttgattttctttctataaattttcagGAGCCTGAAAAACATGTGTTTCACCTTGTTACTGACAAACTGAACTTTGGGGCCATGAACATGTGGTTTTTGCTGAATCCACCTGGGGATGCAACAATGC

upper sequence: GLYMA07G08910.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G147145_T02 (Zea mays), 3'ss of exon 4
gcaccaaaaatatcgtgcatgtgaaag-tgtatctatgat---ttagtaaattatacttttaa--aaccag--gcctcataactttgttattgt--cttcaacgttgcagGATCCTTCAAAGCATGTTTTTCACCTTGTTACCGATAAACTAAATTTTGGAGCCATGAACATGTGGTTTCTTTTAAACCCTCCTGAAAAAGCTACAATCC
        | | |  ||||| |  ||| || |  ||||||   ||  |   || |||  || |     ||      | | |   || || || |  ||  ||  |||||||| |||  ||| ||||| ||||| |||||||| || ||||| || ||||| |||||||||||||||||| |  | || || ||||   | || |||||||
-----gttagtttaatgcatcttcaagctggaaatatgatctcttcattgtttgtaccattgactggtcaattatattacactcttatttttcttgctataaatttgcagGAGCCTGAAAAACATGTATTTCATCTTGTTACTGACAAACTGAACTTTGGGGCCATGAACATGTGGTTTTTGCTGAATCCACCTGGGGATGCAACAATCC

upper sequence: GLYMA07G08910.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G379577_T01 (Zea mays), 3'ss of exon 7
gcaccaaaaatatcgtgcatgtgaaagtgtatctatgatttagtaaattatacttttaaaaccaggcctcataactttgttatt-gtcttcaacgttgcagGATCCTTCAAAGCATGTTTTTCACCTTGTTACCGATAAACTAAATTTTGGAGCCATGAACATGTGGTTTCTTTTAAACCCTCCTGAAAAAGCTACAATCC
          |||  | ||||        | |   | | ||| | ||||  | |  | |||  ||   || |||| ||| | || |   |   | || ||| | ||    || |||||||| || ||||| || || ||  |||| ||||||||||||||||||||||||||  | ||||| ||||  || ||||| ||||
---------gtattttccatgcac-----ttttagtcaattattcaattgcattcctcaaagtag--ttcctaacattgatgtttggaatgtccttttcagAAACCAGAGAAACATGTTTTCCATCTTGTGACTGACAAGTTAAACTTTGGAGCCATGAACATGTGGTTTCTGCTGAACCCACCTGGCAAGGCTACCATCC

upper sequence: GLYMA07G08910.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G386971_T01 (Zea mays), 3'ss of exon 7
gcaccaaaaatatcgtgcatgtgaaagtgtatctatgatttagtaaattatacttttaaaaccaggc-ctcataactttgttattgtcttcaacgttgcagGATCCTTCAAAGCATGTTTTTCACCTTGTTACCGATAAACTAAATTTTGGAGCCATGAACATGTGGTTTCTTTTAAACCCTCCTGAAAAAGCTACAATCC
          |||  ||| |||       | |   | | ||| | ||||  |||     ||  ||   || ||     ||||  || | |     || ||||| ||    || |||||||| || ||||| || || ||  |||| ||||||||||||||||||||||||||  | ||||| ||||  || || || ||||
---------gtattttgcgtgtac-----ttttagtcaattattcaattgcactccactaagtagtttctaatggtgatgtt--tggcatgtctttttcagGAACCAGAGAAACATGTTTTCCATCTTGTGACTGACAAGTTAAACTTTGGAGCCATGAACATGTGGTTTCTGCTGAACCCACCTGGCAAGGCCACCATCC

upper sequence: GLYMA07G08910.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv15s0048g01300.t01 (Vitis vinifera), 3'ss of exon 8
---gcaccaaaaatatcgtgcatgtgaaagtgtatctatgatttagtaaattatacttttaaaaccaggcctcataactttgttattgtcttcaacgttgcagGATCCTTCAAAGCATGTTTTTCACCTTGTTACCGATAAACTAAATTTTGGAGCCATGAACATGTGGTTTCTTTTAAACCCTCCTGAAAAAGCTACAATCC
   | |  |   | |  |    ||| |        | |      |  | || ||  | ||              ||| |||| || |  | || |  |||||||| ||   ||| ||||| || || || ||||| ||||| || ||||||||||||||||| ||||||||||| || ||||| || | |||||| || ||||
tttggataagcgaaaggggatttgttaggaaagcacaaaagggcatcacat-atgttcttcctttttcattcactaagtttgctaataccctcga--ttgcagGAACCAGAAAAACATGTATTCCATCTGGTTACTGATAAGCTGAATTTTGGAGCCATGAATATGTGGTTTCTGTTGAACCCCCCAGGAAAAGCAACTATCC

upper sequence: GLYMA07G08910.1 (Glycine max), 3'ss of exon 5
lower sequence: PP1S128_25V6.1 (Physcomitrella patens), 3'ss of exon 7
---------------------------------------------------------------------------------gcaccaaaaatatcgtgcatgtgaaagtgtatctatgatttagtaaattatacttttaaaaccaggcctcataactttgttattgtcttcaacgttgcagGATCCTTCAAAGCATGTTTTTCACCTTGTTACCGATAAACTAAATTTTGGAGCCATGAACATGTGGTTTCTTTTAAACCCTCCTGAAAAAGCTACAATCC
                                                                                  |   ||  ||   |   |  |||    |||| ||||||  |||     ||   | |     ||   |  | | || | | |   |  ||    |||||||| ||    || || ||||||||| |||||||||| || ||||||||||| |||||||  ||||||||| |   ||| ||||| |     |||   || |
gtatggagtctatcaagatctattcttttctgatagaggcctatggcctcagatattctatgttttgttttaaagcgacgctcgttaagtatgctgctgaaatgacttggtatatatgatcgagttttccatggatctg---tcatagcaaacacctatttcaactttatctttcttgcagGAGCCAGAGAAACACGTTTTTCACATTGTTACCGACAAGCTAAATTTTGGTGCCATGATGATGTGGTTTTTAGCAAATCCTCCCGGGGCTGCTGTCATAC

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|12689076|gb|BG155341.1|BG155341
EST:     ATGTCTTGGCTGCATCTGTTGTTGTCAACTCAACTATTATGAATGCAAAG                         GATCCTTCAAAGCATGTTTTTCACCTTGTTACCGATAAACTAAATTTTGGA
genomic: ATGTCTTGGCTGCATCTGTTGTTGTCAACTCAACTATTATGAATGCAAAGgtgacttgga ... aacgttgcagGATCCTTCAAAGCATGTTTTTCACCTTGTTACCGATAAACTAAATTTTGGA
EST: gi|8283918|gb|BE021477.1|BE021477
EST:     TGTCTTGGCTGCATCTGGTGTTGTCAACTCAACTATTATGAATGNCAAAG                         -ATCCTNCAAAGCATGT
genomic: TGTCTTGGCTGCATCTGTTGTTGTCAACTCAACTATTATGAATG-CAAAGgtgacttgga ... aacgttgcagGATCCTTCAAAGCATGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aattatacttttaaaaccaggcctcataactttgttattgtcttcaacgttgcagGATCCTTCAAAGCATGTTTTTCACCTTGTTACCGATAAACTAAATTTTGGAGCCATGAACATGTGGTTTCTTTTAAACCCTCCTGAAAAAGCTACAATCC
                       tcataac  putative branch site (score: 2)
                         ataactttgttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcaccaaaaatatcgtgcatgtgaaagtgtatctatgatttagtaaattatacttttaaaaccaggcctcataactttgttattgtcttcaacgttgcagGATCCTTCAAAGCATGTTTTTCACCTTGTTACCGATAAACTAAATTTTGGAGCCATGAACATGTGGTTTCTTTTAAACCCTCCTGAAAAAGCTACAATCC

-caccaaa
- - - - - - - -tgcatgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccaggcc