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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaagatacatagaaaaaataattttgcttttgctgtctagtattgcttccaaaaatgaagttctacattttgtcacatagtagaattacttcttatccagGATAAGTCATGGCGTGTTCGTTACATGGTTGCTAATCAACTATATGAGCTATGTGAAGCTGTTGGTCCTGACCCCACCAG

Basic information

species Glycine max
transcript GLYMA09G31760.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G31760.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os09g07510.1 (Oryza sativa), 3'ss of exon 4
------------------------------------------------------aaagatacatagaaaaaataatt--ttgct-------tttgctgtctagtattgcttccaa-aaatgaagttctaca-ttttgtcacatagta----gaattacttcttatccagGATAAGTCATGGCGTGTTCGTTACATGGTTGCTAATCAACTATATGAGCTATGTGAAGCTGTTGGTCCTGACCCCACCAG
                                                      | |  ||  |  | | | | |||  |||||         || ||    |  |||||||      |||   | | | | || || ||  |  ||       | |||  |||   |||| || |||||||| |||||||| |||||||| |||||| | |||||||| || || || ||||||||||| |   | ||
gtaaattacacccctacttggtacctcagtgtcatctacttgatatcacatataatatttatttgcagacattcattagttgctagaggttcctgatgctccgagttgcttctgttgtatgtgttaccataattatgacatcttttactctctgtaactcattaaatagGACAAATCATGGCGAGTTCGTTATATGGTTGCCAATCAATTGTATGAGCTCTGCGAGGCAGTTGGTCCTGAACATTCTAG

upper sequence: GLYMA09G31760.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G164352_T04 (Zea mays), 3'ss of exon 4
--aaagatacatagaaaaaataatt--ttgcttttgctgtctagtattgcttccaaaaatgaagttctacattttgtcacatagtagaattacttcttatccagGATAAGTCATGGCGTGTTCGTTACATGGTTGCTAATCAACTATATGAGCTATGTGAAGCTGTTGGTCCTGACCCCACCAG
    || | |         ||||||  ||  ||||||    |  |   | ||      || |      |||  | |  || |  | | | |   | || |  ||||||| ||||||||||||||||| |||||||| |||||| |||||||||| ||||| |||||||| ||||| || || ||
ttgtagttgctagaggttgataatttcttagttttgcaacttgttgcag-ttaagtgcatcaccactaacaaat-gctacttgcttgtact--cttttgtttagGATAAATCATGGCGTGTTCGTTATATGGTTGCCAATCAATTATATGAGCTCTGTGAGGCTGTTGGCCCTGAGCCTACAAG

upper sequence: GLYMA09G31760.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G122135_T01 (Zea mays), 3'ss of exon 4
------------------------------------------------------------------------------------aaagatacatagaaaaaataattttgctt--ttgctgtctagtattgc---ttccaaaaatgaagttctacatt-ttgtcacatagta---gaat-tact--tcttatccagGATAAGTCATGGCGTGTTCGTTACATGGTTGCTAATCAACTATATGAGCTATGTGAAGCTGTTGGTCCTGACCCCACCAG
                                                                                      || | |         |||||||  |    | ||    |||| ||||   || |   | |  ||| |   |    ||  | ||  ||   | || ||||    || |  ||||||| ||||||||||||||||| ||||| || |||||  |||||||||| ||||| |||||||| ||||| ||||| ||
gtacattgctcccatgttggaccctatacattttgcagcaagtaatttgctttctttgtggatatattattgggagacatgtttttagttgctagaggttgataatttctcggagtcgcctcttagttttgcaacttgctgcagttcagtgcattaccgctgataaatgctacttgcatatactcgctttgtttagGATAAATCATGGCGTGTTCGTTATATGGTCGCCAATCAGTTATATGAGCTCTGTGAGGCTGTTGGCCCTGAGCCCACAAG

upper sequence: GLYMA09G31760.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G102858_T01 (Zea mays), 3'ss of exon 4
--------------------------------------------------------------------------aaagatac-atagaaaaaataattttgcttttgctgtctagtattgcttccaaaaa-tgaagttct---acattttgtcacatagtaga--------attactt-------cttatc----cagGATAAGTCATGGCGTGTTCGTTACATGGTTGCTAATCAACTATATGAGCTATGTGAAGCTGTTGGTCCTGACCCCACCAG
                                                                          |||  ||| | || || | |    |    | ||||       | |  || ||     | |||||     ||| |     |||| ||  |        ||| |||       |||| |    |||||||| || |||||||| || || ||||| || |||||||| ||||| |||||||||||||||||| |||| ||||| ||
gtatatcttacacacttttggtggcttaataaatgttgggagaaaagataaagttgtcaatactaattctcgtaaaaattactagagtaagatttccataagatctgctactagacaataatttcatgtgcttaagtttcagcacactaccatacatggttaatgatttcaattgcttatgttttcttaacatctcagGATAAATCTTGGCGTGTGCGCTATATGGTGGCAAATCAACTGTATGAACTATGTGAAGCTGTTGGTACTGAACCCACAAG

upper sequence: GLYMA09G31760.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv17s0000g03870.t01 (Vitis vinifera), 3'ss of exon 5
---aaagatacatagaaaaaataattttgcttttgctgtctagtattgcttccaaaaatgaagttctacattttgtcacatagtagaattacttcttatccagGATAAGTCATGGCGTGTTCGTTACATGGTTGCTAATCAACTATATGAGCTATGTGAAGCTGTTGGTCCTGACCCCACCAG
   |   ||||     |   |||||| |  |     |   ||| | ||  ||  || |||   |  |  ||  |     || |   ||||  ||| |   ||||||||||| ||||||||||| || |||||||| |||||| ||||||||||||||||||||||||||||||| || |||||
caaactcatactattgagtcataattctcataaaaatagttagaagtg--tcacaatatggtttatttgatcattgtgtat-gagaaattttttcctgaacagGATAAGTCTTGGCGTGTTCGCTATATGGTTGCAAATCAATTATATGAGCTATGTGAAGCTGTTGGTCCTGAGCCTACCAG

upper sequence: GLYMA09G31760.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv03s0038g00200.t01 (Vitis vinifera), 3'ss of exon 1
aaagatacatagaaaaaataattttgcttttgctgtctagtattgcttccaaaaatgaagttctacat-tttgtcacatagtagaattacttcttatccagGATAAGTCATGGCGTGTTCGTTACATGGTTGCTAATCAACTATATGAGCTATGTGAAGCTGTTGGTCCTGACCCCACCAG--------------------
                                                           ||   |||| ||  || ||||    |   | ||||    ||||||||||| ||||||||||| || |||||||| |||||| ||||||||||||||||||||||||||||||| || |||||                    
-----------------------------------------------------------gtagcacatattcttcccataaattatgaatttct--ctcagGATAAGTCTTGGCGTGTTCGCTATATGGTTGCAAATCAATTATATGAGCTATGTGAAGCTGTTGGTCCTGAGCCTACCAGGTCAGACTTGGTTCCTGCAT

upper sequence: GLYMA09G31760.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv04s0008g07090.t01 (Vitis vinifera), 3'ss of exon 2
---------------------------------------------aaagatacatagaaaaaataattttgcttttgctgtctagtattgcttccaaaaatgaagttctacattttgtcacatagtagaattacttcttatccagGATAAGTCATGGCGTGTTCGTTACATGGTTGCTAATCAACTATATGAGCTATGTGAAGCTGTTGGTCCTGACCCCACCAG
                                              |  ||  |  | | ||||  | ||| |    || |  ||    ||| |||  | |    |   | |||   || ||||    |   | ||||    ||||||||||| ||||||||||| || |||||||| |||||| ||||||||||||||||||                      
cgatcctagaaccactatgctatagtagcttggctactttagtaatagtatttaaggtataaattttgttgatacgcctttaaagctaagctaccatgagTCGCATCACATATTCC-TCCCATAAATTATGAATTTCT--CTCAGGATAAGTCTTGGCGTGTTCGCTATATGGTTGCAAATCAATTATATGAGCTATGTGAAG----------------------

upper sequence: GLYMA09G31760.1 (Glycine max), 3'ss of exon 4
lower sequence: PP1S117_137V6.1 (Physcomitrella patens), 3'ss of exon 3
aaagatacatagaaaaaat---aattttgcttttgctgtctagtattgcttccaaaaatgaagttctacattttgtcacatagtagaattacttctta--tccagGATAAGTCATGGCGTGTTCGTTACATGGTTGCTAATCAACTATATGAGCTATGTGAAGCTGTTGGTCCTGACCCCACCAG
     ||  | | || | |    | ||    |  | | | |   | |   | ||||  |  ||||  |  || | | |  |  | || |  ||    |  ||||||| |||||||||||||||||||||||||| ||||| ||  | || ||||||||||| || || || || || || |||||
---tctatttgggaagattccagagttcctatcggatttatcacactaagttcaaatgtagagtt--atcttattttagtttctcgattgcctgtggacttccagGACAAGTCATGGCGTGTTCGTTACATGGTAGCTAACCAGTTGTACGAGCTATGTGAGGCGGTCGGGCCAGAGCCTACCAG

upper sequence: GLYMA09G31760.1 (Glycine max), 3'ss of exon 4
lower sequence: EFJ35758 (Selaginella moellendorffii), 3'ss of exon 3
aaagatacatagaaaaaataattttgcttttgctgtctagtattgcttccaaaaatgaagttctacattttgtcacatagtagaattacttcttatccagGATAAGTCATGGCGTGTTCGTTACATGGTTGCTAATCAACTATATGAGCTATGTGAAGCTGTTGGTCCTGACCCCACCAG
                                       ||||  ||       ||    || |   |  |||  | |  |    |   |  || | ||||| ||||| ||||| || ||||| ||||||||||||||||||||||| || |||||| ||||||| || ||    || ||
---------------------------------------gtatgtctc------attcttttattgttcctgttgc-tgatgcggtgcgtgtttctacagGACAAGTCCTGGCGGGTACGTTATATGGTTGCTAATCAACTATATGAACTCTGTGAAACTGTTGGACCGGAATGTACTAG

upper sequence: GLYMA09G31760.1 (Glycine max), 3'ss of exon 4
lower sequence: EFJ10709 (Selaginella moellendorffii), 3'ss of exon 3
aaagatacatagaaaaaataattttgcttttgctgtctagtattgcttccaaaaatgaagttctacattttgtcacatagtagaattacttcttatccagGATAAGTCATGGCGTGTTCGTTACATGGTTGCTAATCAACTATATGAGCTATGTGAAGCTGTTGGTCCTGACCCCACCAG
                                       ||||  ||        |   ||||    |  ||   |   |     ||  |||   | ||||| ||||| ||||| || ||||| ||||||||||||||||||||||| || |||||| ||||||| || ||    || ||
---------------------------------------gtatgtctcattcttttattgttcctgttgctgatgcggtgcgtgtttgtttc---tacagGACAAGTCCTGGCGGGTACGTTATATGGTTGCTAATCAACTATATGAACTCTGTGAAACTGTTGGACCGGAATGTACTAG

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|207792759|gb|GD767451.1|GD767451
EST:     CTCAAGATTGCGTGGCACATATTCTTCCTGTCATAGTCAATTTTTCTCAG                         GATAAGTCATGGCGTGTTCGTTACATGGTTGCTAAT
genomic: CTCAAGATTGCGTGGCACATATTCTTCCTGTCATAGTCAATTTTTCTCAGgtttgttggc ... tcttatccagGATAAGTCATGGCGTGTTCGTTACATGGTTGCTAAT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttccaaaaatgaagttctacattttgtcacatagtagaattacttcttatccagGATAAGTCATGGCGTGTTCGTTACATGGTTGCTAATCAACTATATGAGCTATGTGAAGCTGTTGGTCCTGACCCCACCAG
                                           cttcttatcc  CT-rich tract
     aaaaatgaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaagatacatagaaaaaataattttgcttttgctgtctagtattgcttccaaaaatgaagttctacattttgtcacatagtagaattacttcttatccagGATAAGTCATGGCGTGTTCGTTACATGGTTGCTAATCAACTATATGAGCTATGTGAAGCTGTTGGTCCTGACCCCACCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT
- - - - - - aaaaaat
- - - - - - - - - - - - - - - tgctgtc
- - - - - - - - - - - - - - - - - - - - - - - - - - -aatgaag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctacatt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgtcaca