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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaacatagtgttatctacactaactctttcctttctggcttcataacagtttatcaaccactgtttcctgctttttgtttcagTTGAAAGAATACATTGATGACACAGAAGATTTCATCAACATTCAACTG

Basic information

species Glycine max
transcript GLYMA13G44820.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G44820.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os06g44150.1 (Oryza sativa), 3'ss of exon 3
gtaaacatagtgttatctacactaactctttcctttctggctt-cataacagtttatcaaccactgttt--cctgctttttgtttcagTTGAAAGAATACATTGATGACACAGAAGATTTCATCAACATTCAACTG
||||  |      | ||  ||  | | |  |   |  ||  || ||| ||      | |     ||| |  ||| | |||| |||||| |||| || |||||||||||||| |||||||| |||||||||||  ||
gtaatgaaccacctctccccaaaatcccaattaatcttgtttttcattactagcagttacaggatgtctgaccttcattttctttcagCTGAAGGAGTACATTGATGACACTGAAGATTTTATCAACATTCAGTTG

upper sequence: GLYMA13G44820.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G064467_T01 (Zea mays), 3'ss of exon 3
--gtaaacatagtgttatctaca--ctaactct-ttcctttctggc--ttcataacagtttatcaaccactgtttcctgctttttgtttcagTTGAAAGAATACATTGATGACACAGAAGATTTCATCAACATTCAACTG
    ||||   |  || | || |   || || | || || | |  |   | || |  ||| | |||    || | |  ||   || |||||| | || || || ||||||||||||||||||||||||||||| ||||||
gtacaaactatgaattgtgtatatgttagctttgtttctgttttacagattattatggttga-caatt-ttgctactcgcacattttttcagCTAAAGGAGTATATTGATGACACAGAAGATTTCATCAACATACAACTG

upper sequence: GLYMA13G44820.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G170326_T02 (Zea mays), 3'ss of exon 3
------------gtaaacatagtgttatctacactaactctttcctttctggcttcataacagtttatcaaccactgtttcctgctttttgtttcagTTGAAAGAATACATTGATGACACAGAAGATTTCATCAACATTCAACTG
             | | ||   |||  |  |        | |    |  |      |||  |||  |          | |  |  |  || |||||| | ||||| |||||||||||||| ||||| |||||||||||||| |||
gtaccaagccatatcaccagcatgtcttaaatctggttacgtataataatactgcaataggagtcaaaggggtctgatctatttttacttctttcagCTTAAAGAGTACATTGATGACACTGAAGACTTCATCAACATTCAGCTG

upper sequence: GLYMA13G44820.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G108477_T01 (Zea mays), 3'ss of exon 3
----------gtaaacatagtgttatctaca-ctaactctttcctttctgg------cttcataacagtttatcaaccactgtttcctgctttt---tgtttcagTTGAAAGAATACATTGATGACACAGAAGATTTCATCAACATTCAACTG
           ||     ||  |    || | ||  || |    | | | |        | |||  |||  |          |   ||| ||||   | |||||| | ||||| ||||| |||||||| ||||| |||||||||||||| |||
gtaccgagccatatctccagcatatcttaaatctggctatgctatgtgtagtaataatgtgataggagtgaaaggggtctgatgatctgtttttccttctttcagCTTAAAGAGTACATCGATGACACTGAAGACTTCATCAACATTCAGCTG

upper sequence: GLYMA13G44820.1 (Glycine max), 3'ss of exon 4
lower sequence: AT1G16010.3 (Arabidopsis thaliana), 3'ss of exon 5
gtaaac--atagtgttatctacactaactctt--tcctttctggcttcataacagtttatcaaccactgtttcctgctttttgtttcagTTGAAAGAATACATTGATGACACAGAAGATTTCATCAACATTCAACTG
|||     || |        |   | ||| ||  || ||  | |||  | | |  ||||   | |  |||| |   ||||   || ||||| || || |||||||||||||| ||||||||||| ||||||||||||
gtactttaatggctcctctcatttttacttttgatctttcttcgctagacagc--tttaatcatctgtgttcctctctttactttacagTTAAAGGAGTACATTGATGACACTGAAGATTTCATTAACATTCAACTG

upper sequence: GLYMA13G44820.1 (Glycine max), 3'ss of exon 4
lower sequence: AT1G80900.1 (Arabidopsis thaliana), 3'ss of exon 3
------gtaaacatagtgttatcta-cactaactctttcctttc--tggcttcataacagtttatcaaccac-tgtttcctgctttttgtttcagTTGAAAGAATACATTGATGACACAGAAGATTTCATCAACATTCAACTG
        |||| | |  ||    | || | |   | |  |||     ||||  ||| ||    | || ||| ||   |   ||||    ||||||| || || ||||| ||||| || ||||||||||||||||||||| ||
gtaactaaaaacctcgcctttgtgatcattcatcatcttgttttaacagcttt-taaaagcggtttaatcacctgcaactctctttactcttcagTTAAAGGAGTACATCGATGATACCGAAGATTTCATCAACATTCAATTG

upper sequence: GLYMA13G44820.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv09s0018g00600.t01 (Vitis vinifera), 3'ss of exon 3
gtaaac-atagtgttatctacact----aactctttcctttctg---gcttcataacagttta-------tcaaccactgtttcctgctttttgtttcagTTGAAAGAATACATTGATGACACAGAAGATTTCATCAACATTCAACTG
|||  |   |   || | |||| |     || |||  ||||       |||||     | |         | |     |  || || | | | ||||||| |||| ||||||||||||||||||||||||||||| |||||||| |||
gtatcctgcatctttctttacatttgtagacccttgtcttttaatatacttcaggtggggtggagaaaatttattagttagtttcttcatgtcgtttcagCTGAAGGAATACATTGATGACACAGAAGATTTCATTAACATTCAGCTG

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|6071171|gb|AW100558.1|AW100558
EST:     TGGAAGCATACTTTGTTGTCATTGATAGCACTCTAAATAAGTTGACATCG                         TTGAAAGAATACATTGATGACACAGAAGATTTCATCAACATTCAACTG
genomic: TGGAAGCATACTTTGTTGTCATTGATAGCACTCTAAATAAGTTGACATCGgtaaacatag ... tttgtttcagTTGAAAGAATACATTGATGACACAGAAGATTTCATCAACATTCAACTG
EST: gi|9985740|gb|BE659848.1|BE659848
EST:     TGGAAGCATACTTTGTTGTCATTGATAGCACTCTAAATAAGTTGACATCG                         TTGAAAGAATACATTGATGACACAGAAGATTTCATCAACATTCAACTG
genomic: TGGAAGCATACTTTGTTGTCATTGATAGCACTCTAAATAAGTTGACATCGgtaaacatag ... tttgtttcagTTGAAAGAATACATTGATGACACAGAAGATTTCATCAACATTCAACTG
EST: gi|18038753|gb|BM307047.1|BM307047
EST:     TGGAAGCATACTTTGTTGTCATTGATAGCACTCTAAATAAGTTGACATCG                         TTGAAAAGA-TACATTGATGACACAGAAGATTTCATCAACATTCAACTG
genomic: TGGAAGCATACTTTGTTGTCATTGATAGCACTCTAAATAAGTTGACATCGgtaaacatag ... tttgtttcagTTGAAA-GAATACATTGATGACACAGAAGATTTCATCAACATTCAACTG
EST: gi|14990737|gb|BI316410.1|BI316410
EST:     TGGAAGCATACTTTGTTGTCATTGATAGCACTCTAAATAAGTTGACATCG                         TCTGAAAGAATACATTGATGACACAGAAGATTTCATCAACATTCAACTG
genomic: TGGAAGCATACTTTGTTGTCATTGATAGCACTCTAAATAAGTTGACATCGgtaaacatag ... tttgtttcagT-TGAAAGAATACATTGATGACACAGAAGATTTCATCAACATTCAACTG
EST: gi|58014711|gb|CX701453.1|CX701453
EST:     TGGAAGCATACTTTGTTGTCATTGATAGCACTCTAAATAAGTTGACATCG                         TTGAAAGAATACATTGATGACACAGAAGATTTCATCAACATTCAACTG
genomic: TGGAAGCATACTTTGTTGTCATTGATAGCACTCTAAATAAGTTGACATCGgtaaacatag ... tttgtttcagTTGAAAGAATACATTGATGACACAGAAGATTTCATCAACATTCAACTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcctttctggcttcataacagtttatcaaccactgtttcctgctttttgtttcagTTGAAAGAATACATTGATGACACAGAAGATTTCATCAACATTCAACTG
            tcataac  putative branch site (score: 2)
                                ctgtttcctgcttttt  putative PPT
                                           tttttgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaacatagtgttatctacactaactctttcctttctggcttcataacagtttatcaaccactgtttcctgctttttgtttcagTTGAAAGAATACATTGATGACACAGAAGATTTCATCAACATTCAACTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA