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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgatttcttttacatttggatcttttccatattctttcagtttttttttccagttcttttttattttgcctttttgttttttcacagtgggtaggtagatgaatggttgagcttctgttttcagagtatcattttctggttttcatgtattttagGTTCGAACTGTAAGAGTTGAGAAGAGGATAAATGAGATTGTTAACAGGCTAAACAAGACAAAAGTGGAAAGGAAACCTGATTTGAAAG

Basic information

species Glycine max
transcript GLYMA04G08530.3
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G08530.3 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G157332_T05 (Zea mays), 3'ss of exon 3
gtgatttcttttacatttggatcttttccatattctttcagtttttttttccagttcttttttattttgcctttttgttttttcacagtgggtaggtagatgaatggttgagcttctgttttcagagtatcattttctggttttcatgtattttagGTTCGAACTGTAAGAGTTGAGAAGAGGATAAATGAGATTGTTAACAGGCTAAACAAGACAAAAGTGGAAAGGAAACCTGATTTGAAAG------------
                                                     ||| ||||| |||   | |  || |  || ||  ||    |    |||||||  |  ||||||   | | | |     |  |  |  ||||| | | ||  ||||||| ||| | | ||| || |||||||| ||||||||||| ||| |  | || |||||||| |||||| ||||||||||||| || |            
---------------------------------------------------tcgttattttt-attgcacatgcttatcattacat-gtactaaaactgatgaataat--agcttcgactataatatctgtaactcatccttttctttt-ttgaagGTTCGCACTATTAAAGTGGAAAAGAGGATCAATGAGATTGTGAACCGCTTGAATAAGACAAAGGTGGAACGGAAACCTGATTTAAAGGGTATGTCACATT

upper sequence: GLYMA04G08530.3 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G157332_T03 (Zea mays), 3'ss of exon 1
gtgatttcttttacatttggatcttttccatattctttcagtttttttttccagttcttttttattttgcctttttgttttttcacagtgggtaggtagatgaatggttgagcttctgttttcagagtatcattttctggttttcatgtattttagGTTCGAACTGTAAGAGTTGAGAAGAGGATAAATGAGATTGTTAACAGGCTAAACAAGACAAAAGTGGAAAGGAAACCTGATTTGAAAG
                                                     ||| ||||| |||   | |  || |  || ||  ||    |    |||||||  |  ||||||   | | | |     |  |  |  ||||| | | ||  ||||||| ||| | | ||| || |||||||| ||||||||||| ||| |  | || |||||||| |||||| ||||||||||||| || |
---------------------------------------------------tcgttattttt-attgcacatgcttatcattacat-gtactaaaactgatgaataat--agcttcgactataatatctgtaactcatccttttctttt-ttgaagGTTCGCACTATTAAAGTGGAAAAGAGGATCAATGAGATTGTGAACCGCTTGAATAAGACAAAGGTGGAACGGAAACCTGATTTAAAGG

upper sequence: GLYMA04G08530.3 (Glycine max), 3'ss of exon 4
lower sequence: Vv04s0008g03810.t01 (Vitis vinifera), 3'ss of exon 3
gtgatttcttttacatttggatcttttccatattctttcagtttttttttccagttcttttttat--tttgcc-tttttgttttttcacagtgggtaggtagatgaatggttgagcttctgttttcagagtatcattttctggttttcatgtattttagGTTCGAACTGTAAGAGTTGAGAAGAGGATAAATGAGATTGTTAACAGGCTAAACAAGACAAAAGTGGAAAGGAAACCTGATTTGAAAG
                                     | || || ||| |    ||||  | | |  |||||   |||| ||| ||    ||| | | | | ||||| | | ||  | |||         | |  ||||   | ||      | ||||||| || ||||| ||||| |||||| | ||||||||||| ||||| ||  | |||| ||||||||| ||||||||||| ||||| ||||
------------------------------------gtgagcttctttattttcttctgctctgtgctttgcaacttttatttctttttggtgagcatgcatatgaaagataga--tactg--------atgtagtttttgtgctt------aatttagGTACGCACTGTGAGAGTGGAGAAGCGAATAAATGAGATAGTTAATAGATTGAACAGGACAAAAGTAGAAAGGAAACCAGATTTAAAAG

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|192327626|gb|FK020659.1|FK020659
EST:     AAACTGCTTCAATGGATGTTGGCCAAGTTGGTTTTCACAACTCAAAAATG                         GTTCGAACTGTAAGAGTTGAGAAGAGGATAAATGAGATTGTTAACAGGCTA
genomic: AAACTGCTTCAATGGATGTTGGCCAAGTTGGTTTTCACAACTCAAAAATGgtgatttctt ... tgtattttagGTTCGAACTGTAAGAGTTGAGAAGAGGATAAATGAGATTGTTAACAGGCTA
EST: gi|192331951|gb|FK026735.1|FK026735
EST:     AAACTGCTTCAATGGATGTTGGCCAAGTTGGTTTTCACAACTCAAAAATG                         GTTCGAACTGTAAGAGTTGAGAAGAGGATAAATGAGATTGTTAACAGGCTA
genomic: AAACTGCTTCAATGGATGTTGGCCAAGTTGGTTTTCACAACTCAAAAATGgtgatttctt ... tgtattttagGTTCGAACTGTAAGAGTTGAGAAGAGGATAAATGAGATTGTTAACAGGCTA
EST: gi|208250509|gb|GE046930.1|GE046930
EST:     ACTGCTTCAATGGATGTTGGCCAAGTTGGTTTTCACAAACTCAAAAATAG                         GTTCGAACTGTAAGAGTTGAGAAGAGGATAAAT
genomic: ACTGCTTCAATGGATGTTGGCCAAGTTGGTTTTCACAA-CTCAAAAAT-Ggtgatttctt ... tgtattttagGTTCGAACTGTAAGAGTTGAGAAGAGGATAAAT
EST: gi|192299133|gb|FG992879.1|FG992879
EST:     AAACTGCTTCAATGGATGTTGGCCAAGTTGGTTTTCACAACTCAAAAATG                         GTTCGAACTGTAAGAGTTGAGAAGAGGATAAATGAGATTGTTAACAGGCTA
genomic: AAACTGCTTCAATGGATGTTGGCCAAGTTGGTTTTCACAACTCAAAAATGgtgatttctt ... tgtattttagGTTCGAACTGTAAGAGTTGAGAAGAGGATAAATGAGATTGTTAACAGGCTA
EST: gi|18713863|gb|BM522747.1|BM522747
EST:     AAACTGCTTCAATGGATGTTGGCCAAGTTGGTTTTCACAACTCAAAAATG                         GTTCGAACTGTAAGAGTTGAGAAGAGGATAAATGAGATTGTTAACAGGCTA
genomic: AAACTGCTTCAATGGATGTTGGCCAAGTTGGTTTTCACAACTCAAAAATGgtgatttctt ... tgtattttagGTTCGAACTGTAAGAGTTGAGAAGAGGATAAATGAGATTGTTAACAGGCTA
EST: gi|208048593|gb|GD847524.1|GD847524
EST:     AAACTGCTTCAATGGATGTTGGCCAAGTTGGTTTTCACAACTCAAAAATG                         GTTCGAACTGTAAGAGTTGAGAAGAGGATAAATGAGATTGTTAACAGGCTA
genomic: AAACTGCTTCAATGGATGTTGGCCAAGTTGGTTTTCACAACTCAAAAATGgtgatttctt ... tgtattttagGTTCGAACTGTAAGAGTTGAGAAGAGGATAAATGAGATTGTTAACAGGCTA
EST: gi|23725673|gb|BU760799.1|BU760799
EST:     AAACTGCTTCAATGGATGTTGGCCAAGTTGGTTTTCACAACTCAAAAATG                         GTTCGAACTGTAAGAGTTGAGAAGAGGATAAATGAGATTGTTAACAGGCTA
genomic: AAACTGCTTCAATGGATGTTGGCCAAGTTGGTTTTCACAACTCAAAAATGgtgatttctt ... tgtattttagGTTCGAACTGTAAGAGTTGAGAAGAGGATAAATGAGATTGTTAACAGGCTA
EST: gi|192315597|gb|FK007425.1|FK007425
EST:     AAACTGCTTCAATGGATGTTGGCCAAGTTGGTTTTCACAACTCAAAAATG                         GTTCGAACTGTAAGAGTTGAGAAGAGGATAAATGAGATTGTTAACAGGCTA
genomic: AAACTGCTTCAATGGATGTTGGCCAAGTTGGTTTTCACAACTCAAAAATGgtgatttctt ... tgtattttagGTTCGAACTGTAAGAGTTGAGAAGAGGATAAATGAGATTGTTAACAGGCTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaatggttgagcttctgttttcagagtatcattttctggttttcatgtattttagGTTCGAACTGTAAGAGTTGAGAAGAGGATAAATGAGATTGTTAACAGGCTAAACAAGACAAAAGTGGAAAGGAAACCTGATTTGAAAG
                                       ttttcat  CT-rich tract
                                       ttttcatgtatttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgatttcttttacatttggatcttttccatattctttcagtttttttttccagttcttttttattttgcctttttgttttttcacagtgggtaggtagatgaatggttgagcttctgttttcagagtatcattttctggttttcatgtattttagGTTCGAACTGTAAGAGTTGAGAAGAGGATAAATGAGATTGTTAACAGGCTAAACAAGACAAAAGTGGAAAGGAAACCTGATTTGAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA