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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...caatgccttttcatttatatatttttatcccgacaaaattgcattatgatcgttgtagcaaagatatttacttagttatatgttaccttatttcatccagGTGTGGGAGGTGAAAGCTGCCGACCTGACCATTAGCCCTGTTCACCGTGCTGCAGTGGGCATAGTAGATCCGAACAAG

Basic information

species Glycine max
transcript GLYMA12G08600.1
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G08600.1 (Glycine max), 3'ss of exon 14
lower sequence: LOC_Os10g34750.2 (Oryza sativa), 3'ss of exon 14
caatgccttttcatttatatatttttatc------ccgacaaaattgcattatgatcgttgtagcaaagatatttacttagttatatgttaccttatttcatccagGTGTGGGAGGTGAAAGCTGCCGACCTGACCATTAGCCCTGTTCACCGTGCTGCAGTGGGCATAGTAGATCCGAACAAG
  ||   |||| |     |  |||  ||        | |   |  |    | | ||  |   |     ||  ||| ||   |||||| ||   ||  | |   ||||| ||||||||||||||||| ||  ||| |||||| ||||| || ||||||||    || ||||| ||||||||||||
ggatatattttgaccctaaagtttaaattaaggggtctaggcagctttgatttaattttctgattgttgaggtttgct--attatattttg--ttgatcc--tcagGTTTGGGAGGTGAAAGCTGCTGATTTGAGCATTAGTCCTGTGCATCGTGCTGCCAATGGTATAGTTGATCCGAACAAG

upper sequence: GLYMA12G08600.1 (Glycine max), 3'ss of exon 14
lower sequence: GRMZM2G071304_T01 (Zea mays), 3'ss of exon 14
-caatgccttttcatttatatatttttatcccgacaaaattgcattatgatcgttgtagcaaagatatttacttagttatatgttaccttatttcatccagGTGTGGGAGGTGAAAGCTGCCGACCTGACCATTAGCCCTGTTCACCGTGCTGCAGTGGGCATAGTAGATCCGAACAAG
   |    |   |       |  || || | |   | |   | |        |||    |      | ||| |||  | ||| ||  |||  ||    ||||| |||||||| ||||||||||| |||| ||| |||||||| || ||||||||    || ||||| ||||| || |||
ttcacatttgccctgaagattgcttgtaacacagtagatgggaaagggcgcggttaagcctgttgcagttaattaaat-tattttttcttgcttttcacagGTCTGGGAGGTCAAAGCTGCCGATCTGAGCATAAGCCCTGTACATCGTGCTGCCAATGGTATAGTCGATCCAAATAAG

upper sequence: GLYMA12G08600.1 (Glycine max), 3'ss of exon 14
lower sequence: Vv06s0061g00690.t01 (Vitis vinifera), 3'ss of exon 14
caatgccttttcatttatatatttttatcccgacaaaattgcattatgatcgttgtagcaaagatatt-tacttagt-tatatgttaccttatttcatc-cagGTGTGGGAGGTGAAAGCTGCCGACCTGACCATTAGCCCTGTTCACCGTGCTGCAGTGGGCATAGTAGATCCGAACAAG
 | |   | |  ||  ||| |  | | | |     | || ||||| ||||| |   ||   | || || || | | | || || | |  | |||   |  ||||| ||||||||||||||||| ||| ||||||||||||||||||| ||||||||||| || ||||| ||||| ||||||
-agtaa-tctggatgaataaacatctgttctcgagacatggcatt-tgatcatcagagtgcatatgttatattaaatgtaaatataaagtaattcttttgcagGTTTGGGAGGTGAAAGCTGCAGACTTGACCATTAGCCCTGTTCATCGTGCTGCAGTTGGAATAGTGGATCCTAACAAG

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|18040766|gb|BM309060.1|BM309060
EST:     ATAGATTTGGAGAAACAATAAATCCTGATGTCTGGTTTGAAGCCAGTGAG                         GTGTGGGAGGTGAAAGCTGCCGACCTGACCATTAGCCCTGTTCACCGTGCT
genomic: ATAGATTTGGAGAAACAATAAATCCTGATGTCTGGTTTGAAGCCAGTGAGgtgagaatta ... tttcatccagGTGTGGGAGGTGAAAGCTGCCGACCTGACCATTAGCCCTGTTCACCGTGCT
EST: gi|51342409|gb|CO983482.1|CO983482
EST:     ATAGATTTGGAGAAACAATAAATCCTGATGTCTGGTTTGAAGCCAGTGAG                         GTGTGGGAGGTGAAAGCTGCCGACCTGACCATTAGCCCTGTTCACCGTGCT
genomic: ATAGATTTGGAGAAACAATAAATCCTGATGTCTGGTTTGAAGCCAGTGAGgtgagaatta ... tttcatccagGTGTGGGAGGTGAAAGCTGCCGACCTGACCATTAGCCCTGTTCACCGTGCT
EST: gi|51338234|gb|CO982100.1|CO982100
EST:     ATAGATTTGGAGAAACAATAAATCCTGATGTCTGGTTTGAAGCCAGTGAG                         GTGTGGGAGGTGAAAGCTGCCGACCTGACCATTAGCCCTGTTCACCGTGCT
genomic: ATAGATTTGGAGAAACAATAAATCCTGATGTCTGGTTTGAAGCCAGTGAGgtgagaatta ... tttcatccagGTGTGGGAGGTGAAAGCTGCCGACCTGACCATTAGCCCTGTTCACCGTGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgatcgttgtagcaaagatatttacttagttatatgttaccttatttcatccagGTGTGGGAGGTGAAAGCTGCCGACCTGACCATTAGCCCTGTTCACCGTGCTGCAGTGGGCATAGTAGATCCGAACAAG
                                        ccttatttc  CT-rich tract
              aaagatatttacttag  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
caatgccttttcatttatatatttttatcccgacaaaattgcattatgatcgttgtagcaaagatatttacttagttatatgttaccttatttcatccagGTGTGGGAGGTGAAAGCTGCCGACCTGACCATTAGCCCTGTTCACCGTGCTGCAGTGGGCATAGTAGATCCGAACAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
caatgcc
- - - - - - - - - - - - - - cccgaca
- - - - - - - - - - - - - - - - - - - -tgcatta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgttacc