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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTAACCGAAGGTTTCCTTTGGATCCCCTCTTTGGGTGGTCCTACTACCATTGCTGCTAGACAAAGTGGAGCTGGAATTTCTTGGCTTTTTCCATTTGTGgtaagaaagatatcttttgcttcatagttgaaataataagttgtagttgggctttttccccctaatcctgtgagtcattatgatctttcgaagcagtcta...

Basic information

species Glycine max
transcript GLYMA11G14960.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G14960.1 (Glycine max), 5'ss of exon 6
lower sequence: LOC_Os01g05800.1 (Oryza sativa), 5'ss of exon 6
GCTAACCGAAGGTTTCCTTTGGATCCCCTCTTTGGGTGGTCCTACTACCATTGCTGCTAGACAAAGTGGAGCTGGAATTTCTTGGCTTTTTCCATTTGTGgtaagaaagatatcttttgcttcatagttgaaataataagtt-gtagttgggctttttccccctaatcctgtgagtcattatgatctttcgaagcagtcta-
 || || ||||| ||  | ||||| || |||||||| || ||||| || ||||||||| | |||||||| ||||| ||||||||||| || || |||||||||| |||  |         || | |  |  |  || || ||  | | ||  ||        |   |     | |   ||  |    ||  |     | |  
ACTGACAGAAGGATTTTTCTGGATTCCATCTTTGGGAGGCCCTACAACAATTGCTGCTCGGCAAAGTGGTGCTGGCATTTCTTGGCTCTTGCCTTTTGTGgtaataaaattgatcacacgttaaca--tatatcaacaatttcattgctgatctaggaaaatcaggtttatagtgcacttgagcgaatttaacctcattttc

upper sequence: GLYMA11G14960.1 (Glycine max), 5'ss of exon 6
lower sequence: GRMZM2G110063_T01 (Zea mays), 5'ss of exon 7
GCTAACCGAAGGTTTCCTTTGGATCCCCTCTTTGGGTGGTCCTACTACCATTGCTGCTAGACAAAGTGGAGCTGGAATTTCTTGGCTTTTTCCATTTGTGgtaagaaagatatcttttgcttcatagttgaaataataagttgtagttgggctttttccccctaatcctgtgagtcat-tatgatctttcgaagcagtcta--
  | || ||||| ||  | ||||| || ||  ||||||||||||| || ||||| ||| | |||||||| ||||| ||||| ||||| || ||||||||||||   ||   ||   |||| | |   |  ||||     |||  | |   | || |      || |    |          |||     |  |  ||| |   
ATTGACAGAAGGATTTTTCTGGATTCCATCACTGGGTGGTCCTACAACAATTGCAGCTCGGCAAAGTGGTGCTGGGATTTCGTGGCTCTTCCCATTTGTGgtattgaa---attgattgcattaacatataaattggctgtttcattcctggttctgaaaaatagtttgatctactgcacttgagtggccatactagtatgtc

upper sequence: GLYMA11G14960.1 (Glycine max), 5'ss of exon 6
lower sequence: Vv06s0004g04460.t01 (Vitis vinifera), 5'ss of exon 6
GCTAACCGAAGGTTTCCTTTGGATCCCCTCTTTGGGTGGTCCTACTACCATTGCTGCTAGACAAAGTGGAGCTGGAATTTCTTGGCTTTTTCCATTTGTGgtaag-aaagatatcttttgcttcatagttgaaataataagttgtagttgggctttttcccccta-atcctgtgagtcattatgatctttcgaagcagtcta---
| | || ||||| ||  ||||||| |||||||||||||| || ||||| ||||||||| ||||||||||| |||| |||||||||||| |||| ||||||||||  ||| |||  |  ||      | |||  |   ||| |  ||  |  ||   ||| |   | ||   || |      || || | |  | | |    |   
GTTGACAGAAGGGTTTTTTTGGATTCCCTCTTTGGGTGGGCCAACTACAATTGCTGCTCGACAAAGTGGATCTGGCATTTCTTGGCTTATTCCGTTTGTGgtaatcaaaaataattactg----ggacttgtgaagctaactgatatctctgccgcttctcaacatatgtagttatcttgcatcatttgtt-atgaacctcatgg

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|22526016|gb|BU084827.1|BU084827
EST:     TTGCTGCTAGACAAAGTGGAGCTGGAATTTCTTGGCTTTTTCCATTTGTG                         GACGGGCATCCACCTTTGGGTTGGCAAGATACTGCAGCATATCTTGTTTTA
genomic: TTGCTGCTAGACAAAGTGGAGCTGGAATTTCTTGGCTTTTTCCATTTGTGgtaagaaaga ... ggtcatgcagGACGGGCATCCACCTTTGGGTTGGCAAGATACTGCAGCATATCTTGTTTTA
EST: gi|23052844|gb|BU577335.1|BU577335
EST:     TTGCTGCTAGACAAAGTGGAGCTGGAATCTCTTGGCTTTTTCCATTTGTG                         GACGGACATCCACCTTTGGGTTGGCAAGATACTGCAGCATATCTTGTTTTA
genomic: TTGCTGCTAGACAAAGTGGAGCTGGAATTTCTTGGCTTTTTCCATTTGTGgtaagaaaga ... ggtcatgcagGACGGGCATCCACCTTTGGGTTGGCAAGATACTGCAGCATATCTTGTTTTA
EST: gi|208292230|gb|GE092064.1|GE092064
EST:     TTGCTGCTAGACAAAGTGGAGCTGGAATTTCCTGGCTTTTTCCATTTGTG                         GACGGGCATCCACCTTTGGGTTGGCAAGATACTGCAGCATATCTTGTTTTA
genomic: TTGCTGCTAGACAAAGTGGAGCTGGAATTTCTTGGCTTTTTCCATTTGTGgtaagaaaga ... ggtcatgcagGACGGGCATCCACCTTTGGGTTGGCAAGATACTGCAGCATATCTTGTTTTA

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
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCTAACCGAAGGTTTCCTTTGGATCCCCTCTTTGGGTGGTCCTACTACCATTGCTGCTAGACAAAGTGGAGCTGGAATTTCTTGGCTTTTTCCATTTGTGgtaagaaagatatcttttgcttcatagttgaaataataagttgtagttgggctttttccccctaatcctgtgagtcattatgatctttcgaagcagtcta

- - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttccccc