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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaatgttggacatttactttgttttattcagtattttgttgtttaaattcaaatttaacctcgatgatacaactgtcccagGCAGCTTTAAATACTGAAGATCCACAATATCAAGATAAAAGAATGGTGGCTCAAAGAAATGGAAAGTTATCAGTTCAAGTTTTTCAT

Basic information

species Glycine max
transcript GLYMA19G22520.2
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G22520.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv14s0171g00310.t01 (Vitis vinifera), 3'ss of exon 7
gtaaatgttggacatttactttgttttattcagtattttgttgtttaaattc------aaatttaacctc---gatgatacaact-----------gtcccagGCAGCTTTAAATACTGAAGATCCACAATATCAAGATAAAAGAATGGTGGCTCAAAGAAATGGAAAGTTATCAGTTCAAGTTTTTCAT
|||| |  | ||    |||  | |||||| ||  |||||  |||||    |        || |   |||      ||||| ||||           ||  ||||||||| | || ||||| ||||| |||||||| || || |||||||| |||||||||||||||||  || |||| |||   ||||||
gtaa-tacttgagtcctacccttttttatacaaaattttactgtttgctcttttgggtgaactcttcctttttattgatataactttataatctctgtttcagGCAGCTCTTAACACTGAGGATCCTCAATATCAGGACAAGAGAATGGTTGCTCAAAGAAATGGAAAACTAACAGTGCAAAAATTTCAT
















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|8282740|gb|BE020301.1|BE020301
EST:     ACTATGGTTTTGTTGATGAAAATAATTCCAATGATCGTCTTATAGTTGAG                         GCAGCCTTTAAAT
genomic: ACTATGGTTTTGTTGATGAAAATAATTCCAATGATCGTCTTATAGTTGAGgtaaatgttg ... actgtcccagGCAGC-TTTAAAT
EST: gi|8283385|gb|BE020946.1|BE020946
EST:     ACTATGGTTTTGTTGATGAAAATAATTCCAATGATCGTCTTATAGTTGAG                         GCAGCTTTAAATACTGAA
genomic: ACTATGGTTTTGTTGATGAAAATAATTCCAATGATCGTCTTATAGTTGAGgtaaatgttg ... actgtcccagGCAGCTTTAAATACTGAA
EST: gi|197661912|gb|FD480321.1|FD480321
EST:     ACTATGGTTTTGTTGATGAAAATAATTCCAATGATCGTCTTATAGTTGAG                         GCAGCTTTAAATACTGAAGATCCACAATATCAAGATAAAAGAATGGTGGCT
genomic: ACTATGGTTTTGTTGATGAAAATAATTCCAATGATCGTCTTATAGTTGAGgtaaatgttg ... actgtcccagGCAGCTTTAAATACTGAAGATCCACAATATCAAGATAAAAGAATGGTGGCT
EST: gi|20815055|gb|BQ299533.1|BQ299533
EST:     ACTATGGTTTTGTTGATGAAAATAATTCCAATGATCGTCTTATAGTTGAG                         GCAGCTTTAAATACTGAAGATCCACAATATCAAGATAAAAGAATGGTGGCT
genomic: ACTATGGTTTTGTTGATGAAAATAATTCCAATGATCGTCTTATAGTTGAGgtaaatgttg ... actgtcccagGCAGCTTTAAATACTGAAGATCCACAATATCAAGATAAAAGAATGGTGGCT
EST: gi|21994328|gb|BQ785856.1|BQ785856
EST:     ACTATGGTTTTGTTGATGAAAATAATTCCAATGATCGTCTTATAGTTGAG                         GCAGCTTTAAATACTGAAGATCCACAATATCAAGATAAAAGAATGGTGGCT
genomic: ACTATGGTTTTGTTGATGAAAATAATTCCAATGATCGTCTTATAGTTGAGgtaaatgttg ... actgtcccagGCAGCTTTAAATACTGAAGATCCACAATATCAAGATAAAAGAATGGTGGCT
EST: gi|19348347|gb|BM892879.1|BM892879
EST:     ACTATGGTTTTGTTGATGAAAATAATTCCAATGATCGTCTTATAGTTGAG                         GCAGCTTTAAATACTGAAGATCCACAATATCAAGATAAAAGAATGGTGGCT
genomic: ACTATGGTTTTGTTGATGAAAATAATTCCAATGATCGTCTTATAGTTGAGgtaaatgttg ... actgtcccagGCAGCTTTAAATACTGAAGATCCACAATATCAAGATAAAAGAATGGTGGCT
EST: gi|20814963|gb|BQ299441.1|BQ299441
EST:     ACTATGGTTTTGTTGATGAAAATAATTCCAATGATCGTCTTATAGTTGAG                         GCAGCTTTAAATACTGAAGATCCACAATATCAAGATAAAAGAATGGTGGCT
genomic: ACTATGGTTTTGTTGATGAAAATAATTCCAATGATCGTCTTATAGTTGAGgtaaatgttg ... actgtcccagGCAGCTTTAAATACTGAAGATCCACAATATCAAGATAAAAGAATGGTGGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcagtattttgttgtttaaattcaaatttaacctcgatgatacaactgtcccagGCAGCTTTAAATACTGAAGATCCACAATATCAAGATAAAAGAATGGTGGCTCAAAGAAATGGAAAGTTATCAGTTCAAGTTTTTCAT
                          atttaac  putative branch site (score: 3)
                                              ctgtccc  putative PPT
     tattttgttgtttaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaatgttggacatttactttgttttattcagtattttgttgtttaaattcaaatttaacctcgatgatacaactgtcccagGCAGCTTTAAATACTGAAGATCCACAATATCAAGATAAAAGAATGGTGGCTCAAAGAAATGGAAAGTTATCAGTTCAAGTTTTTCAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA