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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttattaggattttgcataacttttgatgccaatatacttcttttactaacctctggagttaagtctacctcgtacttaatttatgaaaaatttattccagGCTACCCCTATAATTTGGATTTCGATTATGGTGCACTCACGCAACTTCAGCACTTTTCCATAAACAACCTTGGAGATCCATTTATTGAAAGCAACTATGG

Basic information

species Glycine max
transcript GLYMA15G05630.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G05630.2 (Glycine max), 3'ss of exon 2
lower sequence: PP1S13_150V6.1 (Physcomitrella patens), 3'ss of exon 1
ttattag--gattttgcataacttttgatgccaatatacttcttttactaacctctggagttaagtctacctcgtacttaatttatgaaaaatttattccagGCTACCCCTATAATTTGGATTTCGATTATGGTGCACTCACGCAACTTCAGCACTTTTCCATAAACAACCTTGGAGATCCATTTATTGAAAGCAACTATGG
|  ||||    | |||| |   |  |||   |  |||  |||  |  |  ||   |    ||   |    |   |  ||||  |   |    |   || |||| |||||||||||| | || ||||||||||| |||||  |||| || || ||||||||||| || ||  | || |||||||| || ||||||||||| ||
tctttagttagtgttgc-tcggtagtgaactcgttatcgttcaatgtcgcacacttact-ttgccttcgtcgaatctttaacgttacatttctcctttgcagGGTACCCCTATAATCTTGACTTCGATTATGGAGCACTGTCGCAGCTACAACACTTTTCCATCAATAATTTGGGCGATCCATTCATCGAAAGCAACTACGG

upper sequence: GLYMA15G05630.2 (Glycine max), 3'ss of exon 2
lower sequence: EFJ11717 (Selaginella moellendorffii), 3'ss of exon 1
ttattaggattttgcataacttttgatgccaatatacttcttttactaacctctggagttaagtctacctcgtacttaatttatgaaaaatttattccagGCTACCCCTATAATTTGGATTTCGATTATGGTGCACTCACGCAACTTCAGCACTTTTCCATAAACAACCTTGGAGATCCATTTATTGAAAGCAACTATGG
                              || | | |   ||      |||      ||  |  |   |     || |  | |    | |  | | |||| || || || ||  |||||||||| || ||||| ||| |||| || ||||| |||||||| ||||| || |||||||| || || || |||||||||||
----------------------------gtaagagattctcttcttcttccttgctgctttggagtgttt---gtttgagctcttgcgattggaatgcagGGTATCCATACAACCTGGATTTCGACTACGGTGCTCTCTCGCAGCTACAGCATTTTTCCATCAACAATCTGGGAGATCCTTTCATCGAGAGCAACTATGG

upper sequence: GLYMA15G05630.2 (Glycine max), 3'ss of exon 2
lower sequence: EFJ22493 (Selaginella moellendorffii), 3'ss of exon 1
ttattaggattttgcataacttttgatgccaatatacttcttttactaacctctggagttaagtctacctcgtacttaatttatgaaaaatttattccagGCTACCCCTATAATTTGGATTTCGATTATGGTGCACTCACGCAACTTCAGCACTTTTCCATAAACAACCTTGGAGATCCATTTATTGAAAGCAACTATGG
                              || | | ||  ||      |||      ||  |  |   |     || |  | |    | |  | | |||| || || || ||  |||||||||| || ||||| ||| |||| || ||||| |||||||| ||||| || |||||||| || || || |||||||||||
----------------------------gtaagaaattttcttcttcctccttgctgctttggagtgttt---gtttgagctcttgcgattggaatgcagGGTATCCATACAACCTGGATTTCGACTACGGTGCTCTCTCGCAGCTACAGCATTTTTCCATCAACAATCTGGGAGATCCTTTCATCGAGAGCAACTATGG

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|9986777|gb|BE660885.1|BE660885
EST:     GTTGGCCAGATACAAAAGAGCCTTGACTGAAAGGACAAAGCACCATTTAG                         GCTACCCCTATAATTTGGATTTCGATTATGGTGCACTCACGCAACTTCAGC
genomic: GTTGGCCAGATACAAAAGAGCCTTGACTGAAAGGACAAAGCACCATTTAGgtttgacaat ... tttattccagGCTACCCCTATAATTTGGATTTCGATTATGGTGCACTCACGCAACTTCAGC
EST: gi|18735474|gb|BM528785.1|BM528785
EST:     GTTGGCCAGATACAAAAGAGCCTTGACTGAAAGGACAAAGCACCATTTAG                         GCTACCCCTATAATTTGGATTTCGATTATGGTGCACTCACGCAACTTCAGC
genomic: GTTGGCCAGATACAAAAGAGCCTTGACTGAAAGGACAAAGCACCATTTAGgtttgacaat ... tttattccagGCTACCCCTATAATTTGGATTTCGATTATGGTGCACTCACGCAACTTCAGC
EST: gi|213593221|gb|DB969907.1|DB969907
EST:     GTTGGCCAGATACAAAAGAGCCTTGACTGAAAGGACAAAGCACCATTTAG                         GCTACCCCTATAATTTGGATTTCGATTATGGTGCACTCACGCAACTTCAGC
genomic: GTTGGCCAGATACAAAAGAGCCTTGACTGAAAGGACAAAGCACCATTTAGgtttgacaat ... tttattccagGCTACCCCTATAATTTGGATTTCGATTATGGTGCACTCACGCAACTTCAGC
EST: gi|19348938|gb|BM893470.1|BM893470
EST:     GTTGGCCAGATACAAAAGAGCTTTGACTGAAAGGACAAAGCATCATTTAG                         GGTACCCCTATAATTTGGATTTCGATTATGGTGCGCTCACGCAACTTCAGC
genomic: GTTGGCCAGATACAAAAGAGCCTTGACTGAAAGGACAAAGCACCATTTAGgtttgacaat ... tttattccagGCTACCCCTATAATTTGGATTTCGATTATGGTGCACTCACGCAACTTCAGC
EST: gi|298187541|gb|HO034690.1|HO034690
EST:     GTTGGCCAGATACAAAAGAGCCTTGACTGAAAGGACAAAGCACCATTTAG                         GCTACCCCTATAATTTGGATTTCGATTATGGTGCACTCACGCAACTTCAGC
genomic: GTTGGCCAGATACAAAAGAGCCTTGACTGAAAGGACAAAGCACCATTTAGgtttgacaat ... tttattccagGCTACCCCTATAATTTGGATTTCGATTATGGTGCACTCACGCAACTTCAGC
EST: gi|213599567|gb|DB964366.1|DB964366
EST:     GTTGGCCAGATACAAAAGAGCCTTGACTGAAAGGACAAAGCACCATTTAG                         GCTACCCCTATNATTTGGATTTCGATTATGGTGCACTCACGCAACTTCAGC
genomic: GTTGGCCAGATACAAAAGAGCCTTGACTGAAAGGACAAAGCACCATTTAGgtttgacaat ... tttattccagGCTACCCCTATAATTTGGATTTCGATTATGGTGCACTCACGCAACTTCAGC
EST: gi|192298859|gb|FG987604.1|FG987604
EST:     GTTGGCCAGATACAAAAGAGCCTTGACTGAAAGGACAAAGCACCATTTAG                         GCTACCCCTATAATTTGGATTTCGATTATGGTGCACTCACACAACTTCAGC
genomic: GTTGGCCAGATACAAAAGAGCCTTGACTGAAAGGACAAAGCACCATTTAGgtttgacaat ... tttattccagGCTACCCCTATAATTTGGATTTCGATTATGGTGCACTCACGCAACTTCAGC
EST: gi|298189793|gb|HO038196.1|HO038196
EST:     GTTGGCCAGATACAAAAGAGCCTTGACTGAAAGGATAAAGCACCATTTAG                         GCTACCCCTATAATTTGGATTTCGATTATGGTGCACTCACGCAACTTCAGC
genomic: GTTGGCCAGATACAAAAGAGCCTTGACTGAAAGGACAAAGCACCATTTAGgtttgacaat ... tttattccagGCTACCCCTATAATTTGGATTTCGATTATGGTGCACTCACGCAACTTCAGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctaacctctggagttaagtctacctcgtacttaatttatgaaaaatttattccagGCTACCCCTATAATTTGGATTTCGATTATGGTGCACTCACGCAACTTCAGCACTTTTCCATAAACAACCTTGGAGATCCATTTATTGAAAGCAACTATGG
                                             tttattcc  CT-rich tract
                        tcgtacttaatttatg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttattaggattttgcataacttttgatgccaatatacttcttttactaacctctggagttaagtctacctcgtacttaatttatgaaaaatttattccagGCTACCCCTATAATTTGGATTTCGATTATGGTGCACTCACGCAACTTCAGCACTTTTCCATAAACAACCTTGGAGATCCATTTATTGAAAGCAACTATGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - tgcataa
- - - - - - - - - - - -tgatgcc
- - - - - - - - - - - - - - - - - - - - - - - - - ctctgga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - atgaaaaa