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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aacacagttgcggtgtttatgttggtcaattttgacaaagctttccttacccctaatgatgacccttgctcctaacagacattatctctggcattttcagACACTGTCCTCTGGTTTGGATGATTATCCACGAGCTTCACACCCAAGTGAAGATGAACGCCACTTGGATCTTAGATGTTGGATGTTACTTGCAGCAGACT

Basic information

species Glycine max
transcript GLYMA05G27900.1
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA05G27900.2 (Glycine max), 3'ss of exon 14
lower sequence: Vv01s0010g03300.t01 (Vitis vinifera), 3'ss of exon 14
aacacagttgcggtgtttatgtt-ggtcaattttgacaaagctttccttacccctaatgatgacccttgctcctaacagacattatctctggcattttcagACACTGTCCTCTGGTTTGGATGATTATCCACGAGCTTCACACCCAAGTGAAGATGAACGCCACTTGGATCTTAGATGTTGGATGTTACTTGCAGCAGACT
|  |   |  |  |||| ||||| |||    | |   ||    ||  || |   ||  ||||    |        |  |||||| | ||   |||| | |||||||||||||||| ||||| ||||| |||||||| |||||||| |||| ||| || | |||  ||||||||||||| |||||| | |||||||| || |
actatgttatcaatgtt-atgttaggttgggtatagaaagatattttttccagatagagatggttatgctgttgcattgacattgtttcgaacattcttagACACTGTCCTCTGGCTTGGACGATTACCCACGAGCATCACACCCTAGTGGAGAAGAGCACCATGTGGATCTTAGATGCTGGATGCTTCTTGCAGCTGAAT

upper sequence: GLYMA05G27900.2 (Glycine max), 3'ss of exon 14
lower sequence: EFJ24054 (Selaginella moellendorffii), 3'ss of exon 15
aacacagttgcggtgtttatgttggtcaattttgacaaagctttccttacccctaatgatgacccttgctcctaacagacattat---ctctggcattttcagACACTGTCCTCTGGTTTGGATGATTATCCACGAGCTTCACACCCAAGTGAAGATGAACGCCACTTGGATCTTAGATGTTGGATGTTACTTGCAGCAGACT
                                                     ||   | |   | | ||  | |   ||  | |   | | ||| |  | |||   |||| |||||||||||||| ||||||||||||||||| |||||||  ||||| || ||| | ||| |  | || ||||||    | |||||  | |
----------------------------------------------------gtaggcacgtttcattctg-tgattaacgctctagacaccggcttcgttagAGTTTGTCGTCTGGTTTGGATGACTATCCACGAGCTTCACATCCAAGTGCTGATGAGCGACACGTTGATTTACGTTGCTGGATGGCCTTGGCAGCGAAAT

upper sequence: GLYMA05G27900.2 (Glycine max), 3'ss of exon 14
lower sequence: EFJ35102 (Selaginella moellendorffii), 3'ss of exon 15
aacacagttgcggtgtttatgttggtcaattttgacaaagctttccttacccctaatgatgacccttgctcctaacagacattat---ctctggcattttcagACACTGTCCTCTGGTTTGGATGATTATCCACGAGCTTCACACCCAAGTGAAGATGAACGCCACTTGGATCTTAGATGTTGGATGTTACTTGCAGCAGACT
                                                     ||   | |   | | ||  | |   ||  | |   | | ||| |  | |||   |||| |||||||||||||| |||||||| |||||||| |||||||  ||||| || ||| | ||| |  | || ||||||    | |||||  | |
----------------------------------------------------gtaggcacgtttcattctg-tgattaacgctctagacaccggcttcgttagAGTTTGTCGTCTGGTTTGGATGACTATCCACGGGCTTCACATCCAAGTGCTGATGAGCGACACGTTGATTTACGTTGCTGGATGGCCTTGGCAGCGAAAT

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|193533398|gb|FK493750.1|FK493750
EST:     ACGATAGGACAATGCGTGAAGTAAATCCTAAG                         ACACTGTCCTCTGGTTTGGATGATTATCCACGAGCTTCACACCCAAGTGAA
genomic: ACGATAGGACAATGCGTGAAGTAAATCCTAAGgttctaatat ... gcattttcagACACTGTCCTCTGGTTTGGATGATTATCCACGAGCTTCACACCCAAGTGAA
EST: gi|208307075|gb|GE103239.1|GE103239
EST:     ACGATAGGACAATGCGTGAAGTAAATCCTAAG                         ACACTGTCCTCTGGTTTGGATGATTATCCACGAGCTTCACACCCAAGTGAA
genomic: ACGATAGGACAATGCGTGAAGTAAATCCTAAGgttctaatat ... gcattttcagACACTGTCCTCTGGTTTGGATGATTATCCACGAGCTTCACACCCAAGTGAA
EST: gi|208195868|gb|GD994429.1|GD994429
EST:     CGGGACGATAGGACAATGCGTGAAGTAAATCCTAAG                         ACACTGTCCTCTGGTTTGGATGATTATCCACGAGCTTCACACCCAAGTGAA
genomic: CGGGACGATAGGACAATGCGTGAAGTAAATCCTAAGgttctaatat ... gcattttcagACACTGTCCTCTGGTTTGGATGATTATCCACGAGCTTCACACCCAAGTGAA
EST: gi|207696288|gb|GD677783.1|GD677783
EST:     ACGATAGGACAATGCGTGAAGTAAATCCTAAG                         ACACTGTCCTCTGGTTTGGATGATTATCCACGAGCTTCACACCCAAGTGAA
genomic: ACGATAGGACAATGCGTGAAGTAAATCCTAAGgttctaatat ... gcattttcagACACTGTCCTCTGGTTTGGATGATTATCCACGAGCTTCACACCCAAGTGAA
EST: gi|207806471|gb|GD777436.1|GD777436
EST:     ACGATAGGACAATGCGTGAAGTAAATCCTAAG                         ACACTGTCCTCTGGTTTGGATGATTATCCACGAGCTTCACACCCAAGTGAA
genomic: ACGATAGGACAATGCGTGAAGTAAATCCTAAGgttctaatat ... gcattttcagACACTGTCCTCTGGTTTGGATGATTATCCACGAGCTTCACACCCAAGTGAA
EST: gi|208126411|gb|GD925655.1|GD925655
EST:     CGGGACGATAGGACAATGCGTGAAGTAAATCCTAAG                         ACACTGTCCTCTGGTTTGGATGATTATCCACGAGCTTCACACCCAAGTGAA
genomic: CGGGACGATAGGACAATGCGTGAAGTAAATCCTAAGgttctaatat ... gcattttcagACACTGTCCTCTGGTTTGGATGATTATCCACGAGCTTCACACCCAAGTGAA
EST: gi|208252611|gb|GE046147.1|GE046147
EST:     ACGATAGGACAATGCGTGAAGTAAATCCTAAG                         ACACTGTCCTCTGGTTTGGATGATTATCCACGAGCTTCACACCCAAGTGAA
genomic: ACGATAGGACAATGCGTGAAGTAAATCCTAAGgttctaatat ... gcattttcagACACTGTCCTCTGGTTTGGATGATTATCCACGAGCTTCACACCCAAGTGAA
EST: gi|193566450|gb|FK522437.1|FK522437
EST:     ACGATAGGACAATGCGTGAAGTAAATCCTAAG                         ACACTGTCCTCTGGTTTGGATGATTATCCACGAGCTTCACACCCAAGTGAA
genomic: ACGATAGGACAATGCGTGAAGTAAATCCTAAGgttctaatat ... gcattttcagACACTGTCCTCTGGTTTGGATGATTATCCACGAGCTTCACACCCAAGTGAA
EST: gi|13480605|gb|BG509948.1|BG509948
EST:     ACTATTGGCACGGACGGGACGATAGGACAATGCGTGAAGTAAATCCTAAG                         ACACTGTCCTCTGGTTTGGATGATTATCCACGAGCTTCACACCCAAGTGAA
genomic: ACTATTGGCACGGACGGGACGATAGGACAATGCGTGAAGTAAATCCTAAGgttctaatat ... gcattttcagACACTGTCCTCTGGTTTGGATGATTATCCACGAGCTTCACACCCAAGTGAA
EST: gi|208089246|gb|GD886507.1|GD886507
EST:     GACGATAGGACAATGCGTGAAGTAAATCCTAAG                         ACACTGTCCTCTGGTTTGGATGATTATCCACGAGCTTCACACCCAAGTGAA
genomic: GACGATAGGACAATGCGTGAAGTAAATCCTAAGgttctaatat ... gcattttcagACACTGTCCTCTGGTTTGGATGATTATCCACGAGCTTCACACCCAAGTGAA
EST: gi|193442359|gb|FK407344.1|FK407344
EST:     CGGGACGATAGGACAATGCGTGAAGTAAATCCTAAG                         ACACTGTCCTCTGGTTTGGATGATTATCCACGAGCTTCACACCCAAGTGAA
genomic: CGGGACGATAGGACAATGCGTGAAGTAAATCCTAAGgttctaatat ... gcattttcagACACTGTCCTCTGGTTTGGATGATTATCCACGAGCTTCACACCCAAGTGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttacccctaatgatgacccttgctcctaacagacattatctctggcattttcagACACTGTCCTCTGGTTTGGATGATTATCCACGAGCTTCACACCCAAGTGAAGATGAACGCCACTTGGATCTTAGATGTTGGATGTTACTTGCAGCAGACT
                        tcctaac  putative branch site (score: 1)
                                              cattttc  putative PPT
        taatgat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aacacagttgcggtgtttatgttggtcaattttgacaaagctttccttacccctaatgatgacccttgctcctaacagacattatctctggcattttcagACACTGTCCTCTGGTTTGGATGATTATCCACGAGCTTCACACCCAAGTGAAGATGAACGCCACTTGGATCTTAGATGTTGGATGTTACTTGCAGCAGACT

- - cagttgc
- - - - - -ggtgttt
- - - - - - - - - atgttgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - tgatgac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccttgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cctaaca