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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaggattatctttggactttcgtacaaaaacatttttgtggaataccgtctcaaattcatgatgattatgttcattttgtctttagGGAACTGTTGTTGAGGGAACTATACAGAAGCTATTTGAAGGGCATCATATGAATTATATCGAATGCATCAATGTGGACTATAAATCAACTAGAAAGGAGT

Basic information

species Glycine max
transcript GLYMA14G04890.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA14G04890.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os01g56490.1 (Oryza sativa), 3'ss of exon 6
-gtaaaggattatctttggactttcgtacaaaaacatttttgtggaataccgtctcaaattcatgatgattatgttcattttgtctttagGGAACTGTTGTTGAGGGAACTATACAGAAGCTATTTGAAGGGCATCATATGAATTATATCGAATGCATCAATGTGGACTATAAATCAACTAGAAAGGAGT
  |  |   |||| ||||   ||   |  || |  ||        ||||  || |||   |||  |||   |  | |  | |   || ||||||||  ||| || || || || ||  ||||||||||||| ||||||||||||||||| || ||||| ||||| ||||| ||||| || || || || |
gttggacatttatttttg---ttatatgtaagataat-------aaatagtgtttca---tca--atgtacaactactctctcgattcagGGAACTACTGTGGAAGGGACAATTCAACAGCTATTTGAAGGTCATCATATGAATTATATTGAGTGCATTAATGTTGACTACAAATCTACAAGGAAAGAAT

upper sequence: GLYMA14G04890.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv06s0009g00960.t01 (Vitis vinifera), 3'ss of exon 6
gtaaaggattatctttggactttcgtacaaaaacatttttgtggaataccgtctcaaattcatgatgattatgttcattttgtctttagGGAACTGTTGTTGAGGGAACTATACAGAAGCTATTTGAAGGGCATCATATGAATTATATCGAATGCATCAATGTGGACTATAAATCAACTAGAAAGGAGT
                     | |  |||  |   || |||||||||    | |||  |   |||  |||||    |  |  |    ||||||||||||| ||||| ||||||||| || ||||||||||||| |||||||| || || |||||||||||||||||||| ||||| || || |||||||
--------------------gtacaaacatgactgttgttgtggaat--tatttcagttc--tgacaattat---taagtgcttgccagGGAACTGTTGTGGAGGGCACTATACAGCAGTTATTTGAAGGGCACCATATGAACTACATTGAATGCATCAATGTGGACTACAAATCTACAAGGAAGGAGT

upper sequence: GLYMA14G04890.1 (Glycine max), 3'ss of exon 6
lower sequence: PP1S104_2V6.1 (Physcomitrella patens), 3'ss of exon 6
--gtaaaggattatctttggactttcgtacaaaaacatttttgtggaataccgtctcaaattcatgatgattatg----ttcatttt--gtctt---tagGGAACTGTTGTTGAGGGAACTATACAGAAGCTATTTGAAGGGCATCATATGAATTATATCGAATGCATCAATGTGGACTATAAATCAACTAGAAAGGAGT
  ||    |    | |   |  | | || |      |||    |    | |       ||||  |||  | | |     |||  |||  | |||   ||||| || |  || ||||| || ||||| || || |||||||| |||||||||||||||||||||||||||||||| || | ||| || ||| | |||||||
gcgttctcggcgttgtggcggttgttgtgcgcgtgaattcagttattgtgcttgggtcaatttgtgagaagtctaaaatttcgatttccgacttacgtagGGCACGGCAGTGGAGGGGACGATACAAAATCTTTTTGAAGGCCATCATATGAATTATATCGAATGCATCAATGTCGATTTTAAGTCCACTCGGAAGGAGT

upper sequence: GLYMA14G04890.1 (Glycine max), 3'ss of exon 6
lower sequence: PP1S123_138V6.1 (Physcomitrella patens), 3'ss of exon 6
--gtaaaggattatctttggactttcgtacaaaaacatttttgtggaataccgtctcaaattcatgatgattatgttcattttgtcttt----agGGAACTGTTGTTGAGGGAACTATACAGAAGCTATTTGAAGGGCATCATATGAATTATATCGAATGCATCAATGTGGACTATAAATCAACTAGAAAGGAGT
   |  |  | | ||| |   || |            ||   | | |     ||     ||   |  || |     || || |||  ||    ||||||||| ||| ||||| || || ||| | || || ||||||||||| ||||| || || || ||||||||||| || |||||||||||  | || ||||
gtatggataaatctctgttagctatgtcttctcggttttcaagagtagctgggtacattatgtttactggtgggaatccttctgtgcttttacagGGAACTGCTGTCGAGGGCACAATCCAGCAACTGTTCGAAGGGCATCACATGAACTACATAGAGTGCATCAATGTTGATTATAAATCAACACGGAAAGAGT

upper sequence: GLYMA14G04890.1 (Glycine max), 3'ss of exon 6
lower sequence: EFJ14291 (Selaginella moellendorffii), 3'ss of exon 4
gtaaaggattatctttggactttcgtacaaaaacatttttgtggaataccgtctcaaattcatgatgatta-tgttcattttgtctttagGGAACTGTTGTTGAGGGAACTATACAGAAGCTATTTGAAGGGCATCATATGAATTATATCGAATGCATCAATGTGGACTATAAATCAACTAGAAAGGAGT
                                    |||  ||  ||    |      |  ||| |   ||      |  |   ||  || | |||| |||||| || || |||||| |||| || ||||| ||||||||||||||||| ||||||||||||||||||||||| || ||| ||||||| |
-----------------------------------gtttactgctattttcttcacgttaaatgttttctaacaccaagctccactacagAGTACTGCTGTTGAAGGTACCATACAGCAGCTTTTCGAAGGCCATCATATGAATTATATTGAATGCATCAATGTGGACTATAAGTCCACTCGAAAGGAAT

upper sequence: GLYMA14G04890.1 (Glycine max), 3'ss of exon 6
lower sequence: EFJ19227 (Selaginella moellendorffii), 3'ss of exon 6
gtaaaggattatctttggactttcgtacaaaaacatttttgtggaataccgtctcaaattcatgatgattatgttcattttgtctttagGGAACTGTTGTTGAGGGAACTATACAGAAGCTATTTGAAGGGCATCATATGAATTATATCGAATGCATCAATGTGGACTATAAATCAACTAGAAAGGAGT
                               |  | ||| ||    |      |||||   ||  | ||    |  | |   |  | ||||||| | |||||| ||||| || ||  |||| ||||| || ||||||||||| || |||||||||||||| || || || ||||| ||  | || ||||
----------------------------gtgagtacttt-gtacgttga-acttcaaagctattcttatct--tctactcacttctcagGGAACCGCTGTTGAAGGAACGATTCAACAGCTTTTTGAGGGTCATCATATGAACTACATCGAATGCATCAACGTCGATTACAAATCTACGCGGAAAGAGT

upper sequence: GLYMA14G04890.1 (Glycine max), 3'ss of exon 6
lower sequence: EFJ18164 (Selaginella moellendorffii), 3'ss of exon 4
gtaaaggattatctttggactttcgtacaaaaacatttttgtggaataccgtctcaaattcatgatgatta-tgttcattttgtctttagGGAACTGTTGTTGAGGGAACTATACAGAAGCTATTTGAAGGGCATCATATGAATTATATCGAATGCATCAATGTGGACTATAAATCAACTAGAAAGGAGT
                                    |||  ||  ||    |      |  ||| |   ||      |  |   ||  || | |||| |||||| || || |||||| |||| || ||||| || |||||||||||||| |||||||||||||||||||| || || ||| ||||||| |
-----------------------------------gtttactgctattttcttcacgttaaatgttttctaacaccaagctccactacagAGTACTGCTGTTGAAGGTACCATACAGCAGCTTTTCGAAGGCCACCATATGAATTATATTGAATGCATCAATGTGGACTACAAGTCCACTCGAAAGGAAT

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|51334822|gb|CO978688.1|CO978688
EST:     TTCAAGAACTGAACAGAGTNNNCTGTGAAAAACTTGAAGACAAGATGAAG                         GGAACTGTTGTTGAGGGAACTATACAGAAGCTATTTGAAGGGCATCATATG
genomic: TTCAAGAACTGAACAGAGTCCTCTGTGAAAAACTTGAAGACAAGATGAAGgtaaaggatt ... ttgtctttagGGAACTGTTGTTGAGGGAACTATACAGAAGCTATTTGAAGGGCATCATATG
EST: gi|207829030|gb|GD798076.1|GD798076
EST:     TTCAAGAACTGAACAGAGTCCTCTGTGAAAAACTTGAAGACAAGATGAAG                         GGAACTGTTGTTGAGGGAACTATACAGAAGCTATTTGAAGGG
genomic: TTCAAGAACTGAACAGAGTCCTCTGTGAAAAACTTGAAGACAAGATGAAGgtaaaggatt ... ttgtctttagGGAACTGTTGTTGAGGGAACTATACAGAAGCTATTTGAAGGG
EST: gi|208319726|gb|GE114573.1|GE114573
EST:     TTCAAGAACTGAACAGAGTCCTCTGTGAAAAACTTGAAGACAAGATGAAG                         GGAACTGTTGTTGAGGGAACTATACAGAAGCTATTTGAAGGGCATCATATG
genomic: TTCAAGAACTGAACAGAGTCCTCTGTGAAAAACTTGAAGACAAGATGAAGgtaaaggatt ... ttgtctttagGGAACTGTTGTTGAGGGAACTATACAGAAGCTATTTGAAGGGCATCATATG
EST: gi|207776334|gb|GD750327.1|GD750327
EST:     TTCAAGAACTGAACAGAGTCCTCTGTGAAAAACTTGAAGACAAGATGAAG                         GGAACTGTTGTTGAGGGAACTATACAGAAGCTATTTGAAGGG
genomic: TTCAAGAACTGAACAGAGTCCTCTGTGAAAAACTTGAAGACAAGATGAAGgtaaaggatt ... ttgtctttagGGAACTGTTGTTGAGGGAACTATACAGAAGCTATTTGAAGGG
EST: gi|193655171|gb|FK599653.1|FK599653
EST:     TTCAAGAACTGAACAGAGTCCTCTGTGAAAAACTTGAAGACAAGATGAAG                         GGAACTGTTGTTGAGGGAACTATACAGAAGCTATTTGAAGGGCATCATATG
genomic: TTCAAGAACTGAACAGAGTCCTCTGTGAAAAACTTGAAGACAAGATGAAGgtaaaggatt ... ttgtctttagGGAACTGTTGTTGAGGGAACTATACAGAAGCTATTTGAAGGGCATCATATG
EST: gi|208251207|gb|GE049630.1|GE049630
EST:     TTCAAGAACTGAACAGAGTCCTCTGTGAAAAACTTGAAGACAAGATGAAG                         GGAACTGTTGTTGAGGGAACTATACAGAAGCTATTTGAAGGGCATCATATG
genomic: TTCAAGAACTGAACAGAGTCCTCTGTGAAAAACTTGAAGACAAGATGAAGgtaaaggatt ... ttgtctttagGGAACTGTTGTTGAGGGAACTATACAGAAGCTATTTGAAGGGCATCATATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttttgtggaataccgtctcaaattcatgatgattatgttcattttgtctttagGGAACTGTTGTTGAGGGAACTATACAGAAGCTATTTGAAGGGCATCATATGAATTATATCGAATGCATCAATGTGGACTATAAATCAACTAGAAAGGAGT
                                       ttcattttgtcttt  CT-rich tract
                                 attatgttcatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaaggattatctttggactttcgtacaaaaacatttttgtggaataccgtctcaaattcatgatgattatgttcattttgtctttagGGAACTGTTGTTGAGGGAACTATACAGAAGCTATTTGAAGGGCATCATATGAATTATATCGAATGCATCAATGTGGACTATAAATCAACTAGAAAGGAGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG