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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttcttgataagatgttgctatctgagaattgtctcttgcttttttagccactttattcacagagattcattttctggttgtttactgtttgcctttaggtggtgtccttttgtttggtcaattagttataatgtttaaaatgccattatctgctttacgtggcagAGTGTTCCTGTGCAAGCTGGGCAAACTCCTCCTCTGTTGCAGTATTTTGGAACACTTTTAACAAGGGGAAAGCTGAATGCCTTTGAATCATTAGAATTAT

Basic information

species Glycine max
transcript GLYMA14G06340.2
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA14G06340.2 (Glycine max), 3'ss of exon 11
lower sequence: LOC_Os12g01390.1 (Oryza sativa), 3'ss of exon 11
gtttcttgataagatgttgctatctgagaattgtctcttgcttttttagccactttattcacagagattcattttctggttgtttactgtttgccttta-ggtggtgtccttttgtttggtcaattagttataatgtttaaaatgccattatctgctttacgtggcagAGTGTTCCTGTGCAAGCTGGGCAAACTCCTCCTCTGTTGCAGTATTTTGGAACACTTTTAACAAGGGGAAAGCTGAATGCCTTTGAATCATTAGAATTAT
                                                       | ||||   |  ||| | |  |||   | |||   |   ||| | | |  ||  ||| || |||     |||| | |   ||||            | |||||||    ||||||||||||||| |||||||||||||| ||||| || |||||||| ||||| ||| |  ||||  |||| ||||| ||||| |  || ||  | ||  |||
------------------------------------------------------attttcatttactttcctgtgttgggactgtacaactaatcttaatgcttatgctcttctgcttgac---ttagctttttcgtttc-----------tgtgctttaaaatgcagAGTGTTCCTGTTCAAGCTGGGCAAACGCCTCCACTCTTGCAGTACTTTGGCACATTGCTAACTCGGGGGAAGCTCAATGCTTACGAGTCTCTTGAGCTAT

upper sequence: GLYMA14G06340.2 (Glycine max), 3'ss of exon 11
lower sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 11
gtttcttgataagatgttgctatctgagaattgtctcttgcttttttagccactttattcacagagattcattttctggttgtttactgtttgccttta-ggtggtgtccttttgtttggtcaattagttataatgtttaaaatgccattatctgctttacgtggcagAGTGTTCCTGTGCAAGCTGGGCAAACTCCTCCTCTGTTGCAGTATTTTGGAACACTTTTAACAAGGGGAAAGCTGAATGCCTTTGAATCATTAGAATTAT
                                                       | ||||   |  ||| | |  |||   | |||   |   ||| | | |  ||  ||| || |||     |||| | |   ||||            | ||||||     ||||||||||||||| |||||||||||||| ||||| || |||||||| ||||| ||| |  ||||  |||| ||||| ||||| |  || ||  | ||  |||
------------------------------------------------------attttcatttactttcctgtgttgggactgtacaactaatcttaatgcttatgctcttctgcttgac---ttagctttttcgtttc-----------tgtgcttttaaatgcagAGTGTTCCTGTTCAAGCTGGGCAAACGCCTCCACTCTTGCAGTACTTTGGCACATTGCTAACTCGGGGGAAGCTCAATGCTTACGAGTCTCTTGAGCTAT

upper sequence: GLYMA14G06340.2 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 9
gtttcttgataagatgttgctatctgagaattgtctcttgcttttttagccactttattcacagagattcattttctggttgtttactgtttgcctttaggtggtgtccttttgtttggtcaattagttataatgtttaaaatgccattatctgctttacgtggcagAGTGTTCCTGTGCAAGCTGGGCAAACTCCTCCTCTGTTGCAGTATTTTGGAACACTTTTAACAAGGGGAAAGCTGAATGCCTTTGAATCATTAGAATTAT
                                                       |  |  ||| ||||||| | |   |  |  | | |  |  | || ||      | ||| ||||    | || || | |||||||        |||  |  |  |  | |||||||||||||||||||||||||||||| || || || |||||||| ||||| ||| |  ||||  | || ||||| ||||||||||| ||  | ||  |||
-----------------------------------------------------cctgctatcag-gattcatgtacatttaatcaattctcagtgtataagt-----tcctttctttgacttaataattcttatgttta--------ttactttatcaaaattgcagAGTGTTCCTGTGCAAGCTGGGCAAACACCCCCACTCTTGCAGTACTTTGGCACATTGCTAACTCGAGGGAAGCTCAATGCCTTTGAGTCTCTTGAGCTAT

upper sequence: GLYMA14G06340.2 (Glycine max), 3'ss of exon 11
lower sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 11
gtttcttgataagatgttgctatctgagaattgtctcttgcttttttagccactttattcacagagattcattttctggttgtttactgtttgcctttaggtggtgtccttttgtttggtcaattagttataatgtttaaaatgccattatctgctttacgtggcagAGTGTTCCTGTGCAAGCTGGGCAAACTCCTCCTCTGTTGCAGTATTTTGGAACACTTTTAACAAGGGGAAAGCTGAATGCCTTTGAATCATTAGAATTAT
                                            | ||    |  |||||| ||  |   ||  ||||      |  ||| |         |  |||     ||||||    |  |||   ||  |  || ||  || | |    ||    | ||||||||||||||| ||||| ||||||||||||||  |||| ||||||||||| || ||||| || || || ||||| ||| | | ||| || || ||| |||
-------------------------------------------gtatatgttccatattca-agcaaagaatcctctgtgaacatgttgtcta--------taatgta----tgtttgtaacaccagtctgaaactacaacatcacactttacaatt----ttgcagAGTGTTCCTGTACAAGCAGGGCAAACTCCTCCATTGTTACAGTATTTTGGGACCCTTTTGACTAGAGGGAAGCTCAATTCATATGAGTCTTTGGAACTAT

upper sequence: GLYMA14G06340.2 (Glycine max), 3'ss of exon 11
lower sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 11
gtttcttgataagatgttgctatctgagaattgtctcttgcttttttagccactttattcacagagattcattttctggttgtttactgtttgcctttaggtggtgtccttttgtttggtcaatta-gttataatgtttaaaatgcca--ttatctgctttacg---tggcagAGTGTTCCTGTGCAAGCTGGGCAAACTCCTCCTCTGTTGCAGTATTTTGGAACACTTTTAACAAGGGGAAAGCTGAATGCCTTTGAATCATTAGAATTAT
                                                                                ||| || |   |  |   ||    | |   |     || | | ||| | |  ||||||   ||  |||  || ||  || ||     | ||||||||||||||| |||||||| |||||||||||  |||| ||||||||||| || ||||| || || || || || ||| | | ||| ||| | ||| |||
-------------------------------------------------------------------------------gtgtctatttcatatcca-agcaactatgtgtaaacatgtttatttatgatgaaatgttggtaacaccaatttttcaactctataattttgcagAGTGTTCCTGTACAAGCTGGACAAACTCCTCCATTGTTACAGTATTTTGGGACTCTTTTGACTAGAGGGAAACTCAATTCATATGAGTCACTGGAACTAT

upper sequence: GLYMA14G06340.2 (Glycine max), 3'ss of exon 11
lower sequence: Vv13s0067g01290.t01 (Vitis vinifera), 3'ss of exon 11
gtttcttgataagatgttgctatctgagaattgtctcttgcttttttagccactttattcacagagattcattttctggttgtttactgtttgcctttaggtggtgtccttttgtttggtcaattagttataatgtttaaaatgccattatctgctttacgtggcagAGTGTTCCTGTGCAAGCTGGGCAAACTCCTCCTCTGTTGCAGTATTTTGGAACACTTTTAACAAGGGGAAAGCTGAATGCCTTTGAATCATTAGAATTAT
                                    ||| |||| ||    | ||| ||   | | |  ||||  ||||   |||   ||  |     || || |  ||      || |||   |  || |  ||| |||               |||   | ||||||||||||| ||||| ||||||| ||||| ||| || | ||||| |||||||||||| |||| || |||||||| ||||| ||||| ||||| |||||||
------------------------------------cttcctttattttttattttttt---aaaaaaccattccctggaattttggggtgggaa---agatgctaacc----actttgtc---ttcttctggtgtctaa---------------ttt---ttgcagAGTGTTCCTATGCAATCTGGGCAGACTCCACCTTTGCTACAGTACTTTGGAACACTTCTAACTAGAGGAAAGCTCAATGCATTTGAGTCATTGGAATTAT

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|20815168|gb|BQ299646.1|BQ299646
EST:     AATCTCCACAAGGAATCCTTCGAACTCCTGACACAGTTGCCAAATTTCAG                         AGTGTTCCTGTGCAAGCTGGGCAAACTCCTCCTCTGTTGCAGTATTTTGGA
genomic: AATCTCCACAAGGAATCCTTCGAACTCCTGACACAGTTGCCAAATTTCAGgtttcttgat ... tacgtggcagAGTGTTCCTGTGCAAGCTGGGCAAACTCCTCCTCTGTTGCAGTATTTTGGA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtttggtcaattagttataatgtttaaaatgccattatctgctttacgtggcagAGTGTTCCTGTGCAAGCTGGGCAAACTCCTCCTCTGTTGCAGTATTTTGGAACACTTTTAACAAGGGGAAAGCTGAATGCCTTTGAATCATTAGAATTAT
                                      tctgcttt  CT-rich tract
       tcaattagttataatg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttcttgataagatgttgctatctgagaattgtctcttgcttttttagccactttattcacagagattcattttctggttgtttactgtttgcctttaggtggtgtccttttgtttggtcaattagttataatgtttaaaatgccattatctgctttacgtggcagAGTGTTCCTGTGCAAGCTGGGCAAACTCCTCCTCTGTTGCAGTATTTTGGAACACTTTTAACAAGGGGAAAGCTGAATGCCTTTGAATCATTAGAATTAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA