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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gaattactattaaagtctacatacactatatagtctatgttacatcaaatcatatgatgattttttctaagtagcaattatatatgtgttattatttcagCAATTGAGACAACTCTATGGTCGATTGAATGGGGCATTGCTGAGCTTGTGAACCACCCAGAGATCCAGCAGAAGGTGAGGGATGAAATTGATAGAGTTCT

Basic information

species Glycine max
transcript GLYMA14G38580.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA14G38580.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G010468_T01 (Zea mays), 3'ss of exon 2
---------------------------------------------------gaattactattaaagtctacatacactatatagtctatgttacatcaaatcatatgatgattttttcta-agtagcaattatatatgtgtt-attattt-cagCAATTGAGACAACTCTATGGTCGATTGAATGGGGCATTGCTGAGCTTGTGAACCACCCAGAGATCCAGCAGAAGGTGAGGGATGAAATTGATAGAGTTCT
                                                     | |     | || | ||  |       | ||| | |||  |  |    |||      ||  || | | |||    | ||  | ||||||  |  | | |||| || ||||| || || |||||||| || ||||   | || ||||| ||||||||||| ||||||||||||||| || || | ||  | || |  || ||
gtaaattatatttcagactaagttaacctcgcttcaggtttagtatgacaaagactgtcgctgaaatttaagtctg----aaagtttctgtcgcgccgcgccatgctcgtatgcttccaagagtcaagactaagtttgtgtttgtcgtctacagCGATCGAGACCACGCTGTGGTCGATCGAGTGGGCGGTCGCCGAGCTGGTGAACCACCCGGAGATCCAGCAGAAGCTGCGGCAGGAGCTGGACACGGTGCT

upper sequence: GLYMA14G38580.1 (Glycine max), 3'ss of exon 3
lower sequence: PP1S158_96V6.1 (Physcomitrella patens), 3'ss of exon 3
--------------------------gaattactattaaagtctacatacactatatagtctatgttacatcaaatcatat---gatgattt------tttctaagtagcaattatatatgtgttattat-----------ttcagCAATTGAGACAACTCTATGGTCGATTGAATGGGGCATTGCTGAGCTTGTGAACCACCCAGAGATCCAGCAGAAGGTGAGGGATGAAATTGATAGAGTTCT
                          |||||        | | |     ||| |   | | ||| |  ||  || |   ||    |  || |      | || ||  |   |  |   |||||| | | |           | |||| || ||  ||||| |   ||| |||||||||||||| ||||||||||||||||||||| |  | ||  |     ||  ||  ||  ||  |  |||  |
gtgcgaatccacaaactggttcagtcgaattgtagccggaatttgttctcacaactgactatatctcccacgaattgtgatcaaaacaatctgcccgttgtccaaacactgacgaggaatgtgtcaatgtgaccacatctatgcagCGATAGAATCAACTTTGCTGTCAATTGAATGGGGCATAGCTGAGCTTGTGAACCACCCAAACGTGCAAAAACGACTGCAGGCGGAGCTTCTTGAAGTGAT

upper sequence: GLYMA14G38580.1 (Glycine max), 3'ss of exon 3
lower sequence: PP1S56_125V6.1 (Physcomitrella patens), 3'ss of exon 2
gaattactattaaagtctacatacactatatagtctatgttacatcaaatcatatgatgattttttctaagtagcaattatatatgtgttattatttcagCAATTGAGACAACTCTATGGTCGATTGAATGGGGCATTGCTGAGCTTGTGAACCACCCAGAGATCCAGCAGAAGGTGAGGGATGAAATTGATAGAGTTCT-----------------------------------
                                                                                              || |||||||||| |||||||| ||||||||||| | ||| ||||| |||||||||||| | || ||| |    | |||   ||| |  ||  | ||    |||||                                   
---------------------------------------------------------------------------------------------gttgcagcaattgatacaactctgtggtcgattgagtagGGGATTGCGGAGCTTGTGAACAATCCGGAGCTA-GACGGAATCCGAGAG--GAGCTAGACGCCGTTCTTGGAAAGGGCAATATGGTGATCGAGCCCGACACAT

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|13479760|gb|BG509103.1|BG509103
EST:     GATCAACGAAGACAACGTCCTTTACATTGTTGAAAACATTAATGTCGCTG                         CAATTGAGACAACTCTATGGTCGATTGAATGGGGCATTGCTGAGCTTGTGA
genomic: GATCAACGAAGACAACGTCCTTTACATTGTTGAAAACATTAATGTCGCTGgtatgatgct ... attatttcagCAATTGAGACAACTCTATGGTCGATTGAATGGGGCATTGCTGAGCTTGTGA
EST: gi|192320877|gb|FK013071.1|FK013071
EST:     ATTGTTGAAAACATTAATGTCGCTG                         CAATTGAGACAACTCTATGGTCGATTGAATGGGGCATTGCTGAGCTTGTGA
genomic: ATTGTTGAAAACATTAATGTCGCTGgtatgatgct ... attatttcagCAATTGAGACAACTCTATGGTCGATTGAATGGGGCATTGCTGAGCTTGTGA
EST: gi|254318383|gb|GR832551.1|GR832551
EST:     GATCAACGAAGACAACGTCCTTTACATTGTTGAAAACATTAATGTCGCTG                         CAATTGAGACAACTCTATGGTCGATTGAATGGGGCATTGCTGAGCTTGTGA
genomic: GATCAACGAAGACAACGTCCTTTACATTGTTGAAAACATTAATGTCGCTGgtatgatgct ... attatttcagCAATTGAGACAACTCTATGGTCGATTGAATGGGGCATTGCTGAGCTTGTGA
EST: gi|37997489|gb|CF809078.1|CF809078
EST:     GATCAACGAAGACAACGTCCTTTACATTGTTGAAAACATCAATGTCGCTG                         CAATTGAGACAACTCTATGGTCGATTGAATGGGGCATTGCTGAGCTTGTGA
genomic: GATCAACGAAGACAACGTCCTTTACATTGTTGAAAACATTAATGTCGCTGgtatgatgct ... attatttcagCAATTGAGACAACTCTATGGTCGATTGAATGGGGCATTGCTGAGCTTGTGA
EST: gi|4286987|gb|AI441125.1|AI441125
EST:     GATCAACGAAGACAACGTCCTTTACATTGTTGAAAACATTAATGTCGCTG                         CAATTGAGACAACTCTATGGTCGATTGAATGGGGCATTGCTGAGCTTGTGA
genomic: GATCAACGAAGACAACGTCCTTTACATTGTTGAAAACATTAATGTCGCTGgtatgatgct ... attatttcagCAATTGAGACAACTCTATGGTCGATTGAATGGGGCATTGCTGAGCTTGTGA
EST: gi|37996475|gb|CF808064.1|CF808064
EST:     GATCAACGAAGACAACGTCCTTTACATTGTTGAAAACATCAATGTCGCTG                         CAATTGAGACAACTCTATGGTCGATTGAATGGGGCATTGCTGAGCTTGTGA
genomic: GATCAACGAAGACAACGTCCTTTACATTGTTGAAAACATTAATGTCGCTGgtatgatgct ... attatttcagCAATTGAGACAACTCTATGGTCGATTGAATGGGGCATTGCTGAGCTTGTGA
EST: gi|14126646|gb|BG791084.1|BG791084
EST:     GATCAACGAAGACAACGTCCTTTACATTGTTGAAAACATCAATGTCGCTG                         CAATTGAGACAACTCTATGGTCGATTGAATGGGGCATTGCTGAGCTTGTGA
genomic: GATCAACGAAGACAACGTCCTTTACATTGTTGAAAACATTAATGTCGCTGgtatgatgct ... attatttcagCAATTGAGACAACTCTATGGTCGATTGAATGGGGCATTGCTGAGCTTGTGA
EST: gi|4282941|gb|AI440594.1|AI440594
EST:     GATCAACGAAGACAACGTCCTTTACATTGTTGAAAACATTAATGTCGCTG                         CAATTGAGACAACTCTATGGTCGATTGAATGGGGCATTGCTGAGCTTGTGA
genomic: GATCAACGAAGACAACGTCCTTTACATTGTTGAAAACATTAATGTCGCTGgtatgatgct ... attatttcagCAATTGAGACAACTCTATGGTCGATTGAATGGGGCATTGCTGAGCTTGTGA
EST: gi|15664543|gb|BI701914.1|BI701914
EST:     GATCAACGAAGACAACGTCCTTTACATTGTTGAAAACATTAATGTCGCTG                         CAATTGAGACAACTCTATGGTCGATTGAATGGGGCATTGCTGAGCTTGTGA
genomic: GATCAACGAAGACAACGTCCTTTACATTGTTGAAAACATTAATGTCGCTGgtatgatgct ... attatttcagCAATTGAGACAACTCTATGGTCGATTGAATGGGGCATTGCTGAGCTTGTGA
EST: gi|37995343|gb|CF806932.1|CF806932
EST:     GATCAACGAAGACAACGTCCTTTACATTGTTGAAAACATCAATGTCGCTG                         CAATTGAGACAACTCTATGGTCGATTGAATGGGGCATTGCTGAGCTTGTGA
genomic: GATCAACGAAGACAACGTCCTTTACATTGTTGAAAACATTAATGTCGCTGgtatgatgct ... attatttcagCAATTGAGACAACTCTATGGTCGATTGAATGGGGCATTGCTGAGCTTGTGA
EST: gi|13311397|gb|BG405048.1|BG405048
EST:     GATCAACGAAGACAACGTCCTTTACATTGTTGAAAACATTAATGTCGCTG                         CAATTGAGACAACTCTATGGTCGATTGAATGGGGCATTGCTGAGCTTGTGA
genomic: GATCAACGAAGACAACGTCCTTTACATTGTTGAAAACATTAATGTCGCTGgtatgatgct ... attatttcagCAATTGAGACAACTCTATGGTCGATTGAATGGGGCATTGCTGAGCTTGTGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caaatcatatgatgattttttctaagtagcaattatatatgtgttattatttcagCAATTGAGACAACTCTATGGTCGATTGAATGGGGCATTGCTGAGCTTGTGAACCACCCAGAGATCCAGCAGAAGGTGAGGGATGAAATTGATAGAGTTCT
                                              ttatttc  CT-rich tract
                              aattatatatgtgtta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gaattactattaaagtctacatacactatatagtctatgttacatcaaatcatatgatgattttttctaagtagcaattatatatgtgttattatttcagCAATTGAGACAACTCTATGGTCGATTGAATGGGGCATTGCTGAGCTTGTGAACCACCCAGAGATCCAGCAGAAGGTGAGGGATGAAATTGATAGAGTTCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC
- - - - - - - - - -catacac
- - - - - - - - - - - - - - - - gtctatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tatgtgt