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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTATTCTGGCCTGAACAATCCGAGTTTGTAAGGATGGCAGCAAGATTTGGAGCCAAAATAGTACCTTTTGGTGTAGTTGGAGAAGATGACATTGGTCAAgtaagttttggtcttttctgaaccaatcattttcctctatgaatttattatagcctgaaaatgcttgtatcaggcaaagcatgaccaattgtttttatat...

Basic information

species Glycine max
transcript GLYMA16G05580.1
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G05580.1 (Glycine max), 5'ss of exon 11
lower sequence: LOC_Os09g33530.1 (Oryza sativa), 5'ss of exon 11
GTTATTCTGGCCTGAACAATCCGAGTTTGTAAGGATGGCAGCAAGATTTGGAGCCAAAATAGTACCTTTTGGTGTAGTTGGAGAAGATGACATTGGTCAAgtaagt---tttggtcttttctgaaccaatcattttcctctatgaatttattatagcctgaaaatgcttgtatcaggcaaagcatgaccaattgtttttatat-
||| || ||||| || || || || ||||| ||||||||| |||| |||||||| | |||| |||| ||||| ||||||||||||||||| ||  || | || |||   ||    || ||    |||||| |||      |   ||| |  | |    |  | ||  || | |  |   || | |  |    ||| |  || | 
GTTGTTTTGGCCAGAGCAGTCTGAATTTGTGAGGATGGCATCAAGGTTTGGAGCAACAATAATACCATTTGGAGTAGTTGGAGAAGATGATATATGTGATgtgagtgcattcttactattaactaccaattattaatagatgcaaatctcctttgctgtctacatttttttttgcgaggaacctttgc----tgtctacatgtt

upper sequence: GLYMA16G05580.1 (Glycine max), 5'ss of exon 11
lower sequence: AT3G26840.1 (Arabidopsis thaliana), 5'ss of exon 11
GTTATTCTGGCCTGAACAATCCGAGTTTGTAAGGATGGCAGCAAGATTTGGAGCCAAAATAGTACCTTTTGGTGTAGTTGGAGAAGATGACATTGGTCAAgtaagttttggtcttttctgaaccaatcattttcctctatgaatttattatagcctgaaaatgcttgtatcaggcaaagcatgaccaattgtttttatat
| | || ||||| ||||  ||||||||||| ||  | ||| | | ||||||||||||||| || ||||||||||| ||||||||||| || ||  |  ||||||| |||    | | ||  ||  || ||     ||    |  |   | | || | |      |||  |  | ||  | ||||      |         
GCTGTTTTGGCCAGAACGGTCCGAGTTTGTGAGAGTTGCATCTAAATTTGGAGCCAAAATTGTTCCTTTTGGTGTTGTTGGAGAAGACGATATCTGCGAAgtaagctttctcatatgctatac--attataaatatccg-aacctcggtttggcgtaa----ctttggtttggacattgaatgattctcag---------

upper sequence: GLYMA16G05580.1 (Glycine max), 5'ss of exon 11
lower sequence: AT5G41120.1 (Arabidopsis thaliana), 5'ss of exon 11
GTTATTCTGGCCTGAACAATCCGAGTTTGTAAGGATGGCAGCAAGATTTGGAGCCAAAATAGTACCTTTTGGTGTAGTTGGAGAAGATGACATTGGTCAAgtaagttttggtcttttctgaaccaatcattttcctctatgaatttattatagcctgaaaatgcttgtatcaggcaaagcatgaccaattgtttttatat---
|||||| ||||| ||||| || |||||||||||||| ||| | | ||||||||| |||||  | |||||||| || ||||||||||||||  || || |||||||        | |  |   |     | ||||  |       || ||| | |   |   || ||  ||  ||    |  | |  | | ||||    |    
GTTATTTTGGCCAGAACATTCGGAGTTTGTAAGGATAGCATCTAAATTTGGAGCAAAAATCATTCCTTTTGGAGTTGTTGGAGAAGATGATCTTTGTGAAgtaagcaaaaaaatctcttttccgttctactttcaacacctgcattcttaaaactc-attttgtttcaattgggttttgagtta--actcgtttgagcaatgg

upper sequence: GLYMA16G05580.1 (Glycine max), 5'ss of exon 11
lower sequence: AT3G26820.1 (Arabidopsis thaliana), 5'ss of exon 13
GTTATTCTGGCCTGAACAATCCGAGTTTGTAAGGATGGCAGCAAGATTTGGAGCCAAAATAGTACCTTTTGGTGTAGTTGGAGAAGATGACATTGGTCAAgtaagttttggtcttttctgaaccaatcattttcctctatgaatttattatagcctgaaaatgcttgtatcaggcaaa-gcatgaccaattgtttttatat-------
| | || ||||| ||||||||||||||||| ||  | ||| | | ||||||||| ||||| || ||||| ||||| ||||||||||| |||||   | | ||||||       || |||  || ||| |||    ||||  | | | | ||  |||  |  |   | | |    || | |||| |  ||     || | ||       
GCTGTTTTGGCCAGAACAATCCGAGTTTGTGAGAGTTGCATCTAAATTTGGAGCGAAAATCGTTCCTTTCGGTGTTGTTGGAGAAGACGACATCTTTAATgtaagt------attctctacacaaat-attaagatctac-actatttcatttccttcatgtaactatttatcacatatgcattattaaccccattcaaatttctact

upper sequence: GLYMA16G05580.1 (Glycine max), 5'ss of exon 11
lower sequence: Vv14s0068g01430.t01 (Vitis vinifera), 5'ss of exon 11
GTTATTCTGGCCTGAACAATCCGAGTTTGTAAGGATGGCAGCAAGATTTGGAGCCAAAATAGTACCTTTTGGTGTAGTTGGAGAAGATGACATTGGTCAAgtaagttttggtcttttctgaaccaatcattttcctctatgaatttattatagcctgaaaatgcttgtatcaggcaaagcatgaccaattgtttttatat-------
||| || ||||| |||||||| ||||||||  | || || || || ||||||||||||||  |||| ||||| || ||||||||||||||  ||||||| ||||  ||   |  | |       |||    |||    ||   ||  |||| |  |   | | ||  || |||          |  || |     |  ||       
GTTGTTTTGGCCAGAACAATCTGAGTTTGTCCGAATTGCGGCTAGGTTTGGAGCCAAAATTATACCCTTTGGAGTTGTTGGAGAAGATGATTTTGGTCAGgtaaacttgattactat-------aatgtccttcaatcatagcttctttattgattattagttctcctaccagttgccatgcaagtaagttcgcatgcatgctaaca

upper sequence: GLYMA16G05580.1 (Glycine max), 5'ss of exon 11
lower sequence: Vv14s0068g01440.t01 (Vitis vinifera), 5'ss of exon 11
GTTATTCTGGCCTGAACAATCCGAGTTTGTAAGGATGGCAGCAAGATTTGGAGCCAAAATAGTACCTTTTGGTGTAGTTGGAGAAGATGACATTGGTCAAgtaagttttggtcttttctgaaccaatcattttcctctatgaatttattatagcctgaaaatgctt-gtatcaggcaaagcatgaccaattgtttttatat-----
||| || ||||| |||  ||| |||||| |  | ||||| || ||||||||||||||||| ||||| ||||| || |||||||||||||| |||||||| |||     ||| |||  ||    ||||    ||  |   ||  ||  ||||    |     |     ||| ||  || | || |  ||  | |   |  |      
GTTGTTTTGGCCAGAATCATCTGAGTTTATCCGAATGGCGGCTAGATTTGGAGCCAAAATTGTACCCTTTGGGGTGGTTGGAGAAGATGATATTGGTCAGgta-----tgggcttgactactacaatatcctttatgactgtcttctttatcaattattggtttccagtaccatacagacca-gctcatgtatccatccacccaca

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|51345114|gb|CO985847.1|CO985847
EST:     GAGCCAAAATAGTACCTTTTGGTGTAGTTGGAGAAGATGACATTGGTCAA                         GTAGTTTTTGATTATGACGACTTGGTGAAAATTCCTTACTTTAGGTCTGAA
genomic: GAGCCAAAATAGTACCTTTTGGTGTAGTTGGAGAAGATGACATTGGTCAAgtaagttttg ... gtcttttcagGTAGTTTTTGATTATGACGACTTGGTGAAAATTCCTTACTTTAGGTCTGAA
EST: gi|254346772|gb|GR856494.1|GR856494
EST:     AGCCAAAATAGTACCTTTTGGTGTAGTTGGAGAAGATGACATTGGGTCAA                         GTAGTTTTTGATTATGACGACTTG-TGAAA-TTCCTTTACTTTAG-TCTG
genomic: AGCCAAAATAGTACCTTTTGGTGTAGTTGGAGAAGATGACATTGG-TCAAgtaagttttg ... gtcttttcagGTAGTTTTTGATTATGACGACTTGGTGAAAATTCCTT-ACTTTAGGTCTG
EST: gi|15813571|gb|BI785846.1|BI785846
EST:     GAGCCAAAATAGTACCTTTTGGTGTAGTTGGAGAAGATGACATTGGTCAA                         GTAGTTTTTGATTATGACGACTTGGTGAAAATTCCT
genomic: GAGCCAAAATAGTACCTTTTGGTGTAGTTGGAGAAGATGACATTGGTCAAgtaagttttg ... gtcttttcagGTAGTTTTTGATTATGACGACTTGGTGAAAATTCCT
EST: gi|254346773|gb|GR856495.1|GR856495
EST:     GAGCCAAAATAGTACCTTTTGGTGTAGTTGGAGAAGATGACATTGGTCAA                         GTAGTTTTTGATTATGACGACTTGGTGAAAATTCCTTACTTTAGGTCTGAA
genomic: GAGCCAAAATAGTACCTTTTGGTGTAGTTGGAGAAGATGACATTGGTCAAgtaagttttg ... gtcttttcagGTAGTTTTTGATTATGACGACTTGGTGAAAATTCCTTACTTTAGGTCTGAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTATTCTGGCCTGAACAATCCGAGTTTGTAAGGATGGCAGCAAGATTTGGAGCCAAAATAGTACCTTTTGGTGTAGTTGGAGAAGATGACATTGGTCAAgtaagttttggtcttttctgaaccaatcattttcctctatgaatttattatagcctgaaaatgcttgtatcaggcaaagcatgaccaattgtttttatat

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG