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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGATGCCCTGCCTTCTGAGTATGATTCACGAGTTAAGGCCATGGAAGTTGATGAAAAGCCAACGGAGGACTACAATGACATTGGTGGTTTAGAGAAGCAGgtgcactataattaccgacaatttatcgatgcactctttctctttttcttatttacaattaggtaacagggcttccgatgatgtgatcaataacttggtctttgccaacag

Basic information

species Glycine max
transcript GLYMA03G39500.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G39500.1 (Glycine max), 5'ss of exon 4
lower sequence: LOC_Os02g56000.2 (Oryza sativa), 5'ss of exon 4
GGATGCCCTGCCTTCTGAGTATGATTCACGAGTTAAGGCCATGGAAGTTGATGAAAAGCCAACGGAGGACTACAATGACATTGGTGGTTTAGAGAAGCAGgtgc------actataa----ttaccgacaa-----tttatcgatgcactctttctctttttcttatttacaattaggtaacagggcttccg-atgatgtga---tcaataacttggtctttgccaacag-------------------------------------------
 ||  | || ||||| || ||||||||||| |||||||| ||||| || ||||||||||| || ||||| |||||||||||||||||  | ||||| |||||        ||| |||     ||  ||  |     ||  |        ||    |  | || |||| ||       |||||     ||||  ||    | |   |  || | ||| | ||||   |  |                                           
AGACACGCTACCTTCAGAATATGATTCACGGGTTAAGGCAATGGAGGTAGATGAAAAGCCTACAGAGGATTACAATGACATTGGTGGCCTTGAGAAACAGgtatttatttactttaaagatctaatgatgaaaacattagttaggatggtcaccattctgttgttatgtaagtagcagtaacttcatttccatatctcataagtgttcatcagttgctgtttgttcattgttatctgctctcttatgttctacttttatattgtctaatgcag

upper sequence: GLYMA03G39500.1 (Glycine max), 5'ss of exon 4
lower sequence: LOC_Os06g07630.1 (Oryza sativa), 5'ss of exon 4
GGATGCCCTGCCTTCTGAGTATGATTCACGAGTTAAGGCCATGGAAGTTGATGAAAAGCCAACGGAGGACTACAATGACATTGGTGGTTTAGAGAAGCAGgtgcact-----ataattaccgacaatttatcgatgcactctttctctttttcttatttacaattaggtaacagggcttccgatgatgtgatcaataacttggtctttgccaacag----------------------------------------------------------------------
|||  | ||||| || ||||||||||||||||| ||||| ||||| || |||||||| || || |||||||||||||| ||||| ||| | || |||||||| || |     |||| |   || | || |  | | |  | ||     |     |||| ||||  |  |     ||      ||   |  ||   || |      |    |||                                                                         
GGACACACTGCCATCAGAGTATGATTCACGAGTAAAGGCAATGGAGGTGGATGAAAAACCCACAGAGGACTACAATGATATTGGAGGTCTTGAAAAGCAGgtacattgcttaataaatgttgaaagttcagtgttcc-tttttggaactggaaatattgacaaccatctctttagggaat-aatagagcaatttgtatcgcttcatgcatcaagcatgttacatttccatccatcttttccttttcataatttatcattctttccatcctattttattgaatatag

upper sequence: GLYMA03G39500.1 (Glycine max), 5'ss of exon 4
lower sequence: GRMZM2G027282_T01 (Zea mays), 5'ss of exon 4
GGATGCCCTGCCTTCTGAGTATGATTCACGAGTTAAGGCCATGGAAGTTGATGAAAAGCCAACGGAGGACTACAATGACATTGGTGGTTTAGAGAAGCAGgtgcactataatt----accgacaatttatcgatgcactctttctctttttctt-atttacaat-taggtaacagggcttccgatgatgtgatcaataacttggtctttgccaacag
 ||| |  ||||||| |||||||| ||||| |||||||| |||||||| ||||| || || || ||||| |||||||||||||| ||  | ||||| |||||    |    |     || |    || |  | |  |      ||  | || |  ||||   |  | |  | || |   |   |||||||     |||||   |             
AGATACATTGCCTTCAGAGTATGACTCACGGGTTAAGGCAATGGAAGTAGATGAGAAACCTACTGAGGATTACAATGACATTGGCGGACTTGAGAAACAGgtaatttgctttccagaactgggggttaactgttatatcagcactactgttgtggatttgttacattgcaagcaagcagtaatatgatgtttggtataacacag-------------

upper sequence: GLYMA03G39500.1 (Glycine max), 5'ss of exon 4
lower sequence: GRMZM2G032505_T02 (Zea mays), 5'ss of exon 4
GGATGCCCTGCCTTCTGAGTATGATTCACGAGTTAAGGCCATGGAAGTTGATGAAAAGCCAACGGAGGACTACAATGACATTGGTGGTTTAGAGAAGCAGgtgcactataattaccgacaatttatcgatgcactctttctctttttcttatttacaattaggtaacagggcttccgatgatgtgatcaataacttggtctttgccaacag
 ||| |  |||| || ||||| ||||||||||| ||||| |||||||| ||||||||||| || || || || ||||||||||| ||| | || ||||||                                                                                                               
AGATACATTGCCATCAGAGTACGATTCACGAGTGAAGGCAATGGAAGTGGATGAAAAGCCCACTGAAGATTATAATGACATTGGGGGTCTTGAAAAGCAGnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn-----------

upper sequence: GLYMA03G39500.1 (Glycine max), 5'ss of exon 4
lower sequence: AT3G05530.1 (Arabidopsis thaliana), 5'ss of exon 4
GGATGCCCTGCCTTCTGAGTATGATTCACGAGTTAAGGCCATGGAAGTTGATGAAAAGCCAACGGAGGACTACAATGACATTGGTGGTTTAGAGAAGCAGgtgcactataattaccgacaatttatcgatgcactctttctctttttcttatttacaattaggtaacagggcttccgatgatgtgatcaataacttggtctttgccaacag
|||| || |||| || |||||||| ||  | ||||| |||||||| || |||||||| ||||| || || |||||||||||||| ||  |||||||||||||    |   |  |  |      | |  ||   || | |    ||| |||  |    |  |  |||  | | ||   ||     || ||                      
GGATACCTTGCCATCCGAGTATGACTCTAGGGTTAAAGCCATGGAGGTCGATGAAAAACCAACTGAAGATTACAATGACATTGGAGGACTAGAGAAGCAGgtatgtttataccattg------tgttaatctgctgtattgactttgcttcgtagtga--aactaattgagttt---atttctggaacag---------------------

upper sequence: GLYMA03G39500.1 (Glycine max), 5'ss of exon 4
lower sequence: Vv14s0060g02260.t01 (Vitis vinifera), 5'ss of exon 4
GGATGCCCTGCCTTCTGAGTATGATTCACGAGTTAAGGCCATGGAAGTTGATGAAAAGCCAACGGAGGACTACAATGACATTGGTGGTTTAGAGAAGCAGgtgcactataatt--accgacaatttatcgatgcactctttctctttttcttatttacaattaggtaacagggctt-ccgatgatgtgatcaataacttggtctttgccaacag
 ||| |  |||| |||||||||||||| ||||| ||||| ||||| ||||||||||| ||||| || ||||||||||| || || ||  | ||||||||||     |  ||||      | | ||||| || |   |  ||   | |    | |||   | |    |  |   ||| ||  | ||   | ||                      
AGATACTTTGCCATCTGAGTATGATTCTCGAGTAAAGGCTATGGAGGTTGATGAAAAACCAACAGAAGACTACAATGATATCGGAGGGCTGGAGAAGCAGgcaagtttcaattttgtgcatattttatggaagtggttgttgcttgtccgatttttgatactttcaactaaaacttgcctctaattacaacag---------------------

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|23727048|gb|BU761539.1|BU761539
EST:     ATGAAAAGCCAACGGAGGACTACAATGACATTGGTGGTTTAGAGAAGCAG                         ATCCAAGAATTAGTTGAAGCAATTGTTTTGCCAA
genomic: ATGAAAAGCCAACGGAGGACTACAATGACATTGGTGGTTTAGAGAAGCAGgtgcactata ... ttgccaacagATCCAAGAATTAGTTGAAGCAATTGTTTTGCCAA
EST: gi|17400340|gb|BM177122.1|BM177122
EST:     ATGAAAAGCCAACGGAGGACTACAATGACATTGGTGGTTTAGAGAAGCAG                         ATCCAAGAATTAGTTGAAGCAATTGTTTTGCCAATGACCTGCAAAGAGCGG
genomic: ATGAAAAGCCAACGGAGGACTACAATGACATTGGTGGTTTAGAGAAGCAGgtgcactata ... ttgccaacagATCCAAGAATTAGTTGAAGCAATTGTTTTGCCAATGACCTGCAAGGAGCGG
EST: gi|16281884|gb|BI944719.1|BI944719
EST:     ATGAAAAGCCAACGGAGGACTACAATGACATTGGTGGTTTAGAGAAGCAG                         ATCCAAGAATTAGTTGAAGCAATTGTTTTGCCAATGACCTGCAAGGAGCGG
genomic: ATGAAAAGCCAACGGAGGACTACAATGACATTGGTGGTTTAGAGAAGCAGgtgcactata ... ttgccaacagATCCAAGAATTAGTTGAAGCAATTGTTTTGCCAATGACCTGCAAGGAGCGG
EST: gi|208272900|gb|GE072328.1|GE072328
EST:     ATGAAAAGCCAACGGAGGACTACAATGACATTGGTGGTTTAGAGAAGCAG                         ATCCAAGAATTAGTTGAAGCAATTGTTTTGCCAATGACCTGCAAGGAGCGG
genomic: ATGAAAAGCCAACGGAGGACTACAATGACATTGGTGGTTTAGAGAAGCAGgtgcactata ... ttgccaacagATCCAAGAATTAGTTGAAGCAATTGTTTTGCCAATGACCTGCAAGGAGCGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGATGCCCTGCCTTCTGAGTATGATTCACGAGTTAAGGCCATGGAAGTTGATGAAAAGCCAACGGAGGACTACAATGACATTGGTGGTTTAGAGAAGCAGgtgcactataattaccgacaatttatcgatgcactctttctctttttcttatttacaattaggtaacagggcttccgatgatgtgatcaataacttggtctttgccaacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC