Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgatgagtcctatattgcgaatttgctaatatttcatgattttatgttctctggatgccattcttatattggcttctatgcagATGATCCACATAATGACCCAAATGTGTCGGGAGATCCATACAAGACATTGTTTGTGGCTAAACTC

Basic information

species Glycine max
transcript GLYMA11G07200.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G07200.2 (Glycine max), 3'ss of exon 4
lower sequence: AT3G50670.1 (Arabidopsis thaliana), 3'ss of exon 4
gtgatgagtcctatatt----gcgaatttgctaatatt-tcatgattttatgttctctggatgccattcttatattggcttctatgcagATGATCCACATAATGACCCAAATGTGTCGGGAGATCCATACAAGACATTGTTTGTGGCTAAACTC
|| ||      ||| ||    | |    |  ||||    || |   |||  |   |||   |   | | |  | ||   || ||||||||||| ||  ||||||| |||||||   | ||||||||||||||||||||||| ||  | | ||| 
gtaatctactatatgttatttgtgttccttttaatgccctcttaggtttgagaattcttagt--taatttgttttttttttatatgcagATGACCCCAATAATGATCCAAATGCTACTGGAGATCCATACAAGACATTGTTCGTTTCAAGACTT

upper sequence: GLYMA11G07200.2 (Glycine max), 3'ss of exon 4
lower sequence: Vv04s0023g01580.t01 (Vitis vinifera), 3'ss of exon 4
---------------------------gtgatgagtcctatattgcgaatttgctaatatttcatgattttatgttctctggatgccattcttatattggcttctatgcagATGATCCACATAATGACCCAAATGTGTCGGGAGATCCATACAAGACATTGTTTGTGGCTAAACTC
                           ||  |  ||       || || ||||     |||| || ||   |  || |  |        | |     |  ||||||||||||||||||| |||||||||||||| | |||||||| |||||||||||||||||||| ||||  || 
gtgataagctattttctccctctcctagtatttggtgtctaggtg-gattttgtatccattttattatca-acatttttggtgccttgctttacacgtatcttctatgcagATGATCCAAATAATGACCCAAATATTTCGGGAGACCCATACAAGACATTGTTTGTAGCTAGGCTT
















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|209727268|gb|BW655253.1|BW655253
EST:     GCTAAGGCTTGAGAAGGGAGCTGCAAAGGCTGCTGAGGAGCTTGAGAAAT                         ATGATCCACATAATGACCCAAATGTGTCGGGAGATCCATACAAGACATTGT
genomic: GCTAAGGCTTGAGAAGGGAGCTGCAAAGGCTGCTGAGGAGCTTGAGAAATgtgatgagtc ... ttctatgcagATGATCCACATAATGACCCAAATGTGTCGGGAGATCCATACAAGACATTGT
EST: gi|209728976|gb|BW655019.1|BW655019
EST:     GCTAAGGCTTGAGAAGGGAGCTGCAAAGGCTGCTGAGGAGCTTGAGAAAT                         ATGATCCACATAATGACCCAAATGTGTCGGGAGATCCATACAAGACATTGT
genomic: GCTAAGGCTTGAGAAGGGAGCTGCAAAGGCTGCTGAGGAGCTTGAGAAATgtgatgagtc ... ttctatgcagATGATCCACATAATGACCCAAATGTGTCGGGAGATCCATACAAGACATTGT
EST: gi|209698445|gb|BW667242.1|BW667242
EST:     GCTAAGGCTTGAGAAGGGAGCTGCAAAGGCTGCTGAGGAGCTTGAGAAAT                         ATGATCCACATAATGACCCAAATGTGTCGGGAGATCCATACAAGACATTGT
genomic: GCTAAGGCTTGAGAAGGGAGCTGCAAAGGCTGCTGAGGAGCTTGAGAAATgtgatgagtc ... ttctatgcagATGATCCACATAATGACCCAAATGTGTCGGGAGATCCATACAAGACATTGT
EST: gi|11412754|gb|BF424765.1|BF424765
EST:     GCTAAGGCTTGAGAAGGGAGCTGCANAGGCTGCTGAGGAGCTTGAGAAAT                         ATGATCCACATAATGACCCAGATGTGTCGGGAGATCCATACAAGACATTGT
genomic: GCTAAGGCTTGAGAAGGGAGCTGCAAAGGCTGCTGAGGAGCTTGAGAAATgtgatgagtc ... ttctatgcagATGATCCACATAATGACCCAAATGTGTCGGGAGATCCATACAAGACATTGT
EST: gi|213603451|gb|DB970492.1|DB970492
EST:     GCTAAGGCTTGAGAAGGGAGCTGCAAAGGCTGCTGAGGAGCTTGAGAAAT                         ATGATCCACATAATGACCCAAATGTGTCGGGAGATCCATACAAGACATTGT
genomic: GCTAAGGCTTGAGAAGGGAGCTGCAAAGGCTGCTGAGGAGCTTGAGAAATgtgatgagtc ... ttctatgcagATGATCCACATAATGACCCAAATGTGTCGGGAGATCCATACAAGACATTGT
EST: gi|18039679|gb|BM307973.1|BM307973
EST:     GCTAAGGCTTGAGAAGGGAGCTGCAAAGGCTGCTGAGGAGCTTGAGAAAT                         ATGATCCACATAATGACCCAAATGTGTCGGGAGATCCATACAAGACATTGT
genomic: GCTAAGGCTTGAGAAGGGAGCTGCAAAGGCTGCTGAGGAGCTTGAGAAATgtgatgagtc ... ttctatgcagATGATCCACATAATGACCCAAATGTGTCGGGAGATCCATACAAGACATTGT
EST: gi|213618444|gb|DB963373.1|DB963373
EST:     GCTAAGGCTTGAGAAGGGAGCTGCAAAGGCTGCTGAGGAGCTTGAGAAAT                         ATGATCCACATAATGACCCAAATGTGTCGGGAGATCCATACAAGACATTGT
genomic: GCTAAGGCTTGAGAAGGGAGCTGCAAAGGCTGCTGAGGAGCTTGAGAAATgtgatgagtc ... ttctatgcagATGATCCACATAATGACCCAAATGTGTCGGGAGATCCATACAAGACATTGT
EST: gi|8826552|gb|BE210282.1|BE210282
EST:     GCTAAGGCTTGAGAAGGGAGCTGCAAAGGCTGCTGAAGAGCTTGAGAAAT                         ATGATCCACATAATGACCCAAATGTGTCGGGAGATCCATACAAGACATTGT
genomic: GCTAAGGCTTGAGAAGGGAGCTGCAAAGGCTGCTGAGGAGCTTGAGAAATgtgatgagtc ... ttctatgcagATGATCCACATAATGACCCAAATGTGTCGGGAGATCCATACAAGACATTGT
EST: gi|26058824|gb|CA801738.1|CA801738
EST:     GCTAAGGCTTGAGAAGGGAGCTGCAAAGGCTGCTGAGGAGCTTGAGAAAT                         ATGATCCACATAATGACCCAAATGTGTCGGGAGATCCATACAAGACATTGT
genomic: GCTAAGGCTTGAGAAGGGAGCTGCAAAGGCTGCTGAGGAGCTTGAGAAATgtgatgagtc ... ttctatgcagATGATCCACATAATGACCCAAATGTGTCGGGAGATCCATACAAGACATTGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atatttcatgattttatgttctctggatgccattcttatattggcttctatgcagATGATCCACATAATGACCCAAATGTGTCGGGAGATCCATACAAGACATTGTTTGTGGCTAAACTC
 tgctaat  putative branch site (score: 2)
                                            cttctat  putative PPT
                               attcttatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgatgagtcctatattgcgaatttgctaatatttcatgattttatgttctctggatgccattcttatattggcttctatgcagATGATCCACATAATGACCCAAATGTGTCGGGAGATCCATACAAGACATTGTTTGTGGCTAAACTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC