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'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacaatttaaattgtttgatttttattacaagtatatttgctctattatttgttcttttaaaaacatttgtctttctattctgctgagagatgatgatttaatgtcttctaaatgtattttcttttgaatttgctacagGTTATTTTCTTCACGGATCCAGTTGATGAGTACTTGATGCAATACCTGATGGATTATGAAGACAAGAAGTTCCAAAATGTGTCCAAGGAGGGTTTGAAAC

Basic information

species Glycine max
transcript GLYMA14G40320.1
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA14G40320.1 (Glycine max), 3'ss of exon 13
lower sequence: LOC_Os06g50300.1 (Oryza sativa), 3'ss of exon 13
gtacaatttaaattgtttgatttttattacaagtatatttgctctattatttgttcttttaaaaacatttgtctttctattctgctgagagatgatgatttaatgtcttctaaatgtattttcttttgaatttgctacagGTTATTTTCTTCACGGATCCAGTTGATGAGTACTTGATGCAATACCTGATGGATTATGAAGACAAGAAGTTCCAAAATGTGTCCAAGGAGGGTTTGAAAC
                                |||  |   |   |||  ||| | |||||  | |   |    |   |||   |||            ||||      ||||   || |||  ||    |||| | |||||||| | |||||| || || ||||| |||||||||||||||||||| ||||| || || |||||||||||||| || || |||||||||||| | ||||
------------------------------gggtac-tgcaccacatttattgcttttttatgagctcctccaatagaattactctggatccctggagcttaa------ctaa---tacttttgttatcttttgttgcagGTTATCTACTTCACTGACCCTGTTGACGAGTACTTGATGCAATACCTCATGGACTACGAGGACAAGAAGTTCCAGAACGTCTCCAAGGAGGGTCTCAAAC

upper sequence: GLYMA14G40320.1 (Glycine max), 3'ss of exon 13
lower sequence: GRMZM2G141931_T02 (Zea mays), 3'ss of exon 13
gtacaatttaaattgtttgatttttattacaagtatatttgctctattatttgttcttttaaaaacatttgtctttctattctgctgagagatgatgatttaatgtcttctaaatgtattttcttttgaatttgctacagGTTATTTTCTTCACGGATCCAGTTGATGAGTACTTGATGCAATACCTGATGGATTATGAAGACAAGAAGTTCCAAAATGTGTCCAAGGAGGGTTTGAAAC
                                |||| |||   ||  |  | |||  |  |    ||||    | |||    |   ||     | |  |   | ||         |  |  | ||||   |||| | ||||| || |||||||| || || || || |||||| ||||||| ||||||||||| || || |||||||||||||| || ||||||||||||||  |||| |
--------------------------------gtat-tttatgctgctggtggtttatccacttccattatagtgtctgagatctggaatacagcttgtgggaagtaacgctgtcgcttgatttttttg-tttg-tgcagGTCATCTTCTTCACCGACCCCGTGGACGAGTACCTGATGCAGTACCTGATGGACTACGAGGACAAGAAGTTCCAGAACGTGTCCAAGGAGGGACTGAAGC

upper sequence: GLYMA14G40320.1 (Glycine max), 3'ss of exon 13
lower sequence: GRMZM2G399073_T02 (Zea mays), 3'ss of exon 15
gtacaatttaaattgtttgatttttattacaagtatat-ttgctctattatttgttcttttaaaaacatttgtctttctattctgct-gagagatgatgatttaatgtct-tctaaatgtattttcttttgaatttgctacagGTTATTTTCTTCACGGATCCAGTTGATGAGTACTTGATGCAATACCTGATGGATTATGAAGACAAGAAGTTCCAAAATGTGTCCAAGGAGGGTTTGAAAC
                           || |  | |||  ||||   ||||    | |  | | |   |  |   |   || | ||| ||||  |    |      |  | | |   | | |||| |||||  |||||   |||| || |||||||| || ||  | || |||||| ||||||| ||||||||||| || || |||| ||||||||| || ||||||||||||||  |||| |
--------------------------gtatatatgtatgctgctggtttatccactttcattacagtgtggggtctggaatacagcttgagaagtaccaacgctgcgcttgttttgttttgttttgttttgtttttgc---agGTCATCTTCTTCACCGACCCTATGGACGAGTACCTGATGCAGTACCTGATGGACTACGAGGACAGGAAGTTCCAGAACGTGTCCAAGGAGGGCCTGAAGC

upper sequence: GLYMA14G40320.1 (Glycine max), 3'ss of exon 13
lower sequence: AT4G24190.1 (Arabidopsis thaliana), 3'ss of exon 13
gtacaatttaaattgtttgatttttattacaagtatatttgctctattatttgttcttttaaaaacatttgtctttctattctgctgagagatgatgatttaatgtcttctaaatgtattttcttttgaatttgctacagGTTATTTTCTTCACGGATCCAGTTGATGAGTACTTGATGCAATACCTGATGGATTATGAAGACAAGAAGTTCCAAAATGTGTCCAAGGAGGGTTTGAAAC
                                                        |||  |   ||   |  |    ||||| ||   |    ||||| |        |  ||    || || |     | | |  ||||| || |||||||| || ||||||||||| |||||||||||||||||||||||||| |||||||| |||||||| |||||||||||||| ||  ||||  
-------------------------------------------------------gtttgcattgcacacgaata---attcttctttaa----atgatctccaactcgcataacacgttctcatacttgtgttcc-cagGTCATCTTCTTCACAGACCCAGTTGATGAATACTTGATGCAATACCTGATGGATTACGAAGACAAAAAGTTCCAGAATGTGTCCAAGGAAGGACTGAAGG

upper sequence: GLYMA14G40320.1 (Glycine max), 3'ss of exon 13
lower sequence: Vv18s0001g14500.t01 (Vitis vinifera), 3'ss of exon 13
gtacaatttaaattgtttgatttttattacaagtatatttgctctattatttgttcttttaaaaacatttgtctttctattctgctgagagatgatgatttaatgtcttctaaatgtattttcttttgaatt----tgctacagGTTATTTTCTTCACGGATCCAGTTGATGAGTACTTGATGCAATACCTGATGGATTATGAAGACAAGAAGTTCCAAAATGTGTCCAAGGAGGGTTTGAAAC
              || |||||   |  | |    || ||||| | | |   || |||   |  |   | |||||  | || | || ||  |  ||   ||  | | |   || |   |||  || |||||     |  | |||||||||||||| || || ||||| ||||||||| ||||||||||||||||||| ||||||||||| || ||||| |||||||| ||||| ||  ||||||
--------------gtatgattggaaa-agataactacttgcttt-tcaaccgtcctt--gattagtctggtcttattcttttcctaaggtactatc-cttggtttttaacaacttgttttctttctgaatcattctattgcagGTTATTTTCTTTACTGACCCAGTGGATGAGTACCTGATGCAATACCTGATGGACTATGAAGACAAAAAATTCCAGAATGTGTCAAAGGAAGGCCTGAAAC

upper sequence: GLYMA14G40320.1 (Glycine max), 3'ss of exon 13
lower sequence: PP1S126_38V6.1 (Physcomitrella patens), 3'ss of exon 13
gtacaatttaaattgtttgatttttattacaagtatatttgctctattatttgttcttttaaaaacatttgtctttctattctgctgagagatgatgatttaatgtcttctaaatgtattttcttttgaatttgctacagGTTATTTTCTTCACGGATCCAGTTGATGAGTACTTGATGCAATACCTGATGGATTATGAAGACAAGAAGTTCCAAAATGTGTCCAAGGAGGGTTTGAAAC
    ||       | | ||||| ||  || |    | ||||    ||   |    ||      ||| ||| |  || |        |  |||       | ||    |    |||| || |  ||  |  |||    ||||| || |  || || || |||||||||||||||||||  ||| ||||||  || ||||| ||||| |||||||||||||  |||||||| | | | || |
--gtaaagcgctgtatctgattgtt--tatagtagtttttggaacat-gctcaagctc-----aacttttatggttttggcgcatagtcagaca---tctcaacactt----aatgaatatgattgcgggttt----cagGTCATCTATTTGACAGACCCAGTTGATGAGTACTTGACCCAAAACCTGACTGAGTATGAGGACAAAAAGTTCCAAAATGCTTCCAAGGACGATCTCAAGC

upper sequence: GLYMA14G40320.1 (Glycine max), 3'ss of exon 13
lower sequence: EFJ17496 (Selaginella moellendorffii), 3'ss of exon 14
gtacaatttaaattgtttgatttttattacaagtatatttgctctattatttgttcttttaaaaacatttgtctttctattctgctgagagatgatgatttaatgtcttctaaatgtattttcttttgaatttgctacagGTTATTTTCTTCACGGATCCAGTTGATGAGTACTTGATGCAATACCTGATGGATTATGAAGACAAGAAGTTCCAAAATGTGTCCAAGGAGGGTTTGAAAC
                                                                          | || || | ||  | ||| || ||   | ||      ||||  ||   |  ||         |||||||||||||||||||| ||||| |||||||| ||||  || |||||||  || |  || ||||||||| ||   ||  | |||||||| || ||||| |
-------------------------------------------------------------------------gtacttttttcctttgggataataatccgaggtgact--aatgccttggttcatg-------cgcagGTTATTTTCTTCACGGACCCAGTCGATGAGTATTTGACTCAGTACCTGACCGAGTTCGATGACAAGAAGCTCGTCAACATCTCCAAGGAAGGATTGAAGC

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|15661681|gb|BI699052.1|BI699052
EST:     AACTGGAAAACTCTCCCTTCCTTGAGCGGCTTAAGAAGAAAAATTTTGAG                         GTTATTTTCTTCACGGATCCA
genomic: AACTGGAAAACTCTCCCTTCCTTGAGCGGCTTAAGAAGAAAAATTTTGAGgtacaattta ... tttgctacagGTTATTTTCTTCACGGATCCA
EST: gi|11688292|gb|BF595968.1|BF595968
EST:     AACTGGAAAACTCTCCCTTCCTTGAGCGGCTTAAGAAGAAAAATTTTGAG                         GTTATTTTCTTCACGGATCCAGTTGATGAGTACTTGATGCAATACCTGATG
genomic: AACTGGAAAACTCTCCCTTCCTTGAGCGGCTTAAGAAGAAAAATTTTGAGgtacaattta ... tttgctacagGTTATTTTCTTCACGGATCCAGTTGATGAGTACTTGATGCAATACCTGATG
EST: gi|37995336|gb|CF806925.1|CF806925
EST:     AACTGGAAAACTCTCCCTTCCTTGAGCGGCTTAAGAAGAAAAATTTTGAG                         GTTATTTTCTTCACGGATCCAGTTGATGAGTACTTGATGCAATACCTGATG
genomic: AACTGGAAAACTCTCCCTTCCTTGAGCGGCTTAAGAAGAAAAATTTTGAGgtacaattta ... tttgctacagGTTATTTTCTTCACGGATCCAGTTGATGAGTACTTGATGCAATACCTGATG
EST: gi|193550593|gb|FK508890.1|FK508890
EST:     AACTGGAAAACTCTCCCTTCCTTGAGCGGCTTAAGAAGAAAAATTTTGAG                         GTTATTTTCTTCACGGATCCAGTTG
genomic: AACTGGAAAACTCTCCCTTCCTTGAGCGGCTTAAGAAGAAAAATTTTGAGgtacaattta ... tttgctacagGTTATTTTCTTCACGGATCCAGTTG
EST: gi|192313365|gb|FK005137.1|FK005137
EST:     AACTGGAAAACTCTCCCTTCCTTGAGCGGCTTAAGAAGAAAAATTTTGAG                         GTTATTTTCTTCACGGATCCAGTTGATGAGTACTTGATGCAATACCTGATG
genomic: AACTGGAAAACTCTCCCTTCCTTGAGCGGCTTAAGAAGAAAAATTTTGAGgtacaattta ... tttgctacagGTTATTTTCTTCACGGATCCAGTTGATGAGTACTTGATGCAATACCTGATG
EST: gi|192313364|gb|FK005136.1|FK005136
EST:     AACTGGAAAACTCTCCCTTCCTTGAGCGGCTTAAGAAGAAAAATTTTGAG                         GTTATTTTCTTCACGGATCCAGTTGATGAGTACTTGATGCAATACCTGATG
genomic: AACTGGAAAACTCTCCCTTCCTTGAGCGGCTTAAGAAGAAAAATTTTGAGgtacaattta ... tttgctacagGTTATTTTCTTCACGGATCCAGTTGATGAGTACTTGATGCAATACCTGATG
EST: gi|7925492|gb|AW831518.1|AW831518
EST:     AACTGGAAAACTCTCCCTTCCTTGAGCGGCTTAAGAAGAAAAATTTTGAG                         GTTATTTTCTTCACGGATCCAGTTGATGAGTACTTGATGCAATACCTGATG
genomic: AACTGGAAAACTCTCCCTTCCTTGAGCGGCTTAAGAAGAAAAATTTTGAGgtacaattta ... tttgctacagGTTATTTTCTTCACGGATCCAGTTGATGAGTACTTGATGCAATACCTGATG
EST: gi|208175635|gb|GD973418.1|GD973418
EST:     AACTGGAAAACTCTCCATTCCTTGAGCGGCTTAAGAAGAAAAATTTTGAG                         GTTATTTTCTTCACGGATCCAGTTGATGAATACTTGATGCAATACCTGATG
genomic: AACTGGAAAACTCTCCCTTCCTTGAGCGGCTTAAGAAGAAAAATTTTGAGgtacaattta ... tttgctacagGTTATTTTCTTCACGGATCCAGTTGATGAGTACTTGATGCAATACCTGATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgagagatgatgatttaatgtcttctaaatgtattttcttttgaatttgctacagGTTATTTTCTTCACGGATCCAGTTGATGAGTACTTGATGCAATACCTGATGGATTATGAAGACAAGAAGTTCCAAAATGTGTCCAAGGAGGGTTTGAAAC
                      ttctaaa  putative branch site (score: 2)
                         taaatgtattttcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacaatttaaattgtttgatttttattacaagtatatttgctctattatttgttcttttaaaaacatttgtctttctattctgctgagagatgatgatttaatgtcttctaaatgtattttcttttgaatttgctacagGTTATTTTCTTCACGGATCCAGTTGATGAGTACTTGATGCAATACCTGATGGATTATGAAGACAAGAAGTTCCAAAATGTGTCCAAGGAGGGTTTGAAAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG