Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagattaacattattctctcgatcctcataaattggttccattcggagtgtgtgatttagttcacttacgccgctataataataatctgattgattctaattgaaatttgcgtctcagTGAGTCACCATGGTGAGGGTTAGTGTGCTGAACGATGCTCTGAAGAGCATGTACAATGCTGAGAAAAGGGGAAAGCGCCAAGTCATGATTAGGCCATCCT

Basic information

species Glycine max
transcript GLYMA17G02200.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G02200.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G083497_T02 (Zea mays), 3'ss of exon 1
gtaagattaacattattctctcgatcctcataaattggttccattcggagtgtgtgatttagttcacttacgccgctataataataatctgattgattctaattgaaatttgcgtctcagTGAG-TCACCATGGTGAGGGTTAGTGTGCTGAACGATGCTCTGAAGAGCATGTACAATGCTGAGAAAAGGGGAAAGCGCCAAGTCATGATTAGGCCATCCT---
                 |  | | || |  ||  | | |   | | |   | |   ||     |||||    ||   | |  |    | ||||   | | | |  |  |||  ||    |  || ||| |||||||||||| |||||||| |||||||| || |||  |||||||||||| ||||| ||||| ||| | || |||||||| ||||| || |   
----------------acctttggtcgtgctacgtagatgtaaatggctatttcgaatgctactcact----ccagcacagca----tgtgatccttacaattgcatctttttgttcacgcaagGTCATCATGGTGAGGGTCAGTGTGCTCAACGATGCGCTCAAGTCCATGTACAATGCAGAGAAGAGGGGCAAGAGGCAGGTCATGATCAGGCCGTCGTCCA

upper sequence: GLYMA17G02200.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G328578_T01 (Zea mays), 3'ss of exon 1
gtaagattaacattattctctcgatcctcataaattggttccattcggagtgt---gtgatttagttcacttacgccgctataataataatctgattgattctaattgaaatttgcgtctcagTGAGTCACCATGGTGAGGGTTAGTGTGCTGAACGATGCTCTGAAGAGCATGTACAATGCTGAGAAAAGGGGAAAGCGCCAAGTCATGATTAGGCCATCCT
             | | |  |   |  |  || ||   | | | | |  || |    |||| |  ||  ||    |||  || | |    | ||| ||  |||  |||   ||   ||   |    | || |||||||||||| |||||||| || |||||||| |||  ||||||||||||||| || |  || || || || |||||||| |||||     
-------------tgtacctttagttgtgttacataaatgcaaatggctgtttcctctgatattcttgtctgtgtccggcatgagacccttatgactgtatctctttg---ttcagGT---AAAAGGACAGCATGGTGAGGGTCAGTGTGCTCAATGATGCTCTCAAGTCCATGTACAATGCTGAAAAGATAGGGAAACGTCAGGTCATGATCAGGCCG----

upper sequence: GLYMA17G02200.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G018228_T01 (Zea mays), 3'ss of exon 1
gtaagattaacattattctctcgatcctcataaattggttccattcggagtgtgtgatttagttcacttacgccgctataataataatctgattgattctaattgaaatttgcgtctcagTGA---GTCACCATGGTGAGGGTTAGTGTGCTGAACGATGCTCTGAAGAGCATGTACAATGCTGAGAAAAGGGGAAAGCGCCAAGTCATGATTAGGCCATCCT------------------------------------------
                                                                                                         |  | |  ||    || |   | || |||||||||||| || ||||| || |||||||| |||  ||||||||||||||| || |  || || || || |||||||| ||||| || |                                          
--------------------------------------------------------------------------------------------------------tatctctttgttcaggtaaaaggacagcatggtgagggtcagcgtgctcaatgatgctctcaagtccatgtacaatgctgaaaagatagggaaacgtcagGTCATGATCAGGCCGTCATCCAAGGTGATCATCAAGTTCCTGACGGTCATGCAGCGCCATG

upper sequence: GLYMA17G02200.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G018228_T03 (Zea mays), 3'ss of exon 1
gtaagattaacattattctctcgatcctcataaattggttccattcggagtgtgtgatttagttcacttacgccgctataataataatctgattgattctaattgaaatttgcgtctcagTGAGTCACCATGGTGAGGGTTAGTGTGCTGAACGATGCTCTGAAGAGCATGTACAATGCTGAGAAAAGGGGAAAGCGCCAAGTCATGATTAGGCCATCCT
             | | |  | | |  |  || ||   | | | | |  || |    |    |||   |  |   ||   || | |  || |    |     |     ||   ||   |    | || |||||||||||| || ||||| || |||||||| |||  ||||||||||||||| || |  || || || || |||||||| |||||     
-------------tgtacctttggttgtgttacataaatgcaaatggctgtttcctctgatattcttgtctgtgtctggcatgagacccttacaactgtatctctttgttcagGT---AAAAGGACAGCATGGTGAGGGTCAGCGTGCTCAATGATGCTCTCAAGTCCATGTACAATGCTGAAAAGATAGGGAAACGTCAGGTCATGATCAGGCCG----

upper sequence: GLYMA17G02200.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G018228_T04 (Zea mays), 3'ss of exon 1
gtaagattaacattattctctcgatcctcataaattggttccattcggagtgtgtgatttagttcacttacgccgctataataataatctgattgattctaattgaaatttgcgtctcagTGAGTCACCATGGTGAGGGTTAGTGTGCTGAACGATGCTCTGAAGAGCATGTACAATGCTGAGAAAAGGGGAAAGCGCCAAGTCATGATTAGGCCATCCT--------
                      |     |||||||         | |     | |||| |  ||  ||    | |  || | |    |   | ||  |||  |||   ||   ||   |    | || |||||||||||| || ||||| || |||||||| |||  ||||||||||||||| || |  || || || || |||||||| ||||| || |        
---------------------tgtgttacataaatgcaaatggct-gtttcctctgatattcttgtctgtgtctggcatgagacccttacaactgtatctctttg---ttcaggt---aaaaggacagCATGGTGAGGGTCAGCGTGCTCAATGATGCTCTCAAGTCCATGTACAATGCTGAAAAGATAGGGAAACGTCAGGTCATGATCAGGCCGTCATCCAAGGTG

upper sequence: GLYMA17G02200.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv13s0019g00530.t01 (Vitis vinifera), 3'ss of exon 2
gtaagattaacattattct-ctcgatcctcataaattggttccattcggagtgtgtgatttagttcacttacgccgctataataataatctgattgattctaattgaaatttgc----gtctcagTGAGTCACCATGGTGAGGGTTAGTGTGCTGAACGATGCTCTGAAGAGCATGTACAATGCTGAGAAAAGGGGAAAGCGCCAAGTCATGATTAGGCCATCCT
             | |||| || |||    ||   ||  |   |||     |||| |||||  |    | |      | |   | || | |||   |  |   ||  | ||||     | ||   | ||| |  |||||||| |||||||| ||||| |||||||| ||||||||||||||||| |||||  | || ||||| || || ||||| |         
--------gtttctgttctgcttgatttctat---tttttcttatttatcatgtgggatttcatg---tcaaagttttgtgcaagtagtttgac--aacccttttatattttgtagCGGCCTTGTTTAGTGAAGATGGTGAGAGTTAGTGTCCTGAATGATGCTCTCAAGAGCATGTACAATGCAGAGAAGCGTGGGAAGCGACAGGTGATGATCA---------

upper sequence: GLYMA17G02200.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv08s0040g02460.t01 (Vitis vinifera), 3'ss of exon 1
gtaagattaacattattctctcgatcctcataaattggttccattcggagtgtgtgatttagttcacttacgccgctataataataatctgattgattctaattgaaatttgcgtctcagTGAGTCACCATGGTGAGGGTTAGTGTGCTGAACGATGCTCTGAAGAGCATGTACAATGCTGAGAAAAGGGGAAAGCGCCAAGTCATGATTAGGCCATCCT
        | |  | ||  || |||  | |||  |   | ||   |    | ||  || |   |     ||   | | | | | | | ||  ||| ||    ||   |   || | ||  |  |  |  |||||||| || |||||  |||| |||||||| ||||||||||| ||||| |||||  |||||||||| || || ||||| |         
-------catctgtgttggct-gatagttatatctccctccctccctccctctgaaatatgtcttgaagacatggttttca-attgaacttcttgctttacctttgcagCAGCCTTTCTTT--GCAAGGATGGTGAGAGTCAGTGTCTTGAATGATGCTCTAAAGAGCATGTATAATGCAGAGAAGCGGGGAAAGCGACAGGTTATGATCA---------

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|298175254|gb|HO018135.1|HO018135
EST:     AGCACTGGCGCAGCTACCCTGAGGCTTCCCTTCTCTTCTCTTCTCTGTCG                         TGAGTCACCATGGTGAGGGTTAGTGTGCTGAACGATGCTCTGAAGAGCATG
genomic: AGCACTGGCGCAGCTACCCTGAGGCTTCTCTTCTCTTCTCTTCTCTGTCGgtaagattaa ... tgcgtctcagTGAGTCACCATGGTGAGGGTTAGTGTGCTGAACGATGCTCTGAAGAGCATG
EST: gi|58024827|gb|CX711568.1|CX711568
EST:     CTCTTCTCTTCTCTGTCG                         TGAGTCACCATGGTGAGGGTTAGTGTGCTGAACGATGCTCTGAAGAGCATG
genomic: CTCTTCTCTTCTCTGTCGgtaagattaa ... tgcgtctcagTGAGTCACCATGGTGAGGGTTAGTGTGCTGAACGATGCTCTGAAGAGCATG
EST: gi|31464244|gb|CD406272.1|CD406272
EST:     TCTCTTCTCTGTCG                         TGAGTCACCATGGTGAGGGTTAGTGTGCTGAACGATGCTCTGAAGAGCATG
genomic: TCTCTTCTCTGTCGgtaagattaa ... tgcgtctcagTGAGTCACCATGGTGAGGGTTAGTGTGCTGAACGATGCTCTGAAGAGCATG
EST: gi|193342091|gb|FK307653.1|FK307653
EST:     CTCTTCTCTTCTCTGTCG                         TGAGTCACCATGGTGAGGGTTAGTGTGCTGAACGATGCTCTGAAGAGCATG
genomic: CTCTTCTCTTCTCTGTCGgtaagattaa ... tgcgtctcagTGAGTCACCATGGTGAGGGTTAGTGTGCTGAACGATGCTCTGAAGAGCATG
EST: gi|208112392|gb|GD913721.1|GD913721
EST:     CTTCTCTGTCG                         TGAGTCACCATGGTGAGGGTTAGTGTGCTGAACGATGCTCTGAAGAGCATG
genomic: CTTCTCTGTCGgtaagattaa ... tgcgtctcagTGAGTCACCATGGTGAGGGTTAGTGTGCTGAACGATGCTCTGAAGAGCATG
EST: gi|14259906|gb|BG882814.1|BG882814
EST:     CTTCTCTTCTCTGTCG                         TGAGTCACCATGGTGAGGGTTAGTGTGCTGAACGATGCTCTGAAGAGCATG
genomic: CTTCTCTTCTCTGTCGgtaagattaa ... tgcgtctcagTGAGTCACCATGGTGAGGGTTAGTGTGCTGAACGATGCTCTGAAGAGCATG
EST: gi|208031659|gb|GD831209.1|GD831209
EST:     CTCTTCTCTGTCG                         TGAGTCACCATGGTGAGGGTTAGTGTGCTGAACGATGCTCTGAAGAGCATG
genomic: CTCTTCTCTGTCGgtaagattaa ... tgcgtctcagTGAGTCACCATGGTGAGGGTTAGTGTGCTGAACGATGCTCTGAAGAGCATG
EST: gi|298174142|gb|HO017478.1|HO017478
EST:     AGCACTGGCGCAGCTACCCTGAGGCTTCTCTTCTCCTCTCTTCTCTGTCG                         TGAGTCACCATGGTGAGGGTTAGTGTGCTGAACGATGCTCTGAAGAGCATG
genomic: AGCACTGGCGCAGCTACCCTGAGGCTTCTCTTCTCTTCTCTTCTCTGTCGgtaagattaa ... tgcgtctcagTGAGTCACCATGGTGAGGGTTAGTGTGCTGAACGATGCTCTGAAGAGCATG
EST: gi|4260154|gb|AI416650.1|AI416650
EST:     TCTCTTCTCTGTCG                         TGAGTCACCATGGTGAGGGTTAGTGTGCTGAACGATGCTCTGAAGAGCATG
genomic: TCTCTTCTCTGTCGgtaagattaa ... tgcgtctcagTGAGTCACCATGGTGAGGGTTAGTGTGCTGAACGATGCTCTGAAGAGCATG
EST: gi|12774192|gb|BG239119.1|BG239119
EST:     TCTTCTCTTCTCTGTCG                         TGAGTCACCATGGTGAGGGTTAGTGTGCTGAACGATGCTCTGAAGAGCATG
genomic: TCTTCTCTTCTCTGTCGgtaagattaa ... tgcgtctcagTGAGTCACCATGGTGAGGGTTAGTGTGCTGAACGATGCTCTGAAGAGCATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acttacgccgctataataataatctgattgattctaattgaaatttgcgtctcagTGAGTCACCATGGTGAGGGTTAGTGTGCTGAACGATGCTCTGAAGAGCATGTACAATGCTGAGAAAAGGGGAAAGCGCCAAGTCATGATTAGGCCATCCT
                               ttctaat  putative branch site (score: 2)
           tataataataatctga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagattaacattattctctcgatcctcataaattggttccattcggagtgtgtgatttagttcacttacgccgctataataataatctgattgattctaattgaaatttgcgtctcagTGAGTCACCATGGTGAGGGTTAGTGTGCTGAACGATGCTCTGAAGAGCATGTACAATGCTGAGAAAAGGGGAAAGCGCCAAGTCATGATTAGGCCATCCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG