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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGCCAACAGCTCAAAGACATGGAAGGAAGTTTGCTTTGCTTGTGTTGATGCAGAGGAGTTTCGTTTGGCCCAAATTTGTGGACTAAACATTATTATTCAGgtaatatgttgatttcagttttttgatgaactgtgtgtgcccatgcacacgcgtgcgtgtatatataggaacgtttttcttcatttctgatgcagaccga...

Basic information

species Glycine max
transcript GLYMA14G06340.2
intron # 24
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA14G06340.1 (Glycine max), 5'ss of exon 24
lower sequence: LOC_Os11g01380.1 (Oryza sativa), 5'ss of exon 24
AGCCAACAGCTCAAAGACATGGAAGGAAGTTTGCTTTGCTTGTGTTGATGCAGAGGAGTTTCGTTTGGCCCAAATTTGTGGACTAAACATTATTATTCAGgta-atatgttgatttcagttttttgatgaactgtgtgtgcccatgcacacgcgtgcgtgtatatataggaacgtttttcttcatttctgatgcagaccga
 || |||||  | || |||||||||||||| |||||||||||||||||||| |||||||| ||  | || ||||| ||||| || || |||||| | |||||| ||||   |     |  | || ||   |     | |  |  | ||      | | | | || ||       | |  |  | ||| |  |  ||     
GGCTAACAGTGCTAAAACATGGAAGGAAGTCTGCTTTGCTTGTGTTGATGCCGAGGAGTTCCGGCTAGCACAAATATGTGGTCTCAATATTATTGTCCAGgtatatatacaggagcaacctgttagaactaaaacatatttcagtacaagtcttttcttatctagattt---tttctaacacccttttttgtatag-----

upper sequence: GLYMA14G06340.1 (Glycine max), 5'ss of exon 24
lower sequence: LOC_Os12g01390.1 (Oryza sativa), 5'ss of exon 24
AGCCAACAGCTCAAAGACATGGAAGGAAGTTTGCTTTGCTTGTGTTGATGCAGAGGAGTTTCGTTTGGCCCAAATTTGTGGACTAAACATTATTATTCAGgta-atatgttgatttcagttttttgatgaactgtgtgtgcccatgcacacgcgtgcgtgtatatataggaacgtttttcttcatttctgatgcagaccga
 || |||||  | || |||||||||||||| |||||||||||||||||||| |||||||| ||  | || ||||| ||||| || || |||||| | |||||| ||||   |     |  | || ||   |     | |  |  | ||      | | | | || ||     |      | |  ||| || |  ||     
GGCTAACAGTGCTAAAACATGGAAGGAAGTCTGCTTTGCTTGTGTTGATGCCGAGGAGTTCCGGCTAGCACAAATATGTGGTCTCAATATTATTGTCCAGgtatatatacaggaccaacctgttagaactaaaacatatttcagtacaagtcttttcttatctagattttttctaacacccttttttttg-tatag-----

upper sequence: GLYMA14G06340.1 (Glycine max), 5'ss of exon 24
lower sequence: GRMZM2G325285_T01 (Zea mays), 5'ss of exon 14
AGCCAACAGCTCAAAGACATGGAAGGAAGTTTGCTTTGCTTGTGTTGATGCAGAGGAGTTTCGTTTGGCCCAAATTTGTGGACTAAACATTATTATTCAGgtaatatgttgatttcagttttttgatgaactgtgtgtg----cccatgcacacgcgtgcgtgtatatataggaac--gtttttcttcatttctgatgcagaccga--------
 || |||||  | || ||||||||||| || ||||||||||||||||| || |||||||| ||| | || ||||||||||| || || |||||||||||||||      |     ||  |  || || |  | | |||     |   |  | |   | || | |||   || || |   |||||  |||| |||| |   |             
GGCTAACAGTGCCAAAACATGGAAGGAGGTCTGCTTTGCTTGTGTTGACGCCGAGGAGTTCCGTCTTGCACAAATTTGTGGTCTCAATATTATTATTCAGgtatacaagtaggagcacatacttaataatttttttgtagtatctgctttatagcagagcttctatcactatgatctatttttttctcatatctgcttttgtatttttgtttag

upper sequence: GLYMA14G06340.1 (Glycine max), 5'ss of exon 24
lower sequence: GRMZM2G111355_T02 (Zea mays), 5'ss of exon 5
AGCCAACAGCTCAAAGACATGGAAGGAAGTTTGCTTTGCTTGTGTTGATGCAGAGGAGTTTCGTTTGGCCCAAATTTGTGGACTAAACATTATTATTCAGgtaatatgttgatttcagttttttgatgaactgt-gt-gtgccca-tgcacacgcgtgcgtgtatatataggaacg--tttttcttcatttctgatgcagaccga--------------------------------------------------------------------------
 || |||||  | || ||||||||| | || ||||||||||||||||| || |||||||| ||| | || ||||||||||| || || |||||||||||||||      |     ||  |  || || |  | | || ||  |   |  | |   | || | |||   || || |   |||||  |||| |||| |   |                                                                               
GGCTAACAGTGCCAAAACATGGAAGAAGGTCTGCTTTGCTTGTGTTGACGCCGAGGAGTTCCGTCTTGCACAAATTTGTGGTCTCAATATTATTATTCAGgtatacaagtaggagcacatacttaataattttttgtagtatctgctttatagcagagcttctatcactatgatctatttttttctcatatctgcttttgtatttttgtttaggtcgatgatgccttccttacaaagtaaatggtcctctccttgcccccagttatgatctgtttatag

upper sequence: GLYMA14G06340.1 (Glycine max), 5'ss of exon 24
lower sequence: GRMZM5G822591_T01 (Zea mays), 5'ss of exon 1
AGCCAACAGCTCAAAGACATGGAAGGAAGTTTGCTTTGCTTGTGTTGATGCAGAGGAGTTTCGTTTGGCCCAAATTTGTGGACTAAACATTATTATTCAGgtaatatgttgatttcagttttttgatgaactgt-gt-gtgccca-tgcacacgcgtgcgtgtatatataggaacg----tttttcttcatttctgatgcagaccga--------
 || |||||  | || ||||||||||| || ||||||||||||||||| || |||||||| ||| | || ||||||||||| || || |||||| ||||||||      |     ||  |  ||||| |  | | || ||  |   |  | |   | || | |||   |  || |     |||||  |||| |||| |   |             
GGCTAACAGTGCCAAAACATGGAAGGAGGTCTGCTTTGCTTGTGTTGACGCCGAGGAGTTCCGTCTTGCACAAATTTGTGGTCTCAATATTATTGTTCAGgtatacaagtaggagcacatacttgataattttttgtagtatctgctttatagcagagcttctatcactgtgatctatttttttttctcatatctgcttttgtatttttgtttag

upper sequence: GLYMA14G06340.1 (Glycine max), 5'ss of exon 24
lower sequence: GRMZM2G057576_T02 (Zea mays), 5'ss of exon 22
AGCCAACAGCTCAAAGACATGGAAGGAAGTTTGCTTTGCTTGTGTTGATGCAGAGGAGTTTCGTTTGGCCCAAATTTGTGGACTAAACATTATTATTCAGgtaatatgttgatttcagttttttgatgaactgtgtgtgcccatgcacacgcgtgcgtgtatatataggaacgtttttctt--catttctgatgcagaccga------
 || |||||  | || ||||||||||| || ||||||||||||||||| || |||||||| ||| | || ||||| ||||| || || |||||| ||||||||      |         |  |||||||  | |   |   | |              || | |||   |   || ||  |  |||  ||| |               
GGCTAACAGTGCTAAAACATGGAAGGAGGTCTGCTTTGCTTGTGTTGACGCGGAGGAGTTCCGTCTTGCACAAATATGTGGTCTCAATATTATTGTTCAGgtatacaagtaggagggcatacttgatgatttttccctagtctttgttttattgcaaagtttctatgatatatttctttctgacatacctgctcttttttttgtttag

upper sequence: GLYMA14G06340.1 (Glycine max), 5'ss of exon 24
lower sequence: GRMZM2G395549_T01 (Zea mays), 5'ss of exon 9
------------------------------------------------------------------------AGCCAACAGCTCAAAGACATGGAAGGAAGTTTGCTTTGCTTGTGTTGATGCAGAGGAGTTTCGTTTGGCCCAAATTTGTGGACTAAACATTATTATTCAGgta-atatgttgat-------ttcagttttttgatgaactgtgtgtgcccatgcacacgcgtgcgtgtatatatagg-aacgtttttcttcatttctgatgcagaccga
                                                                         || |||||  | || || |||||||| || ||||||||||||||||| |  |||||||| ||| | || ||||| ||||| || || |||||| ||||| || | | || |          |   |||||   |   || ||| |        |    |     | ||| | |     || |   |  || ||| |  |  ||     
AAACTGGGCTAAGCTGGCTGTTACCCTGGTTAAGCTGAAGCAATACCAAGGTGCTGTGGATGCTGCTCGCAAGGCTAACAGTGCTAAAACGTGGAAGGAGgtctgctttgcttgtgttgacgtggaggagttccgtcttgcacaaatatgtggtctcaatattattgttcagatatacaagtaggagggcatacttgatttttccctattctttgttttattgcaaagtttctatgatatatttctttctgacatagctgctctttttttgtttag-----

upper sequence: GLYMA14G06340.1 (Glycine max), 5'ss of exon 24
lower sequence: AT3G11130.1 (Arabidopsis thaliana), 5'ss of exon 24
AGCCAACAGCTCAAAGACATGGAAGGAAGTTTGCTTTGCTTGTGTTGATGCAGAGGAGTTTCGTTTGGCCCAAATTTGTGGACTAAACATTATTATTCAGgta---atatgttgatttcagttttttgatgaactgtgtgtgcccatgcacacgcgtgcgtgtatatataggaacgtttttcttcatttctgatgcagaccga---
||| |||||  ||||||||||||||||||| |||||||||||||||||||| ||||| || ||  |||| ||||| |||||||| |||||||| || |||||    | ||      | |   ||   ||  || | | | |    ||      |  |   | |  || | | |  |  ||| |  | |  |  ||       |   
AGCAAACAGTGCAAAGACATGGAAGGAAGTCTGCTTTGCTTGTGTTGATGCTGAGGAATTCCGACTGGCTCAAATCTGTGGACTTAACATTATCATACAGgtggataaataacagatcctagttcccgagaaagttt-tttagttataattgggtttcaatttcaattttgta-tgcctttttgtaatatttttgtgctttaatag

upper sequence: GLYMA14G06340.1 (Glycine max), 5'ss of exon 24
lower sequence: AT3G08530.1 (Arabidopsis thaliana), 5'ss of exon 24
AGCCAACAGCTCAAAGACATGGAAGGAAGTTTGCTTTGCTTGTGTTGATGCAGAGGAGTTTCGTTTGGCCCAAATTTGTGGACTAAACATTATTATTCAGgtaatatgttgatttcagttttttgatgaact-------gtgtgtgcccatgcacacgcgtgcgtg-tatatataggaacgtttttc-ttcatttctgatgcagaccga-------------
||| |||||  ||||||||||||||||||| ||||||||||| |||||||| ||||| || || ||||| ||||| ||||| || |||||||| |||||||| |     |||| | | |      |  |  |           ||         ||   |||  || | ||||    || || | || || |||||      |  |                
AGCAAACAGTGCAAAGACATGGAAGGAAGTCTGCTTTGCTTGCGTTGATGCTGAGGAATTCCGGTTGGCTCAAATATGTGGTCTTAACATTATCATTCAGgtgaatacctgatcttactgagcacaaaagtttccccttacaggttttagatttcaattgtgtatgctttatagcccaatgtatctcatttatttcctggttaatcttttggtgcttaatag

upper sequence: GLYMA14G06340.1 (Glycine max), 5'ss of exon 24
lower sequence: Vv13s0067g01290.t01 (Vitis vinifera), 5'ss of exon 24
AGCCAACAGCTCAAAGACATGGAAGGAAGTTTGCTTTGCTTGTGTTGATGCAGAGGAGTTTCGTTTGGCCCAAATTTGTGGACTAAACATTATTATTCAGgtaatatgttgatttc-agttttttgatgaactgtgtgtgcccatgcacacgcgtgcgtgtatatataggaacgtttttcttcatttctgatgcagaccga-------------------------------------------------------
 || ||||||||||||||||||||||| |||||||||||||||||||||||||| ||||| || || || || || ||||| || ||||||||||| |||||||| | ||| |||  |    |  | ||   ||  |     |||  | | |  |   ||| |  | |    | | | | |    |||  |  |  |                                                           
GGCTAACAGCTCAAAGACATGGAAGGAGGTTTGCTTTGCTTGTGTTGATGCAGAAGAGTTCCGCTTAGCTCAGATATGTGGTCTCAACATTATTATACAGgtaatgtattgttttttaagggtagggtgggatg-ataacatcataaaaatggattgttgtttcaaaatttccttctgtatgagcttccaagcctaatgttttcgcttttttattatcaggtctaatttcctagtgtattgatttgaattttgtag

upper sequence: GLYMA14G06340.1 (Glycine max), 5'ss of exon 24
lower sequence: PP1S270_53V6.1 (Physcomitrella patens), 5'ss of exon 25
AGCCAACAGCTCAAAGACATGGAAGGAAGTTTGCTTTGCTTGTGTTGATGCAGAGGAGTTTCGTTTGGCCCAAATTTGTGGACTAAACATTATTATTCAGgtaatatgttgatttcagttttttgatgaactgtgtgtgccc-atgcacacgcgtgcgtgtatatataggaacgtttttc-ttcatttctgatgcagaccga-------------------------
||| || ||||| || ||||||| ||||||||| |||||||| || ||| | ||||| ||||| ||||| ||||||||||| || || || |||||||||||| |   ||  |     |  | |     || |  | |     ||| |  |   |   |  |     |  | | |   |  ||||||| |||    ||  ||                         
AGCAAATAGCTCTAAAACATGGAGGGAAGTTTGTTTTGCTTGCGTGGATACCGAGGAATTTCGGTTGGCTCAAATTTGTGGCCTTAAGATCATTATTCAGgtattggcttagtcaacataatgtatcatacagaatttaatggatgaaacctgatatcttcaggatcaacaccatgcctagttcatttttgaatttgaatgaaatgggctttttgtggctgtggaag

upper sequence: GLYMA14G06340.1 (Glycine max), 5'ss of exon 24
lower sequence: PP1S147_10V6.1 (Physcomitrella patens), 5'ss of exon 12
AGCCAACAGCTCAAAGACATGGAAGGAAGTTTGCTTTGCTTGTGTTGATGCAGAGGAGTTTCGTTTGGCCCAAATTTGTGGACTAAACATTATTATTCAGgtaatatgttgatttcagttttttgatgaactgtgtgtgcccatgcacacgc-gtgcgtgtatatataggaacgtttttcttcatttctgatgcagaccga--
 ||||| ||| ||  ||||||||||||||| |||||||||||||| || || || ||||| ||  |||| ||||||||||| || ||  ||||| | |||||| |   | | |||| | | ||  ||        |   | ||||      |   ||    ||   |   |    | |  |   || || || |  || ||  
GGCCAATAGCGCACGGACATGGAAGGAAGTCTGCTTTGCTTGTGTGGACGCCGAAGAGTTCCGCCTGGCTCAAATTTGTGGTCTCAATGTTATTGTCCAGgta-tggataggtttctgctgttacattttgcaattagcctcatgattttactacgcaaccatgcttttcattactatcatatgtt-ctaat-cgtactgaag

upper sequence: GLYMA14G06340.1 (Glycine max), 5'ss of exon 24
lower sequence: PP1S7_102V6.1 (Physcomitrella patens), 5'ss of exon 12
AGCCAACAGCTCAAAGACATGGAAGGAAGTTTGCTTTGCTTGTGTTGATGCAGAGGAGTTTCGTTTGGCCCAAATTTGTGGACTAAACATTATTATTCAGgtaatatgttgatttcagttttttgatgaactgtgtgtgcccatgcacacgcgtgcgtgtatatataggaacgtttttcttcatt--tctgatgcagaccga-----
 ||||||||  ||  ||| ||||||||||| |||||||||||||| ||||| || ||||||||| |||| ||||||||||| || ||  ||||| | ||||||  |      ||  | |  || ||    |  |  ||   | ||      |       | | |||        ||| ||| |||  | || ||      ||     
GGCCAACAGTGCACGGACGTGGAAGGAAGTCTGCTTTGCTTGTGTGGATGCCGAAGAGTTTCGTCTGGCTCAAATTTGTGGTCTCAATGTTATTGTCCAGgtatgaaaagccttctaatgcttcgacatccgatcagttttcttgagttttc-------tgtttatcaaggttctttccttgattagtttgttgtttcatgatgtgc

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|6912831|gb|AW394315.1|AW394315
EST:     CAGAGGAGTNTCGTTTGGCCCAAATTTGTGGACTAAACATTATTATTCAG                         GTGGATGACTTGGAAGAAGTCAGTGAATATTACCAAAACAGAGGTTGCTTC
genomic: CAGAGGAGTTTCGTTTGGCCCAAATTTGTGGACTAAACATTATTATTCAGgtaatatgtt ... aatttcatagGTGGATGACTTGGAAGAAGTCAGTGAATATTACCAAAACAGAGGTTGCTTC




















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGCCAACAGCTCAAAGACATGGAAGGAAGTTTGCTTTGCTTGTGTTGATGCAGAGGAGTTTCGTTTGGCCCAAATTTGTGGACTAAACATTATTATTCAGgtaatatgttgatttcagttttttgatgaactgtgtgtgcccatgcacacgcgtgcgtgtatatataggaacgtttttcttcatttctgatgcagaccga

- - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG