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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCCTGAACGTACAGGTAGTGTAACAATTGTTGGTGCTGTTTCGCCACCTGGAGGAGATTTCTCAGACCCTGTGACATCTGCAACCCTCAGCATAGTTCAGgtaaaactattctttcaaatatggttaaaatgggtaactgcctgcaaagtaagtcagcctaaggttgtcttgactaattcccgcaaattgttaaaaccct...

Basic information

species Glycine max
transcript GLYMA07G00430.1
intron # 14
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G00430.1 (Glycine max), 5'ss of exon 14
lower sequence: LOC_Os06g45120.1 (Oryza sativa), 5'ss of exon 13
CCCTGAACGTACAGGTAGTGTAACAATTGTTGGTGCTGTTTCGCCACCTGGAGGAGATTTCTCAGACCCTGTGACATCTGCAACCCTCAGCATAGTTCAGgtaaaactattctttcaaatatggttaaaatgggtaactgcctgcaaagtaagtcagcctaaggttgtcttgactaattcccgcaaattgttaaaaccct--
 || || || ||||| ||||| ||||||||||||||||| || ||||||||||| ||||| ||||| ||||| || |||||||| || || || || |||||||    | |  |  | ||      ||  |  | |      |   ||     ||   ||     |   |||  | ||   |  || |  |   ||      
TCCAGATCGGACAGGCAGTGTCACAATTGTTGGTGCTGTCTCTCCACCTGGAGGTGATTTTTCAGATCCTGTTACCTCTGCAACTCTTAGTATTGTGCAGgtaaggaaactgct--agattaatccaacctttgaattaaattttcaaacctttctaactgcatgttcattgtttgataatcttaactcctctcaattgcag

upper sequence: GLYMA07G00430.1 (Glycine max), 5'ss of exon 14
lower sequence: LOC_Os02g07870.1 (Oryza sativa), 5'ss of exon 13
CCCTGAACGTACAGGTAGTGTAACAATTGTTGGTGCTGTTTCGCCACCTGGAGGAGATTTCTCAGACCCTGTGACATCTGCAACCCTCAGCATAGTTCAGgtaa---aactattctttcaaatatggttaaaatgggtaactgcctgcaaagtaagtcagcctaaggttgtcttgactaattcccgcaaattgttaaaaccct
 ||  ||||    || ||||| |||||||| || ||||| || |||||||| || ||||| ||||| ||||| || ||||||||||| || || ||||||||||   | |   |   ||    ||| |||| |  | | |  |  | ||  ||   | | ||  | ||| |  |   ||                        
TCCAAAACGGGACGGAAGTGTTACAATTGTAGGGGCTGTCTCTCCACCTGGTGGTGATTTTTCAGATCCTGTTACCTCTGCAACCCTTAGTATTGTTCAGgtaaggaagcagctaagtctgtcatgattaataatgtttatcgttt-cagtgttgttaaaccacatgttcttgtttgtag-----------------------

upper sequence: GLYMA07G00430.1 (Glycine max), 5'ss of exon 14
lower sequence: GRMZM2G421857_T02 (Zea mays), 5'ss of exon 13
CCCTGAACGTACAGGTAGTGTAACAATTGTTGGTGCTGTTTCGCCACCTGGAGGAGATTTCTCAGACCCTGTGACATCTGCAACCCTCAGCATAGTTCAGgtaaaactattctttcaaatatggttaaaatgggt-aactgcctgcaaagtaagtcagcctaaggttgtcttgactaattcccgcaaattgttaaaaccct---------------------
 || ||  | |  || ||||| ||||||||||| ||||| || || ||||| || ||||| ||||||||||| || || ||||||||||| || |||||||||| |  |  ||  |||||    | || ||   | |     |||   | ||   |||||| |  ||  |     |  ||    |||  | ||||| |                        
TCCAGACAGGAATGGCAGTGTCACAATTGTTGGAGCTGTCTCTCCTCCTGGTGGTGATTTTTCAGACCCTGTTACCTCCGCAACCCTCAGTATTGTTCAGgtaaga--aggctgccaaattacttcaatatacttcagtcctctgatcattagtccagcctga--tttacagcgtttgttgtttcaatatattaaatcatatgctgctctttttttttgcag

upper sequence: GLYMA07G00430.1 (Glycine max), 5'ss of exon 14
lower sequence: GRMZM2G128877_T02 (Zea mays), 5'ss of exon 13
CCCTGAACGTACAGGTAGTGTAACAATTGTTGGTGCTGTTTCGCCACCTGGAGGAGATTTCTCAGACCCTGTGACATCTGCAACCCTCAGCATAGTTCAGgtaaaactattctttcaaatatggttaaaatgggtaactgcctgcaaagtaagtcagcctaaggttgtcttgacta--attcccgcaaattgttaaaaccct----------------
 || ||  | || || ||||| ||||||||||| || || || || || || || ||||| ||||||||||| || |||||||||||||| || |||||||||| ||    ||  ||| ||    |  |||   | | | ||   |   |  |||   |     ||    ||  |    || |   | ||||||||| |                   
TCCAGACAGGACTGGCAGTGTCACAATTGTTGGAGCCGTCTCTCCTCCAGGTGGTGATTTTTCAGACCCTGTTACCTCTGCAACCCTCAGTATTGTTCAGgtaagacgg--ctgccaattac---ttcaatacttcagtcccccaatcattggtccatcctgatttacagtgtttgttgtttcaatatattgttaaatcatgtgctgcttttttgcag

upper sequence: GLYMA07G00430.1 (Glycine max), 5'ss of exon 14
lower sequence: AT1G78900.2 (Arabidopsis thaliana), 5'ss of exon 14
CCCTGAACGTACAGGTAGTGTAACAATTGTTGGTGCTGTTTCGCCACCTGGAGGAGATTTCTCAGACCCTGTGACATCTGCAACCCTCAGCATAGTTCAGgtaa-------------aactattct------ttcaaatatggttaaaatgg--gtaactgcctgcaaag-taagtcagcctaaggttgtcttgactaattcccgcaaatt-----gttaaaaccct-------------------------------------------------------------
 || |||||||  || ||||| |||||||||||||| |||||||| ||||||||||| || ||||| |||||||| || |||||||| || || || ||||| |               ||  |        ||| | | | | | | || |  |||  ||   |   || | |  |||     | ||   || |  |  | ||||| | |      || || |  |                                                             
ACCAGAACGTAACGGAAGTGTTACAATTGTTGGTGCAGTTTCGCCTCCTGGAGGAGACTTTTCAGATCCTGTGACTTCAGCAACCCTTAGTATTGTGCAGgtgattatttggttcatgtctgcttccctatcttccattgtagattacatagtcgtatatgttggttgagatgaaccagatggtgtttagttttag-atctgccgcagactcgtatatttaagcattttttttctccactttgaaatgcttactcttccattctggttgtttctcttttcttctgcag

upper sequence: GLYMA07G00430.1 (Glycine max), 5'ss of exon 14
lower sequence: Vv09s0054g00890.t01 (Vitis vinifera), 5'ss of exon 14
CCCTGAACGTACAGGTAGTGTAACAATTGTTGGTGCTGTTTCGCCACCTGGAGGAGATTTCTCAGACCCTGTGACATCTGCAACCCTCAGCATAGTTCAGgtaaaactattctttcaaatatggtt---aaaatgggtaactgcctgcaaa---gtaagtcagcctaaggttgtcttgactaattcccgcaaattgttaaaaccct
 || |||||||  |||||||| ||||||||||| ||||| || || ||||||||||||||||| || ||||||||||||||||| |||||||| || ||||||||  ||   ||    ||     |   || ||    |  |  ||   ||   |||  |  |   | |||    ||   ||||      ||| || ||  |    
ACCAGAACGTAACGGTAGTGTCACAATTGTTGGGGCTGTGTCTCCTCCTGGAGGAGATTTCTCTGATCCTGTGACATCTGCAACTCTCAGCATTGTCCAGgtaaagataaaattctgtatgcatcttctaatattaaaatgtagctattaatacgtatattggtgaagggtcaaattt-ttaatg--tagaaaatgatagcat---

upper sequence: GLYMA07G00430.1 (Glycine max), 5'ss of exon 14
lower sequence: Vv04s0008g02580.t01 (Vitis vinifera), 5'ss of exon 14
CCCTGAACGTACAGGTAGTGTAACAATTGTTGGTGCTGTTTCGCCACCTGGAGGAGATTTCTCAGACCCTGTGACATCTGCAACCCTCAGCATAGTTCAGgtaaaa-ctattctttcaaatatggttaaaatgggtaactgcctgcaaagtaagtcagcctaaggttgtcttgactaattcccgcaaattgttaaaaccct
 || ||||| ||||||||||| || ||||| ||||| ||||| ||||| || |||||||| ||||| || |||||||| || || || || || || |||||||   | |   |||| |  ||  | |   | |   | | |  |     | ||| | |   |  | ||        |  |  | ||| | |   | | ||
GCCAGAACGCACAGGTAGTGTCACCATTGTGGGTGCAGTTTCTCCACCAGGTGGAGATTTTTCAGATCCAGTGACATCAGCTACACTTAGTATTGTCCAGgtaatctccaaattttccagcattttcatttttgcccatttcacgtctcatgagt-aacaacatttagttaaaggagacacaggaaaagtttcctagcact

upper sequence: GLYMA07G00430.1 (Glycine max), 5'ss of exon 14
lower sequence: PP1S44_102V6.1 (Physcomitrella patens), 5'ss of exon 14
CCCTGAACGTACAGGTAGTGTAACAATTGTTGGTGCTGTTTCGCCACCTGGAGGAGATTTCTCAGACCCTGTGACATCTGCAACCCTCAGCATAGTTCAGgtaaaactattctttcaaatatggttaaaatgggtaactgcctgcaaagtaagtcagcctaaggttgtcttgacta-attcccgca--aattgttaaaaccct-----------
|||  | || || |||||||| || |||||||| |||||||| || ||||| ||||| |||||||||||||| ||  | || || ||  | || ||||||||     | | |||   ||| | ||     |   ||  |       |  |  |  |||      |  | || | || | | |  ||  ||    |||||  |            
CCCGAACCGGACTGGTAGTGTTACCATTGTTGGAGCTGTTTCACCTCCTGGTGGAGACTTCTCAGACCCTGTAACTGCAGCTACTCTTGGTATCGTTCAGgttggtatttacttcagaatgttgtgttcttctctagttaataattatatgggaaagcaagttatctttttaattatacttcaacagtaaggactaaaatacgtggggattcag

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|15813358|gb|BI785633.1|BI785633
EST:     GAGGAGATTTCTCAGACCCTGTGACATCTGCAACCCTCAGCATAGTTCAG                         GTTTTCTGGGGGTTGGACAAAAAGCTTGCC
genomic: GAGGAGATTTCTCAGACCCTGTGACATCTGCAACCCTCAGCATAGTTCAGgtaaaactat ... taattggcagGTTTTCTGGGGGTTGGACAAAAAGCTTGCC
EST: gi|58018020|gb|CX704762.1|CX704762
EST:     GAGGAGATTTTTCAGACCCTGTGACATCTGCAACCCTCAGCATAGTTCAG                         G-TTTCTGGGGGTT-GACAAAAAGCTTGCCCAGAGGAAGCACTTTCNTTCT
genomic: GAGGAGATTTCTCAGACCCTGTGACATCTGCAACCCTCAGCATAGTTCAGgtaaaactat ... taattggcagGTTTTCTGGGGGTTGGACAAAAAGCTTGCCCAGAGGAAGCACTTTCCTTCT
EST: gi|51345142|gb|CO985875.1|CO985875
EST:     GAGGAGATTNNNCAGACCCTGTGACATCTGCAANNNNCAGCATAGTTCAG                         GTTTTCTGGGGGTTGGACAAAAAGCTTGCCCAGAGGAAGCACTTTCCTTCT
genomic: GAGGAGATTTCTCAGACCCTGTGACATCTGCAACCCTCAGCATAGTTCAGgtaaaactat ... taattggcagGTTTTCTGGGGGTTGGACAAAAAGCTTGCCCAGAGGAAGCACTTTCCTTCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCCTGAACGTACAGGTAGTGTAACAATTGTTGGTGCTGTTTCGCCACCTGGAGGAGATTTCTCAGACCCTGTGACATCTGCAACCCTCAGCATAGTTCAGgtaaaactattctttcaaatatggttaaaatgggtaactgcctgcaaagtaagtcagcctaaggttgtcttgactaattcccgcaaattgttaaaaccct

- - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT