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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGGACGCCGCCAAGAAGATCCGCAAGCCCTACACCATCACAAAGTCAAGGGAGAACTGGACCGAACCCGAACACGACAAGTTCCTCGAAGCAATTCAACTgtaatcatgttcgctcctttttttttttaatttatcttttaatttttgtttgcttatgaaaattcggtaattgaggttaggagttcggttgaagcattgg...

Basic information

species Glycine max
transcript GLYMA09G24400.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G24400.1 (Glycine max), 5'ss of exon 1
lower sequence: LOC_Os06g01670.1 (Oryza sativa), 5'ss of exon 1
AGGACGCCGCCAAGAAGATCCGCAAGCCCTACACCATCACAAAGTCAAGGGAGAACTGGACCGAACCCGAACACGACAAGTTCCTCGAAGCAATTCAACTgtaatcatgttcgctcctttttttttttaatttatcttttaatttttgtttgcttatgaaaattcggtaattgaggttaggagttcggttgaagcattgg--
| ||||  |  | || | |  | ||||||||||||||||| |||||  |||||| ||||||||| ||||| ||||||||||||||||| ||  | || |||||| |||    || |||| || |   |   ||| ||  |    |   |     |      | |     ||  |  ||   |   || ||       ||   
ACGACGGGGGAAGGAGGGTGAGGAAGCCCTACACCATCACCAAGTCGCGGGAGAGCTGGACCGACCCCGAGCACGACAAGTTCCTCGAGGCGCTGCAGCTgtaagcatccatgcgccttcttctaact--cttaactgctgccctgcctccatcttctgctacttctccatccaatttcatatgccgttttgcctgctgtat

upper sequence: GLYMA09G24400.1 (Glycine max), 5'ss of exon 1
lower sequence: LOC_Os06g45840.2 (Oryza sativa), 5'ss of exon 1
AGGACGCCGCCAAGAAGATCCGCAAGCCCTACACCATCACAAAGTCAAGGGAGAACTGGACCGAACCCGAACACGACAAGTTCCTCGAAGCAATTCAACTgtaatcatgttcgctcct--ttttttttttaatttatcttttaatttttgtttgcttatgaaaattcggtaattgaggttaggagttcggttgaagcattgg-
 ||| |  || | |||| |  | ||||| ||||||||||| ||||| ||||||| |||||| || ||||| ||||||||||||||||| ||  | || |||| |       |  | ||       | | |   |   | | | || | ||   ||    |      ||      | |||| ||  |    | |  || || | 
GGGAGGAGGCGAGGAAGGTGAGGAAGCCGTACACCATCACCAAGTCGAGGGAGAGCTGGACGGAGCCCGAGCACGACAAGTTCCTCGAGGCGCTGCAGCTgtgagtgcccccaattctgcccccgtctctcgctctccctcttatctctgcgcgcgcgcggcg---cgccccccgtggttggggatagtttggcggctttcgt

upper sequence: GLYMA09G24400.1 (Glycine max), 5'ss of exon 1
lower sequence: GRMZM2G135052_T01 (Zea mays), 5'ss of exon 1
AGGACGCCGCCAAGAAGATCCGCAAGCCCTACACCATCACAAAGTCAAGGGAGAACTGGACCGAACCCGAACACGACAAGTTCCTCGAAGCAATTCAACTgtaatcatgttcgctcctttttttttttaatttatcttttaatttttgtt----tgcttatgaaaattcggtaattgaggttaggagttcggttgaagcattgg
|||| | | ||  ||   | |||||||||||||||||||| |||||  | |||| ||||||||| ||||| ||||||||||||||||| ||| | || |||| |       | |||  |   |   |   |   ||    |  |  |        |       |  |  | |   |     ||   ||  | |  |||      
AGGAGGGCCCCCGGAGAGTGCGCAAGCCCTACACCATCACCAAGTCGCGCGAGAGCTGGACCGACCCCGAGCACGACAAGTTCCTCGAGGCACTGCAGCTgtgagtcgacccactctctccctccctccctccctcccccatctcctccggcggcggcggcttacctctgctttgtctcactaatggtatgttcaaagtt----

upper sequence: GLYMA09G24400.1 (Glycine max), 5'ss of exon 1
lower sequence: GRMZM2G057408_T01 (Zea mays), 5'ss of exon 1
AGGACGCCGCCAAGAAGATCCGCAAGCCCTACACCATCACAAAGTCAAGGGAGAACTGGACCGAACCCGAACACGACAAGTTCCTCGAAGCAATTCAACTgtaatcatgttcgctcctttttt-tttttaatttatcttttaatttttgtttgcttatgaaaattcggtaattgaggttaggagttcggttgaagcattgg-
|||| |  |    |||| || | ||||| ||||||||||| |||||  |||||| |||||| || || || ||||||||||||||||| ||  | || |||| |         | || | |    |       | ||    | |      | | |  ||    |||| | | ||| ||   | | |   |||     |||  
AGGAGGAGGTTCGGAAGGTCAGGAAGCCGTACACCATCACCAAGTCGCGGGAGAGCTGGACGGAGCCGGAGCACGACAAGTTCCTCGAGGCCCTGCAGCTgtgagtgccccgaccccctctgcgctccccccctgtccccgattcgggagtaggtagtgccgtttcgatgagtgaagt--agcggttacttgctctgttgcc

upper sequence: GLYMA09G24400.1 (Glycine max), 5'ss of exon 1
lower sequence: GRMZM2G118693_T02 (Zea mays), 5'ss of exon 1
AGGACGCCGCCAAGAAGATCCGCAAGCCCTACACCATCACAAAGTCAAGGGAGAACTGGACCGAACCCGAACACGACAAGTTCCTCGAAGCAATTCAACTgtaatcatgttcgctcctttttttttttaatttatcttttaatttttgtttgcttatgaaaattcggtaattgaggttaggagttcggttgaagcattgg-
|||| |||  ||||||| | || ||||| ||||||||||| |||||  |||||| |||||| || |  || ||||||||||||||||| ||  | || |||||| || |  |   || |    |   |    | | |||| |||  ||   | | |      |   |     |   ||  |   |    ||     |||  
AGGAAGCCAGCAAGAAGGTGCGGAAGCCGTACACCATCACCAAGTCGCGGGAGAGCTGGACGGAGCAGGAGCACGACAAGTTCCTCGAGGCCCTGCAGCTgtaagcaggagcaacccctgacatgggttccatttattttgattgatgcg-gttcacaggcctaaagcgtcgggctttgtggtgttttctgtctttttgat

upper sequence: GLYMA09G24400.1 (Glycine max), 5'ss of exon 1
lower sequence: Vv16s0050g01180.t01 (Vitis vinifera), 5'ss of exon 1
AGGACGCCGCCAAGAAGATCCGCAAGCCCTACACCATCACAAAGTCAAGGGAGAACTGGACCGAACCCGAACACGACAAGTTCCTCGAAGCAATTCAACTgtaat-catgttcgctcctttttttttttaatttatcttttaatttttgtttgctt-atgaaaattcggtaattgaggttaggagttcggttgaagcattgg
||||  | || ||||||||||| ||||||||||| || || ||||  || ||||| |||||||| ||||| ||||||||||||||||||||  |||| ||||||  |   |   |||   |    ||||  ||      ||  ||||| | || || ||      |   |  ||  | |||    || |  |  || |||  
AGGATCCGGCTAAGAAGATCCGGAAGCCCTACACTATTACCAAGTGCAGAGAGAAGTGGACCGAGCCCGAGCACGACAAGTTCCTCGAAGCTCTTCAGCTgtaagacgcttcaactcgaatagggttttggttggggcattt-tttttatgtgtttgattgcgtgtttatttttttgtttatctctttgtgttgagaattt-

upper sequence: GLYMA09G24400.1 (Glycine max), 5'ss of exon 1
lower sequence: EFJ36434 (Selaginella moellendorffii), 5'ss of exon 1
AGGACGCCGCCAAGAAGATCCGCAAGCCCTACACCATCACAAAGTCAAGGGAGAACTGGACCGAACCCGAACACGACAAGTTCCTCGAAGCAATTCAACTgtaatcatgttcgctcctttttttttttaatttatcttttaatttttgtttgcttatgaaaattcggtaattgaggttaggagttcggttgaagcattgg
| |  |   ||||||||||||| ||||||||||||||||| || || ||||||| |||||| || |  || ||||||||||| ||||| ||  | || ||||||        | || |||  |       | |   || ||| |    | |    |                                            
ATGCGGTGTCCAAGAAGATCCGGAAGCCCTACACCATCACGAAATCCAGGGAGAGCTGGACGGAGCAAGAGCACGACAAGTTTCTCGAGGCCTTGCAGCTgtaaga------gatcttttcctcgcgaggtatcggttctaagtccaatctctccag-------------------------------------------

upper sequence: GLYMA09G24400.1 (Glycine max), 5'ss of exon 1
lower sequence: EFJ37776 (Selaginella moellendorffii), 5'ss of exon 1
AGGACGCCGCCAAGAAGATCCGCAAGCCCTACACCATCACAAAGTCAAGGGAGAACTGGACCGAACCCGAACACGACAAGTTCCTCGAAGCAATTCAACTgtaatcatgttcgctcctttttttttttaatttatcttttaatttttgtttgcttatgaaaattcggtaattgaggttaggagttcggttgaagcattgg
  || ||||||| ||||||||||||||||||||||||||| |||||  | ||||||||| | ||    || |||||||| |||||||| ||  | || |||| |    ||||   |  | || |||  | ||     |  |  ||||| ||      | |                                        
--GATGCCGCCAGGAAGATCCGCAAGCCCTACACCATCACCAAGTCGCGCGAGAACTGGGCGGATGAAGAGCACGACAAATTCCTCGAGGCGCTGCATCTgtga----gttcttcctctcttctttacagttc----tcgatattttgcttctccgcgtag---------------------------------------

upper sequence: GLYMA09G24400.1 (Glycine max), 5'ss of exon 1
lower sequence: EFJ32076 (Selaginella moellendorffii), 5'ss of exon 1
AGGACGCCGCCAAGAAGATCCGCAAGCCCTACACCATCACAAAGTCAAGGGAGAACTGGACCGAACCCGAACACGACAAGTTCCTCGAAGCAATTCAACTgtaatcatgttcgctcctttttttttttaatttatcttttaat-ttttgtttgcttatgaaaattcggtaattgaggttaggagttcggttgaagcattgg
              |||||||||||||||||||||||||| |||||  | ||||||||| | ||    || |||||||| |||||||| ||  |||| |||| |          | ||| ||||| | |    |  | |  || ||||  ||      | |                                        
--------------AAGATCCGCAAGCCCTACACCATCACCAAGTCGCGCGAGAACTGGGCGGATGAAGAGCACGACAAATTCCTCGAGGCGCTTCATCTgtgag---------ttcttctttttctcagcacagttctcgatgttttacttctccgcgtag---------------------------------------

upper sequence: GLYMA09G24400.1 (Glycine max), 5'ss of exon 1
lower sequence: EFJ04991 (Selaginella moellendorffii), 5'ss of exon 1
AGGACGCCGCCAAGAAGATCCGCAAGCCCTACACCATCACAAAGTCAAGGGAGAACTGGACCGAACCCGAACACGACAAGTTCCTCGAAGCAATTCAACTgtaatcatgttcgctcctttttttttttaatttatcttttaatttttgtttgcttatgaaaattcggtaattgaggttaggagttcggttgaagcattgg
| |  |   ||||||||||||| ||||||||||||||||| || || ||||||| |||||| || |  || ||||||||||| ||||| ||  | || ||||||      |    ||       | || |||     |  ||| | |                                                     
ATGCGGTGTCCAAGAAGATCCGGAAGCCCTACACCATCACGAAATCCAGGGAGAGCTGGACGGAGCAAGAGCACGACAAGTTTCTCGAGGCCTTGCAGCTgtaagagatcttttccccgcgaggtattgattctaagtccaatctctccag-------------------------------------------------

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|26048127|gb|CA784712.1|CA784712
EST:     GAGAACTGGACCGAACCCCAACACGACAAGTTCCTCGAAGCAATTCAACT                         GTTTGACCGTGACTGGAAAAAGATTGAAGCATTTGTTGGATCAAAGAGTGT
genomic: GAGAACTGGACCGAACCCGAACACGACAAGTTCCTCGAAGCAATTCAACTgtaatcatgt ... cttttttcagGTTTGACCGTGACTGGAAAAAGATTGAAGCATTTGTTGGATCAAAGAGTGT
EST: gi|15337996|gb|BI498652.1|BI498652
EST:     GAGAACTGGACCGAACCCGAACACGACAAGTTCCTCGAAGCAATTCAACT                         GTTTGACCGTGACTGGAAAAAGATTGAAGCATTTGTTGGATCAAAGAGTGT
genomic: GAGAACTGGACCGAACCCGAACACGACAAGTTCCTCGAAGCAATTCAACTgtaatcatgt ... cttttttcagGTTTGACCGTGACTGGAAAAAGATTGAAGCATTTGTTGGATCAAAGAGTGT
EST: gi|254334102|gb|GR849020.1|GR849020
EST:     GAGAACTGGACCGAACCCGAACACGACAAGTTCCTCGAAGCAATTCAACT                         GTTTGACCGTGACTGGAAAAAGATTGAAGCATTTGTTGGATCAAAGAGTGT
genomic: GAGAACTGGACCGAACCCGAACACGACAAGTTCCTCGAAGCAATTCAACTgtaatcatgt ... cttttttcagGTTTGACCGTGACTGGAAAAAGATTGAAGCATTTGTTGGATCAAAGAGTGT
EST: gi|6566705|gb|AW234339.1|AW234339
EST:     GAGAACTGGACCGAACCCGAACACGACAAGTTCCTCGAAGCAATTCAACT                         GTTTGACCGTGACTGGAAAAAGATTGAAGCATTTGTTGGATCAAAGAGTGT
genomic: GAGAACTGGACCGAACCCGAACACGACAAGTTCCTCGAAGCAATTCAACTgtaatcatgt ... cttttttcagGTTTGACCGTGACTGGAAAAAGATTGAAGCATTTGTTGGATCAAAGAGTGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGGACGCCGCCAAGAAGATCCGCAAGCCCTACACCATCACAAAGTCAAGGGAGAACTGGACCGAACCCGAACACGACAAGTTCCTCGAAGCAATTCAACTgtaatcatgttcgctcctttttttttttaatttatcttttaatttttgtttgcttatgaaaattcggtaattgaggttaggagttcggttgaagcattgg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA