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'   		14  
 5'  3'   		15  
 5'  3'   		16  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgtaatgtaataatccaaatttgtataaaaaattatttttcttactgctgttactgtctgctggttcaatacagttatatgtttgctgtttaatttatagGAAAACAAAGAAGGTCTTGAACTTCTGAAGACTGCCATTGCTAAAGCTGGTTACACTGGAAAG

Basic information

species Glycine max
transcript GLYMA16G32960.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G32960.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G064302_T01 (Zea mays), 3'ss of exon 9
---------tgtaatgtaataatccaaatttgtataaaaaattatttttcttactgctgttactgtctgctggttcaatacagttatatgtttgctgtttaatttatagGAAAACAAAGAAGGTCTTGAACTTCTGAAGACTGCCATTGCTAAAGCTGGTTACACTGGAAAG
         |||  | |  | | |  |   |   || |||||   |  ||   |  |  ||  | |||     |  |||    || | |||   |   |  || |  |||||||||||||||| ||||||||  ||||| | ||||| |  || ||||| ||||||||||||
acgctcttttgttttatgttgaccgtagggtacctacaaaatcgatcatcg-gcatccatt--tatctcacaatctaat----ttctgtgtgaaccaat--atatgcagGAAAACAAAGAAGGCCTTGAACTATTGAAGGCAGCCATAGAAAAGGCTGGCTACACTGGAAAG

upper sequence: GLYMA16G32960.1 (Glycine max), 3'ss of exon 9
lower sequence: PP1S1_526V6.1 (Physcomitrella patens), 3'ss of exon 9
-tgtaatgtaataatccaaatttgtataaaaaattatttttcttactgctgtta-ctgtctgctggttcaatacagttatatgtttgctgtttaatttatagGAAAACAAAGAAGGTCTTGAACTTCTGAAGACTGCCATTGCTAAAGCTGGTTACACTGGAAAG
  |||  |   || ||     || | |     |   ||||||  | |   |||  |||   | || |  || || |  || |||   |     |    | |||| |||| ||||||||||||| | ||||||||||||||||| || ||||| ||||| |  |||
tggtatcgctgtactctcggcttttgttggtgacactttttccaaatctggttgtctgggagatgttctaacacggc-at-tgtccacctgggaccacacagGATAACAGAGAAGGTCTTGAATTGCTGAAGACTGCCATTGCGAAGGCTGGCTACACGGACAAG

upper sequence: GLYMA16G32960.1 (Glycine max), 3'ss of exon 9
lower sequence: EFJ14601 (Selaginella moellendorffii), 3'ss of exon 7
tgtaatgtaataatccaaatttgtataaaaaattatttttcttactgctgttactgtctgctggttcaatacagttatat-gtttgct-gtttaatttatagGAAAACAAAGAAGGTCTTGAACTTCTGAAGACTGCCATTGCTAAAGCTGGTTACACTGGAAAG
                                          ||   |||||  | |||  | |||  | |   |||| | ||  | | | |    ||| ||||||| ||||||||||| |||||  |||||||||| ||||  || ||||| ||||| ||||||
-----------------------------------------gtag-actgttgttttctcgtcgttttaaatgtttatgttgtgcgtttgatctgcttacagGAAAATAAAGAAGGTCTGGAACTGTTGAAGACTGCTATTGAGAAGGCTGGCTACACCGGAAAG

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|254320422|gb|GR826871.1|GR826871
EST:     AGGATGCTACTAACGTTGGTGATGAAGGTGGCTTTGCTCCTAATATCCAG                         GAAAACAAAGAAG-TCTTGAACTTCTGAAGACTGCCATTGCTAAAGCTGGT
genomic: AGGATGCTACTAACGTTGGTGATGAAGGTGGCTTTGCTCCTAATATCCAGgtccttacca ... taatttatagGAAAACAAAGAAGGTCTTGAACTTCTGAAGACTGCCATTGCTAAAGCTGGT
EST: gi|254317870|gb|GR832038.1|GR832038
EST:     AGGATGCTACTAACGTTGGTGATGAAGGTGGCTTTGCTCCTAATATCCAG                         GAAAACAAAGAAGGTCTTGAACTTCTGAAGACTGCCATTGCTAAAGCTGGT
genomic: AGGATGCTACTAACGTTGGTGATGAAGGTGGCTTTGCTCCTAATATCCAGgtccttacca ... taatttatagGAAAACAAAGAAGGTCTTGAACTTCTGAAGACTGCCATTGCTAAAGCTGGT
EST: gi|24135559|gb|BU926069.1|BU926069
EST:     AGGATGCTACTAACGTTGGTGATGAAGGTGGCTTTGCTCCTAATATCCAG                         GAAAACAAAGAAGGTCTTGAACTTCTGAAGACTGCCATTGCTAAAGCTGGT
genomic: AGGATGCTACTAACGTTGGTGATGAAGGTGGCTTTGCTCCTAATATCCAGgtccttacca ... taatttatagGAAAACAAAGAAGGTCTTGAACTTCTGAAGACTGCCATTGCTAAAGCTGGT
EST: gi|58021375|gb|CX708116.1|CX708116
EST:     GATGCTACT-ACGTNNGGTGATGAAGGTGGC-TTGCTTCNTAATATCCAG                         GAAAACAAAGAAGGTCTTGAACTTCTGAAGACTGCCATTGCTAAAGCTGGT
genomic: GATGCTACTAACGT-TGGTGATGAAGGTGGCTTTGC-TCCTAATATCCAGgtccttacca ... taatttatagGAAAACAAAGAAGGTCTTGAACTTCTGAAGACTGCCATTGCTAAAGCTGGT
EST: gi|254343118|gb|GR859280.1|GR859280
EST:     GGATGCTACTAACGTTGGTGATGAAAGGTGGCTTTGCTCCTAATATCCAG                         GAAAACAAAGAAAGGTCTTGAACTTCTGAAGACTGCCATTGCTAAAGCTGG
genomic: GGATGCTACTAACGTTGGTGATGAA-GGTGGCTTTGCTCCTAATATCCAGgtccttacca ... taatttatagGAAAACAAAGAA-GGTCTTGAACTTCTGAAGACTGCCATTGCTAAAGCTGG
EST: gi|15812359|gb|BI784634.1|BI784634
EST:     AGGATGCTACTAACGTTGGTGATGAAGGTGGCTTTGCTCCTAATATCCAG                         GAAAACAAAGAAGGTCTTGAACTTCTGAAGACTGCCATTGCTAAAGCTGGT
genomic: AGGATGCTACTAACGTTGGTGATGAAGGTGGCTTTGCTCCTAATATCCAGgtccttacca ... taatttatagGAAAACAAAGAAGGTCTTGAACTTCTGAAGACTGCCATTGCTAAAGCTGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgctgttactgtctgctggttcaatacagttatatgtttgctgtttaatttatagGAAAACAAAGAAGGTCTTGAACTTCTGAAGACTGCCATTGCTAAAGCTGGTTACACTGGAAAG
                                          gtttaat  putative branch site (score: 4)
                                         tgtttaatttata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgtaatgtaataatccaaatttgtataaaaaattatttttcttactgctgttactgtctgctggttcaatacagttatatgtttgctgtttaatttatagGAAAACAAAGAAGGTCTTGAACTTCTGAAGACTGCCATTGCTAAAGCTGGTTACACTGGAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - atccaaa
- - - - - - - - - - - - - aaaaaat
- - - - - - - - - - - - - - - - - - - - - - ctgctgt
- - - - - - - - - - - - - - - - - - - - - - -tgctgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgctgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caataca