Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgcaaacttcatgttatcattgatttattttctaaaatatctcagatgttttctaatcatattatgtgtctctattttcagCCCAGATGGAATGATCTAGATGTGAATCAGCATGTTAACAATGTGAAGTATGTTGGGTGGATTCTGGAG

Basic information

species Glycine max
transcript GLYMA04G21910.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G21910.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os11g43820.1 (Oryza sativa), 3'ss of exon 5
----------------------------------------------------------gtatgcaaacttcat-gttatcattgatttattttctaaaatatctcagatgttttctaatcatattatgtgtctctattttcagCCCAGATGGAATGATCTAGATGTGAATCAGCATGTTAACAATGTGAAGTATGTTGGGTGGATTCTGGAG
                                                           |||  ||     || || ||  ||||| |     || |  ||| | | ||| | | | ||    |  ||| |  ||     ||||| ||||||  ||| || ||||| ||||||||||| |||||||| || ||| |||||||||| || |||
gtaagtcagctagacatagttacatactaaattatcattatgcctcaactgcaatcatttatctaagaaaaatagtaatatttgatctcacccctcatttattttaaatgatctttgatggactcttgt-ttactgcaa-cagCCTAGATGGGGTGACCTCGATGTCAATCAGCATGTGAACAATGTTAAATATATTGGGTGGATCCTTGAG

upper sequence: GLYMA04G21910.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os02g43090.1 (Oryza sativa), 3'ss of exon 6
------------------------------------------------------------gtatgcaaacttcatgttatcattgatttattttctaaaatatctcagatgttttctaatcatattatgtgtctctattttcagCCCAGATGGAATGATCTAGATGTGAATCAGCATGTTAACAATGTGAAGTATGTTGGGTGGATTCTGGAG
                                                             | |   ||   || || || |||||| |     || |  ||| | | ||| | | | ||    |  ||| |  ||     ||||| ||||||  ||| || ||||| ||||||||||| |||||||| || ||| |||||||||| || |||
gtaagtcagctagacatggttacatactgaattatcattatgcctcaactgctatcatttatctaagaaaaaca-gtaataattgatctcacccctcatttattttaaatgatatttgatggactcttgt-ttactgcaa-cagCCTAGATGGGGTGACCTCGATGTCAATCAGCATGTGAACAATGTTAAATATATTGGGTGGATCCTTGAG

upper sequence: GLYMA04G21910.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv11s0016g04480.t01 (Vitis vinifera), 3'ss of exon 5
-----------------------------gtatgcaaacttcatgttatcattgatttattttctaaaat--atctcagatgttttctaatcatattatgtgtctctattttcagCCCAGATGGAATGATCTAGATGTGAATCAGCATGTTAACAATGTGAAGTATGTTGGGTGGATTCTGGAG
                              |||  | |  |  | |    | |  ||| |||||||      || |  | | | |  |  | ||||||| | | || |||| ||||| ||||||| |||| ||||||| |||||||||||||||||||| |||||  | || ||||| || |||
gtaagtcaaatgttgttgaattatgaaggttattgacatgttttatgtgtagtagttttttttctattgctgatttttggtttctcattctgatattatat-tttcaatttacagCCTAGATGGAGTGATTTAGATGTCAATCAGCATGTTAACAATGTTAAGTACATCGGTTGGATCCTTGAG

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|193387516|gb|FK350889.1|FK350889
EST:     A-CTAACCAAACTTGATGAATCCNCTAATTTCATTCGCACTGGTTTAAGT                         CCCAGATGGAATGATCTAGATGTGAATCAGCA
genomic: AACTAACCAAACTTGATGATTCCGCTAATTTCATTCGCACTGGTTTAAGTgtatgcaaac ... ctattttcagCCCAGATGGAATGATCTAGATGTGAATCAGCA
EST: gi|298193688|gb|HO040336.1|HO040336
EST:     AACTAACCAAACTTGATGATTCCGCTAATTTCATTCGCACTGGTTTAAGT                         CCCAGATGGAATGATCTAGATGTGAATCAGCATGTTAACAATGTGAAGTAT
genomic: AACTAACCAAACTTGATGATTCCGCTAATTTCATTCGCACTGGTTTAAGTgtatgcaaac ... ctattttcagCCCAGATGGAATGATCTAGATGTGAATCAGCATGTTAACAATGTGAAGTAT
EST: gi|208277935|gb|GE074900.1|GE074900
EST:     AACTAACCAAACTTGATGAATCCGCTAATTTCATTCGCACTGGTTTAAGT                         CCCAGATGGAATGATCTAGATGTGAATCAGCATGTTAACAATGTGA
genomic: AACTAACCAAACTTGATGATTCCGCTAATTTCATTCGCACTGGTTTAAGTgtatgcaaac ... ctattttcagCCCAGATGGAATGATCTAGATGTGAATCAGCATGTTAACAATGTGA
EST: gi|207714240|gb|GD695019.1|GD695019
EST:     ATGAATCCGCTAATTTCATTCGCACTGGTTTAAGT                         CCCAGATGGAATGATCTAGATGTGAATCAGCATGTTAACAATGTGAAGTAT
genomic: ATGATTCCGCTAATTTCATTCGCACTGGTTTAAGTgtatgcaaac ... ctattttcagCCCAGATGGAATGATCTAGATGTGAATCAGCATGTTAACAATGTGAAGTAT
EST: gi|208251806|gb|GE045525.1|GE045525
EST:     TCCGCTAATTTCATTCGCACTGGTTTAAGT                         CCCAGATGGAATGATCTAGATGTGAATCAGCATGTTAACAATGTGAAGTAT
genomic: TCCGCTAATTTCATTCGCACTGGTTTAAGTgtatgcaaac ... ctattttcagCCCAGATGGAATGATCTAGATGTGAATCAGCATGTTAACAATGTGAAGTAT
EST: gi|208334226|gb|GE130813.1|GE130813
EST:     GATGAATCCGCTAATTTCATTCGCACTGGTTTAAGT                         CCCAGATGGAATGATCTAGATGTGAATCAGCATGTTAACAATGTGAAGTAT
genomic: GATGATTCCGCTAATTTCATTCGCACTGGTTTAAGTgtatgcaaac ... ctattttcagCCCAGATGGAATGATCTAGATGTGAATCAGCATGTTAACAATGTGAAGTAT
EST: gi|193361853|gb|FK326105.1|FK326105
EST:     AACTAACCAAACTTGATGAATCCGCTAATTTCATTCGCACTGGTTTAAGT                         CCCAGATGGAATGATCTAGATGTGAATCAGCATGTT
genomic: AACTAACCAAACTTGATGATTCCGCTAATTTCATTCGCACTGGTTTAAGTgtatgcaaac ... ctattttcagCCCAGATGGAATGATCTAGATGTGAATCAGCATGTT
EST: gi|208292274|gb|GE095958.1|GE095958
EST:     AACTAACCAAACTTGATGAATCCGCTAATCTCATTCGCACTGGTTTAAGT                         CCCAGATGGAATGATCTAGATGTGAATCAGCATGTTAACAATGTGAAGTAT
genomic: AACTAACCAAACTTGATGATTCCGCTAATTTCATTCGCACTGGTTTAAGTgtatgcaaac ... ctattttcagCCCAGATGGAATGATCTAGATGTGAATCAGCATGTTAACAATGTGAAGTAT
EST: gi|208183018|gb|GD981100.1|GD981100
EST:     AACTAACCAAACTTGATGAATCCGCTAATTTCATTCGCACT-GTTTAAGT                         CCCAGATGGAATGATCTAGATGTGAATCAGCATGTTAACAATGTGAAGTAT
genomic: AACTAACCAAACTTGATGATTCCGCTAATTTCATTCGCACTGGTTTAAGTgtatgcaaac ... ctattttcagCCCAGATGGAATGATCTAGATGTGAATCAGCATGTTAACAATGTGAAGTAT
EST: gi|208073857|gb|GD871526.1|GD871526
EST:     AACTAACCAAACTTGACGAATCCGCTAATTTCATTCGCACTGGTTTAAGT                         CCCAGATGGAATGATCTAGATGTGAATCAGCATGTTAACAATGTGAAGTAT
genomic: AACTAACCAAACTTGATGATTCCGCTAATTTCATTCGCACTGGTTTAAGTgtatgcaaac ... ctattttcagCCCAGATGGAATGATCTAGATGTGAATCAGCATGTTAACAATGTGAAGTAT
EST: gi|208146311|gb|GD948416.1|GD948416
EST:     AACTAACCAAACTTGATGAATCCGCTAATTTCATTCGCACTGGTTTAAGT                         CCCAGATGGAATGATCTAGATGTGAATCAGCATGTTAACAATGTGA
genomic: AACTAACCAAACTTGATGATTCCGCTAATTTCATTCGCACTGGTTTAAGTgtatgcaaac ... ctattttcagCCCAGATGGAATGATCTAGATGTGAATCAGCATGTTAACAATGTGA
EST: gi|193677182|gb|FK620488.1|FK620488
EST:     AACTAACCAAACTTGATGAATCCGCTAATTTCATTCGCACTGGTTTAAGT                         CCCAGATGGAATGATCTAGATGTGAATCAGCATGTTA
genomic: AACTAACCAAACTTGATGATTCCGCTAATTTCATTCGCACTGGTTTAAGTgtatgcaaac ... ctattttcagCCCAGATGGAATGATCTAGATGTGAATCAGCATGTTA
EST: gi|208196511|gb|GD993168.1|GD993168
EST:     ACTAACCAAACTTGATGAATCCGTCTAATTTCATTCGCACTGGTTTAAGT                         CCCAGATGGAATGATCTAGATGTGAATCAGCATGTTAACAATGTGAAGTAT
genomic: ACTAACCAAACTTGATGATTCCG-CTAATTTCATTCGCACTGGTTTAAGTgtatgcaaac ... ctattttcagCCCAGATGGAATGATCTAGATGTGAATCAGCATGTTAACAATGTGAAGTAT
EST: gi|193689961|gb|FK631822.1|FK631822
EST:     ATTCGCACTGGTTTAAGT                         CCCAGATGGAATGATCTAGATGTGAATCAGCATGTTAACAATGTGAAGTAT
genomic: ATTCGCACTGGTTTAAGTgtatgcaaac ... ctattttcagCCCAGATGGAATGATCTAGATGTGAATCAGCATGTTAACAATGTGAAGTAT
EST: gi|193491529|gb|FK453883.1|FK453883
EST:     AACTAACCAAACTTGATGAATCCGCTAATTTCATTCGCACTGGTTTAAGT                         CCCAGATGGAATGATCTAGATGTGAATCAGCATGTTAACAATGTGAAGTAT
genomic: AACTAACCAAACTTGATGATTCCGCTAATTTCATTCGCACTGGTTTAAGTgtatgcaaac ... ctattttcagCCCAGATGGAATGATCTAGATGTGAATCAGCATGTTAACAATGTGAAGTAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attttctaaaatatctcagatgttttctaatcatattatgtgtctctattttcagCCCAGATGGAATGATCTAGATGTGAATCAGCATGTTAACAATGTGAAGTATGTTGGGTGGATTCTGGAG
                        ttctaat  putative branch site (score: 2)
                                          tctctattttc  putative PPT
                      ttttctaatcatatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgcaaacttcatgttatcattgatttattttctaaaatatctcagatgttttctaatcatattatgtgtctctattttcagCCCAGATGGAATGATCTAGATGTGAATCAGCATGTTAACAATGTGAAGTATGTTGGGTGGATTCTGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA