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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acttgtttgctcattctttaccatcttactctgttctttttagttttgtttttgtgatacatttactgcagttataataatttctcctttaactggtcagGCACACCTGGTGATTGGAGTCACATTATCAAGCAGATTGGAATGTTTACTTTCACTGGATTGAATGCGGAACAAGTTTCCTTCATGACTAAAGAGTACCA

Basic information

species Glycine max
transcript GLYMA04G08560.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G08560.1 (Glycine max), 3'ss of exon 10
lower sequence: LOC_Os01g55540.2 (Oryza sativa), 3'ss of exon 10
acttgtttgctcattctttaccatcttactctgttctttttagttttgtttttgtgatacatttactgcagttataataatttctcctttaac-----tggtcagGCACACCTGGTGATTGGAGTCACATTATCAAGCAGATTGGAATGTTTACTTTCACTGGATTGAATGCGGAACAAGTTTCCTTCATGACTAAAGAGTACCA
|   ||||       ||||    ||| | ||  |||| | | | |     |  | | ||||||  | | | |  |||| |||  |    | |          |||  || ||||| || ||||||||||| || |||||||| |||||||| |||||||||||  | ||    || |||||  | |||||||   | || |||||
aggagtttttcttccctttt---tctgaatccattctctatggctaaaagt--gaggtacattgtcagaaatattaatcattgttgacatgataacatcatgcagAAACTCCTGGAGACTGGAGTCACATCATTAAGCAGATCGGAATGTTCACTTTCACTGGGCTCAACAGTGATCAAGTGGCTTTCATGAGGCAGGAATACCA

upper sequence: GLYMA04G08560.1 (Glycine max), 3'ss of exon 10
lower sequence: GRMZM2G094712_T04 (Zea mays), 3'ss of exon 8
---acttgtttgctcattctttaccatcttactctgttctttttagttttgtttttgtgatacatttactgcagttataataatttctcctttaactggtcagGCACACCTGGTGATTGGAGTCACATTATCAAGCAGATTGGAATGTTTACTTTCACTGGATTGAATGCGGAACAAGTTTCCTTCATGACTAAAGAGTACCA
     || |    ||    | ||   |     ||| || | ||| |||| |  |||  | |     ||   |  |   | | | |     |   |  |  |||| || |||||||||||||| || || || ||||| ||||| |||||||||||||||||  |||||   ||||||||  | |||||||   | || |||||
taccattatcgaatctcaatgtattgttcctttcttttgtctttcgtttcgggtttcgggt---catagcacgatggcactcagtctcgttaataacgtgcagGAACCCCTGGTGATTGGAGCCATATCATTAAGCAAATTGGGATGTTTACTTTCACTGGGCTGAATAGCGAACAAGTCGCATTCATGAGGCAGGAATACCA

upper sequence: GLYMA04G08560.1 (Glycine max), 3'ss of exon 10
lower sequence: PP1S132_95V6.1 (Physcomitrella patens), 3'ss of exon 11
acttgtttgctcattctttaccatcttac-tctgttctttttagttttgtt-tttgtgatacatttactgcagttataataatttctcctt--taactggtcagGCACACCTGGTGATTGGAGTCACATTATCAAGCAGATTGGAATGTTTACTTTCACTGGATTGAATGCGGAACAAGTTTCCTTCATGACTAAAGAGTACCA
            |  |   |  |  |||  | | ||||  | |  | |||  |      | |||| | ||   |  |     ||| || ||  ||      ||||||||||||| ||||||| |||| || | ||||||||||||||||| |||||||| ||||||||   |   |||||    ||||||||     | || ||
----acacatgaaagcgacaaaactttatgtgtattctgctcaagtatgtggtccaacttgcattaagtgatttggtctctttttttctttgatattcatgcagGCACACCTGGCGATTGGACTCACGTTCTGAAGCAGATTGGAATGTTCACTTTCACGGGATTGAACAAGTCTCAAGTCGAGTTCATGACCCGTCAATATCA

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|192306581|gb|FG996243.1|FG996243
EST:     TCGCATCATCAATATGCGCCAAGAACTTTTCGATGCTTTACGTTCCAGAG                         GCACACCTGGTGATTGGAGTCACATTATCAAGCAGATTGGAATGTTTACTT
genomic: TCGCATCATCAATATGCGCCAAGAACTTTTCGATGCTTTACGTTCCAGAGgtcagccttt ... aactggtcagGCACACCTGGTGATTGGAGTCACATTATCAAGCAGATTGGAATGTTTACTT
EST: gi|20812962|gb|BQ297440.1|BQ297440
EST:     TCGCATCATCAATATGCGCCAAGAACTTTTCGATGCTTTACGTTCCAGAG                         GCACACCTGGTGATTGGAGTCACATTATCAAGCAGATTGGAATGTTTACTT
genomic: TCGCATCATCAATATGCGCCAAGAACTTTTCGATGCTTTACGTTCCAGAGgtcagccttt ... aactggtcagGCACACCTGGTGATTGGAGTCACATTATCAAGCAGATTGGAATGTTTACTT
EST: gi|9901743|gb|BE610711.1|BE610711
EST:     TCGCATCATCAATATGCGCCAAGAACTTTTCGATGCTTTACGTTCCAGAG                         GCACACCTGGTGATTGGAGTCACATTATCAAGCAGATTGGAATGTTTACTT
genomic: TCGCATCATCAATATGCGCCAAGAACTTTTCGATGCTTTACGTTCCAGAGgtcagccttt ... aactggtcagGCACACCTGGTGATTGGAGTCACATTATCAAGCAGATTGGAATGTTTACTT
EST: gi|13481430|gb|BG510773.1|BG510773
EST:     TCGCATCATCAATATGCGCCAAGAACTTTTCGATGCTTTACGTTCCAGAG                         GCACACCTGGTGATTGGAGTCACATTATCAAGCAGATTGGAATGTTTACTT
genomic: TCGCATCATCAATATGCGCCAAGAACTTTTCGATGCTTTACGTTCCAGAGgtcagccttt ... aactggtcagGCACACCTGGTGATTGGAGTCACATTATCAAGCAGATTGGAATGTTTACTT
EST: gi|192328739|gb|FK023197.1|FK023197
EST:     TCGCATCATCAATATGCGCCAAGAACTTTTCGATGCTTTACGTTCCAGAG                         GCACACCTGGTGATTGGAGTCACATTATCAAGCAGATTGGAATGTTTACTT
genomic: TCGCATCATCAATATGCGCCAAGAACTTTTCGATGCTTTACGTTCCAGAGgtcagccttt ... aactggtcagGCACACCTGGTGATTGGAGTCACATTATCAAGCAGATTGGAATGTTTACTT
EST: gi|22932102|gb|BU549241.1|BU549241
EST:     TCGCATCATCAATATGCGCCAAGAACTTTTCGATGCTTTACGTTCCAGAG                         GCACACCTGGTGANNNGAGTCACATTATCAAGCAGATTGGAATGTTTACTT
genomic: TCGCATCATCAATATGCGCCAAGAACTTTTCGATGCTTTACGTTCCAGAGgtcagccttt ... aactggtcagGCACACCTGGTGATTGGAGTCACATTATCAAGCAGATTGGAATGTTTACTT
EST: gi|192334120|gb|FK026277.1|FK026277
EST:     TCGCATCATCAATATGCGCCAAGAACTTTTCGATGCTTTACGTTCCAGAG                         GCACACCTGGTGATTGGAGTCACATTATCAAGCAGATTGGAATGTTTACTT
genomic: TCGCATCATCAATATGCGCCAAGAACTTTTCGATGCTTTACGTTCCAGAGgtcagccttt ... aactggtcagGCACACCTGGTGATTGGAGTCACATTATCAAGCAGATTGGAATGTTTACTT
EST: gi|17153142|gb|BM143075.1|BM143075
EST:     TCGCATCATCAATATGCGCCAAGAACTTTTCGATGCTTTACGTTCCAGAG                         GCACCCCTGGTGATTGGAGTCACATT
genomic: TCGCATCATCAATATGCGCCAAGAACTTTTCGATGCTTTACGTTCCAGAGgtcagccttt ... aactggtcagGCACACCTGGTGATTGGAGTCACATT
EST: gi|254322787|gb|GR839808.1|GR839808
EST:     TCGCATCATCAATATGCGCCAAGAACTTTTCGATGCTTTACGTTCCAGAG                         GCACACCTGGTGATTGGAGTCACATTATCAAGCAGATTGGAATGTTTACTT
genomic: TCGCATCATCAATATGCGCCAAGAACTTTTCGATGCTTTACGTTCCAGAGgtcagccttt ... aactggtcagGCACACCTGGTGATTGGAGTCACATTATCAAGCAGATTGGAATGTTTACTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgtttttgtgatacatttactgcagttataataatttctcctttaactggtcagGCACACCTGGTGATTGGAGTCACATTATCAAGCAGATTGGAATGTTTACTTTCACTGGATTGAATGCGGAACAAGTTTCCTTCATGACTAAAGAGTACCA
                                         ctttaac  putative branch site (score: 3)
                                   tttctcctttaact  CT-rich tract
                          ttataataatttctcc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acttgtttgctcattctttaccatcttactctgttctttttagttttgtttttgtgatacatttactgcagttataataatttctcctttaactggtcagGCACACCTGGTGATTGGAGTCACATTATCAAGCAGATTGGAATGTTTACTTTCACTGGATTGAATGCGGAACAAGTTTCCTTCATGACTAAAGAGTACCA

- -tgtttgc
- - - - - - - - - - - - - - - - - - - - - - - - -ttttgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tactgca