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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aatctttcctctaatcactaatatctacccactgctagtctgtctaacctagattgttttgaatattaaatgtattattgaccatcttgtgctttcccagGTGAAGAGCGATGTTACCAGATATCGCTATGGAGATGAGCAGCATTTGGATGAGGCATTGAAACGGATATTTCAGTATGGCCAA

Basic information

species Glycine max
transcript GLYMA19G06090.3
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G06090.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv14s0083g00070.t01 (Vitis vinifera), 3'ss of exon 4
aatctttcctctaatcactaatatctaccc--actgctagtctgtctaacc--tagattgttttgaatattaaatgtattattgaccatcttg--tgctttc-ccagGTGAAGAGCGATGTTACCAGATATCGCTATGGAGATGAGCAGCATTTGGATGAGGCATTGAAACGGATATTTCAGTATGGCCAA
        ||    |  || || | | ||   | |  |    ||| | | |  || | | | |||  |  | ||    || || |  |  |||  | ||||  | |||| | ||  |||||||  |||||||| ||||| ||||| |||||| |||| || |||||||||||||| ||||||||||| |  
-------tcttatgtagctgatttttgcctcaattatttcaatgtgtgaacaatatactttattgttttatgaacaatttttttattactttggttactttaactagGTCAGGAATGATGTTATAAGATATCGTTATGGGGATGAACAGCATCTGGAAGAAGCATTGAAACGGATTTTTCAGTATGGTCTG

upper sequence: GLYMA19G06090.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv18s0041g00450.t01 (Vitis vinifera), 3'ss of exon 1
aatctttcctctaatcactaatatctaccc--actgctagtctgtctaacc--tagattgttttgaatattaaatgtattattgaccatcttg--tgctttc-ccagGTGAAGAGCGATGTTACCAGATATCGCTATGGAGATGAGCAGCATTTGGATGAGGCATTGAAACGGATATTTCAGTATGGCCAA----------------
        ||    |  || || | | ||   | |  |    ||| | | |  || | | | |||  |  | |     || || |  |  |||  | ||||  | |||| | ||  |||||||  |||||||| ||||| ||||| || |||||||| || |||||||||||||| ||||||||||| |                  
-------tcttatgtagctgatttttgcctcaattatttcaatgtgtgaacaatatactttattgttttatgaccaatttttttattactttggttactttaactagGTCAGGAATGATGTTATAAGATATCGTTATGGGGATGAACAACATTTGGAAGAAGCATTGAAACGGATTTTTCAGTATGGTCTGGTAGGTTCTGCAACTT

upper sequence: GLYMA19G06090.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv15s0048g01820.t01 (Vitis vinifera), 3'ss of exon 1
aatctttcctctaatcactaatatctaccc--actgctagtctgtctaacc--tagattgttttgaatattaaatgtattattgaccatcttg--tgctttc-ccagGTGAAGAGCGATGTTACCAGATATCGCTATGGAGATGAGCAGCATTTGGATGAGGCATTGAAACGGATATTTCAGTATGGCCAA
        ||    |  || || | | ||   | |  |    ||| | | |  || | | | |||  |  | ||    || || |  |  |||  | ||||  | |||| | ||  |||||||  |||||||| ||||| ||||| || ||| |||| || |||||||||||||| ||||||||||| |  
-------tcttatgtagctgatttttgcctcaattatttcaatgtgtgaacaatatactttattgttttatgaacaatttttttattactttggttactttaactagGTCAGGAATGATGTTATAAGATATCGTTATGGGGATGAACAACATCTGGAAGAAGCATTGAAACGGATTTTTCAGTATGGTCTG

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|7283701|gb|AW596305.1|AW596305
EST:     CAGATGCTCAAAGCTTGAGGGAAAAATGTGCAACTCCAATTCTTAAACAG                         GTGAAGAGCGATGTTACCAGATATCGCTATGGAGATGAGCAGCATTTGGAT
genomic: CAGATGCTCAAAGCTTGAGGGAAAAATGTGCAACTCCAATTCTTAAACAGgtaatctcat ... gctttcccagGTGAAGAGCGATGTTACCAGATATCGCTATGGAGATGAGCAGCATTTGGAT
EST: gi|213594750|gb|DB959833.1|DB959833
EST:     CAGATGCTCAAAGCTTGAGGGAAAAATGTGCAACTCCAATTCTTAAACAG                         GTGAAGAGCGATGTTACCAGATATCGC
genomic: CAGATGCTCAAAGCTTGAGGGAAAAATGTGCAACTCCAATTCTTAAACAGgtaatctcat ... gctttcccagGTGAAGAGCGATGTTACCAGATATCGC
EST: gi|151394955|gb|EV264826.1|EV264826
EST:     CAGATGCTCAAAGCTTGAGGGAAAAATGTGCAACTCCAATTCTTAAACAG                         GTGAAGAGCGATGTTACCAGATATCGCTATGGAGATGAGCAGCATTTGGAT
genomic: CAGATGCTCAAAGCTTGAGGGAAAAATGTGCAACTCCAATTCTTAAACAGgtaatctcat ... gctttcccagGTGAAGAGCGATGTTACCAGATATCGCTATGGAGATGAGCAGCATTTGGAT
EST: gi|213610855|gb|DB963185.1|DB963185
EST:     CAGATGCTCAAAGCTTGAGGGAAAAATGTGCAACTCCAATTCTTAAACAG                         GTGAAGAGCGATGTTACCAGATATCGCTATGGAGATGAGCAGCATTTG
genomic: CAGATGCTCAAAGCTTGAGGGAAAAATGTGCAACTCCAATTCTTAAACAGgtaatctcat ... gctttcccagGTGAAGAGCGATGTTACCAGATATCGCTATGGAGATGAGCAGCATTTG
EST: gi|6481869|gb|AW201140.1|AW201140
EST:     CAGATGCTCAAAGCTTGAGGGAAAAATGTGCAACTCCAATTCTTAAACAG                         GTGAAGAACGATGTTACCAGATATCGCTATGGAGATGAGCAGCATTTGGAT
genomic: CAGATGCTCAAAGCTTGAGGGAAAAATGTGCAACTCCAATTCTTAAACAGgtaatctcat ... gctttcccagGTGAAGAGCGATGTTACCAGATATCGCTATGGAGATGAGCAGCATTTGGAT
EST: gi|209700887|gb|BW683104.1|BW683104
EST:     CAGATGCTCAAAGCTTGAGGGAAAAATGTGCAACTCCAATTCTTTAACAG                         GTGAAGAGCGATGTTACCAGATATCGC
genomic: CAGATGCTCAAAGCTTGAGGGAAAAATGTGCAACTCCAATTCTTAAACAGgtaatctcat ... gctttcccagGTGAAGAGCGATGTTACCAGATATCGC
EST: gi|209722136|gb|BW659325.1|BW659325
EST:     CAGATGCTCAAAGCTTGAGGGAAAAATGTGCAACTCCAATTCTTAAACAG                         GTGAAGAGCGATGTTACCAGATATCGCTATGGAGATGAGCAGCATTTGGAT
genomic: CAGATGCTCAAAGCTTGAGGGAAAAATGTGCAACTCCAATTCTTAAACAGgtaatctcat ... gctttcccagGTGAAGAGCGATGTTACCAGATATCGCTATGGAGATGAGCAGCATTTGGAT
EST: gi|15664219|gb|BI701590.1|BI701590
EST:     CAGATGCTCAAAGCTTGAGGGAAAAATGTGCAACTCCAATTCTTAAACAG                         GTGAAGAGCGATGTTACCAGATATCGCTATGGA
genomic: CAGATGCTCAAAGCTTGAGGGAAAAATGTGCAACTCCAATTCTTAAACAGgtaatctcat ... gctttcccagGTGAAGAGCGATGTTACCAGATATCGCTATGGA
EST: gi|9259930|gb|BE348077.1|BE348077
EST:     CAGATGCTCAAAGCTTGAGGGAAAAATGTGCAACTCCAATTCTTAAACAG                         GTGAAGAGCGATGTTACCAGATATCGCTATGGAGATGAGCAGCATTTGGAT
genomic: CAGATGCTCAAAGCTTGAGGGAAAAATGTGCAACTCCAATTCTTAAACAGgtaatctcat ... gctttcccagGTGAAGAGCGATGTTACCAGATATCGCTATGGAGATGAGCAGCATTTGGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aacctagattgttttgaatattaaatgtattattgaccatcttgtgctttcccagGTGAAGAGCGATGTTACCAGATATCGCTATGGAGATGAGCAGCATTTGGATGAGGCATTGAAACGGATATTTCAGTATGGCCAA
                              tattgac  putative branch site (score: 2)
                                       tcttgtgctttccc  putative PPT
     agattgttttgaatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aatctttcctctaatcactaatatctacccactgctagtctgtctaacctagattgttttgaatattaaatgtattattgaccatcttgtgctttcccagGTGAAGAGCGATGTTACCAGATATCGCTATGGAGATGAGCAGCATTTGGATGAGGCATTGAAACGGATATTTCAGTATGGCCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG