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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAAAGCGTGGGGAAGCTGCTCTTGCTCGTTTGAAGGTTTATGAAGGAATCCCTCCTCCATATGACAAGACCAAGAGAATGGTTGTTCCTGATGCTCTCAAgtaagactttttctactgtttttttatgctaatatatttaattttaatatagtttgataggcctacactagcaacctatttgaaatcattcattgtacat...

Basic information

species Glycine max
transcript GLYMA15G13670.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G13670.1 (Glycine max), 5'ss of exon 2
lower sequence: AT3G24830.1 (Arabidopsis thaliana), 5'ss of exon 2
CAAAGCGTGGGGAAGCTGCTCTTGCTCGTTTGAAGGTTTATGAAGGAATCCCTCCTCCATATGACAAGACCAAGAGAATGGTTGTTCCTGATGCTCTCAAgtaagactttttctactgtttttttatgctaatatatttaattttaatatagtttgataggcctacactagcaacctatttgaaatcattc-attgtacat--
| |||||||| |  ||||||||||| ||||||||||| | ||| ||| | || ||||| |||||||||  ||||||||||||  ||||||||||||||||||||   || | | ||| || || |||  |        |||||||  |   |||  ||  |  |   ||  ||||   |||    |  ||   || |   |  
CCAAGCGTGGTGCTGCTGCTCTTGCACGTTTGAAGGTGTTTGAGGGAGTACCACCTCCTTATGACAAGGTCAAGAGAATGGTCATTCCTGATGCTCTCAAgtaatgtttctgcaact-ttgttctatcttg-------taattttggttatgttcaatgtgttttagctgtcaactggttttcgtttgttttgttttgtttag

upper sequence: GLYMA15G13670.1 (Glycine max), 5'ss of exon 2
lower sequence: AT4G13170.1 (Arabidopsis thaliana), 5'ss of exon 2
CAAAGCGTGGGGAAGCTGCTCTTGCTCGTTTGAAGGTTTATGAAGGAATCCCTCCTCCATATGACAAGACCAAGAGAATGGTTGTTCCTGATGCTCTCAAgtaagactttttctactgtttttttatgctaatatatttaattttaatatagtttg-ataggcctacactagcaacctatttgaaatcattcattgtacat
| |||||||| |  ||||| |||||||| |||||||||| ||| |||||||| ||||| || |||||||  |||||||||||| ||||||||||||| |||||||   | || |  | |||| ||||| |    |   | ||| |   ||||||    |     |    ||   | || ||   | |  || ||       
CCAAGCGTGGTGCTGCTGCACTTGCTCGCTTGAAGGTTTTTGAGGGAATCCCACCTCCTTACGACAAGATTAAGAGAATGGTTATTCCTGATGCTCTTAAgtaagttctcttttgtttttttgttatgttttgtttcatgattctgtaatagttaatgtccaaatgtgttaatgatctgtt--gattttttaatcag----

upper sequence: GLYMA15G13670.1 (Glycine max), 5'ss of exon 2
lower sequence: AT3G07110.1 (Arabidopsis thaliana), 5'ss of exon 2
CAAAGCGTGGGGAAGCTGCTCTTGCTCGTTTGAAGGTTTATGAAGGAATCCCTCCTCCATATGACAAGACCAAGAGAATGGTTGTTCCTGATGCTCTCAAgtaagactttttctactgtt-tttttatgctaatatatttaattttaat-atagtttgataggcctacactagcaacctatttgaaatcattcattgtacat---
| |||||||| |    ||| ||||| || |||||||| | ||||||| | ||| ||||||||||||||| |||||| ||||| |||||||||||||||||||  | | ||||   || |  |||| ||  |  |  | ||   || | | ||| ||  |     ||||| |  |      ||||  ||  ||| || |  ||   
CTAAGCGTGGAGCTAATGCACTTGCCCGCTTGAAGGTCTTTGAAGGAGTTCCTACTCCATATGACAAGATCAAGAGGATGGTCGTTCCTGATGCTCTCAAgtttgtccttttaccctttcattttcattttttttcagtttccttcatttatacttacaagtagctacagtctctgaaactttg--attcttccttcttgatcag

upper sequence: GLYMA15G13670.1 (Glycine max), 5'ss of exon 2
lower sequence: AT5G48760.1 (Arabidopsis thaliana), 5'ss of exon 2
CAAAGCGTGGGGAAGCTGCTCTTGCTCGTTTGAAGGTTTATGAAGGAATCCCTCCTCCATATGACAAGACCAAGAGAATGGTTGTTCCTGATGCTCTCAAgtaaga--ctttttctactgtttttttatgctaatatatttaattttaatatagtttgataggcctacactagcaacctatttgaaatcattcattgtacat
| |||||||| |  |||||  | || ||| ||||||| ||||||||  | ||| ||||||||||||||| |||||| |||||  | ||||||||||||||||  |   ||||| | | | || || |   ||  |  ||       |  | || || |   ||| |  |  |  | | |  | |   |  ||||        
CGAAGCGTGGAGCTGCTGCATTAGCACGTCTGAAGGTATATGAAGGTGTTCCTACTCCATATGACAAGATCAAGAGGATGGTCATCCCTGATGCTCTCAAgtttgttccttttaccatttttgttcttctcttttggatccgtaactgttctacttcg---ggcattgatgattatcattgtggctcttcttcag-------

upper sequence: GLYMA15G13670.1 (Glycine max), 5'ss of exon 2
lower sequence: Vv07s0005g06490.t01 (Vitis vinifera), 5'ss of exon 2
CAAAGCGTGGGGAAGCTGCTCTTGCTCGTTTGAAGGTTTATGAAGGAATCCCTCCTCCATATGACAAGACCAAGAGAATGGTTGTTCCTGATGCTCTCAAgtaagactttt---tctactgtttttttatg---ctaatatatttaattttaatatagtttga----taggcctacactagcaacctatttgaaa-tcattcattgtacat------------------------------
| |||||||| | ||| || ||||| || ||||||| |||||| ||||||||||| |||||||| ||||  ||||| |||||  |||||||||| ||||||| ||  | ||   |||  || || |   ||   || |  |  ||||||    | | |||| |    ||    |    ||   |  | ||| ||  |  ||  |||   ||                              
CCAAGCGTGGAGCAGCAGCCCTTGCACGATTGAAGGCTTATGAGGGAATCCCTCCACCATATGATAAGATGAAGAGGATGGTCATTCCTGATGCACTCAAgttagtttcttgtttctcttgattatcgttgtctctgaatttcttaattggggtttggtttcaagtctattgtttttttaatcatgtgttttaatcttgtttcttgctaattgatttgatggttggttgaaataaaattag

upper sequence: GLYMA15G13670.1 (Glycine max), 5'ss of exon 2
lower sequence: Vv05s0029g00020.t01 (Vitis vinifera), 5'ss of exon 2
CAAAGCGTGGGGAAGCTGCTCTTGCTCGTTTGAAGGTTTATGAAGGAATCCCTCCTCCATATGACAAGACCAAGAGAATGGTTGTTCCTGATGCTCTCAAgtaagactttttctactgtttttttatgctaatatatttaattttaatatagtttgataggcctacactagcaacctatttgaaatcattcattgtacat---------
| |||||||| |  || || |||||  | ||||||| ||| || || || || ||||||||||| ||||  ||||| |||||| ||||||| |||||||||| ||   || | || |    ||||||  |    | |||| |||| || |||    |||         | |      | || ||  | |    | |             
CTAAGCGTGGAGCCGCAGCGCTTGCCAGATTGAAGGCTTACGAGGGGATTCCACCTCCATATGATAAGATGAAGAGGATGGTTATTCCTGACGCTCTCAAgtgag---ttctgtatttgagttttattttttattttttattttttatttaggcctataaattcttgttggtttgagactttaatgcttgagatttttgggaaaatcag

upper sequence: GLYMA15G13670.1 (Glycine max), 5'ss of exon 2
lower sequence: EFJ34798 (Selaginella moellendorffii), 5'ss of exon 3
CAAAGCGTGGGGAAGCTGCTCTTGCTCGTTTGAAGGTTTATGAAGGAATCCCTCCTCCATATGACAAGACCAAGAGAATGGTTGTTCCTGATGCTCTCAAgtaagactttttctactgtttttttatgctaatatatttaattttaatatagtttgataggcctacactagcaacctatttgaaatcattcattgtacat
| ||||| || |  |||||||| |   |  | ||||| |  ||||||  ||| ||||| ||||||||||||||||  ||||| ||||| || ||||||||||||| ||     |  |  || |||   | |  ||   | |   |   || |    | ||                                        
CCAAGCGCGGTGCCGCTGCTCTGGAGAGGCTCAAGGTCTTCGAAGGATGCCCACCTCCGTATGACAAGACCAAGAAGATGGTCGTTCCAGACGCTCTCAAgtaagcctccacttttttcttcttt---caaggatggctgacgatcggatcga--aacag----------------------------------------

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|208323842|gb|GE120047.1|GE120047
EST:     CCAAGAGAATGGTTGTTCCTGATGCTCTCAA                         GGTGTTGAGGCTTCAGAAGGGACACAAGCACTGTGTATTGGGCAGGTTGTC
genomic: CCAAGAGAATGGTTGTTCCTGATGCTCTCAAgtaagacttt ... atggaatcagGGTGTTGAGGCTTCAGAAAGGACACAAGTACTGTGTATTGGGCAGGTTGTC
EST: gi|254343697|gb|GR857453.1|GR857453
EST:     CCTCCTCCATATGACAAGACCAAGAGAATGGTTGTTCCTGATGCTCTCAA                         GGTGTTGAGGCTTCAGAAAGGACACAAGTACTGTGTATTGGGCAGGTTGTC
genomic: CCTCCTCCATATGACAAGACCAAGAGAATGGTTGTTCCTGATGCTCTCAAgtaagacttt ... atggaatcagGGTGTTGAGGCTTCAGAAAGGACACAAGTACTGTGTATTGGGCAGGTTGTC
EST: gi|298163268|gb|HO012001.1|HO012001
EST:     CCTCCTCCATATGACAAGACCAAGAGAATGGTTGTTCCTGATGCTCTCAA                         GGTGTTGAGGCTTCAGAAAGGACACAAGTACTGTGTATTGGGCAGGTTGTC
genomic: CCTCCTCCATATGACAAGACCAAGAGAATGGTTGTTCCTGATGCTCTCAAgtaagacttt ... atggaatcagGGTGTTGAGGCTTCAGAAAGGACACAAGTACTGTGTATTGGGCAGGTTGTC
EST: gi|16347249|gb|BI972844.1|BI972844
EST:     CCTCCTCCATATGACAAGACCAAGAGAATGGTTGTTCCTGATGCTCTCAA                         GGTGTTGAGGCTTCAGAAAGGACACAAGTACTGTGTATTGGGCAGGTTGTC
genomic: CCTCCTCCATATGACAAGACCAAGAGAATGGTTGTTCCTGATGCTCTCAAgtaagacttt ... atggaatcagGGTGTTGAGGCTTCAGAAAGGACACAAGTACTGTGTATTGGGCAGGTTGTC
EST: gi|298168387|gb|HO009317.1|HO009317
EST:     CCTCCTCCATATGACAAGACCAAGAGAATGGTTGTTCCTGATGCTCTCAA                         GGTGTTGAGGCTTCAGAAAGGACACAAGTACTGTGTATTGGGCAGGTTGTC
genomic: CCTCCTCCATATGACAAGACCAAGAGAATGGTTGTTCCTGATGCTCTCAAgtaagacttt ... atggaatcagGGTGTTGAGGCTTCAGAAAGGACACAAGTACTGTGTATTGGGCAGGTTGTC
EST: gi|207817623|gb|GD791432.1|GD791432
EST:     CCAAGAGAATGGTTGTTCCTGATGCTCTCAA                         GGTGTTGAGGCTTCAGAAGGGACACAAGCACTGTGTATTGGGCAGGTTGTC
genomic: CCAAGAGAATGGTTGTTCCTGATGCTCTCAAgtaagacttt ... atggaatcagGGTGTTGAGGCTTCAGAAAGGACACAAGTACTGTGTATTGGGCAGGTTGTC
EST: gi|298166806|gb|HO010245.1|HO010245
EST:     CCTCCTCCATATGACAAGACCAAGAGAATGGTTGTTCCTGATGCTCTCAA                         GGTGTTGAGGCTTCAGAAAGGACACAAGTACTGTGTATTGGGCAGGTTGTC
genomic: CCTCCTCCATATGACAAGACCAAGAGAATGGTTGTTCCTGATGCTCTCAAgtaagacttt ... atggaatcagGGTGTTGAGGCTTCAGAAAGGACACAAGTACTGTGTATTGGGCAGGTTGTC
EST: gi|298168781|gb|HO009711.1|HO009711
EST:     CCTCCTCCATATGACAAGACCAAGAGAATGGTTGTTCCTGATGCTCTCAA                         GGTGTTGAGGCTTCAGAAAGGACACAAGTACTGTGTATTGGGCAGGTTGTC
genomic: CCTCCTCCATATGACAAGACCAAGAGAATGGTTGTTCCTGATGCTCTCAAgtaagacttt ... atggaatcagGGTGTTGAGGCTTCAGAAAGGACACAAGTACTGTGTATTGGGCAGGTTGTC
EST: gi|9986840|gb|BE660948.1|BE660948
EST:     CCTCCTCCATATGACAAGACCAAGAGAATGGTTGTTCCTGATGCTCTCAA                         GGTGTTGAGGCTTCAGAAAGGACACAAGTACTGTGTATTGGGCAGGTTGTC
genomic: CCTCCTCCATATGACAAGACCAAGAGAATGGTTGTTCCTGATGCTCTCAAgtaagacttt ... atggaatcagGGTGTTGAGGCTTCAGAAAGGACACAAGTACTGTGTATTGGGCAGGTTGTC
EST: gi|24205749|gb|BU965002.1|BU965002
EST:     CCTCCTCCATATGACAAGACCAAGAGAATGGTTGTTCCTGATGCTCTCAA                         GGTGTTGAGGCTTCAGAAAGGACACAAGTACTGTGTATTGGGCAGGTTGTC
genomic: CCTCCTCCATATGACAAGACCAAGAGAATGGTTGTTCCTGATGCTCTCAAgtaagacttt ... atggaatcagGGTGTTGAGGCTTCAGAAAGGACACAAGTACTGTGTATTGGGCAGGTTGTC
EST: gi|16348184|gb|BI973779.1|BI973779
EST:     CCTCCTCCATATGACAAGACCAAGAGAATGGTTGTTCCTGATGCTCTCAA                         GGTGTTGAGGCTTCAGAAAGGACACAAGTACTGTGTATTGGGCAGGTTGTC
genomic: CCTCCTCCATATGACAAGACCAAGAGAATGGTTGTTCCTGATGCTCTCAAgtaagacttt ... atggaatcagGGTGTTGAGGCTTCAGAAAGGACACAAGTACTGTGTATTGGGCAGGTTGTC
EST: gi|254343696|gb|GR857452.1|GR857452
EST:     CCTCCTCCATATGACAAGACCAAGAGAATGGTTGTTCCTGATGCTCTCAA                         GGTGTTGAGGCTTCAGAAAGGACACAAGTACTGTGTATTGGGCAGGTTGTC
genomic: CCTCCTCCATATGACAAGACCAAGAGAATGGTTGTTCCTGATGCTCTCAAgtaagacttt ... atggaatcagGGTGTTGAGGCTTCAGAAAGGACACAAGTACTGTGTATTGGGCAGGTTGTC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAAAGCGTGGGGAAGCTGCTCTTGCTCGTTTGAAGGTTTATGAAGGAATCCCTCCTCCATATGACAAGACCAAGAGAATGGTTGTTCCTGATGCTCTCAAgtaagactttttctactgtttttttatgctaatatatttaattttaatatagtttgataggcctacactagcaacctatttgaaatcattcattgtacat

- - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA