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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAGAATCTTGGGACTTGGAGATCTTGGAGTTCAAGGAATTGGCATTGCCATTGGGAAGCTTGATCTATATGTTGCTGCTGCTGGGATAAATCCTCAAAGGgtacgctgttgctcaatgtttcattatttttcctttccaactgttcaggttttgataacattggtatctttatgttgtcggtaaggaaatatcccaattt...

Basic information

species Glycine max
transcript GLYMA03G24630.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G24630.1 (Glycine max), 5'ss of exon 5
lower sequence: LOC_Os07g31380.1 (Oryza sativa), 5'ss of exon 5
CAGAATCTTGGGACTTGGAGATCTTGGAGTTCAAGGAATTGGCATTGCCATTGGGAAGCTTGATCTATATGTTGCTGCTGCTGGGATAAATCCTCAAAGGgtac--gctgttgctcaatgtttcatta-----tttttcctttccaactgttcaggttttgataacattggtatctttatg-ttgtcggtaaggaaatatcccaattt
||| || ||||| || || ||||| || || || || ||||| ||||||||||| ||| | ||||||||||||||||||||||| |||||||| || ||||||    || ||| |  ||| | | |||     || ||    ||   |  |||    | |  |||  ||          || || |  |||| ||  | |        
CAGGATATTGGGCCTGGGTGATCTCGGGGTGCATGGTATTGGTATTGCCATTGGAAAGTTGGATCTATATGTTGCTGCTGCTGGAATAAATCCCCAGAGGgtaaaaacttttggtttatggtaccttagaagattgttagactcttccctttctccctcttctaattttacatctcccgtgcttttttgtaatgactttt--------

upper sequence: GLYMA03G24630.1 (Glycine max), 5'ss of exon 5
lower sequence: GRMZM2G406672_T02 (Zea mays), 5'ss of exon 5
CAGAATCTTGGGACTTGGAGATCTTGGAGTTCAAGGAATTGGCATTGCCATTGGGAAGCTTGATCTATATGTTGCTGCTGCTGGGATAAATCCTCAAAGGgtacgctgttgctcaatgtttcattat--ttttcctttccaactgttcaggttttgataacattggtatct-ttatgttgtcggtaaggaaatatcccaattt---
||| || ||||| ||||| |||||||| || || || ||||||||||| ||||| ||  | ||| ||||||||||||||||||| |||||||||||||||||  | ||      |||| ||| |||    | |  ||||  | | |||   | ||    |  ||  | ||  ||          |    |  | |  ||       
CAGGATATTGGGTCTTGGTGATCTTGGGGTGCATGGTATTGGCATTGCTATTGGAAAATTGGATTTATATGTTGCTGCTGCTGGAATAAATCCTCAAAGGgtgtgttg------aatggttctttagaactctaatttcagattattcccctctttcccatcttattttcagttccacctaaactggccaccttttgcagccaaat

upper sequence: GLYMA03G24630.1 (Glycine max), 5'ss of exon 5
lower sequence: AT2G13560.1 (Arabidopsis thaliana), 5'ss of exon 5
CAGAATCTTGGGACTTGGAGATCTTGGAGTTCAAGGAATTGGCATTGCCATTGGGAAGCTTGATCTATATGTTGCTGCTGCTGGGATAAATCCTCAAAGGgtacgc-tgttgctcaatgtttcattatttttcc--tttccaactgttcaggt--tttgataacattggtatctttatgttgtcggtaaggaaatatcccaattt
| | || ||||| ||||||||||| || ||||| |||||||| |||||  | |||||||||||| |||||||||| || ||||| |||||||||||| ||||||           ||| |||  ||||||| ||  | ||||  | |     |  | |||||  |||  ||| |  |  |  | | | ||               
CCGGATTTTGGGTCTTGGAGATCTAGGTGTTCATGGAATTGGAATTGCTGTAGGGAAGCTTGATTTATATGTTGCCGCAGCTGGAATAAATCCTCAACGGgtacttgcaccatctaatattttcttattttccccatctccatttttctgtatgatgtgatacaattcttatgtgcacatgctggtttag---------------

upper sequence: GLYMA03G24630.1 (Glycine max), 5'ss of exon 5
lower sequence: Vv15s0021g00500.t01 (Vitis vinifera), 5'ss of exon 5
CAGAATCTTGGGACTTGGAGATCTTGGAGTTCAAGGAATTGGCATTGCCATTGGGAAGCTTGATCTATATGTTGCTGCTGCTGGGATAAATCCTCAAAGGgtacgctgttgctcaatgtttcattatttttcctttccaactgttcaggttttgataacattggtatctttatgttgtcggtaaggaaatatcccaattt---
|||||| ||||| |||||||||||||||||||| || ||||| ||||| ||||||||||| ||| ||||||||||||||||||| |||||||||||||| |||   |   |||  |  | ||| |  | ||| | || || | ||   | |   |||  | | | | |  | |  ||    |  |  |   | ||  | |   
CAGAATATTGGGTCTTGGAGATCTTGGAGTTCAGGGCATTGGGATTGCAATTGGGAAGCTGGATTTATATGTTGCTGCTGCTGGAATAAATCCTCAAAGAgtatcttcccgctttacatgtcact--tgttcttatctaagtattttagatg-aatatgactagaaaccatgttctgaattttggctagactgcccctctaaa

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|19270517|gb|BM886773.1|BM886773
EST:     TTGGGAAGCTTGATCTATATGTTGCTGCTGCTGGGATAAATCCTCAAAGG                         GTACTTCCGGTGATGATTGATGTTGGTACTAATAATGAGAAGTTACTCGAA
genomic: TTGGGAAGCTTGATCTATATGTTGCTGCTGCTGGGATAAATCCTCAAAGGgtacgctgtt ... cttgcaatagGTACTTCCGGTGATGATTGATGTTGGTACTAATAATGAGAAGTTACTCGAA
EST: gi|19345893|gb|BM890773.1|BM890773
EST:     TTGGGAAGCTTGATCTATATGTTGCTGCTGCTGGGATAAATCCTCAAAGG                         GTACTTCCGGTGATGATTGATGTTGGTACTAATAATGAGAAGTTACTCGAA
genomic: TTGGGAAGCTTGATCTATATGTTGCTGCTGCTGGGATAAATCCTCAAAGGgtacgctgtt ... cttgcaatagGTACTTCCGGTGATGATTGATGTTGGTACTAATAATGAGAAGTTACTCGAA
EST: gi|13788373|gb|BG650965.1|BG650965
EST:     TTGGGAAGCTTGATCTATATGTTGCTGCTGCTGGGATAAATCCTCAAA-G                         GTACTTCCGGTGATGATTGATGTTGGTACTAATAATGAGAAGTTACTCGAA
genomic: TTGGGAAGCTTGATCTATATGTTGCTGCTGCTGGGATAAATCCTCAAAGGgtacgctgtt ... cttgcaatagGTACTTCCGGTGATGATTGATGTTGGTACTAATAATGAGAAGTTACTCGAA
EST: gi|17519704|gb|BM188746.1|BM188746
EST:     TTGGGAAGCTTGATCTATATGTTGCTGCTGCTGGGATAAATCCTCAAAGG                         GTACTTCCGGTGATGATTGATGTTGGTACTAATAATGAGAAGTTACTCGAA
genomic: TTGGGAAGCTTGATCTATATGTTGCTGCTGCTGGGATAAATCCTCAAAGGgtacgctgtt ... cttgcaatagGTACTTCCGGTGATGATTGATGTTGGTACTAATAATGAGAAGTTACTCGAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAGAATCTTGGGACTTGGAGATCTTGGAGTTCAAGGAATTGGCATTGCCATTGGGAAGCTTGATCTATATGTTGCTGCTGCTGGGATAAATCCTCAAAGGgtacgctgttgctcaatgtttcattatttttcctttccaactgttcaggttttgataacattggtatctttatgttgtcggtaaggaaatatcccaattt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cctttcc