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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGCGGAGAGTAGAGGGAATGGCGTCCGAGGGCGTGCTCCTGGGGATGGGCAACCCCCTCCTCGACATCTCCGCCGTCGTCGACGACGCCTTCCTCACCAAgtacgcgcgcgctcgtctcctcctgctccttagtcctgatctaccgctgatcccttttttttttttgccttttcgttttgcgttcgtttggatccgaatg...

Basic information

species Oryza sativa
transcript LOC_Os02g41590.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g41590.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G540538_T02 (Zea mays), 5'ss of exon 1
AGCGGAGAGTAGAGGGAATGGCGTCCGAGGGCGTGCTCCTGGGGATGGGCAACCCCCTCCTCGACATCTCCGCCGTCGTCGACGACGCCTTCCTCACCAAgtacgcg--cgcgctcgtctcctcctgctccttagtcctgatctaccgctgatcccttttttttttttgccttttcgttttgcgttcgtttggatccgaatg
 | | ||||  ||      |||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||| || ||||| |||  ||  | |    ||||  |   || |    |          |||     |  |  |  | |  |||| ||  ||| |||| | |  |    |||
GGAGAAGAGAGGAAATGGCGGCGACCGAGGGCGTGCTCCTGGGGATGGGCAACCCCCTCCTCGACATCTCCGCCGTCGTCGATGACGCCTTCCTGACAAAgtaagcggtcgtaccctcgccctctcgtgtctgatctgtttataggaattgagttactcctagtcgtagtgttttggt--tgctttcggtggttttgctatg

upper sequence: LOC_Os02g41590.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G135132_T01 (Zea mays), 5'ss of exon 1
AGCGGAGAGTAGAGGGAATGGCGTCCGAGGGCGTGCTCCTGGGGATGGGCAACCCCCTCCTCGACATCTCCGCCGTCGTCGACGACGCCTTCCTCACCAAgtacg-cgcgcgctcgtctcctcctgctccttagtcctgatctaccgctgatcccttttttttttttgccttttcgttttgcgttcgtttggatccgaatg
|| | ||||  ||      ||||  ||||||||||||||||||||||||||||||||||||||||||||||||||| ||||| |||||||||||  | ||||| | ||  ||    || ||||   | |  |  ||    | ||    | |  |||  |  |  |  | ||  | | |||  |    ||||   || | | 
AGAGAAGAGAGGAAATGGCGGCGAGCGAGGGCGTGCTCCTGGGGATGGGCAACCCCCTCCTCGACATCTCCGCCGTTGTCGATGACGCCTTCCTGGCAAAgtaagtcggtcgtctctcacctctctcactctgatctgtttataggaattactcctagtcgtagtg-gtctggttgctttcggcggttttgcggcctagtc

upper sequence: LOC_Os02g41590.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GLYMA13G20780.1 (Glycine max), 5'ss of exon 1
AGCGGAGAGTAGAGGGAATGGCGTCCGAGGGCGTGCTCCTGGGGATGGGCAACCCCCTCCTCGACATCTCCGCCGTCGTCGACGACGCCTTCCTCACCAAgtacgcgcgcgctcgtctcctcctgctccttagtcctgat-ctaccgctgatcccttttttttttttgccttttcgttttgc-gttcgtttggatccgaatg
           |    ||||| ||  || ||||| ||||| || ||| ||||||| |||||||||||||| ||||||||||||||||| ||| |    |||||     || |||   |  |  |    |||  |  || | |||    | ||   | ||  |  | | | |     ||  |  ||   ||   ||    |  
CCTTCTTCACCGCATCAATGGAGTTGGACGGCGTTCTCCTCGGCATGTGCAACCCTCTCCTCGACATCTCTGCCGTCGTCGACGACGCTTTCTTGCAAAAgtattactgc-ctcacatttttttctctctttcttttgttactattattaattattcttaataatgt-catgagtattgagtagtatattactattttgagc

upper sequence: LOC_Os02g41590.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GLYMA10G06580.1 (Glycine max), 5'ss of exon 1
AGCGGAGAGTAGAGGGAATGGCGTCCGAGGGCGTGCTCCTGGGGATGGGCAACCCCCTCCTCGACATCTCCGCCGTCGTCGACGACGCCTTCCTCACCAAgtacgcgcgcgctcgtctcctcctgctccttagtcctgatctaccgctgatcccttttttttttttgccttttcgttttgcgttcgtttggatccgaatg
         | |    ||||| ||  || ||||| ||||| || ||| ||||||| |||||||||||||| ||||||||||||||||| ||| |    |||||    | |  ||      | ||    ||   ||    |||     | ||   |  |  | | |||  | |     |    |  | || || |      
CCTTCTTCCTCGCATCAATGGAGTTGGACGGCGTTCTCCTCGGCATGTGCAACCCTCTCCTCGACATCTCTGCCGTCGTCGACGACGCTTTCTTGCAAAAgtattaccactatctcacatttctctctctctctctctttcttttatttattgataataatgtgttgaatatattactattatgagcttagaactatgaa

upper sequence: LOC_Os02g41590.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GLYMA03G33910.1 (Glycine max), 5'ss of exon 1
AGCGGAGAGTAGA-GGGAATGGCGTCCGAGGGCGTGCTCCTGGGGATGGGCAACCCCCTCCTCGACATCTCCGCCGTCGTCGACGACGCCTTCCTCACCAAgtacgcgcgcgctcgtctcctcctgctccttagtcctgatctaccgctgatcccttttttttttttgccttttcgttttgcgttcgtttggat--ccgaatg---------------------------------------------------------------------
   |   |  | | |  ||||| |||||| ||| | |||||||| || || ||||| ||||||||||||||||||||||||||| | | |||| | |  ||||||   |   |||     |||    | |   | | |  |   || ||   | | |  |||  |||  | || |      |||||  | || |  | | |||                                                                     
-TTGATCATCACATGAAAATGGTGTCCGAAGGCATTCTCCTGGGCATTGGTAACCCTCTCCTCGACATCTCCGCCGTCGTCGACCAAGACTTCTTTAAAAAgtaccatctgactcactcactctcttttccatgccgttttgctccactctcctcgtcgtttcgtttaaccttgcacac--cgttccataggtttactggatggatcaacgacgtcgtaaatcgctttgttcgcttctgaatgatttttttacttgtttttgtgtttgatag

upper sequence: LOC_Os02g41590.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GLYMA19G36630.1 (Glycine max), 5'ss of exon 1
-AGCGGAGAGTAGAGGGAATGGCGTCCGAGGGCGTGCTCCTGGGGATGGGCAACCCCCTCCTCGACATCTCCGCCGTCGTCGACGACGCCTTCCTCACCAAgtacgcgcgcgctcgtctcctcctgctccttagtcctgatcta--ccgctgatcccttttttttttttgccttt-tcgttttgc-gttcgtttggatccgaatg----------------------------------------------
  |   |||  | |   ||||| |||||| |||   |||||||| ||||| ||||| |||||||||||||||||||||||||| || | |||| | |  |||||    ||| ||| |||     | |      ||  || || |  |  ||  ||  ||  ||  ||| |       ||||  |  | |     |||  || ||                                               
TTGATCAGATCATAAC-AATGGTGTCCGAAGGCACTCTCCTGGGCATGGGTAACCCTCTCCTCGACATCTCCGCCGTCGTCGATGAAGACTTCTTAAAAAAgtatcaccgcactc-tctttaatttccatgccgttttgctccattctcctcgtcgtttcgttactttagagaacaccgttccgtagcttcaccgga--cggataaactacgtcgtttatcgttctgaatgatttttgtgtgttgtgacag

upper sequence: LOC_Os02g41590.1 (Oryza sativa), 5'ss of exon 1
lower sequence: Vv13s0019g04470.t01 (Vitis vinifera), 5'ss of exon 1
AGCGGAGAGTAGAGGGAATGGCGTCCGAGGGCGTGCTCCTGGGGATGGGCAACCCCCTCCTCGACATCTCCGCCGTCGTCGACGACGCCTTCCTCACCAAgtacgcgcgcgctcgtctcctcctgctccttagtcctgatctaccgct--gatcccttttttttttttgccttttcgttttgcgttcgtttggatccgaatg
      |  |      |||||| | ||| ||  | |||||||| |||||||||||||| |||||||| ||  | ||||||||||| |  |||||    |||||      | ||| | |  |  |||   | | | ||  ||| |   |   || |    ||||  ||    ||||  | |||  | ||||   |||    ||
CCTCTTGGATCTCTTCAATGGCTTACGAAGGAATCCTCCTGGGCATGGGCAACCCCCTGCTCGACATTTCTTCTGTCGTCGACGAAGAATTCCTTCAAAAgtaactctactctcctttgtta-tgcggttca-ttctcctctgcttttcaaatgctgcgttttgattctgtttttgttcttggatccgttcttatcgttgtg

upper sequence: LOC_Os02g41590.1 (Oryza sativa), 5'ss of exon 1
lower sequence: Vv13s0019g04480.t01 (Vitis vinifera), 5'ss of exon 1
AGCGGAGAGTAGAGGGAATGGCGTCCGAGGGCGTGCTCCTGGGGATGGGCAACCCCCTCCTCGACATCTCCGCCGTCGTCGACGACGCCTTCCTCACCAAgtacgcgcgcgctcgtctcctcc-tgctccttagtcctgatctaccgctgatcccttttttttttttgccttttcgttttgcgttcgtttggatccgaatg
      |  |      |||||| | ||| ||  | |||||||| ||||||||||||||||||||||| ||  | ||||||||||| |  |||||    | |||      | ||| | |  ||   | | | | |||||   ||    |  || |    ||||  ||    ||||  | |||  | ||||   ||     ||
CCTCTTGGATCTCTTCAATGGCTTACGAAGGAATCCTCCTGGGCATGGGCAACCCCCTCCTCGACATTTCTTCTGTCGTCGACGAAGAATTCCTTCAAAGgtaactctactctcctttgttctgcggttcgtcgtcctctgct-tttcaaatgctgcgttttgattctgtttttgttcttggatccgttcttatggttgtg

upper sequence: LOC_Os02g41590.1 (Oryza sativa), 5'ss of exon 1
lower sequence: PP1S74_140V6.1 (Physcomitrella patens), 5'ss of exon 1
AGCGGAGAGTAGAGGG-AATGGCGTCCGAGGGCGTGCTCCTGGGGATGGGCAACCCCCTCCTCGACATCTCCGCCGTCGTCGACGACGCCTTCCTCACCAAgtacgcgcgcgctcgtctcctcctgctccttagtcctgatctac-cgctgatcccttttttttttttgccttttcgttttgcgttcgtttggatccgaatg
 ||      |     | ||||||||||||||| |||||  |||| ||||| |||||||| ||||||||||||  ||| ||||||||||| ||||||   |||||   |  |      ||| |    || |       || | | |  |||  |   ||   | | | ||     | || ||   ||  |||      |    
-GCATTCTCTCTCTCGCAATGGCGTCCGAGGGTGTGCTTTTGGGCATGGGAAACCCCCTGCTCGACATCTCCTGCGTGGTCGACGACGCATTCCTCGAGAAgtaacggttcctctccctcgtttctcttcacttctttggtttccgtgctcgtgtgttgagtgtgtgtgtgagctagtctttttttttttttcggttgtgc-

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|428330|gb|D24478.1|D24478
EST:     AACCCCCTNCTCGACATCTCCGCCGTCGTCGACGACGCCTTCCTCACCAA                         GTATGACGTCAAGCTGAACAATGCAATTCTCGCTGAGGAAAAGCACTTGCC
genomic: AACCCCCTCCTCGACATCTCCGCCGTCGTCGACGACGCCTTCCTCACCAAgtacgcgcgc ... aatgttttagGTATGACGTCAAGCTGAACAATGCAATTCTCGCTGAGGAAAAGCACTTGCC
EST: gi|163918496|gb|EG710298.1|EG710298
EST:     AACCCCCTCCTCGACATCTCCGCCGTCGTCGACGACGCCTTCCTCACCAA                         GTATGACGTCAAGCTGAACAATGCAATTCTCGCTGAGGAAAAGCACTTGCC
genomic: AACCCCCTCCTCGACATCTCCGCCGTCGTCGACGACGCCTTCCTCACCAAgtacgcgcgc ... aatgttttagGTATGACGTCAAGCTGAACAATGCAATTCTCGCTGAGGAAAAGCACTTGCC
EST: gi|428228|gb|D24376.1|D24376
EST:     AACCCCCTCCTCGACATCTCCGCCGTCGTCGACGACGCCTTCCTCACCAA                         GTATGACGTCAAGCTGAACAATGCAATTCTCGCTGAGGAAAAGCACTTGCC
genomic: AACCCCCTCCTCGACATCTCCGCCGTCGTCGACGACGCCTTCCTCACCAAgtacgcgcgc ... aatgttttagGTATGACGTCAAGCTGAACAATGCAATTCTCGCTGAGGAAAAGCACTTGCC
EST: gi|88733084|gb|CI756261.1|CI756261
EST:     AACCCCCTCCTCGACATCTCCGCCGTCGTCGACGACGCCTTCCTCACCAA                         GTATGACGTCAAGCTGAACAATGCAATTCTCGCTGAGGAAAAGCACTTGCC
genomic: AACCCCCTCCTCGACATCTCCGCCGTCGTCGACGACGCCTTCCTCACCAAgtacgcgcgc ... aatgttttagGTATGACGTCAAGCTGAACAATGCAATTCTCGCTGAGGAAAAGCACTTGCC
EST: gi|88394239|gb|CI603428.1|CI603428
EST:     AACCCCCTCCTCGACATCTCCGCCGTCGTCGACGACGCCTTCCTCACCAA                         GTATGACGTCAAGCTGAACAATGCAATTCTCGCTGAGGAAAAGCACTTGCC
genomic: AACCCCCTCCTCGACATCTCCGCCGTCGTCGACGACGCCTTCCTCACCAAgtacgcgcgc ... aatgttttagGTATGACGTCAAGCTGAACAATGCAATTCTCGCTGAGGAAAAGCACTTGCC
EST: gi|66922324|gb|CX109172.1|CX109172
EST:     AACCCCCTCCTCGACATCTCCGCCGTCGTCGACGACGCCTTCCTCACCAA                         GTATGACGTCAAGCTGAACAATGCAATTCTCGCTGAGGAAAAGCACTTGCC
genomic: AACCCCCTCCTCGACATCTCCGCCGTCGTCGACGACGCCTTCCTCACCAAgtacgcgcgc ... aatgttttagGTATGACGTCAAGCTGAACAATGCAATTCTCGCTGAGGAAAAGCACTTGCC
EST: gi|55410432|gb|CV722808.1|CV722808
EST:     AACCCCCTCCTCGACATCTCCGCCGTCGTCGACGACGCCTTCCTCACCAA                         GTATGACGTCAAGCTGAACAATGCAATTCTCGCTGAGGAAAAGCACTTGCC
genomic: AACCCCCTCCTCGACATCTCCGCCGTCGTCGACGACGCCTTCCTCACCAAgtacgcgcgc ... aatgttttagGTATGACGTCAAGCTGAACAATGCAATTCTCGCTGAGGAAAAGCACTTGCC
EST: gi|33820427|gb|CF336024.1|CF336024
EST:     AACCCCCTCCTCGACATCTCCGCCGTCGTCGACGACGCCTTCCTCACCAA                         GTATGACGTCAAGCTGAACAATGCAATTCTCGCTGAGGAAAAGCACTTGCC
genomic: AACCCCCTCCTCGACATCTCCGCCGTCGTCGACGACGCCTTCCTCACCAAgtacgcgcgc ... aatgttttagGTATGACGTCAAGCTGAACAATGCAATTCTCGCTGAGGAAAAGCACTTGCC
EST: gi|58657974|gb|CK046654.1|CK046654
EST:     AACCCCCTCCTCGACATCTCCGCCGTCGTCGACGACGCCTTCCTCACCAA                         GTATGACGTCAAGCTGAACAATGCAATGCGCGCTGAGGAAAAGCACTTGCC
genomic: AACCCCCTCCTCGACATCTCCGCCGTCGTCGACGACGCCTTCCTCACCAAgtacgcgcgc ... aatgttttagGTATGACGTCAAGCTGAACAATGCAATTCTCGCTGAGGAAAAGCACTTGCC

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 74 (upstream exon), 61 (downstream exon)
Score: 101

AGCGGAGAGTAGAGGGAATGGCGTCCGAGGGCGTGCTCCTGGGGATGGGCAACCCCCTCCTCGACATCTCCGCCGTCGTCGACGACGCCTTCCTCACCAAgtacgcgcgc ... aatgttttagGTATGACGTCAAGCTGAACAATGCAATTCTCGCTGAGGAAAAGCACTTGCCTAT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGCGGAGAGTAGAGGGAATGGCGTCCGAGGGCGTGCTCCTGGGGATGGGCAACCCCCTCCTCGACATCTCCGCCGTCGTCGACGACGCCTTCCTCACCAAgtacgcgcgcgctcgtctcctcctgctccttagtcctgatctaccgctgatcccttttttttttttgccttttcgttttgcgttcgtttggatccgaatg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctcctcc