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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TATCCATGATGGAGCAGTCACTGGGAAAGCAGCAGATGTTCTTGCTGCTGCCAACACAGCGGCAGAAGTTGCTCTGAGGCTTGTTAGACCTGGGAAGAAGgtgcattgaaaagcgttgctttatttacttgctctctttttgcaatttatgctgttcacatttagtgtctaggtcaactgtgcacacaaatgttgtgctt...

Basic information

species Oryza sativa
transcript LOC_Os05g28280.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g28280.1 (Oryza sativa), 5'ss of exon 5
lower sequence: AC233895.1_FGT001 (Zea mays), 5'ss of exon 4
TATCCATGATGGAGCAGTCACTGGGAAAGCAGCAGATGTTCTTGCTGCTGCCAACACAGCGGCAGAAGTTGCTCTGAGGCTTGTTAGACCTGGGAAGAAGgtgcat-----tgaaaagcgtt--gctttattt-acttgctctctttttgcaat--ttatgctgttcacatttagtgtctaggtc--aactgtgcacacaaatgttgtgctt-------------------------------------------------------------------------------------
 ||     ||||  | ||||| || |  || |  ||||| |||||||||||||||||||| |||||||| ||  || ||||||| |||||||||||||| ||   |     || |||||     | ||| ||| ||  | | | ||||  ||||  || | |  ||  | || ||  | ||  |   ||   ||    ||| || ||  ||                                                                                      
AATTACAAATGGGCCTGTCACAGGAAGGGCTGGTGATGTGCTTGCTGCTGCCAACACAGCAGCAGAAGTCGCAATGCGGCTTGTGAGACCTGGGAAGAAAgtaagtgtttttgcaaagcccaaagttttgtttcacaagttatattttatcaatcattgttcccttatccttaagcatatatctttgaaagatgt-ttcaagtggtgatctaactaagtatttcctttctcattttttacatgtactgatttgttcatttcgttggtatttatatatatatatatatatatattcag

upper sequence: LOC_Os05g28280.1 (Oryza sativa), 5'ss of exon 5
lower sequence: EFJ10608 (Selaginella moellendorffii), 5'ss of exon 4
TATCCATGATGGAGCAGTCACTGGGAAAGCAGCAGATGTTCTTGCTGCTGCCAACACAGCGGCAGAAGTTGCTCTGAGGCTTGTTAGACCTGGGAAGAAGgtgcattgaaaagcgttgctttatttacttgctctctttttgcaatttatg-ctgttcacatttagtgtctaggtcaactgtgcacacaaatgttgtgctt
  |||| || ||  |||| ||||| | |||||| |||||| | || ||||||||||| ||||||||||||||||| ||||| || || ||||| |||||||||  || |  ||     ||   | ||  || ||  |  |  |  ||| |  |||||    |||  ||  |||                            
CCTCCAGGAGGGTCCAGTGACTGGAAGAGCAGCGGATGTTTTAGCAGCTGCCAACACTGCGGCAGAAGTTGCTCTCAGGCTCGTGAGGCCTGGAAAGAAGgtgtctttaccagt----ctgagtataggtggtcgttactcacggtttctttctgtttgtgtttc-tgaatag----------------------------

upper sequence: LOC_Os05g28280.1 (Oryza sativa), 5'ss of exon 5
lower sequence: EFJ35350 (Selaginella moellendorffii), 5'ss of exon 4
TATCCATGATGGAGCAGTCACTGGGAAAGCAGCAGATGTTCTTGCTGCTGCCAACACAGCGGCAGAAGTTGCTCTGAGGCTTGTTAGACCTGGGAAGAAGgtgcattgaaaagcgttgctttatttacttgctctctttttgcaatttatg-ctgttcacatttagtgtctaggtcaactgtgcacacaaatgttgtgctt
  |||| || ||  |||| ||||| | |||||| |||||| | || ||||||||||| ||||||||||||||||| ||||| || || ||||| |||||||||  || |  ||     ||   | ||  || ||  |  |  |  ||| |  |||||    |||  ||  |||                            
CCTCCAGGAGGGTCCAGTGACTGGAAGAGCAGCGGATGTTTTAGCAGCTGCCAACACTGCGGCAGAAGTTGCTCTCAGGCTCGTGAGGCCTGGAAAGAAGgtgtctttaccagt----ctgagtataggtggtcgttactcacggtttctttctgtttgtctttc-tgaatag----------------------------

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|58685952|gb|CK074639.1|CK074639
EST:     CCAACACAGCGGCAGAAGTTGCTCTGAGGCTTGTTAGACCTGGGAAGAAG                         AACAAGGATGTCACCGAAGCGATTCAGAAAGTTGCTGCTGCTTATGACTGC
genomic: CCAACACAGCGGCAGAAGTTGCTCTGAGGCTTGTTAGACCTGGGAAGAAGgtgcattgaa ... tcttttgcagAACAAGGATGTCACCGAAGCGATTCAGAAAGTTGCTGCTGCTTATGACTGC
EST: gi|58597052|gb|CK007580.1|CK007580
EST:     CCAACACAGCGGCAGAAGTTGCTCTGAGGCTTGTTAGACCTGGGAAGAAG                         AACAAGGATGTCACCGAAGCGATTCAGAAAGTTGCTGCTGCTTATGACTGC
genomic: CCAACACAGCGGCAGAAGTTGCTCTGAGGCTTGTTAGACCTGGGAAGAAGgtgcattgaa ... tcttttgcagAACAAGGATGTCACCGAAGCGATTCAGAAAGTTGCTGCTGCTTATGACTGC
EST: gi|58694139|gb|CK082826.1|CK082826
EST:     CCAACACAGCGGCAGAAGTTGCTCTGAGGCTTGTTAGACCTGGGAAGAAG                         AACAAGGATGTCACCGAAGCGATTCAGAAAGTTGCTGCTGCTTATGACTGC
genomic: CCAACACAGCGGCAGAAGTTGCTCTGAGGCTTGTTAGACCTGGGAAGAAGgtgcattgaa ... tcttttgcagAACAAGGATGTCACCGAAGCGATTCAGAAAGTTGCTGCTGCTTATGACTGC
EST: gi|58587681|gb|CF985989.1|CF985989
EST:     AGCGGCAGAAGTTGCTCTGAGGCTTGTTAGACCTGGGAAGAAG                         AACAAGGATGTCACCGAAGCGATTCAGAAAGTTGCTGCTGCTTATGACTGC
genomic: AGCGGCAGAAGTTGCTCTGAGGCTTGTTAGACCTGGGAAGAAGgtgcattgaa ... tcttttgcagAACAAGGATGTCACCGAAGCGATTCAGAAAGTTGCTGCTGCTTATGACTGC
EST: gi|6850180|gb|AU082299.1|AU082299
EST:     CAACACAGCGGCCAGAAGTTGCTTTGAGGCTTGTTAGACCT-GGAAGAAG                         ACCAAGGATGTCACCGAAGCGATTCAGAAAGTTGCTGCTGCTTATGACTGC
genomic: CAACACAGCGG-CAGAAGTTGCTCTGAGGCTTGTTAGACCTGGGAAGAAGgtgcattgaa ... tcttttgcagAACAAGGATGTCACCGAAGCGATTCAGAAAGTTGCTGCTGCTTATGACTGC
EST: gi|58684011|gb|CK072698.1|CK072698
EST:     CCAACACAGCGGCAGAAGTTGCTCTGAGGCTTGTTAGACCTGGGAAGAAG                         AACAAGGATGTCACCGAAGCGATTCAGAAAGTTGCTGCTGCTTATGACTGC
genomic: CCAACACAGCGGCAGAAGTTGCTCTGAGGCTTGTTAGACCTGGGAAGAAGgtgcattgaa ... tcttttgcagAACAAGGATGTCACCGAAGCGATTCAGAAAGTTGCTGCTGCTTATGACTGC
EST: gi|58678661|gb|CK067348.1|CK067348
EST:     CCAACACAGCGGCAGAAGTTGCTCTGAGGCTTGTTAGACCTGGGAAGAAG                         AACAAGGATGTCACCGAAGCGATTCAGAAAGTTGCTGCTGCTTATGACTGC
genomic: CCAACACAGCGGCAGAAGTTGCTCTGAGGCTTGTTAGACCTGGGAAGAAGgtgcattgaa ... tcttttgcagAACAAGGATGTCACCGAAGCGATTCAGAAAGTTGCTGCTGCTTATGACTGC
EST: gi|58605226|gb|CK033259.1|CK033259
EST:     GCAACACAGCGGCAGAAGTTGGTCTGAGGCTTGTTAGACCTGGGAAGAAG                         AACAAGGATGTCACCGAAGCGATTCAGAAAGTT
genomic: CCAACACAGCGGCAGAAGTTGCTCTGAGGCTTGTTAGACCTGGGAAGAAGgtgcattgaa ... tcttttgcagAACAAGGATGTCACCGAAGCGATTCAGAAAGTT
EST: gi|33793355|gb|CF322559.1|CF322559
EST:     GGCAGAAGTTGCTCTGAGGCTTGTTAGACCTGGGAAGAAG                         AACAAGGATGTCACCGAAGCGATTCAGAAAGTTGCTGCTGCTTATGACTGC
genomic: GGCAGAAGTTGCTCTGAGGCTTGTTAGACCTGGGAAGAAGgtgcattgaa ... tcttttgcagAACAAGGATGTCACCGAAGCGATTCAGAAAGTTGCTGCTGCTTATGACTGC
EST: gi|88721086|gb|CI744385.1|CI744385
EST:     CCAACACAGCGGCAGAAGTTGCTCTGAGGCTTGTTAGACCTGGGAAGAAG                         AACAAGGATGTCACCGAAGCGATTCAGAAAGTTGCTGCTGCTTATGACTGC
genomic: CCAACACAGCGGCAGAAGTTGCTCTGAGGCTTGTTAGACCTGGGAAGAAGgtgcattgaa ... tcttttgcagAACAAGGATGTCACCGAAGCGATTCAGAAAGTTGCTGCTGCTTATGACTGC
EST: gi|58686553|gb|CK075240.1|CK075240
EST:     CCAACACAGCGGCAGAAGTTGCTCTGAGGCTTGTTAGACCTGGGAAGAAG                         AACAAGGATGTCACCGAAGCGATTCAGAAAGTTGCTGCTGCTTATGACTGC
genomic: CCAACACAGCGGCAGAAGTTGCTCTGAGGCTTGTTAGACCTGGGAAGAAGgtgcattgaa ... tcttttgcagAACAAGGATGTCACCGAAGCGATTCAGAAAGTTGCTGCTGCTTATGACTGC
EST: gi|13806640|gb|AU181604.1|AU181604
EST:     CCAACACAGCGGCAGAAGTTGCTCTGAGGCTTGTTAGACCTGGGAAGAAG                         AACAAGGATGTCACCGAAGCGATTCAGAAAGTTGCTGCTGCTTATGACTGC
genomic: CCAACACAGCGGCAGAAGTTGCTCTGAGGCTTGTTAGACCTGGGAAGAAGgtgcattgaa ... tcttttgcagAACAAGGATGTCACCGAAGCGATTCAGAAAGTTGCTGCTGCTTATGACTGC

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), 67 (downstream exon)
Score: 60

TATCCATGATGGAGCAGTCACTGGGAAAGCAGCAGATGTTCTTGCTGCTGCCAACACAGCGGCAGAAGTTGCTCTGAGGCTTGTTAGACCTGGGAAGAAGgtgcattgaa ... tcttttgcagAACAAGGATGTCACCGAAGCGATTCAGAAAGTTGCTGCTGCTTATGACTGCAAAATTGTGGAAGGAGTTCTCAGCCATCAGCTGAAACAGTTTGTCATTG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TATCCATGATGGAGCAGTCACTGGGAAAGCAGCAGATGTTCTTGCTGCTGCCAACACAGCGGCAGAAGTTGCTCTGAGGCTTGTTAGACCTGGGAAGAAGgtgcattgaaaagcgttgctttatttacttgctctctttttgcaatttatgctgttcacatttagtgtctaggtcaactgtgcacacaaatgttgtgctt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG