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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tagtattgacagcgtcttatttgtgacttgtgagtgaaaaattacataccgtatgtctagttcaagtaattcactttatgtatatgtttccccctttcagCTGAGATTGTAATGTTTGATGGCCACATTGTGGTGTATAAGTTCATCCAAGACCTCCATTTTTTTGTTACTGGAGGAGAGGAGGAGAATGAGCTTATTTT

Basic information

species Oryza sativa
transcript LOC_Os05g38610.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g38610.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM5G883149_T04 (Zea mays), 3'ss of exon 2
tagtattgacagcgtcttatttgtgacttgtgagtgaaa--aattacataccgtatgtctagttcaagtaattcactttatgtatatgtttccccctttcagCTGAGATTGTAATGTTTGATGGCCACATTGTGGTGTATAAGTTCATCCAAGACCTCCATTTTTTTGTTACTGGAGGAGAGGAGGAGAATGAGCTTATTTT
   |  | |     || |   |||||  | |   ||       || | |    | | | |  |||||||| |||| | | | ||| |||||| |  |  |||| |||||||||||||||||||| || |||||||| || ||||||||||||||||| || |||||||||||||||||||| ||||||||||||||||||||
-tctcataatgaactcatgagtgtgatgtattgatgtgcctgtttgcgtgttttttcttttcttcaagtatttca-tatgtttatttgtttctctttaacagCAGAGATTGTAATGTTTGATGGTCAAATTGTGGTATACAAGTTCATCCAAGACCTGCACTTTTTTGTTACTGGAGGAGAAGAGGAGAATGAGCTTATTTT

upper sequence: LOC_Os05g38610.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM5G883149_T03 (Zea mays), 3'ss of exon 2
tagtattgacagcgtcttatttgtgacttgtgagtgaaa--aattacataccgtatgtctagttcaagtaattcactttatgtatatgtttccccctttcagCTGAGATTGTAATGTTTGATGGCCACATTGTGGTGTATAAGTTCATCCAAGACCTCCATTTTTTTGTTACTGGAGGAGAGGAGGAGAATGAGCTTATTTT---
      | |     || |   |||||  | |   ||       || | |    | | | |  |||||||| |||| | | | ||| |||||| |  |  |||| |||||||||||||||||||| || |||||||| || ||||||||||||||||| || |||||||||||||||||||| ||||||||||||||||||||   
----cataatgaactcatgagtgtgatgtattgatgtgcctgtttgcgtgttttttcttttcttcaagtatttca-tatgtttatttgtttctctttaacagcagAGATTGTAATGTTTGATGGTCAAATTGTGGTATACAAGTTCATCCAAGACCTGCACTTTTTTGTTACTGGAGGAGAAGAGGAGAATGAGCTTATTTTAGC

upper sequence: LOC_Os05g38610.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G431350_T03 (Zea mays), 3'ss of exon 2
----tagtattgacagcgtcttatttgtg-acttgtgagtgaaaaattacataccgtatgtctagttcaagtaattcactttatgtatatgtttccccctttcagCTGAGATTGTAATGTTTGATGGCCACATTGTGGTGTATAAGTTCATCCAAGACCTCCATTTTTTTGTTACTGGAGGAGAGGAGGAGAATGAGCTTATTTT
    |    ||||   |  ||||    || |  | ||| ||    | |   |   ||   |||  |||||||| ||||  || | | | |||||| |  |  ||| |||||||||||||||||| || || |||||||| || ||||||||||||||||| || |||||||||||||||||||| || |||||||||||||||||
tgactgaccttgatttctccttaaacatgcagatatgactgtttgagt---ttttgttcttctc-ttcaagtatttcatatt-tttctttgtttctctttaacagTTGAGATTGTAATGTTTGACGGTCAAATTGTGGTATACAAGTTCATCCAAGACCTGCACTTTTTTGTTACTGGAGGAGAAGAAGAGAATGAGCTTATTTT

upper sequence: LOC_Os05g38610.1 (Oryza sativa), 3'ss of exon 2
lower sequence: PP1S8_105V6.1 (Physcomitrella patens), 3'ss of exon 2
tagtattgacagcgtcttatttgtgactt--gtgagtgaaaaattacataccgtatgtctagttcaagtaattcactttatgtatatgtttccccctttcagCTGAGATTGTAATGTTTGATGGCCACATTGTGGTGTATAAGTTCATCCAAGACCTCCATTTTTTTGTTACTGGAGGAGAGGAGGAGAATGAGCTTATTTT
|   ||  |       | || |   | ||   | | | |    ||     |  | ||  || |     ||    |   || |   ||  ||     || |||||||||||| ||||||||||||  | |||||||| || |||||||||  |||||||||||| | ||| || ||||| ||||| ||||| || || ||| |
tctcataaaacattgttgatctccaagttccataaataacttgttttcagctatttggataatcgctatagcgaataatacgatgataatttt--tttgcagCTGAGATTGGAATGTTTGATGGATATATTGTGGTCTACAAGTTCATCTCAGACCTCCATTTCTATGTCACGGGAGGTGAGGATGAGAACGAACTGATTGT

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|58696220|gb|CK084907.1|CK084907
EST:     CGAGAAGTCGGTGTTCGTCAAGACCCAGAAAGCCACTGCCGGAGCAGAAG                         CTGAGATTGTAATGTTTGATGGCCACATTGTGGTGTATAAGTTCATCCAAG
genomic: CGAGAAGTCGGTGTTCGTCAAGACCCAGAAAGCCACTGCCGGAGCAGAAGgtaatgcgca ... cccctttcagCTGAGATTGTAATGTTTGATGGCCACATTGTGGTGTATAAGTTCATCCAAG
EST: gi|87022689|gb|CI293579.1|CI293579
EST:     CGAGAAGTCGGTGTTCGTCAAGACCCAGAAAGCCACTGCCGGAGCAGAAG                         CTGAGATTGTAATGTTTGATGGCCACATTGTGGTGTATAAGTTCATCCAAG
genomic: CGAGAAGTCGGTGTTCGTCAAGACCCAGAAAGCCACTGCCGGAGCAGAAGgtaatgcgca ... cccctttcagCTGAGATTGTAATGTTTGATGGCCACATTGTGGTGTATAAGTTCATCCAAG
EST: gi|33688934|gb|CF317173.1|CF317173
EST:     CGAGAAGTCGGTGTTCGTCAAGACCCAGAAAGCCACTGCCGGAGCAGAAG                         CTGAGATTGTAATGTTTGATGGCCACATTGTGGTGTATAAGTTCATCCAGG
genomic: CGAGAAGTCGGTGTTCGTCAAGACCCAGAAAGCCACTGCCGGAGCAGAAGgtaatgcgca ... cccctttcagCTGAGATTGTAATGTTTGATGGCCACATTGTGGTGTATAAGTTCATCCAAG
EST: gi|88579853|gb|CI691844.1|CI691844
EST:     CGAGAAGTCGGTGTTCGTCAAGACCCAGAAAGCCACTGCCGGAGCAGAAG                         CTGAGATTGTAATGTTTGATGGCCACATTGTGGTGTATAAGTTCATCCAAG
genomic: CGAGAAGTCGGTGTTCGTCAAGACCCAGAAAGCCACTGCCGGAGCAGAAGgtaatgcgca ... cccctttcagCTGAGATTGTAATGTTTGATGGCCACATTGTGGTGTATAAGTTCATCCAAG
EST: gi|396941400|gb|HO188609.1|HO188609
EST:     CGAGAAGTCGGTGTTCGTCAAGACCCAGAAAGCCACTGCCGGAGCAGAAG                         CTGAGATTGTAATGTTTGATGGCCACATTGTGGTGTATAAGTTCATCCAAG
genomic: CGAGAAGTCGGTGTTCGTCAAGACCCAGAAAGCCACTGCCGGAGCAGAAGgtaatgcgca ... cccctttcagCTGAGATTGTAATGTTTGATGGCCACATTGTGGTGTATAAGTTCATCCAAG
EST: gi|88355336|gb|CI679042.1|CI679042
EST:     CGAGAAGTCGGTGTTCGTCAAGACCCAGAAAGCCACTGCCGGAGCAGAAG                         CTGAGATTGTAATGTTTGATGGCCACATTGTGGTGTATAAGTTCATCCAAG
genomic: CGAGAAGTCGGTGTTCGTCAAGACCCAGAAAGCCACTGCCGGAGCAGAAGgtaatgcgca ... cccctttcagCTGAGATTGTAATGTTTGATGGCCACATTGTGGTGTATAAGTTCATCCAAG
EST: gi|33692848|gb|CF321087.1|CF321087
EST:     CGAGAAGTCGGTGTTCGTCAAGACCCAGAAAGCCACTGCCGGAGCAGAAG                         CTGAGATTGTAATGTTTGATGGCCACATTGTGGTGTATAAGTTCATCCAAG
genomic: CGAGAAGTCGGTGTTCGTCAAGACCCAGAAAGCCACTGCCGGAGCAGAAGgtaatgcgca ... cccctttcagCTGAGATTGTAATGTTTGATGGCCACATTGTGGTGTATAAGTTCATCCAAG
EST: gi|88586226|gb|CI703916.1|CI703916
EST:     CGAGAAGTCGGTGTTCGTCAAGACCCAGAAAGCCACTGCCGGAGCAGAAG                         CTGAGATTGTAATGTTTGATGGCCACATTGTGGTGTATAAGTTCATCCAAG
genomic: CGAGAAGTCGGTGTTCGTCAAGACCCAGAAAGCCACTGCCGGAGCAGAAGgtaatgcgca ... cccctttcagCTGAGATTGTAATGTTTGATGGCCACATTGTGGTGTATAAGTTCATCCAAG
EST: gi|88737539|gb|CI759420.1|CI759420
EST:     CGAGAAGTCGGTGTTCGTCAAGACCCAGAAAGCCACTGCCGGAGCAGAAG                         CTGAGATTGTAATGTTTGATGGCCACATTGTGGTGTATAAGTTCATCCAAG
genomic: CGAGAAGTCGGTGTTCGTCAAGACCCAGAAAGCCACTGCCGGAGCAGAAGgtaatgcgca ... cccctttcagCTGAGATTGTAATGTTTGATGGCCACATTGTGGTGTATAAGTTCATCCAAG
EST: gi|29682909|gb|CB679184.1|CB679184
EST:     CGAGAAGTCGGTGTTCGTCAAGACCCAGAAAGCCACTGCCGGAGCAGAAG                         CTGAGATTGTAATGTTTGATGGCCACATTGTGGTGTATAAGTTCATCCAAG
genomic: CGAGAAGTCGGTGTTCGTCAAGACCCAGAAAGCCACTGCCGGAGCAGAAGgtaatgcgca ... cccctttcagCTGAGATTGTAATGTTTGATGGCCACATTGTGGTGTATAAGTTCATCCAAG
EST: gi|33820855|gb|CF336232.1|CF336232
EST:     CGAGAAGTCGGTGTTCGTCAAGACCCAGAAAGCCACTGCCGGAGCAGAAG                         CTGAGATTGTAATGTTTGATGGCCACATTGTGGTGTATAAGTTCATCCAAG
genomic: CGAGAAGTCGGTGTTCGTCAAGACCCAGAAAGCCACTGCCGGAGCAGAAGgtaatgcgca ... cccctttcagCTGAGATTGTAATGTTTGATGGCCACATTGTGGTGTATAAGTTCATCCAAG
EST: gi|33678548|gb|CF306787.1|CF306787
EST:     CGAGAAGTCGGTGTTCGTCAAGACCCAGAAAGCCACTGCCGGAGCAGAAG                         CTGAGATTGTAATGTTTGATGGCCACATTGTGGTGTATAAGTTCATCCAAG
genomic: CGAGAAGTCGGTGTTCGTCAAGACCCAGAAAGCCACTGCCGGAGCAGAAGgtaatgcgca ... cccctttcagCTGAGATTGTAATGTTTGATGGCCACATTGTGGTGTATAAGTTCATCCAAG
EST: gi|218504818|gb|FG952248.1|FG952248
EST:     CGAGAAGTCGGTGTTCGTCAAGACCCAGAAAGCCACTGCCGGAGCAGAAG                         CTGAGATTGTAATGTTTGATGGCCACATTGTGGTGTATAAGTTCATCCAAG
genomic: CGAGAAGTCGGTGTTCGTCAAGACCCAGAAAGCCACTGCCGGAGCAGAAGgtaatgcgca ... cccctttcagCTGAGATTGTAATGTTTGATGGCCACATTGTGGTGTATAAGTTCATCCAAG
EST: gi|218500698|gb|FG952590.1|FG952590
EST:     CGAGAAGTCGGTGTTCGTCAAGACCCAGAAAGCCACTGCCGGAGCAGAAG                         CTGAGATTGTAATGTTTGATGGCCACATTGTGGTGTATAAGTTCATCCAAG
genomic: CGAGAAGTCGGTGTTCGTCAAGACCCAGAAAGCCACTGCCGGAGCAGAAGgtaatgcgca ... cccctttcagCTGAGATTGTAATGTTTGATGGCCACATTGTGGTGTATAAGTTCATCCAAG
EST: gi|88338043|gb|CI677027.1|CI677027
EST:     CGAGAAGTCGGTGTTCGTCAAGACCCAGAAAGCCACTGCCGGAGCAGAAG                         CTGAGATTGTAATGTTTGATGGCCACATTGTGGTGTATAAGTTCATCCAAG
genomic: CGAGAAGTCGGTGTTCGTCAAGACCCAGAAAGCCACTGCCGGAGCAGAAGgtaatgcgca ... cccctttcagCTGAGATTGTAATGTTTGATGGCCACATTGTGGTGTATAAGTTCATCCAAG
EST: gi|38473747|gb|CF957879.1|CF957879
EST:     CGAGAAGTCGGTGTTCGTCAAGACCCAGAAAGCCACTGCCGGAGCAGAAG                         CTGAGATTGTAATGTTTGATGGCCACATTGTGGTGTATAAGTTCATCCAAG
genomic: CGAGAAGTCGGTGTTCGTCAAGACCCAGAAAGCCACTGCCGGAGCAGAAGgtaatgcgca ... cccctttcagCTGAGATTGTAATGTTTGATGGCCACATTGTGGTGTATAAGTTCATCCAAG
EST: gi|58585721|gb|CF984029.1|CF984029
EST:     CGAGAAGTCGGTGTTCGTCAAGACCCAGAAAGCCACTGCCGGAGCAGAAG                         CTGAGATTGTAATGTTTGATGGCCACATTGTGGTGTATAAGTTCATCCAAG
genomic: CGAGAAGTCGGTGTTCGTCAAGACCCAGAAAGCCACTGCCGGAGCAGAAGgtaatgcgca ... cccctttcagCTGAGATTGTAATGTTTGATGGCCACATTGTGGTGTATAAGTTCATCCAAG
EST: gi|88311493|gb|CI572549.1|CI572549
EST:     CGAGAAGTCGGTGTTCGTCAAGACCCAGAAAGCCAGTGCCGGAGCAGAAG                         CTGAGATTGTAATGTTTGATGGCCACATTGTGGTGTATAAGTTCATCCAAG
genomic: CGAGAAGTCGGTGTTCGTCAAGACCCAGAAAGCCACTGCCGGAGCAGAAGgtaatgcgca ... cccctttcagCTGAGATTGTAATGTTTGATGGCCACATTGTGGTGTATAAGTTCATCCAAG
EST: gi|88352776|gb|CI678799.1|CI678799
EST:     CGAGAAGTCGGTGTTCGTCAAGACCCAGAAAGCCACTGCCGGAGCAGAAG                         CTGAGATTGTAATGTTTGATGGCCACATTGTGGTGTATAAGTTCATCCAAG
genomic: CGAGAAGTCGGTGTTCGTCAAGACCCAGAAAGCCACTGCCGGAGCAGAAGgtaatgcgca ... cccctttcagCTGAGATTGTAATGTTTGATGGCCACATTGTGGTGTATAAGTTCATCCAAG
EST: gi|88429206|gb|CI690095.1|CI690095
EST:     CGAGAAGTCGGTGTTCGTCAAGACCCAGAAAGCCACTGCCGGAGCAGAAG                         CTGAGATTGTAATGTTTGATGGCCACATTGTGGTGTATAAGTTCATCCAAG
genomic: CGAGAAGTCGGTGTTCGTCAAGACCCAGAAAGCCACTGCCGGAGCAGAAGgtaatgcgca ... cccctttcagCTGAGATTGTAATGTTTGATGGCCACATTGTGGTGTATAAGTTCATCCAAG
EST: gi|88333877|gb|CI645291.1|CI645291
EST:     CGAGAAGTCGGTGTTCGTCAAGACCCAGAAAGCCACTGCCGGAGCAGAAG                         CTGAGATTGTAATGTTTGATGGCCACATTGTGGTGTATAAGTTCATCCAAG
genomic: CGAGAAGTCGGTGTTCGTCAAGACCCAGAAAGCCACTGCCGGAGCAGAAGgtaatgcgca ... cccctttcagCTGAGATTGTAATGTTTGATGGCCACATTGTGGTGTATAAGTTCATCCAAG
EST: gi|88458357|gb|CI695744.1|CI695744
EST:     CGAGAAGTCGGTGTTCGTCAAGACCCAGAAAGCCACTGCCGGAGCAGAAG                         CTGAGATTGTAATGTTTGATGGCCACATTGTGGTGTATAAGTTCATCCAAG
genomic: CGAGAAGTCGGTGTTCGTCAAGACCCAGAAAGCCACTGCCGGAGCAGAAGgtaatgcgca ... cccctttcagCTGAGATTGTAATGTTTGATGGCCACATTGTGGTGTATAAGTTCATCCAAG
EST: gi|33683273|gb|CF311512.1|CF311512
EST:     CGAGAAGTCGGTGTTCGTCAAGACCCAGAAAGCCACTGCCGGAGCAGAAG                         CTGAGATTGTAATGTTTGATGGCCACATTGTGGTGTATAAGTTCATCCAAG
genomic: CGAGAAGTCGGTGTTCGTCAAGACCCAGAAAGCCACTGCCGGAGCAGAAGgtaatgcgca ... cccctttcagCTGAGATTGTAATGTTTGATGGCCACATTGTGGTGTATAAGTTCATCCAAG

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: 72 (upstream exon), 71 (downstream exon)
Score: 33

GTCAAGTACTACACGGATGATTGGCCTACTCTCTCGGCGAAGCTGGCCTTCGAGAAGTCGGTGTTCGTCAAGACCCAGAAAGCCACTGCCGGAGCAGAAGgtaatgcgca ... cccctttcagCTGAGATTGTAATGTTTGATGGCCACATTGTGGTGTATAAGTTCATCCAAGACCTCCATTTTTTTGTTACTGGAGGAGAGGAGGAGAATGAGCTTATTTT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ataccgtatgtctagttcaagtaattcactttatgtatatgtttccccctttcagCTGAGATTGTAATGTTTGATGGCCACATTGTGGTGTATAAGTTCATCCAAGACCTCCATTTTTTTGTTACTGGAGGAGAGGAGGAGAATGAGCTTATTTT
                                     tatgtttccccctttc  CT-rich tract
                             tttatgtatatgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tagtattgacagcgtcttatttgtgacttgtgagtgaaaaattacataccgtatgtctagttcaagtaattcactttatgtatatgtttccccctttcagCTGAGATTGTAATGTTTGATGGCCACATTGTGGTGTATAAGTTCATCCAAGACCTCCATTTTTTTGTTACTGGAGGAGAGGAGGAGAATGAGCTTATTTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT
- - - - - - - - - - - -tgacttg
- - - - - - - - - - - - - - - - -gtgaaaaa
- - - - - - - - - - - - - - - - - - - - - - cataccg