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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgattccatatactttactgatcttgtgtaactgttacatgtcttaacatatagatcttaaattataatccctcttgtagTGTACAAGAAACACTACCCTCCTGCCCTAAAGGATGATGTTTGGAGATTGGAGAAGATTGGAAAGGATGGTGCATTTCACAAGAAGCTAAACTCAAATGG

Basic information

species Oryza sativa
transcript 13113.m00220
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g36660.1 (Oryza sativa), 3'ss of exon 5
lower sequence: AC202073.4_FGT001 (Zea mays), 3'ss of exon 4
gtatgattccatatactttactgatcttgtgtaactgttacatgtcttaacatatagatcttaaattataat-----------ccctcttgtagTGTACAAGAAACACTACCCTCCTGCCCTAAAGGATGATGTTTGGAGATTGGAGAAGATTGGAAAGGATGGTGCATTTCACAAGAAGCTAAACTCAAATGG
           |||  ||   |  | |  ||| | ||||| ||    ||||||||||   |||||    |||           | || |||||||||| ||||| || || |||||||| ||||||||||| || |||||||| || |||||||||||||||||| |||| |||||||   ||||||||| |||
----------gtatgtttatttagtgtgatgtcattgttaaataatctaacatataggctttaaacatgaatacgttaactaactcttttgtagTGTATAAGAAGCATTATCCTCCTGCACTAAAGGATGAGGTATGGAGATTAGAAAAGATTGGAAAGGATGGTTCATTCCACAAGAGATTAAACTCAAGTGG

upper sequence: LOC_Os04g36660.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA07G30990.2 (Glycine max), 3'ss of exon 3
gtatgattccatatactttactgatcttgtgtaactgttacatgtcttaacata-tagatcttaaattataatccctcttgtagTGTACAAGAAACACTACCCTCCTGCCCTAAAGGATGATGTTTGGAGATTGGAGAAGATTGGAAAGGATGGTGCATTTCACAAGAAGCTAAACTCAAATGG
   | | | ||||   |      || |  | || || |     |  ||    || |  | ||| ||||  |       | ||||| ||||||||||||||||| |||||| | || ||||| || |||||| ||||||||||||| ||||||||  |||||||||| | ||||||   |  |||
--gtaagttcataacttccttatatttgttatatctttctagagaattgttgtaatgaaacttcaattgaa-------tcgtagTATACAAGAAACACTACCCGCCTGCCTTGAATGATGAGGTCTGGAGACTGGAGAAGATTGGCAAGGATGGGTCATTTCACAAAAGGCTAAATAAAGCTGG

upper sequence: LOC_Os04g36660.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA17G07290.1 (Glycine max), 3'ss of exon 6
------gtatgattccatatacttta---ctgatcttgtgtaactgtt------------aca-tgtcttaacatat---agatcttaaattataatccctcttgtagTGTACAAGAAACACTACCCTCCTGCCCTAAAGGATGATGTTTGGAGATTGGAGAAGATTGGAAAGGATGGTGCATTTCACAAGAAGCTAAACTCAAATGG
       |||| ||| | ||  ||||    |  ||| |  | | || |            ||| |||  || ||| |   | || ||| ||| | | |  | |   ||| || ||||| || || || |||||  | |  ||||| || ||||||||||||||||| || ||||||||  ||||||| |||||||| ||       ||
gtagggttatgcttctacatcttttagtttttctctagcatcagtgctctccctgctcctacactgtaatagcatcttttaaattttatattttgacctttttctcagTATATAAGAAGCATTATCCACCTGCATTGACTGATGAAGTGTGGAGATTGGAGAAGATAGGCAAGGATGGGTCATTTCATAAGAAGCTGAATAGTGCAGG

upper sequence: LOC_Os04g36660.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA15G07330.2 (Glycine max), 3'ss of exon 5
gtatgattccatatactttactgatcttgtgtaactgttacatgtcttaacatatagatcttaaattataatccctcttgtagTGTACAAGAAACACTACCCTCCTGCCCTAAAGGATGATGTTTGGAGATTGGAGAAGATTGGAAAGGATGGTGCATTTCACAAGAAGCTAAACTCAAATGG
   | | | |||| |||| | || |  |||   |   || | | | | |  |||           |||||  |    ||| ||| |||||||| |||||||| |||||| | || ||||| || |||||| ||||||||||||| ||||||||| | |||||||| | ||||||   |   ||
--gtaagtacataaacttcattgtttatgttctatcctt-cttctgtaatgatac----------ttata--cttgattgcagTATACAAGAAGCACTACCCACCTGCCTTGAATGATGAGGTCTGGAGACTGGAGAAGATTGGCAAGGATGGTTCCTTTCACAAAAGGCTAAATAAAGCAGG

upper sequence: LOC_Os04g36660.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA08G06320.1 (Glycine max), 3'ss of exon 4
gtatgattccatatactttactgatcttgtgtaactgttacatgtcttaacata-tagatcttaaattataatccctcttgtagTGTACAAGAAACACTACCCTCCTGCCCTAAAGGATGATGTTTGGAGATTGGAGAAGATTGGAAAGGATGGTGCATTTCACAAGAAGCTAAACTCAAATGG
   | | | ||||   |      || |  | || || |     |  ||    || |  | ||| ||||  |       || |||| ||||||||||||||||| |||||| | || ||||| || |||||| ||||||||||||| ||||||||  |||||||||| | ||||||   |  |||
--gtaagttcataacttccttatatttgttatatctttctagagaattgttgtaatgaaacttcaattgaa-------ttatagTATACAAGAAACACTACCCGCCTGCCTTGAATGATGAGGTCTGGAGACTGGAGAAGATTGGTAAGGATGGGTCATTTCACAAAAGGCTAAATAAAGCTGG

upper sequence: LOC_Os04g36660.1 (Oryza sativa), 3'ss of exon 5
lower sequence: AT5G57580.1 (Arabidopsis thaliana), 3'ss of exon 5
gtatgattccatatactttactgatcttgtgtaactgttacatgt----cttaacatatagatcttaaattataatccctct---tgtagTGTACAAGAAACACTACCCTCCTGCCCTAAAGGATGATGTTTGGAGATTGGAGAAGATTGGAAAGGATGGTGCATTTCACAAGAAGCTAAACTCAAATGG
||||| |   | |  ||   ||  |||| |   |||||  ||| |     |||     |  |  || |   | | | | | |   || |||||||||||| || || || ||||| || || |||||||| ||||||||||| ||||| || |||||||| ||||| || || ||||| |   |  | ||
gtatggtcttaaaagctccccttttcttctc--actgtaccatctggtgtttacttcttttagtttgatgcacatttcttttatgtgcagTGTACAAGAAGCATTATCCACCTGCTCTGAATGATGATGTGTGGAGATTGGACAAGATCGGCAAGGATGGGGCATTCCATAAAAAGCTTACTGCTGAAGG

upper sequence: LOC_Os04g36660.1 (Oryza sativa), 3'ss of exon 5
lower sequence: AT2G18750.1 (Arabidopsis thaliana), 3'ss of exon 5
gtatgattccatatactttactgatcttgtgtaactgttacat----gtcttaacatatagatc-ttaaattataatccctcttgtagTGTACAAGAAACACTACCCTCCTGCCCTAAAGGATGATGTTTGGAGATTGGAGAAGATTGGAAAGGATGGTGCATTTCACAAGAAGCTAAACTCAAATGG
   | | | | |    |    |||| ||  || | || |  ||     ||||    | |   |     |||  |  |   || |  ||||||||||||||| ||||| |||||  |  | ||||| || ||||| ||||| |||||||||||||| || || || || ||||| || ||   |   ||
--gtaagttcttgctttcctttgatatta-gtcattgatgtatctgaatctttgtttttcttttgcctaatgtttttttttcctacagTGTACAAGAAACATTACCCACCTGCTTTGGATGATGAGGTCTGGAGGTTGGAAAAGATTGGAAAGGACGGGGCTTTCCATAAGAAACTCAATAAAGCAGG

upper sequence: LOC_Os04g36660.1 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv00s0181g00220.t01 (Vitis vinifera), 3'ss of exon 6
--------------------gtatgattccatatactttactgatcttgtgtaactgt-tacatgtcttaacatatagatcttaaatt------ataatccctcttgtagTGTACAAGAAACACTACCCTCCTGCCCTAAAGGATGATGTTTGGAGATTGGAGAAGATTGGAAAGGATGGTGCATTTCACAAGAAGCTAAACTCAAATGG
                      || |||   ||    ||  |     ||  ||| ||| |  || | ||   ||   | |  | |||       || ||   | |   ||| |||||||| ||||||||||||||  | || ||||| |||||| |||||||||||||||| || |||||  |||| ||||||| | | ||   |  |||
gtgagttgatgttcagtgtcaaattattatttacttctttttatatatgcataaatgtgtgtatctgttgggatgatggtggtgaatctgaaagatcatttttttcccagTATACAAGAAGCACTACCCTCCTGCATTGAATGATGAAGTTTGGCGATTGGAGAAGATTGGCAAAGATGGGTCATTCCACAAGAGGTTGAATAAAGCTGG

upper sequence: LOC_Os04g36660.1 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv11s0052g01380.t01 (Vitis vinifera), 3'ss of exon 4
--------gtatgattccatatactttactgatc---ttgtgtaactgttacatgtcttaac-------atatagatcttaaattataatccctctt---gtagTGTACAAGAAACACTACCCTCCTGCCCTAAAGGATGATGTTTGGAGATTGGAGAAGATTGGAAAGGATGGTGCATTTCACAAGAAGCTAAACTCAAATGG
               ||| | |  |||| | ||    || | | | ||||   | ||||| |       | ||     | ||  |    |   ||     |||||||| ||||||||||| || |||||  |||  |||||||| |||||||||||||||||||| ||||||||| |||| ||||||| ||||||         
gtaggttcaggctcatccttgtcttttatttattgaattattttattgttctttttcttatctgtgatgacatgttattgaatctgctgtttttccctgggtagTGTATAAGAAACACTATCCACCTGCATTAACTGATGATGTGTGGAGATTGGAGAAGATTGGCAAGGATGGTTCATTCCACAAGAGGCTAAATAATTCCCA

upper sequence: LOC_Os04g36660.1 (Oryza sativa), 3'ss of exon 5
lower sequence: PP1S21_379V6.1 (Physcomitrella patens), 3'ss of exon 6
----------gtatgattccatatactttactgatcttgtgtaactgttacatgtcttaacatatagatcttaaatta------taatccc-tcttgtagTGTACAAGAAACACTACCCTCCTGCCCTAAAGGATGATGTTTGGAGATTGGAGAAGATTGGAAAGGATGGTGCATTTCACAAGAAGCTAAACTCAAATGG
           ||| | |  |   | | |    |  ||||| || | | | |     ||  |||| | |  | |          |  || | |  || ||||||||||||||| ||||| || ||||| |  ||||| |||||| | ||||| || ||||| ||||| ||||| |||||||||   || ||   |  | |
tgcatttttgttatcacttgaagaagtgtgaacaatttgtggaaatataaaaatgagtataatattgtttctgagcctcgttgttggtctcattctgcagTGTACAAGAAACATTACCCGCCAGCCCTGACTGATGAGGTTTGGCGGTTGGATAAAATTGGCAAGGACGGTGCTTTTCACAAGCGTCTCAATCAATCTCG

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|29661530|gb|CB657805.1|CB657805
EST:     TAAGGAGGCGAAAACGGAGGCTTTTACTGTTAAAGATCACAGAGGAGAAT                         TGTACAAGAAACACTACCCTCCTGCCCTAAAGGATGATGTTTGGAGATTGG
genomic: TAAGGAGGCGAAAACGGAGGCTTTTACTGTTAAAGATCACAGAGGAGAATgtatgattcc ... cctcttgtagTGTACAAGAAACACTACCCTCCTGCCCTAAAGGATGATGTTTGGAGATTGG
EST: gi|86596775|gb|CI286688.1|CI286688
EST:     AGGAGGCGAAAACGGAGGCTTTTACTGTTAAAGATCACAGAGGAGAAT                         TGTACAAGAAACACTACCCTCCTGCCCTAAAGGATGATGTTTGGAGATTGG
genomic: AGGAGGCGAAAACGGAGGCTTTTACTGTTAAAGATCACAGAGGAGAATgtatgattcc ... cctcttgtagTGTACAAGAAACACTACCCTCCTGCCCTAAAGGATGATGTTTGGAGATTGG
EST: gi|58659064|gb|CK047744.1|CK047744
EST:     TAAGGAGGCGAAAACGGAGGCTTTTACTGTTAAAGATCACAGAGGAGAAT                         TGTACAAGAAACACTACCCTCCTGCCCTAAAGGATGATGTTTGGAGATTGG
genomic: TAAGGAGGCGAAAACGGAGGCTTTTACTGTTAAAGATCACAGAGGAGAATgtatgattcc ... cctcttgtagTGTACAAGAAACACTACCCTCCTGCCCTAAAGGATGATGTTTGGAGATTGG
EST: gi|29637477|gb|CB642486.1|CB642486
EST:     TAAGGAGGCGAAAACGGAGGCTTTTACTGTTAAAGATCACAGAGGAGAAT                         TGTACAAGAAACACTACCCTCCTGCCCTAAAGGATGATGTTTGGAGATTGG
genomic: TAAGGAGGCGAAAACGGAGGCTTTTACTGTTAAAGATCACAGAGGAGAATgtatgattcc ... cctcttgtagTGTACAAGAAACACTACCCTCCTGCCCTAAAGGATGATGTTTGGAGATTGG
EST: gi|66915738|gb|CX102586.1|CX102586
EST:     TAAGGAGGCGAAAACGGAGGCTTTTACTGTTAAAGATCACAGAGGAGAAT                         TGTACAAGAAACACTACCCTCCTGCCCTAAAGGATGATGTTTGGAGATTGG
genomic: TAAGGAGGCGAAAACGGAGGCTTTTACTGTTAAAGATCACAGAGGAGAATgtatgattcc ... cctcttgtagTGTACAAGAAACACTACCCTCCTGCCCTAAAGGATGATGTTTGGAGATTGG
EST: gi|29622953|gb|CB627964.1|CB627964
EST:     TAAGGAGGCGAAAACGGAGGCTTTTACTGTTAAAGATCACAGAGGAGAAT                         TGTACAAGAAACACTACCCTCCTGCCCTAAAGGATGATGTTTGGAGATTGG
genomic: TAAGGAGGCGAAAACGGAGGCTTTTACTGTTAAAGATCACAGAGGAGAATgtatgattcc ... cctcttgtagTGTACAAGAAACACTACCCTCCTGCCCTAAAGGATGATGTTTGGAGATTGG
EST: gi|58612983|gb|CK040695.1|CK040695
EST:     TAAGGAGGCGAAAACGGAGGCTTTTACTGTTAAAGATCACAGAGGAGAAT                         TGTACAAGAAACACTACCCTCCTGCCCTAAAGGATGATGTTTGGAGATTGG
genomic: TAAGGAGGCGAAAACGGAGGCTTTTACTGTTAAAGATCACAGAGGAGAATgtatgattcc ... cctcttgtagTGTACAAGAAACACTACCCTCCTGCCCTAAAGGATGATGTTTGGAGATTGG

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), 69 (downstream exon)
Score: 34

TTTAGACTTGGTTTGCGAGTCTCTTCAGGATTTTGTGAAGGTGTCCGTGTTAAGGAGGCGAAAACGGAGGCTTTTACTGTTAAAGATCACAGAGGAGAATgtatgattcc ... cctcttgtagTGTACAAGAAACACTACCCTCCTGCCCTAAAGGATGATGTTTGGAGATTGGAGAAGATTGGAAAGGATGGTGCATTTCACAAGAAGCTAAACTCAAATGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgtaactgttacatgtcttaacatatagatcttaaattataatccctcttgtagTGTACAAGAAACACTACCCTCCTGCCCTAAAGGATGATGTTTGGAGATTGGAGAAGATTGGAAAGGATGGTGCATTTCACAAGAAGCTAAACTCAAATGG
                tcttaac  putative branch site (score: 34)
                                           tccctcttgt  putative PPT
                tcttaacatatagatc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgattccatatactttactgatcttgtgtaactgttacatgtcttaacatatagatcttaaattataatccctcttgtagTGTACAAGAAACACTACCCTCCTGCCCTAAAGGATGATGTTTGGAGATTGGAGAAGATTGGAAAGGATGGTGCATTTCACAAGAAGCTAAACTCAAATGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC