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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattgagtgattgttaatgcaagtactacatttattctacaactagactgatctgaatccttgaatactgtacttgtgaatgtaacacagGGAAGCGATACAGCTTACCTAACTCAAGAATAATGATCCATCAACCTCTCGGAGGAGCCCAAGGACAAGAGACTGATCTTGAGATCCAG

Basic information

species Oryza sativa
transcript LOC_Os03g19510.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g19510.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G121456_T03 (Zea mays), 3'ss of exon 7
gtaattg-agtgattgttaatgcaagtactacatttattctacaactagactgatctgaatccttgaa--tactgtacttgtgaa--tgtaacacagGGAAGCGATACAGCTTACCTAACTCAAGAATAATGATCCATCAACCTCTCGGAGGAGCCCAAGGACAAGAGACTGATCTTGAGATCCAG
|||   | |||||||| ||||  ||    |  |  | |     |  ||  |     |   |  | |||   |    ||  |||||  | |||  |||| ||||||||||||||||| |||||||| |||||||||||||||||||| ||||| ||||||||||| ||||||||||||||||| |||
gtaccagtagtgattgctaataaaatacatgtaggtgtagcttacatatccaagcttcgttaatagaagtcataaaaccggtgaaaatataatgcagGAAAGCGATACAGCTTACCAAACTCAAGGATAATGATCCATCAACCTCTTGGAGGGGCCCAAGGACAGGAGACTGATCTTGAGATTCAG

upper sequence: LOC_Os03g19510.1 (Oryza sativa), 3'ss of exon 7
lower sequence: Vv07s0005g01530.t01 (Vitis vinifera), 3'ss of exon 7
----gtaattgagt-gattgttaatgcaagtactaca----tttattctacaac-tagactgatctgaatccttgaatactgtacttgtgaatg------taac-acagGGAAGCGATACAGCTTACCTAACTCAAGAATAATGATCCATCAACCTCTCGGAGGAGCCCAAGGACAAGAGACTGATCTTGAGATCCAG
    ||||||   | |  | ||  ||  |||  |       |  | |      | ||  ||  |  |  | |||  | | |||   ||| |         ||||   ||| ||  |||| ||||| || |||||||| || ||||||||||| |||||||| ||||| |||||     | |||||  | || || |||
gtaagtaatttcctaggcttttgttgttagtggtttggagttccacttcgtggcatatgctttttggtgtgctttgaca-tgtgtctgtcacctccctcttaactgaagGAAAAAGATATAGCTTGCCAAACTCAAGGATCATGATCCATCAGCCTCTCGGTGGAGCTCAAGGTGGGCAAACTGACATAGATATTCAG
















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|86254683|gb|CI060994.1|CI060994
EST:     TATGGGAGCTTTTCTGCTTAGTGCTGGGACAAAAG                         GGAAGCGATACAGCTTACCTAACTCAAGAATAATGATCCATCAACCTCTCG
genomic: TATGGGAGCTTTTCTGCTTAGTGCTGGGACAAAAGgtaattgagt ... tgtaacacagGGAAGCGATACAGCTTACCTAACTCAAGAATAATGATCCATCAACCTCTCG
EST: gi|33682025|gb|CF310264.1|CF310264
EST:     TATGGGAGCTTTTCTGCTTAGTGCTGGGACAAAAG                         GGAAGCGATACAGCTTACCTAACTCAAGAATAATGATCCATCAACCTCTCG
genomic: TATGGGAGCTTTTCTGCTTAGTGCTGGGACAAAAGgtaattgagt ... tgtaacacagGGAAGCGATACAGCTTACCTAACTCAAGAATAATGATCCATCAACCTCTCG
EST: gi|218500705|gb|FG952597.1|FG952597
EST:     TATGGGAGCTTTTCTGCTTAGTGCTGGGACAAAAG                         GGAAGCGATACAGCTTACCTAACTCAAGAATAATGATCCATCAACCTCTCG
genomic: TATGGGAGCTTTTCTGCTTAGTGCTGGGACAAAAGgtaattgagt ... tgtaacacagGGAAGCGATACAGCTTACCTAACTCAAGAATAATGATCCATCAACCTCTCG
EST: gi|44675627|gb|CR289061.1|CR289061
EST:     TATGGGAGCTTTTCTGCTTAGTGCTGGGACAAAAG                         GGAAGCGATACAGCTTACCTAACTCAAGAATAATGATCCATCAACCTCTCG
genomic: TATGGGAGCTTTTCTGCTTAGTGCTGGGACAAAAGgtaattgagt ... tgtaacacagGGAAGCGATACAGCTTACCTAACTCAAGAATAATGATCCATCAACCTCTCG
EST: gi|33682024|gb|CF310263.1|CF310263
EST:     TATGGGAGCTTTTCTGCTTAGTGCTGGGACAAAAG                         GGAAGCGATACAGCTTACCTAACTCAAGAATAATGATCCATCAACCTCTCG
genomic: TATGGGAGCTTTTCTGCTTAGTGCTGGGACAAAAGgtaattgagt ... tgtaacacagGGAAGCGATACAGCTTACCTAACTCAAGAATAATGATCCATCAACCTCTCG
EST: gi|86596355|gb|CI268655.1|CI268655
EST:     TATGGGAGCTTTTCTGCTTAGTGCTGGGACAAAAG                         GGAAGCGATACAGCTTACCTAACTCAAGAATAATGATCCATCAACCTCTCG
genomic: TATGGGAGCTTTTCTGCTTAGTGCTGGGACAAAAGgtaattgagt ... tgtaacacagGGAAGCGATACAGCTTACCTAACTCAAGAATAATGATCCATCAACCTCTCG
EST: gi|8858878|gb|AU096196.1|AU096196
EST:     TATGGGAGCTTTTCTGCTTAGTGCTGGGACAAAAG                         GGAAGCGATACAGCTTACCTAACTCAAGAATAATGATCCATCAACCTCTCG
genomic: TATGGGAGCTTTTCTGCTTAGTGCTGGGACAAAAGgtaattgagt ... tgtaacacagGGAAGCGATACAGCTTACCTAACTCAAGAATAATGATCCATCAACCTCTCG
EST: gi|33801418|gb|CF326580.1|CF326580
EST:     TATGGGAGCTTTTCTGCTTAGTGCTGGGACAAAAG                         GGAAGCGATACAGCTTACCTAACTCAAGAATAATGATCCATCAACCTCTCG
genomic: TATGGGAGCTTTTCTGCTTAGTGCTGGGACAAAAGgtaattgagt ... tgtaacacagGGAAGCGATACAGCTTACCTAACTCAAGAATAATGATCCATCAACCTCTCG
EST: gi|88832375|gb|CI019316.1|CI019316
EST:     TATGGGAGCTTTTCTGCTTAGTGCTGGGACAAAAG                         GGAAGCGATACAGCTTACCTAACTCAAGAATAATGATCCATCAACCTCTCG
genomic: TATGGGAGCTTTTCTGCTTAGTGCTGGGACAAAAGgtaattgagt ... tgtaacacagGGAAGCGATACAGCTTACCTAACTCAAGAATAATGATCCATCAACCTCTCG
EST: gi|89198430|gb|CI007490.1|CI007490
EST:     CAAGTATGGGAGCTTTTCTGCTTAGTGCTGGGACAAAAG                         GGAAGCGATACAGCTTACCTAACTCAAGAATAATGATCCATCAACCTCTCG
genomic: CAAGTATGGGAGCTTTTCTGCTTAGTGCTGGGACAAAAGgtaattgagt ... tgtaacacagGGAAGCGATACAGCTTACCTAACTCAAGAATAATGATCCATCAACCTCTCG
EST: gi|109711590|gb|CI013195.1|CI013195
EST:     CTGCAAGTATGGGAGCTTTTCTGCTTAGTGCTGGGACAAAAG                         GGAAGCGATACAGCTTACCTAACTCAAGAATAATGATCCATCAACCTCTCG
genomic: CTGCAAGTATGGGAGCTTTTCTGCTTAGTGCTGGGACAAAAGgtaattgagt ... tgtaacacagGGAAGCGATACAGCTTACCTAACTCAAGAATAATGATCCATCAACCTCTCG
EST: gi|86423150|gb|CI060723.1|CI060723
EST:     TAT-GGAGCTTTTCTGCTTAGTGCTGGGACAAAAG                         GGAAGCGATACAGCTTACCTAACTCAAGAATAATGATCCATCAACCTCTCG
genomic: TATGGGAGCTTTTCTGCTTAGTGCTGGGACAAAAGgtaattgagt ... tgtaacacagGGAAGCGATACAGCTTACCTAACTCAAGAATAATGATCCATCAACCTCTCG
EST: gi|86413585|gb|CI019170.1|CI019170
EST:     TATGGGAGCTTTTCTGCTTAGTGCTGGGACAAAAG                         GGAAGCGATACAGCTTACCTAACTCAAGAATAATGATCCATCAACCTCTCG
genomic: TATGGGAGCTTTTCTGCTTAGTGCTGGGACAAAAGgtaattgagt ... tgtaacacagGGAAGCGATACAGCTTACCTAACTCAAGAATAATGATCCATCAACCTCTCG

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: 67 (upstream exon), 40 (downstream exon)
Score: 7

TATGGGAGCTTTTCTGCTTAGTGCTGGGACAAAAGgtaattgagt ... tgtaacacagGGAAGCGATACAGCTTACCTAACTCAAGAATAATGATCCATCAACCTCTCGGAGGAGCCCAAGGACAAGAGACTGATCTTGAGATCCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctacaactagactgatctgaatccttgaatactgtacttgtgaatgtaacacagGGAAGCGATACAGCTTACCTAACTCAAGAATAATGATCCATCAACCTCTCGGAGGAGCCCAAGGACAAGAGACTGATCTTGAGATCCAG
                                            atgtaac  putative branch site (score: 7)
                         ttgaata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaattgagtgattgttaatgcaagtactacatttattctacaactagactgatctgaatccttgaatactgtacttgtgaatgtaacacagGGAAGCGATACAGCTTACCTAACTCAAGAATAATGATCCATCAACCTCTCGGAGGAGCCCAAGGACAAGAGACTGATCTTGAGATCCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC