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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tggtcctatctatcacttggaaaagcttgtgctgagtataggctggagtgaccatttctaacagatgatttgtcacatgatattttgtttattgctgtagGTTATTCCTGATGTTGCAACGTTTCCCAGTTGAATCGAAAGGACGGCGCAAGAAATTGCAGGAG

Basic information

species Oryza sativa
transcript LOC_Os10g39220.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g39220.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G174286_T03 (Zea mays), 3'ss of exon 8
-tggtcc-tatctatcacttggaaaagcttgtgctgagtataggctggagtgaccatttctaacagatgatttgtcacatgatattttgtttattgctgtagGTTATTCCTGATGTTGCAACGTTTCCCAGTTGAATCGAAAGGACGGCGCAAGAAATTGCAGGAG
 ||||   ||   || | ||    |  || |   ||  | |||    |  | ||| |||| |     |||  || |   |||| || ||| | || ||||||||| ||| |||||||||| ||||| || || ||||| |||||| | || |||||||||||||||
ttggtttgtaggcat-attttatcatcctagctatgcatgtagtacagtttaaccctttc-atttattgagatgacttttgatgttctgtctgtttctgtagGTTGTTCATGATGTTGCAGCGTTTTCCTGTAGAATCAAAAGGAAGACGAAAGAAATTGCAGGAG

upper sequence: LOC_Os10g39220.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G003076_T02 (Zea mays), 3'ss of exon 7
tggtcctatctatcacttggaaaagcttgtgctgagtataggc--tggagtgaccatttcta-ac--agatg---atttgtcacat---gatattttgtttattgctgtagGTTATTCCTGATGTTGCAACGTTTCCCAGTTGAATCGAAAGGACGGCGCAAGAAATTGCAGGAG
           |  |  || | ||| | ||  |    |   ||  |  |    ||||| ||| ||   ||||    || |    ||   |||||| ||| | || |||||||||||| ||||||||||| ||||| || || || ||||||||| || | |||||||||||||||
----------caggatgtgtagaag-tggttttatacactagccataaatcacccattgctatactaggatgcctgttggctggattttgatattctgtctgtttctgtagGTTATTTCTGATGTTGCAGCGTTTTCCTGTAGATTCGAAAGGAAGGAGAAAGAAATTGCAGGAG

upper sequence: LOC_Os10g39220.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G003076_T03 (Zea mays), 3'ss of exon 7
tggtcctatctatcacttggaaaagcttgtgctgagtataggctggagtgaccatttctaacagatgatttgtcacatgatattttgtttattgctgtagGTTATTCCTGATGTTGCAACGTTTCCCAGTTGAATCGAAAGGACGGCGCAAGAAATTGCAGGAG
                     ||| |      ||    ||  || |  || |  ||     | |  |||||      ||||||| ||| | || |||||||||||| ||||||||||| ||||| || || || ||||||||| || | |||||||||||||||
------------------cataaatcacccattgc---tatactaggatgcctgtt---ggctg--gattt------tgatattctgtctgtttctgtaggttatttctgatgttgcagcgttttcctgtagATTCGAAAGGAAGGAGAAAGAAATTGCAGGAG

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|89176193|gb|CI043214.1|CI043214
EST:     GTGTATCACTGTTT-CGGCTTTTGGG-TTCTTCTCTACGGTGGGAG                         GTTATTCCTGATGTTGCAACGTTTCCCAGTTGAATCGAAAGGACGGCGCAA
genomic: GTGTATCACTGTTTGCGGCTTTTGGGTTTCTTCTCTACGGTGGGAGgtaatacttc ... attgctgtagGTTATTCCTGATGTTGCAACGTTTCCCAGTTGAATCGAAAGGACGGCGCAA
EST: gi|218492361|gb|FG955401.1|FG955401
EST:     GTGTATCACTGTTTGCGGCTTTTGGGTTTCTTCTCTACGGTGGGAG                         GTTATTCCTGATGTTGCAACGTTTCCCAGTTGAATCGAAAGGACGGCGCAA
genomic: GTGTATCACTGTTTGCGGCTTTTGGGTTTCTTCTCTACGGTGGGAGgtaatacttc ... attgctgtagGTTATTCCTGATGTTGCAACGTTTCCCAGTTGAATCGAAAGGACGGCGCAA
EST: gi|218502314|gb|FG958985.1|FG958985
EST:     GTGTATCACTGTTTGCGGCTTTTGGGTTTTTTCTTTACGGTGGGAG                         GTTATTCCTGATGTTGCAACGTTTCCCAGTTGAATCGAAAGGACGGCGCAA
genomic: GTGTATCACTGTTTGCGGCTTTTGGGTTTCTTCTCTACGGTGGGAGgtaatacttc ... attgctgtagGTTATTCCTGATGTTGCAACGTTTCCCAGTTGAATCGAAAGGACGGCGCAA
EST: gi|5002917|gb|AU068026.1|AU068026
EST:     GTGTATCACTGTTTGCGGCTTTTGGGTTTCTTCTCTACGGTGGGAG                         GTTATNCCTGATGTTGCAACGTTTCCCAGTTGAATCGAAAGGACGGCGCAA
genomic: GTGTATCACTGTTTGCGGCTTTTGGGTTTCTTCTCTACGGTGGGAGgtaatacttc ... attgctgtagGTTATTCCTGATGTTGCAACGTTTCCCAGTTGAATCGAAAGGACGGCGCAA
EST: gi|87035694|gb|CI190316.1|CI190316
EST:     GTGTATCACTGTTTGCGGCTTTTGGGTTTCTTCTCTACGGTGGGAG                         GTTATTCCTGATGTTGCAACGTTTCCCAGTTGAATCGAAAGGACGGCGCAA
genomic: GTGTATCACTGTTTGCGGCTTTTGGGTTTCTTCTCTACGGTGGGAGgtaatacttc ... attgctgtagGTTATTCCTGATGTTGCAACGTTTCCCAGTTGAATCGAAAGGACGGCGCAA
EST: gi|3768123|gb|AU032150.1|AU032150
EST:     GTGTATCACTGTTTGCGGCTTTTGGGTTTCTTCTCTACGGTGGGAG                         GTTATTCCTGATGTTGCAACGTTTCCCAGTTGAATCGAAAGGACGGCGCAA
genomic: GTGTATCACTGTTTGCGGCTTTTGGGTTTCTTCTCTACGGTGGGAGgtaatacttc ... attgctgtagGTTATTCCTGATGTTGCAACGTTTCCCAGTTGAATCGAAAGGACGGCGCAA
EST: gi|87035709|gb|CI190331.1|CI190331
EST:     GTGTATCACTGTTTGCGGCTTTTGGGTTTCTTCTCTACGGTGGGAG                         GTTATTCCTGATGTTGCAACGTTTCCCAGTTGAATCGAAAGGACGGCGCAA
genomic: GTGTATCACTGTTTGCGGCTTTTGGGTTTCTTCTCTACGGTGGGAGgtaatacttc ... attgctgtagGTTATTCCTGATGTTGCAACGTTTCCCAGTTGAATCGAAAGGACGGCGCAA
EST: gi|29664023|gb|CB660298.1|CB660298
EST:     GTGTATCACTGTTTGCGGCTTTTGGGTTTCTTCTCTACGGTGGGAG                         GTTATTCCTGATGTTGCAACGTTTCCCAGTTGAATCGAAAGGACGGCGCAA
genomic: GTGTATCACTGTTTGCGGCTTTTGGGTTTCTTCTCTACGGTGGGAGgtaatacttc ... attgctgtagGTTATTCCTGATGTTGCAACGTTTCCCAGTTGAATCGAAAGGACGGCGCAA
EST: gi|86256146|gb|CI007862.1|CI007862
EST:     CAGGTGTATCACTGTTTGCGGCTTTT-GGTTTCTTCTCTACGGTGGGAG                         GTTATTCCTGATGTTGCAACGTTTCCCAGTTGAATCGAAAGGACGGCGCAA
genomic: CAGGTGTATCACTGTTTGCGGCTTTTGGGTTTCTTCTCTACGGTGGGAGgtaatacttc ... attgctgtagGTTATTCCTGATGTTGCAACGTTTCCCAGTTGAATCGAAAGGACGGCGCAA
EST: gi|218501789|gb|FG963428.1|FG963428
EST:     GTGTATCACTGTTTGCGGCTTTTGGGTTTCTTCTCTACGGTGGGAG                         GTTATTCCTGATGTTGCAACGTTTCCCAGTTGAATCGAAAGGACGGCGCAA
genomic: GTGTATCACTGTTTGCGGCTTTTGGGTTTCTTCTCTACGGTGGGAGgtaatacttc ... attgctgtagGTTATTCCTGATGTTGCAACGTTTCCCAGTTGAATCGAAAGGACGGCGCAA
EST: gi|11118168|gb|AU163356.1|AU163356
EST:     GTGTATCACTGTTTGCGGGCTTTTGGGTTTCTTCTCTACGGTGGGAG                         GTTATTCCTGATGTTGCAACGTTTCCCAGTTGAATCGAAAGGACGGCGCAA
genomic: GTGTATCACTGTTTGC-GGCTTTTGGGTTTCTTCTCTACGGTGGGAGgtaatacttc ... attgctgtagGTTATTCCTGATGTTGCAACGTTTCCCAGTTGAATCGAAAGGACGGCGCAA
EST: gi|89173292|gb|CI041185.1|CI041185
EST:     CTCTACGGTGGGAG                         GTTATTCCTGATGTTGCAACGTTTCCCAGTTGAATCGAAAGGACGGCGCAA
genomic: CTCTACGGTGGGAGgtaatacttc ... attgctgtagGTTATTCCTGATGTTGCAACGTTTCCCAGTTGAATCGAAAGGACGGCGCAA
EST: gi|87032470|gb|CI266110.1|CI266110
EST:     GCTTTTGGG-TTCTTCTCTACGGTGGGAG                         GTTATTCCTGATGTTGCAACGTTTCCCAGTTGAATCGAAAGGACGGCGCAA
genomic: GCTTTTGGGTTTCTTCTCTACGGTGGGAGgtaatacttc ... attgctgtagGTTATTCCTGATGTTGCAACGTTTCCCAGTTGAATCGAAAGGACGGCGCAA
EST: gi|29663945|gb|CB660220.1|CB660220
EST:     GTGTATCACTGTTTGCGGCTTTTGGGTTTCTTCTCTACGGTGGGAG                         GTTATTCCTGATGTTGCAACGTTTCCCAGTTGAATCGAAAGGACGGCGCAA
genomic: GTGTATCACTGTTTGCGGCTTTTGGGTTTCTTCTCTACGGTGGGAGgtaatacttc ... attgctgtagGTTATTCCTGATGTTGCAACGTTTCCCAGTTGAATCGAAAGGACGGCGCAA
EST: gi|87028641|gb|CI266040.1|CI266040
EST:     CGGCTTTT-GGTTTCTTCTCTACGGTGGGAG                         GTTATTCCTGATGTTGCAACGTTTCCCAGTTGAATCGAAAGGACGGCGCAA
genomic: CGGCTTTTGGGTTTCTTCTCTACGGTGGGAGgtaatacttc ... attgctgtagGTTATTCCTGATGTTGCAACGTTTCCCAGTTGAATCGAAAGGACGGCGCAA
EST: gi|11173257|gb|AU164690.1|AU164690
EST:     GTGTATCACTGTTTNCGGCTTTTGGGTTTCTTCTCTACGGTGGGAG                         GTTATTCCTGATGTTGCAACGTTTCCCAGTTGAATCGAAAGGACGGCGCAA
genomic: GTGTATCACTGTTTGCGGCTTTTGGGTTTCTTCTCTACGGTGGGAGgtaatacttc ... attgctgtagGTTATTCCTGATGTTGCAACGTTTCCCAGTTGAATCGAAAGGACGGCGCAA
EST: gi|87035720|gb|CI190342.1|CI190342
EST:     GTGTATCACTGTTTGCGGCTTTTGGGTTTCTTCTCTACGGTGGGAG                         GTTATTCCTGATGTTGCAACGTTTCCCAGTTGAATCGAAAGGACGGCGCAA
genomic: GTGTATCACTGTTTGCGGCTTTTGGGTTTCTTCTCTACGGTGGGAGgtaatacttc ... attgctgtagGTTATTCCTGATGTTGCAACGTTTCCCAGTTGAATCGAAAGGACGGCGCAA
EST: gi|87031400|gb|CI261774.1|CI261774
EST:     ATCACTGTTTGCGGCTTTTGGGTTTCTTCTCTACGGTGGGAG                         GTTATTCCTGATGTTGCAACGTTTCCCAGTTGAATCGAAAGGACGGCGCAA
genomic: ATCACTGTTTGCGGCTTTTGGGTTTCTTCTCTACGGTGGGAGgtaatacttc ... attgctgtagGTTATTCCTGATGTTGCAACGTTTCCCAGTTGAATCGAAAGGACGGCGCAA
EST: gi|44666590|gb|CR280024.1|CR280024
EST:     GTGTATCACTGTTTACGGCTTTTGGGTTTCTTCTCTACGGTGGGAG                         GTTATTCCTGATGTTGCAACGTTTCCCAGTTGAATCGAAAGGACGGCGCAA
genomic: GTGTATCACTGTTTGCGGCTTTTGGGTTTCTTCTCTACGGTGGGAGgtaatacttc ... attgctgtagGTTATTCCTGATGTTGCAACGTTTCCCAGTTGAATCGAAAGGACGGCGCAA
EST: gi|218483378|gb|FG949318.1|FG949318
EST:     GTGTATCACTGTTTGCGGCTTTTGGGTTTCTTCTCTACGGTGGGAG                         GTTATTCCTGATGTTGCAACGTTTCCCAGTTGAATCGAAAGGACGGCGCAA
genomic: GTGTATCACTGTTTGCGGCTTTTGGGTTTCTTCTCTACGGTGGGAGgtaatacttc ... attgctgtagGTTATTCCTGATGTTGCAACGTTTCCCAGTTGAATCGAAAGGACGGCGCAA
EST: gi|87035684|gb|CI190306.1|CI190306
EST:     GTGTATCACTGTTTGCGGCTTTTGGGTTTCTTCTCTACGGTGGGAG                         GTTATTCCTGATGTTGCAACGTTTCCCAGTTGAATCGAAAGGACGGCGCAA
genomic: GTGTATCACTGTTTGCGGCTTTTGGGTTTCTTCTCTACGGTGGGAGgtaatacttc ... attgctgtagGTTATTCCTGATGTTGCAACGTTTCCCAGTTGAATCGAAAGGACGGCGCAA
EST: gi|29663981|gb|CB660256.1|CB660256
EST:     GTGTATCACTGTTTGCGGCTTTTGGGTTTCTTCTATACGGTGGGAG                         GTTATTCCTGATGTTGCAACGTTTCCCAGTTGAATCGAAAGGACGGCGCAA
genomic: GTGTATCACTGTTTGCGGCTTTTGGGTTTCTTCTCTACGGTGGGAGgtaatacttc ... attgctgtagGTTATTCCTGATGTTGCAACGTTTCCCAGTTGAATCGAAAGGACGGCGCAA
EST: gi|86854988|gb|CI263055.1|CI263055
EST:     GTGTATCACTGTTTGCGGCTTTTGGGTGTCTTCTCTACGGTGGGAG                         GTTATTCCTGATGTTGCAACGTTTCCCAGTTGAATCGAAAGGACGGCGCAA
genomic: GTGTATCACTGTTTGCGGCTTTTGGGTTTCTTCTCTACGGTGGGAGgtaatacttc ... attgctgtagGTTATTCCTGATGTTGCAACGTTTCCCAGTTGAATCGAAAGGACGGCGCAA
EST: gi|29659575|gb|CB655850.1|CB655850
EST:     GTGTATCACTGTTTGCGGCTTTTGGGTTTCTTCTCTACGGTGGGAG                         GTTATTCCTGATGTTGCAACGTTTCCCAGTTGAATCGAAAGGACGGCGCAA
genomic: GTGTATCACTGTTTGCGGCTTTTGGGTTTCTTCTCTACGGTGGGAGgtaatacttc ... attgctgtagGTTATTCCTGATGTTGCAACGTTTCCCAGTTGAATCGAAAGGACGGCGCAA

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: 46 (upstream exon), 64 (downstream exon)
Score: 41

GTGTATCACTGTTTGCGGCTTTTGGGTTTCTTCTCTACGGTGGGAGgtaatacttc ... attgctgtagGTTATTCCTGATGTTGCAACGTTTCCCAGTTGAATCGAAAGGACGGCGCAAGAAATTGCAGGAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gagtgaccatttctaacagatgatttgtcacatgatattttgtttattgctgtagGTTATTCCTGATGTTGCAACGTTTCCCAGTTGAATCGAAAGGACGGCGCAAGAAATTGCAGGAG
          ttctaac  putative branch site (score: 41)
                               atgatattttgtttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tggtcctatctatcacttggaaaagcttgtgctgagtataggctggagtgaccatttctaacagatgatttgtcacatgatattttgtttattgctgtagGTTATTCCTGATGTTGCAACGTTTCCCAGTTGAATCGAAAGGACGGCGCAAGAAATTGCAGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
tggtcct
- - - - - - - - - - - - - - gtgctga
- - - - - - - - - - - - - - - - - - - - -gctggag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gatgatt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - acatgat