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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactcttcttttcctcattgcatcttgtttcatccttacagtagcactcaacctcatttctgttttatcactgttatgtgcttgcttttctgcacctgcaaacctgtttgcaaacggtgattaatccgcaccatgttttcctagGGACAACGCAAATGAGATCAAAGCAAAGTACATCATTGAGGCTGCAAACCACCCCACAGACCCTGAGGCAGATGAG

Basic information

species Oryza sativa
transcript LOC_Os03g58040.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g58040.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G178415_T03 (Zea mays), 3'ss of exon 7
gtactcttcttttcctcattgcatcttgtttcatccttacagtagcactcaacctcatttctgttttatcactgttatgtgcttgcttt-tctgcacctgcaaacctgtttgcaaacggtgattaatccgcaccatgttttcc-tagGGACAACGCAAATGAGATCAAAGCAAAGTACATCATTGAGGCTGCAAACCACCCCACAGACCCTGAGGCAGATGAG
|||   |||||   ||||||| |  | ||||   || |||    ||   | |  ||  |||| ||   | | | |||| |  | | | |  ||||| ||  |  |||| ||  ||    |  |     |      ||||||    ||||| || || || || || || |||||||||||||| |||||||| || ||||||||||| || |||||||| |||
gtagatttctt---ctcattgaag-tcgttttcaccctac----gcctacgaagtcgattcttttcagttattattatatcttagttgtgcctgcagctcgaggcctgatta-aactattcgtccgcactttttttgtttttgacagGGATAATGCTAACGACATAAAGGCAAAGTACATCATCGAGGCTGCCAATCACCCCACAGATCCAGAGGCAGACGAG
















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|86600065|gb|CI258405.1|CI258405
EST:     TGATGTCCTCATCCCGGCAGCACTTGGTGGAGTTATAAACAA                         GGACAACGCAAATGAGATCAAAGCAAAGTACATCATTGAGGCTGCAAACCA
genomic: TGATGTCCTCATCCCGGCAGCACTTGGTGGAGTTATAAACAAgtactcttct ... gttttcctagGGACAACGCAAATGAGATCAAAGCAAAGTACATCATTGAGGCTGCAAACCA
EST: gi|58680379|gb|CK069066.1|CK069066
EST:     GAAGAATGTGATGTCCTCATCCCGGCAGCACTTGGTGGAGTTATAAACAA                         GGACAACGCAAATGAGATCAAAGCAAAGTACATCATTGAGGCTGCAAACCA
genomic: GAAGAATGTGATGTCCTCATCCCGGCAGCACTTGGTGGAGTTATAAACAAgtactcttct ... gttttcctagGGACAACGCAAATGAGATCAAAGCAAAGTACATCATTGAGGCTGCAAACCA
EST: gi|286451|gb|D15259.1|D15259
EST:     GAAGAATGTGATGTCCTCATCCCGGCAGCACTTGGTGGAGTTATAAACAA                         GGACAACGCAAATGAGATCAAAGCAAAGTACATCATTGAGGCTGCAAACCA
genomic: GAAGAATGTGATGTCCTCATCCCGGCAGCACTTGGTGGAGTTATAAACAAgtactcttct ... gttttcctagGGACAACGCAAATGAGATCAAAGCAAAGTACATCATTGAGGCTGCAAACCA
EST: gi|163923029|gb|EG712776.1|EG712776
EST:     GAAGAATGTGATGTCCTCATCCCGGCAGCACTTGGTGGAGTTATAAACAA                         GGACAACGCAAATGAGATCAAAGCAAAGTACATCATTGAGGCTGCAAACCA
genomic: GAAGAATGTGATGTCCTCATCCCGGCAGCACTTGGTGGAGTTATAAACAAgtactcttct ... gttttcctagGGACAACGCAAATGAGATCAAAGCAAAGTACATCATTGAGGCTGCAAACCA
EST: gi|29674432|gb|CB670707.1|CB670707
EST:     GAAGAATGTGATGTCCTCATCCCGGCAGCACTTGGTGGAGTTATAAACAA                         GGACAACGCAAATGAGATCAAAGCAAAGTACATCATTGAGGCTGCAACCCT
genomic: GAAGAATGTGATGTCCTCATCCCGGCAGCACTTGGTGGAGTTATAAACAAgtactcttct ... gttttcctagGGACAACGCAAATGAGATCAAAGCAAAGTACATCATTGAGGCTGCAAACCA
EST: gi|8527504|gb|AU092319.1|AU092319
EST:     ATGTCCTNATCCCGGCAGCACTTGGTGGAGTTATAAACAA                         GGACAACGCAAATGAGATCAAAGCAAAGTACATCATTGAGNCTGNAAACCA
genomic: ATGTCCTCATCCCGGCAGCACTTGGTGGAGTTATAAACAAgtactcttct ... gttttcctagGGACAACGCAAATGAGATCAAAGCAAAGTACATCATTGAGGCTGCAAACCA
EST: gi|58593842|gb|CF992150.1|CF992150
EST:     GAGTTATAAACAA                         GGACAACGCAAATGAGATCAAAGCAAAGTACATCATTGAGGCTGCAAGCCA
genomic: GAGTTATAAACAAgtactcttct ... gttttcctagGGACAACGCAAATGAGATCAAAGCAAAGTACATCATTGAGGCTGCAAACCA
EST: gi|3760756|gb|C98010.1|C98010
EST:     AGAATTTGATGTCCTCATCCCGGCAGCATTTGGTGGA-TTATTAACAA                         GGACAACGC-AATGAGATCAAAGC-AAGTACATCATTGA-GCTTGCAAACC
genomic: AGAATGTGATGTCCTCATCCCGGCAGCACTTGGTGGAGTTATAAACAAgtactcttct ... gttttcctagGGACAACGCAAATGAGATCAAAGCAAAGTACATCATTGAGGC-TGCAAACC
EST: gi|86594966|gb|CI258220.1|CI258220
EST:     TCATCCCGGCAGCACTTGTTGGAGTTATTATACAA                         GGACGACGCAAATGAGATCAAAGCTAAGTACATCATTGAGGCTGCAAACC
genomic: TCATCCCGGCAGCACTTGGTGGAGTTA-TAAACAAgtactcttct ... gttttcctagGGACAACGCAAATGAGATCAAAGCAAAGTACATCATTGAGGCTGCAAACC
EST: gi|29679311|gb|CB675586.1|CB675586
EST:     GAAGAATGTGATGTCCTCATCCCGGCAGCACTTGGTGGAGTTATAAACAA                         GGACAACGCAAATGAGATCAAAGCAAAGTACATCATTGAGGCTGCAAACCA
genomic: GAAGAATGTGATGTCCTCATCCCGGCAGCACTTGGTGGAGTTATAAACAAgtactcttct ... gttttcctagGGACAACGCAAATGAGATCAAAGCAAAGTACATCATTGAGGCTGCAAACCA

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: 75 (upstream exon), 69 (downstream exon)
Score: 22

TCAAGGGTTTCGACGGAGGCGATGCAATCGACCCACGCTCACTGCTTACTGAAGAATGTGATGTCCTCATCCCGGCAGCACTTGGTGGAGTTATAAACAAgtactcttct ... gttttcctagGGACAACGCAAATGAGATCAAAGCAAAGTACATCATTGAGGCTGCAAACCACCCCACAGACCCTGAGGCAGATGAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgcacctgcaaacctgtttgcaaacggtgattaatccgcaccatgttttcctagGGACAACGCAAATGAGATCAAAGCAAAGTACATCATTGAGGCTGCAAACCACCCCACAGACCCTGAGGCAGATGAG
                             gattaat  putative branch site (score: 22)
                                            tgttttcct  putative PPT
                            tgattaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtactcttcttttcctcattgcatcttgtttcatccttacagtagcactcaacctcatttctgttttatcactgttatgtgcttgcttttctgcacctgcaaacctgtttgcaaacggtgattaatccgcaccatgttttcctagGGACAACGCAAATGAGATCAAAGCAAAGTACATCATTGAGGCTGCAAACCACCCCACAGACCCTGAGGCAGATGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG