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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactgctacctgcttgttccttcattcgatttatgtgtcctgaaatgcaatctaacaaataactgttctcctcaaacagGTGAGCAGCTTCTCGTTTGGGGAGGCCAACACTGACAGCGTGACGAAAACTGCAAAGAAGATAACTGGCAAGAAATTCACCGATCTCACAGGCAACAACA

Basic information

species Oryza sativa
transcript LOC_Os03g27010.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g27010.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G107473_T01 (Zea mays), 3'ss of exon 4
-------gtactgctacctgcttgtt-ccttcattcgatttatgtgtcctgaaatgcaatctaacaaataactgttctcctcaaacagGTGAGCAGCTTCTCGTTTGGGGAGGCCAACACTGACAGCGTGACGAAAACTGCAAAGAAGATAACTGGCAAGAAATTCACCGATCTCACAGGCAACAACA
          |||| ||     || | ||    |||  ||| ||    |   ||||  ||  ||| |||    ||  |   ||| ||||  |||| |||||||||||| || |||||||||||||||  | | || || |||| ||||||||| ||||||||  ||| ||| ||||| |||||| |||
gtatttgccgctgcaacaaatctggtaccccttttccctttttgctgtccagaatgttattcaaccaatgttcgtcttaaacaa-cagGCCAGCACCTTCTCGTTTGGAGATGCCAACACTGACAGCACGCCAAAGACGGCAAGGAAGATAACCGGCAAGAAGGTCAACGACCTCACCGGCAACGACA
















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|87026012|gb|CI257170.1|CI257170
EST:     ACACAGCAAATGGCACCGGTGCCTCACACACACCTGTGAGAAATGCAAAT                         GTGAGCAGCTTCTCGTTTGGGGAGGCCAACACTGACAGCGTGACGAAAACT
genomic: ACACAGCAAATGGCACCGGTGCCTCACACACACCTGTGAGAAATGCAAATgtactgctac ... cctcaaacagGTGAGCAGCTTCTCGTTTGGGGAGGCCAACACTGACAGCGTGACGAAAACT
EST: gi|29661138|gb|CB657413.1|CB657413
EST:     ACACAGCAAATGGCACCGGTGCCTCACACACACCTGTGAGAAATGCAAAT                         GTGAGCAGCTTCTCGTTTGGGGAGGCCAACACTGACAGCGTGACGAAAACT
genomic: ACACAGCAAATGGCACCGGTGCCTCACACACACCTGTGAGAAATGCAAATgtactgctac ... cctcaaacagGTGAGCAGCTTCTCGTTTGGGGAGGCCAACACTGACAGCGTGACGAAAACT
EST: gi|29661239|gb|CB657514.1|CB657514
EST:     ACACAGCAAATGGCACCGGTGCCTCACACACACCTGTGAGAAATGCAAAT                         GTGAGCAGCTTCTCGTTTGGGGAGGCCAACACTGACAGCGTGACGAAAACT
genomic: ACACAGCAAATGGCACCGGTGCCTCACACACACCTGTGAGAAATGCAAATgtactgctac ... cctcaaacagGTGAGCAGCTTCTCGTTTGGGGAGGCCAACACTGACAGCGTGACGAAAACT
EST: gi|87012920|gb|CI297147.1|CI297147
EST:     ACACAGCAAATGGCACCGGTGCCTCACACACACCTGTGAGAAATGCAAAT                         GTGAGCAGCTTCTCGTTTGGGGAGGCCAACACTGACAGCGTGACGAAAACT
genomic: ACACAGCAAATGGCACCGGTGCCTCACACACACCTGTGAGAAATGCAAATgtactgctac ... cctcaaacagGTGAGCAGCTTCTCGTTTGGGGAGGCCAACACTGACAGCGTGACGAAAACT
EST: gi|66916849|gb|CX103697.1|CX103697
EST:     ACACAGCAAATGGCACCGGTGCCTCACACACACCTGTGAGAAATGCAAAT                         GTGAGCAGCTTCTCGTTTGGGGAGGCCAACACTGACAGCGTGACGAAAACT
genomic: ACACAGCAAATGGCACCGGTGCCTCACACACACCTGTGAGAAATGCAAATgtactgctac ... cctcaaacagGTGAGCAGCTTCTCGTTTGGGGAGGCCAACACTGACAGCGTGACGAAAACT
EST: gi|86854155|gb|CI252146.1|CI252146
EST:     CACACCTGTGAGAAATGCAAAT                         GTGAGCAGCTTCTCGTTTGGGGAGGCCAACACTGACAGCGTGACGAAAACT
genomic: CACACCTGTGAGAAATGCAAATgtactgctac ... cctcaaacagGTGAGCAGCTTCTCGTTTGGGGAGGCCAACACTGACAGCGTGACGAAAACT
EST: gi|29665112|gb|CB661387.1|CB661387
EST:     ACACAGCAAATGGCACCGGTGCCTCACACACACCTGTGAGAAATGCAAAT                         GTGAGCAGCTTCTCGTTTGGGGAGGCCAACACTGACAGCGTGACGAAAACT
genomic: ACACAGCAAATGGCACCGGTGCCTCACACACACCTGTGAGAAATGCAAATgtactgctac ... cctcaaacagGTGAGCAGCTTCTCGTTTGGGGAGGCCAACACTGACAGCGTGACGAAAACT
EST: gi|11025516|gb|AU162117.1|AU162117
EST:     ACACAGCAAATGGCACCGGTGCCTCACACACACCTGTGAGAAATGCAAAT                         GTGAGCAGCTTCTCGTTTGGGGAGGCCAACACTGACAGCGTGACGAAAACT
genomic: ACACAGCAAATGGCACCGGTGCCTCACACACACCTGTGAGAAATGCAAATgtactgctac ... cctcaaacagGTGAGCAGCTTCTCGTTTGGGGAGGCCAACACTGACAGCGTGACGAAAACT
EST: gi|58680529|gb|CK069216.1|CK069216
EST:     ACACAGCAAATGGCACCGGTGCCTCACACACACCTGTGAGAAATGCAAAT                         GTGAGCAGCTTCTCGTTTGGGGAGGCCAACACTGACAGCGTGACGAAAACT
genomic: ACACAGCAAATGGCACCGGTGCCTCACACACACCTGTGAGAAATGCAAATgtactgctac ... cctcaaacagGTGAGCAGCTTCTCGTTTGGGGAGGCCAACACTGACAGCGTGACGAAAACT
EST: gi|38475431|gb|CF959564.1|CF959564
EST:     ACACAGCAAATGGCAC-GGTGCCTCACACACACCTGTGAGAAATGCAAAT                         GTGAGCAGCTTCTCGTTTGGGGAGGCCAACACTGACAGCGTGACGAAAACT
genomic: ACACAGCAAATGGCACCGGTGCCTCACACACACCTGTGAGAAATGCAAATgtactgctac ... cctcaaacagGTGAGCAGCTTCTCGTTTGGGGAGGCCAACACTGACAGCGTGACGAAAACT
EST: gi|29640214|gb|CB645223.1|CB645223
EST:     ACCCAGCAAATGGCCCCGGTGCCTCACACACACCTGTGAGAAATGCAAAT                         GTGAGCAGCTTCTCGTTTGGGGAGGCCAACACTGACAGCGTGACGAAAACT
genomic: ACACAGCAAATGGCACCGGTGCCTCACACACACCTGTGAGAAATGCAAATgtactgctac ... cctcaaacagGTGAGCAGCTTCTCGTTTGGGGAGGCCAACACTGACAGCGTGACGAAAACT
EST: gi|86498964|gb|CI141597.1|CI141597
EST:     ACACAGCAAATGGCACCGGTGCCTCACACACACCTGTGAGAAATGCAAAT                         GTGAGCAGCTTCTCGTTTGGGGAGGCCAACACTGACAGCGTGACGAAAACT
genomic: ACACAGCAAATGGCACCGGTGCCTCACACACACCTGTGAGAAATGCAAATgtactgctac ... cctcaaacagGTGAGCAGCTTCTCGTTTGGGGAGGCCAACACTGACAGCGTGACGAAAACT
EST: gi|11025517|gb|AU162118.1|AU162118
EST:     CACAGCAAATGGCACCGGTGCCTCACACACACTTGTGAGAAATGCAAAT                         GTGAGCCAGCTTCTCGTTTGGGGAGGCCAACA-TGACAGCGTGNCGAAAAC
genomic: CACAGCAAATGGCACCGGTGCCTCACACACACCTGTGAGAAATGCAAATgtactgctac ... cctcaaacagGTGAGC-AGCTTCTCGTTTGGGGAGGCCAACACTGACAGCGTGACGAAAAC
EST: gi|86417826|gb|CI032035.1|CI032035
EST:     ACACACACCTGTGAGAAATGCAAAT                         GTGAGCAGCTTCTCGTTTGGGGAGGCCAACACTGACAGCGTGACGAAAACT
genomic: ACACACACCTGTGAGAAATGCAAATgtactgctac ... cctcaaacagGTGAGCAGCTTCTCGTTTGGGGAGGCCAACACTGACAGCGTGACGAAAACT

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: 71 (upstream exon), 75 (downstream exon)
Score: 54

TGGCCATGGCCTTTTTGACCCTCAAGATGTAAGGCCTAATGGGGCAAGGAACACAGCAAATGGCACCGGTGCCTCACACACACCTGTGAGAAATGCAAATgtactgctac ... cctcaaacagGTGAGCAGCTTCTCGTTTGGGGAGGCCAACACTGACAGCGTGACGAAAACTGCAAAGAAGATAACTGGCAAGAAATTCACCGATCTCACAGGCAACAACA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcgatttatgtgtcctgaaatgcaatctaacaaataactgttctcctcaaacagGTGAGCAGCTTCTCGTTTGGGGAGGCCAACACTGACAGCGTGACGAAAACTGCAAAGAAGATAACTGGCAAGAAATTCACCGATCTCACAGGCAACAACA
                                aaataac  putative branch site (score: 54)
                                      ctgttctcctc  CT-rich tract
                        aatctaacaaataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtactgctacctgcttgttccttcattcgatttatgtgtcctgaaatgcaatctaacaaataactgttctcctcaaacagGTGAGCAGCTTCTCGTTTGGGGAGGCCAACACTGACAGCGTGACGAAAACTGCAAAGAAGATAACTGGCAAGAAATTCACCGATCTCACAGGCAACAACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA