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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgcttgaacctctagatatgtttcttacctttaacatgtcgaaactctagaagagggagagttcctgacttatttattactcatatgaaccagACTTCCAAGGAATATCTTGAGAAGCAGTTGGCAGAAGTGGAGAACAACATAAGAGAGCTACTTCAGCAGGACCCTGGGCTGGCACGCCAGATCCTATCAA

Basic information

species Oryza sativa
transcript LOC_Os02g26440.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g26440.1 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv11s0065g00480.t01 (Vitis vinifera), 3'ss of exon 5
-----gtatgcttgaacctctagatatgtttcttacctttaacatgtcgaaactctagaagagggagagttcctgacttatttattactcatatgaaccagACTTCCAAGGAATATCTTGAGAAGCAGTTGGCAGAAGTGGAGAACAACATAAGAGAGCTACTTCAGCAGGACCCTGGGCTGGCACGCCAGATCCTATCAA
      |  | ||| | |||   |  |      |||    |  |  | | | |||| |  ||      | |    ||| |  | |    ||  |    |||||||||||||||||  | ||||||||| ||||||| || ||||||||| | || ||||| || ||||| || || || || || || || ||| | || |
ggggcttgagtttggatctcacaagctacagtctacaaccacaaacttgtatctct-ggtgaaaatttgattgaaactaagatttgttgcacgttggacagACTTCCAAGGAATACTTAGAGAAGCAGATGGCAGAGGTAGAGAACAACCTGAGGGAGCTGCTGCAGCAAGATCCAGGTCTTGCTCGTCAAATCATGTCGA
















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|55442132|gb|CV734387.1|CV734387
EST:     AGCAAGAACAAAAGCTTAATGACAGTGAAAGTGCAATAGCATCGATGCAG                         ACTTCCAAGGAATATCTTGAGAAGCAGTTGGCAGAAGTGGAGAACAACATA
genomic: AGCAAGAACAAAAGCTTAATGACAGTGAAAGTGCAATAGCATCGATGCAGgtatgcttga ... tatgaaccagACTTCCAAGGAATATCTTGAGAAGCAGTTGGCAGAAGTGGAGAACAACATA
EST: gi|86872790|gb|CI317705.1|CI317705
EST:     AGCAAGAACAAAAGCTTAATGACAGTGAAAGTGCAATAGCATCGATGCAG                         ACTTCCAAGGAATATCTTGAGAAGCAGTTGGCAGAAGTGGAGAACAACATA
genomic: AGCAAGAACAAAAGCTTAATGACAGTGAAAGTGCAATAGCATCGATGCAGgtatgcttga ... tatgaaccagACTTCCAAGGAATATCTTGAGAAGCAGTTGGCAGAAGTGGAGAACAACATA
EST: gi|88440382|gb|CI549263.1|CI549263
EST:     AGCAAGAACAAAAGCTTAATGACAGTGAAAGTGCAATAGCATCGATGCAG                         ACTTCCAAGGAATATCTTGAGAAGCAGTTGGCAGAAGTGGAGAACAACATA
genomic: AGCAAGAACAAAAGCTTAATGACAGTGAAAGTGCAATAGCATCGATGCAGgtatgcttga ... tatgaaccagACTTCCAAGGAATATCTTGAGAAGCAGTTGGCAGAAGTGGAGAACAACATA
EST: gi|33816629|gb|CF334147.1|CF334147
EST:     AGCAAGAACAAAAGCTTAATGACAGTGAAAGTGCAATAGCATCGATGCAG                         ACTTCCAANGGAATATCTTGAGAAGCAGTTGGCAGAAGTGGAGAACAACAT
genomic: AGCAAGAACAAAAGCTTAATGACAGTGAAAGTGCAATAGCATCGATGCAGgtatgcttga ... tatgaaccagACTTCCAA-GGAATATCTTGAGAAGCAGTTGGCAGAAGTGGAGAACAACAT
EST: gi|33805163|gb|CF328459.1|CF328459
EST:     AGCAAGAACAAAAGCTTAATGACAGTGAAAGTGCAATAGCATCGATGCAG                         ACTTCCAAGGAATATCTTGAGAAGCAGTTGGCAGAAGTGGAGAACAACATA
genomic: AGCAAGAACAAAAGCTTAATGACAGTGAAAGTGCAATAGCATCGATGCAGgtatgcttga ... tatgaaccagACTTCCAAGGAATATCTTGAGAAGCAGTTGGCAGAAGTGGAGAACAACATA
EST: gi|88421172|gb|CI567013.1|CI567013
EST:     AGCAAGAACAAAAGCTTAATGACAGTGAAAGTGCAATAGCATCGATGCAG                         ACTTC-AAGGAATATCTTGAGAAG-AGTTG
genomic: AGCAAGAACAAAAGCTTAATGACAGTGAAAGTGCAATAGCATCGATGCAGgtatgcttga ... tatgaaccagACTTCCAAGGAATATCTTGAGAAGCAGTTG
EST: gi|33816630|gb|CF334148.1|CF334148
EST:     AGCAAGAACAAAAGCTTAATGACAGTGAAAGTGCAATAGCATCGATGCAG                         ACTTCCAAGGAATATCTTGAGAAGCAGTTGGCAGAAGTGGAGAACAACATA
genomic: AGCAAGAACAAAAGCTTAATGACAGTGAAAGTGCAATAGCATCGATGCAGgtatgcttga ... tatgaaccagACTTCCAAGGAATATCTTGAGAAGCAGTTGGCAGAAGTGGAGAACAACATA
EST: gi|33805165|gb|CF328460.1|CF328460
EST:     AGCAAGAACAAAAGCTTAATGACAGTGAAAGTGCAATAGCATCGATGCAG                         ACTTCCAAGGAATATCTTGAGAAGCAGTTGGCAGAAGTGGAGAACAACATA
genomic: AGCAAGAACAAAAGCTTAATGACAGTGAAAGTGCAATAGCATCGATGCAGgtatgcttga ... tatgaaccagACTTCCAAGGAATATCTTGAGAAGCAGTTGGCAGAAGTGGAGAACAACATA
EST: gi|58667807|gb|CK056493.1|CK056493
EST:     AGCAAGAACAAAAGCTTAATGACAGTGAAAGTGCAATAGCATCGATGCAG                         ACTTCCAAGGAATATCTTGAGAAGCAGTTGGCAGAAGTGGAGAACAACATA
genomic: AGCAAGAACAAAAGCTTAATGACAGTGAAAGTGCAATAGCATCGATGCAGgtatgcttga ... tatgaaccagACTTCCAAGGAATATCTTGAGAAGCAGTTGGCAGAAGTGGAGAACAACATA
EST: gi|33677160|gb|CF305399.1|CF305399
EST:     AGCAAGAACAAAAGCTTAATGACAGTGAAAGTGCAATAGCATCGATGCAG                         ACTTCCAAGGAATATCTTGAGAAGCAGTTGGCAGAAGTGGAGAACAACATA
genomic: AGCAAGAACAAAAGCTTAATGACAGTGAAAGTGCAATAGCATCGATGCAGgtatgcttga ... tatgaaccagACTTCCAAGGAATATCTTGAGAAGCAGTTGGCAGAAGTGGAGAACAACATA
EST: gi|55442130|gb|CV734386.1|CV734386
EST:     AGCAAGAACAAAAGCTTAATGACAGTGAAAGTGCAATAGCATCGATGCAG                         ACTTCCAAGGAATATCTTGAGAAGCAGTTGGCAGAAGTGGAGAACAACATA
genomic: AGCAAGAACAAAAGCTTAATGACAGTGAAAGTGCAATAGCATCGATGCAGgtatgcttga ... tatgaaccagACTTCCAAGGAATATCTTGAGAAGCAGTTGGCAGAAGTGGAGAACAACATA
EST: gi|86824043|gb|CI260706.1|CI260706
EST:     AGCAAGAACAAAAGCTTAATGACAGTGAAAGTGCAATAGCATCGATGCAG                         ACTTCCAAGGAATATCTTGAGAAGCAGTTGGCAGAAGTGGAGAACAACATA
genomic: AGCAAGAACAAAAGCTTAATGACAGTGAAAGTGCAATAGCATCGATGCAGgtatgcttga ... tatgaaccagACTTCCAAGGAATATCTTGAGAAGCAGTTGGCAGAAGTGGAGAACAACATA

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: 73 (upstream exon), 73 (downstream exon)
Score: 27

ATTTATTTTGGAGCCAAAATCACTCCTGCTGAATGAGCAAGAACAAAAGCTTAATGACAGTGAAAGTGCAATAGCATCGATGCAGgtatgcttga ... tatgaaccagACTTCCAAGGAATATCTTGAGAAGCAGTTGGCAGAAGTGGAGAACAACATAAGAGAGCTACTTCAGCAGGACCCTGGGCTGGCACGCCAGATCCTATCAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcgaaactctagaagagggagagttcctgacttatttattactcatatgaaccagACTTCCAAGGAATATCTTGAGAAGCAGTTGGCAGAAGTGGAGAACAACATAAGAGAGCTACTTCAGCAGGACCCTGGGCTGGCACGCCAGATCCTATCAA
                        tcctgac  putative branch site (score: 27)
                               ttatttattactcata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgcttgaacctctagatatgtttcttacctttaacatgtcgaaactctagaagagggagagttcctgacttatttattactcatatgaaccagACTTCCAAGGAATATCTTGAGAAGCAGTTGGCAGAAGTGGAGAACAACATAAGAGAGCTACTTCAGCAGGACCCTGGGCTGGCACGCCAGATCCTATCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT