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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cctcagataactaaaaaaaacagcccactggttcatatgaaatgtgtagtcctatattatttatacggttgccttatcattatggcttacgctattgcagGTCAGCGTCAGGGTAAGGGACAAAGCTGAACTAGCCACAGTGAGCATTGATGACATCATCACACGTTTTAAGGAGGAAGTAGCAGCTTACAAATGATTTT

Basic information

species Oryza sativa
transcript LOC_Os08g19850.1
intron # 19
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g19850.1 (Oryza sativa), 3'ss of exon 19
lower sequence: GRMZM2G137615_T01 (Zea mays), 3'ss of exon 8
--------------------------------------------cctcagataactaaaaaaaacagcccactggttcatatgaaatgtgtagtcctatatt-atttatacggttgccttatcat-tatggcttacgc-tattgcagGTCAGCGTCAGGGTAAGGGACAAAGCTGAACTAGCCACAGTGAGCATTGATGACATCATCACACGTTTTAAGGAGGAAGTAGCAGCTTACAAATGATTTT
                                            ||    |    |  |  |  |   ||    || |  |   | ||       | | ||  ||||      ||||  | |||  |    | |  |  || |||||||| |||| |||||||| || || || || || |||||| ||||| |||||| | ||||||||||||| | ||||||| | | ||| | |||||||||||
gtaagtcctctttacctcgtgccatttttttaatcttctacataccgtgtacttgtgtaccagtctcaccctcagtcctcagatattgatccacgcaaaatagatttgattccttgctgtttcacatggaccctttgtgtactgcagGTCTGCGTTAGGGTAAGAGATAATGCCGACCTGGCCACAATGAGCGTTGATGGCCTCATCACACGTTTGAGGGAGGAAATCGTAGCCTTCAAATGATTTT
















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|29628276|gb|CB633287.1|CB633287
EST:     AATTCAACTACATTCTTGTCGTTGGTGCACAAGAAGCAGAGACTGGACAG                         GTCAGCGTCAGGGTAAGGGACAAAGCTGAACTAGCCACAGTGAGCATTGAT
genomic: AATTCAACTACATTCTTGTCGTTGGTGCACAAGAAGCAGAGACTGGACAGgtttttaccc ... gctattgcagGTCAGCGTCAGGGTAAGGGACAAAGCTGAACTAGCCACAGTGAGCATTGAT
EST: gi|88974311|gb|CI019984.1|CI019984
EST:     AATTCAACTACATTCTTGTCGTTGGTGCACAAGAAGCAGAGACTGGACAG                         GTCAGCGTCAGGGTAAGGGACAAAGCTGAACTAGCCACAGTGAGCATTGAT
genomic: AATTCAACTACATTCTTGTCGTTGGTGCACAAGAAGCAGAGACTGGACAGgtttttaccc ... gctattgcagGTCAGCGTCAGGGTAAGGGACAAAGCTGAACTAGCCACAGTGAGCATTGAT
EST: gi|58669943|gb|CK058629.1|CK058629
EST:     AATTCAACTACATTCTTGTCGTTGGTGCACAAGAAGCAGAGACTGGACAG                         GTCAGCGTCAGGGTAAGGGACAAAGCTGAACTAGCCACAGTGAGCATTGAT
genomic: AATTCAACTACATTCTTGTCGTTGGTGCACAAGAAGCAGAGACTGGACAGgtttttaccc ... gctattgcagGTCAGCGTCAGGGTAAGGGACAAAGCTGAACTAGCCACAGTGAGCATTGAT
EST: gi|24208843|gb|AU225870.1|AU225870
EST:     AATTCAACTACATTCTTGTCGTTGGTGCACAAGAAGCAGAGACTGGACAG                         GTCAGCGTCAGGGTAAGGGACAAAGCTGAACTAGCCACAGTGAGCATTGAT
genomic: AATTCAACTACATTCTTGTCGTTGGTGCACAAGAAGCAGAGACTGGACAGgtttttaccc ... gctattgcagGTCAGCGTCAGGGTAAGGGACAAAGCTGAACTAGCCACAGTGAGCATTGAT
EST: gi|86430588|gb|CI083011.1|CI083011
EST:     AATTCAACTACATTCTTGTCGTTGGTGCACAAGAAGCAGAGACTGGACAG                         GTCAGCGTCAGGGTAAGGGACAAAGCTGAACTAGCCACAGTGAGCATTGAT
genomic: AATTCAACTACATTCTTGTCGTTGGTGCACAAGAAGCAGAGACTGGACAGgtttttaccc ... gctattgcagGTCAGCGTCAGGGTAAGGGACAAAGCTGAACTAGCCACAGTGAGCATTGAT
EST: gi|88411730|gb|CI521453.1|CI521453
EST:     AATTCAACTACATTCTTGTCGTTGGTGCACAAGAAGCAGAGACTNGACAG                         GTCAGCGTCAGGGTAAGGGACAAANCTGAACTAGCCACAGTGAGCATTGAT
genomic: AATTCAACTACATTCTTGTCGTTGGTGCACAAGAAGCAGAGACTGGACAGgtttttaccc ... gctattgcagGTCAGCGTCAGGGTAAGGGACAAAGCTGAACTAGCCACAGTGAGCATTGAT
EST: gi|88488406|gb|CI425677.1|CI425677
EST:     AATTCAACTACATTCTTGTCGTTGGTGCACAAGAAGCAGAGACTGGACAG                         GTCAGGCGTCAGGGTAAGGGACAAAGCTNAACTAGCCACAGTGAGCATTGA
genomic: AATTCAACTACATTCTTGTCGTTGGTGCACAAGAAGCAGAGACTGGACAGgtttttaccc ... gctattgcagGTCA-GCGTCAGGGTAAGGGACAAAGCTGAACTAGCCACAGTGAGCATTGA
EST: gi|29622569|gb|CB627580.1|CB627580
EST:     AATTCAACTACATTCTTGTCGTTGGTGCACAAGAAGCAGAGACTGGACAG                         GTCAGCGTCAGGGTAAGGGACAAAGCTGAACTAGCCACAGTGAGCATTGAT
genomic: AATTCAACTACATTCTTGTCGTTGGTGCACAAGAAGCAGAGACTGGACAGgtttttaccc ... gctattgcagGTCAGCGTCAGGGTAAGGGACAAAGCTGAACTAGCCACAGTGAGCATTGAT
EST: gi|88382609|gb|CI535817.1|CI535817
EST:     AATTCAACTACATTCTTGTCGTTGGTGCACAAGAAGCAGAGACTGGACAG                         GTCAGCGTCAGGGTAAGGGACAAAGCTGAACTAGCCACAGTGAGCATTGAT
genomic: AATTCAACTACATTCTTGTCGTTGGTGCACAAGAAGCAGAGACTGGACAGgtttttaccc ... gctattgcagGTCAGCGTCAGGGTAAGGGACAAAGCTGAACTAGCCACAGTGAGCATTGAT
EST: gi|8956784|gb|BE230587.1|BE230587
EST:     AATTCAACTACATTCTTGTCGTTGGTGCACAAGAAGCAGAGACTGG-CAG                         GTCAGCGTCAGGGTAAGGGACAAAGCTGA-CTAGCC-CAGTGAGCATTGAT
genomic: AATTCAACTACATTCTTGTCGTTGGTGCACAAGAAGCAGAGACTGGACAGgtttttaccc ... gctattgcagGTCAGCGTCAGGGTAAGGGACAAAGCTGAACTAGCCACAGTGAGCATTGAT
EST: gi|88219267|gb|CI218827.1|CI218827
EST:     AATTCAACTACATTCTTGTCGTTGGTGCACAAGAAGCAGAGACTGGACAG                         GTCAGCGTCAGGGTAAGGGACAAAGCTGAACTAGCCACAGTGAGCATTGAT
genomic: AATTCAACTACATTCTTGTCGTTGGTGCACAAGAAGCAGAGACTGGACAGgtttttaccc ... gctattgcagGTCAGCGTCAGGGTAAGGGACAAAGCTGAACTAGCCACAGTGAGCATTGAT
EST: gi|88197260|gb|CI197110.1|CI197110
EST:     AATTCAACTACATTCTTGTCGTTGGTGCACAAGAAGCAGAGACTGGACAG                         GTCAGCGTCAGGGTAAGGGACAAAGCTGAACTAGCCACAGTGAGCATTGAT
genomic: AATTCAACTACATTCTTGTCGTTGGTGCACAAGAAGCAGAGACTGGACAGgtttttaccc ... gctattgcagGTCAGCGTCAGGGTAAGGGACAAAGCTGAACTAGCCACAGTGAGCATTGAT
EST: gi|58606862|gb|CK034895.1|CK034895
EST:     AATTCAACTACATTCTTGTCGTTGGTGCACAAGAAGCAGAGACTGGACAG                         GTCAGCGTCAGGGTAAGGGACAAAGCTGAACTAGCCACAGTGAGCATTGAT
genomic: AATTCAACTACATTCTTGTCGTTGGTGCACAAGAAGCAGAGACTGGACAGgtttttaccc ... gctattgcagGTCAGCGTCAGGGTAAGGGACAAAGCTGAACTAGCCACAGTGAGCATTGAT
EST: gi|88321457|gb|CI535409.1|CI535409
EST:     AATTCAACTACATTCTTGTCGTTGGTGCACAAGAAGCAGAGACTGGACAG                         GTCAGCGTCAGGGTAAGGGACAAAGCTGAACTAGCCACAGTGAGCATTGAT
genomic: AATTCAACTACATTCTTGTCGTTGGTGCACAAGAAGCAGAGACTGGACAGgtttttaccc ... gctattgcagGTCAGCGTCAGGGTAAGGGACAAAGCTGAACTAGCCACAGTGAGCATTGAT
EST: gi|88974365|gb|CI020038.1|CI020038
EST:     AATTCAACTACATTCTTGTCGTTGGTGCACAAGAAGCAGAGACTGGACAG                         GTCAGCGTCAGGGTAAGGGACAAAGCTGAACTAGCCACAGTGAGCATTGAT
genomic: AATTCAACTACATTCTTGTCGTTGGTGCACAAGAAGCAGAGACTGGACAGgtttttaccc ... gctattgcagGTCAGCGTCAGGGTAAGGGACAAAGCTGAACTAGCCACAGTGAGCATTGAT
EST: gi|58674470|gb|CK063157.1|CK063157
EST:     AATTCAACTACATTCTTGTCGTTGGTGCACAAGAAGCAGAGACTGGACAG                         GTCAGCGTCAGGGTAAGGGACAAAGCTGAACTAGCCACAGTGAGCATTGAT
genomic: AATTCAACTACATTCTTGTCGTTGGTGCACAAGAAGCAGAGACTGGACAGgtttttaccc ... gctattgcagGTCAGCGTCAGGGTAAGGGACAAAGCTGAACTAGCCACAGTGAGCATTGAT

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), 48 (downstream exon)
Score: 19

GTACGGGAGGCTCAATTAGCCCAATTCAACTACATTCTTGTCGTTGGTGCACAAGAAGCAGAGACTGGACAGgtttttaccc ... gctattgcagGTCAGCGTCAGGGTAAGGGACAAAGCTGAACTAGCCACAGTGAGCATTGATGACATCATCACACGTTTTAAGGAGGAAGTAGCAGCTTACAAATGATTTT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtagtcctatattatttatacggttgccttatcattatggcttacgctattgcagGTCAGCGTCAGGGTAAGGGACAAAGCTGAACTAGCCACAGTGAGCATTGATGACATCATCACACGTTTTAAGGAGGAAGTAGCAGCTTACAAATGATTTT
                                      ggcttac  putative branch site (score: 19)
       tatattatttata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cctcagataactaaaaaaaacagcccactggttcatatgaaatgtgtagtcctatattatttatacggttgccttatcattatggcttacgctattgcagGTCAGCGTCAGGGTAAGGGACAAAGCTGAACTAGCCACAGTGAGCATTGATGACATCATCACACGTTTTAAGGAGGAAGTAGCAGCTTACAAATGATTTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - aaaaaaa
- - - - - - - - - - - - - -ctggttc