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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgcaatttactcgttatattatgttgtgttgatcctactgtcataagcttctattgccatttggtttgatgatgcattgtacttgacgatctttttgcagGCATATCTCTAAAGACCCAGGAGCTATATGCACTTGTGTTTGCTGCTCGTTACTTGGACCTGTTCATTCATTTTATATCTCTGTATAACACTGTCATGAA

Basic information

species Oryza sativa
transcript LOC_Os11g28340.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g28340.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G031802_T02 (Zea mays), 3'ss of exon 1
tgcaatttactcgttatattatgttgtgttgatcctactgtcataagcttctattgccatttggtttgatgatgcattg---tacttgacgatctttttgcagGCATATCTCTAAAGACCCAGGAGCTATATGCACTTGTGTTTGCTGCTCGTTACTTGGACCTGTTCATTCATTTTATATCTCTGTATAACACTGTCATGAA
   | | || |  ||||    |       || |  |  | |   ||||||||||||  || ||||||||||   |  ||    || || | |  || ||| |||||||||||| ||||| |||||||| ||||||||||| ||||| || || ||| ||||||||||  |||||||| | |||||||||||||||||||||||
-ttattctagtaattattgcctaacagcatgttaatgtt-tagcaagcttctattgttatatggtttgatgggtctctgattcacatggc-actttcttgtagGCATATCTCTGAAGACACAGGAGCTGTATGCACTTGTTTTTGCAGCACGGTACCTGGACCTGTTTGTTCATTTTGTGTCTCTGTATAACACTGTCATGAA
















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|88359307|gb|CI679833.1|CI679833
EST:     CAGCGTGGTGGTGCTCCTCCTGAAGATCCACACCATCAAGTCCTGCGCAG                         GCATATCTCTAAAGACCCAGGAGCTATATGCACTTGTGTTTGCCTGCTCGT
genomic: CAGCGTGGTGGTGCTCCTCCTGAAGATCCACACCATCAAGTCCTGCGCAGgtaacgcgcc ... ctttttgcagGCATATCTCTAAAGACCCAGGAGCTATATGCACTTGTGTTTGC-TGCTCGT
EST: gi|117216901|gb|CT861591.1|CT861591
EST:     CAGCGTGGTGGTGCTCCTCCTCAAGATCCACACCATCAAGTCCTGCGCAG                         GCATATCTCTAAAGACCCAGGAGCTATATGCACTTGTGTTTGCTGCTCGTT
genomic: CAGCGTGGTGGTGCTCCTCCTGAAGATCCACACCATCAAGTCCTGCGCAGgtaacgcgcc ... ctttttgcagGCATATCTCTAAAGACCCAGGAGCTATATGCACTTGTGTTTGCTGCTCGTT
EST: gi|88332030|gb|CI642255.1|CI642255
EST:     CAGCGTGGTGGTGCTCCTCCTGAAGATCCACACCATCAAGTCCTGCGCAG                         GCATATCTCTAAAGACCCAGGAGCTATATGCACTTGTGTTTGCTGCTCGTT
genomic: CAGCGTGGTGGTGCTCCTCCTGAAGATCCACACCATCAAGTCCTGCGCAGgtaacgcgcc ... ctttttgcagGCATATCTCTAAAGACCCAGGAGCTATATGCACTTGTGTTTGCTGCTCGTT
EST: gi|88331165|gb|CI639576.1|CI639576
EST:     CAGCGTGGTGGTGCTCCTCCTGAAGATCCACACCATCAAGTCCTGCGCAG                         GCATATCTCTAAAGACCCAGGAGCTATATGCACTTGTGTTTGCTGCTCGTT
genomic: CAGCGTGGTGGTGCTCCTCCTGAAGATCCACACCATCAAGTCCTGCGCAGgtaacgcgcc ... ctttttgcagGCATATCTCTAAAGACCCAGGAGCTATATGCACTTGTGTTTGCTGCTCGTT
EST: gi|88381796|gb|CI682469.1|CI682469
EST:     CAGCGTGGTGGTGCTCCTCCTGAAGATCCACACCATCAAGTCCTGCGCAG                         GCATATCTCTAAAGACCCAGGAGCTATATGCACTTGTGTTTGCTGCTCGTT
genomic: CAGCGTGGTGGTGCTCCTCCTGAAGATCCACACCATCAAGTCCTGCGCAGgtaacgcgcc ... ctttttgcagGCATATCTCTAAAGACCCAGGAGCTATATGCACTTGTGTTTGCTGCTCGTT
EST: gi|88414401|gb|CI691564.1|CI691564
EST:     CAGCGTGGTGGTGCTCCTCCTGAAGATCCACACCATCAAGTCCTGCGCAG                         GCATATCTCTAAAGACCCAGGAGCTATATGCACTTGTGTTTGCTGCTCGTT
genomic: CAGCGTGGTGGTGCTCCTCCTGAAGATCCACACCATCAAGTCCTGCGCAGgtaacgcgcc ... ctttttgcagGCATATCTCTAAAGACCCAGGAGCTATATGCACTTGTGTTTGCTGCTCGTT
EST: gi|88367679|gb|CI568451.1|CI568451
EST:     CAGCGTGGTGGTGCTCCTCCTGAAGATCCACACCATCAAGTCCTGCGCAG                         GCATATCTCTAAAGACCCAGGAGCTATATGCACTTGTGTTTGCTGCTCGTT
genomic: CAGCGTGGTGGTGCTCCTCCTGAAGATCCACACCATCAAGTCCTGCGCAGgtaacgcgcc ... ctttttgcagGCATATCTCTAAAGACCCAGGAGCTATATGCACTTGTGTTTGCTGCTCGTT
EST: gi|58599124|gb|CK009652.1|CK009652
EST:     CAGCGTGGTGGTGCTCCTCCTCAAGATCCACACCATCAAGTCCTGCGCAG                         GCATATCTCTAAAGACCCAGGAGCTATATGCACTTGTGTTTGCTGCTCGTT
genomic: CAGCGTGGTGGTGCTCCTCCTGAAGATCCACACCATCAAGTCCTGCGCAGgtaacgcgcc ... ctttttgcagGCATATCTCTAAAGACCCAGGAGCTATATGCACTTGTGTTTGCTGCTCGTT
EST: gi|88589576|gb|CI705472.1|CI705472
EST:     CAGCGTGGTGGTGCTCCTCCTGAAGATCCACACCATCAAGTCCTGCGCAG                         GCATATCTCTAAAGACCCAGGAGCTATATGCACTTGTGTTTGCTGCTCGTT
genomic: CAGCGTGGTGGTGCTCCTCCTGAAGATCCACACCATCAAGTCCTGCGCAGgtaacgcgcc ... ctttttgcagGCATATCTCTAAAGACCCAGGAGCTATATGCACTTGTGTTTGCTGCTCGTT
EST: gi|88354174|gb|CI637740.1|CI637740
EST:     CAGCGTGGTGGTGCTCCTCCTGAAGATCCACACCATCAAGTCCTGCGCAG                         GCATATCTCTAAAGACCCAGGAGCTATATGCACTTGTGTTTGCTGCTCGTT
genomic: CAGCGTGGTGGTGCTCCTCCTGAAGATCCACACCATCAAGTCCTGCGCAGgtaacgcgcc ... ctttttgcagGCATATCTCTAAAGACCCAGGAGCTATATGCACTTGTGTTTGCTGCTCGTT
EST: gi|58589776|gb|CF988084.1|CF988084
EST:     CAGCGTGGTGGTGCTCCTCCTCAAGATCCACACCATCAAGTCCTGCGCAG                         GCATATCTCTAAAGACCCAGGAGCTATATGCACTTGTGTTTGCTGCTCGTT
genomic: CAGCGTGGTGGTGCTCCTCCTGAAGATCCACACCATCAAGTCCTGCGCAGgtaacgcgcc ... ctttttgcagGCATATCTCTAAAGACCCAGGAGCTATATGCACTTGTGTTTGCTGCTCGTT
EST: gi|33684131|gb|CF312370.1|CF312370
EST:     CAGCGTGGTGGTGCTCCTCCTGAAGATCCACACCATCAAGTCCTGCGCAG                         GCATATCTCTAAAGACCCAGGAGCTATATGCACTTGTGTTTGCTGCTCGTT
genomic: CAGCGTGGTGGTGCTCCTCCTGAAGATCCACACCATCAAGTCCTGCGCAGgtaacgcgcc ... ctttttgcagGCATATCTCTAAAGACCCAGGAGCTATATGCACTTGTGTTTGCTGCTCGTT
EST: gi|88433002|gb|CI569671.1|CI569671
EST:     CAGCGTGGTGGTGCTCCTCCTGAAGATCCACACCATCAAGTCCTGCGCAG                         GCATATCTCTAAAGACCCAGGAGCTATATGCACTTGTGTTTGCTGCTCGTT
genomic: CAGCGTGGTGGTGCTCCTCCTGAAGATCCACACCATCAAGTCCTGCGCAGgtaacgcgcc ... ctttttgcagGCATATCTCTAAAGACCCAGGAGCTATATGCACTTGTGTTTGCTGCTCGTT
EST: gi|86829855|gb|CI288545.1|CI288545
EST:     CAGCGTGGTGGTGCTCCTCCTGAAGATCCACACCATCAAGTCCTGCGCAG                         GCATATCTCTAAAGACCCAGGAGCTATATGCACTTGTGTTTGCTGCTCGTT
genomic: CAGCGTGGTGGTGCTCCTCCTGAAGATCCACACCATCAAGTCCTGCGCAGgtaacgcgcc ... ctttttgcagGCATATCTCTAAAGACCCAGGAGCTATATGCACTTGTGTTTGCTGCTCGTT

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), 71 (downstream exon)
Score: 43

GCGGCGGAGATGAACGCGTTCCGGCTAGCCGGGGACATGACCCACCTCCTCAGCGTGGTGGTGCTCCTCCTGAAGATCCACACCATCAAGTCCTGCGCAGgtaacgcgcc ... ctttttgcagGCATATCTCTAAAGACCCAGGAGCTATATGCACTTGTGTTTGCTGCTCGTTACTTGGACCTGTTCATTCATTTTATATCTCTGTATAACACTGTCATGAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agcttctattgccatttggtttgatgatgcattgtacttgacgatctttttgcagGCATATCTCTAAAGACCCAGGAGCTATATGCACTTGTGTTTGCTGCTCGTTACTTGGACCTGTTCATTCATTTTATATCTCTGTATAACACTGTCATGAA
                                   acttgac  putative branch site (score: 43)
                                            tctttttgc  putative PPT
                                           atcttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgcaatttactcgttatattatgttgtgttgatcctactgtcataagcttctattgccatttggtttgatgatgcattgtacttgacgatctttttgcagGCATATCTCTAAAGACCCAGGAGCTATATGCACTTGTGTTTGCTGCTCGTTACTTGGACCTGTTCATTCATTTTATATCTCTGTATAACACTGTCATGAA

- - - - - - - - - - atgttgt
- - - - - - - - - - - - - - - - -cctactg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - ccatttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgatgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtacttg