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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcacctgtcctcactgcattaagggttttttggccccgtttattgtttatcctttattctaacatggcgttctgctgtacagGCTCATGTATTACTGCATTTCATCAATGCGTCACATGCACGGAAGCAGATGAACTCCAGGAGATCAGATCCTTATGGAAACCCATGTAACATGGATTTCA

Basic information

species Oryza sativa
transcript LOC_Os01g66350.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g66350.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G081188_T03 (Zea mays), 3'ss of exon 3
gtaagcacctgtc-ctcactgcattaagggttttttggccccgtttattgtttatcctttattctaacatggcgttctgctgtacagGCTCATGTATTACTGCATTTCATCAATGCGTCACATGCACGGAAGCAGATG---AACTCCAGGAGATCAGATCCTTATGGAAACCCATGTAACATGGATTTCA
|||||||  |||  |||| |||  |     |  | |       ||  || |||  ||  ||| || | |||   |||||||||||||||||||||  || ||||||| || ||||| |||||||| ||||  | || |   ||    | |    || | ||| |  ||    ||    |  || | |  |
gtaagcatttgtttctcagtgcgatgtaattggtatatgtgttttggtttttttacccatatgctca-atgtgtttctgctgtacagGCTCATGTGCTATTGCATTTTATTAATGCATCACATGCTCGGAGACTGAAGCAGAAGCAGAAGCAGGCAAACCCTGACCGA---TCAGAGTATCTGTACTCTA
















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|88347974|gb|CI636067.1|CI636067
EST:     TGCTCAAGGATCAAGCAAAGTCAGATGACATTATCAAAGCGGCTTTCCAT                         GCTCATGTATTACTGCATTTCATCAATGCGTCA
genomic: TGCTCAAGGATCAAGCAAAGTCAGATGACATTATCAAAGCGGCTTTCCATgtaagcacct ... tgctgtacagGCTCATGTATTACTGCATTTCATCAATGCGTCA
EST: gi|88333187|gb|CI641030.1|CI641030
EST:     TGCTCAAGGATCAAGCAAAGTCAGATGACATTATCAAAGCGGCTTTCCAT                         GCTCATGTATTACTGCATTTCATCAATGCGTCACATGCACGGAAGCAGATG
genomic: TGCTCAAGGATCAAGCAAAGTCAGATGACATTATCAAAGCGGCTTTCCATgtaagcacct ... tgctgtacagGCTCATGTATTACTGCATTTCATCAATGCGTCACATGCACGGAAGCAGATG
EST: gi|88332186|gb|CI643603.1|CI643603
EST:     TGCTCAAGGATCAAGCAAAGTCAGATGACATTATCAAAGCGGCTTTCCAT                         GCTCATGTATTACTGCATTTCATCAATGCGTCACATGCACGGAAGCAGATG
genomic: TGCTCAAGGATCAAGCAAAGTCAGATGACATTATCAAAGCGGCTTTCCATgtaagcacct ... tgctgtacagGCTCATGTATTACTGCATTTCATCAATGCGTCACATGCACGGAAGCAGATG
EST: gi|88330936|gb|CI638344.1|CI638344
EST:     TGCTCAAGGATCAAGCAAAGTCAGATGACATTATCAAAGCGGCTTTCCAT                         GCTCATGTATTACTGCATTTCATCAATGCGTCACATGCACGGAAGCAGATG
genomic: TGCTCAAGGATCAAGCAAAGTCAGATGACATTATCAAAGCGGCTTTCCATgtaagcacct ... tgctgtacagGCTCATGTATTACTGCATTTCATCAATGCGTCACATGCACGGAAGCAGATG
EST: gi|88326154|gb|CI657734.1|CI657734
EST:     TGCTCAAGGATCAAGCAAAGTCAGATGACATTATCAAAGCGGCTTTCCAT                         GCTCATGTATTACTGCATTTCATCAATGCGTCACATGCACGGAAGCAGATG
genomic: TGCTCAAGGATCAAGCAAAGTCAGATGACATTATCAAAGCGGCTTTCCATgtaagcacct ... tgctgtacagGCTCATGTATTACTGCATTTCATCAATGCGTCACATGCACGGAAGCAGATG
EST: gi|58679991|gb|CK068678.1|CK068678
EST:     TGCTCAAGGATCAAGCAAAGTCAGATGACATTATCAAAGCGGCTTTCCAT                         GCTCACGTATTACTGCATTTCATCAATGCGTCACATGCACGGAAGCAGATG
genomic: TGCTCAAGGATCAAGCAAAGTCAGATGACATTATCAAAGCGGCTTTCCATgtaagcacct ... tgctgtacagGCTCATGTATTACTGCATTTCATCAATGCGTCACATGCACGGAAGCAGATG
EST: gi|88330845|gb|CI636857.1|CI636857
EST:     TGCTCAAGGATCAAGCAAAGTCAGATGACATTATCAAAGCGGCTTTCCAT                         GCTCATGTATTACTGCATTTCATCAATGCGTCACATGCACGGAAGCAGATG
genomic: TGCTCAAGGATCAAGCAAAGTCAGATGACATTATCAAAGCGGCTTTCCATgtaagcacct ... tgctgtacagGCTCATGTATTACTGCATTTCATCAATGCGTCACATGCACGGAAGCAGATG
EST: gi|88305833|gb|CI633413.1|CI633413
EST:     TGCTCAAGGATCAAGCAAAGTCAGATGACATTATCAAAGCGGCTTTCCAT                         GCTCATGTATTACTGCATTTCATCAATGCGTCACATGCACGGAA
genomic: TGCTCAAGGATCAAGCAAAGTCAGATGACATTATCAAAGCGGCTTTCCATgtaagcacct ... tgctgtacagGCTCATGTATTACTGCATTTCATCAATGCGTCACATGCACGGAA
EST: gi|29681946|gb|CB678221.1|CB678221
EST:     TGCTCAAGGATCAAGCAAAGTCAGATGACATTATCAAAGCGGCTTTCCAT                         GCTCATGTATTACTGCATTTCATC
genomic: TGCTCAAGGATCAAGCAAAGTCAGATGACATTATCAAAGCGGCTTTCCATgtaagcacct ... tgctgtacagGCTCATGTATTACTGCATTTCATC

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: 70 (upstream exon), 67 (downstream exon)
Score: 54

TGAGAGATACATGGTAACATATAACCCCGCAAAGGATAAGGTATATGCTTTGCTCAAGGATCAAGCAAAGTCAGATGACATTATCAAAGCGGCTTTCCATgtaagcacct ... tgctgtacagGCTCATGTATTACTGCATTTCATCAATGCGTCACATGCACGGAAGCAGATGAACTCCAGGAGATCAGATCCTTATGGAAACCCATGTAACATGGATTTCA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttggccccgtttattgtttatcctttattctaacatggcgttctgctgtacagGCTCATGTATTACTGCATTTCATCAATGCGTCACATGCACGGAAGCAGATGAACTCCAGGAGATCAGATCCTTATGGAAACCCATGTAACATGGATTTCA
                             ttctaac  putative branch site (score: 54)
                                          ttctgct  putative PPT
           tttattgtttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagcacctgtcctcactgcattaagggttttttggccccgtttattgtttatcctttattctaacatggcgttctgctgtacagGCTCATGTATTACTGCATTTCATCAATGCGTCACATGCACGGAAGCAGATGAACTCCAGGAGATCAGATCCTTATGGAAACCCATGTAACATGGATTTCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA