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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttttttttttactcgagagagtacgagtgcctgaaaatagggagaaccgatgagtgatattttgcgtatttaatttattagttattgttgtgtcctgcagGGGAAAGGTGAATTTTCGATGGAGTATCTGGAGCACAATACCGTATCGCAGGATGTACAGATGCAACTAGTGAATACGTACAAGGCCAGCAGGGGCACAG

Basic information

species Oryza sativa
transcript LOC_Os03g36780.1
intron # 19
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g36780.1 (Oryza sativa), 3'ss of exon 19
lower sequence: GRMZM2G056393_T02 (Zea mays), 3'ss of exon 19
---ttttttttttactcgagagagtacgagtgcctgaaaatagggagaaccgatgagtgatattttgcgtatttaatttattagttattgt-tgtgtcctgcagGGGAAAGGTGAATTTTCGATGGAGTATCTGGAGCACAATACCGTATCGCAGGATGTACAGATGCAACTAGTGAATACGTACAAGGCCAGCAGGGGCACAG
   | | |  | || | | |     || |||   |     |    |  |  |  |||  ||  | ||  | |   ||||||  ||| |  |   ||||||||||||||||||||||||| |||||||||| |||||||| |||   |||||||||||||| ||||||||||||||||   ||||| ||||   || ||||||||
aactatgtcatatatttgtggactgactagtagttt----ttataaatattggagagaaattgtgtggttttcctatttatctgttttcttgcatgtcctgcagGGGAAAGGTGAATTTACGATGGAGTACCTGGAGCATAATGTTGTATCGCAGGATGTGCAGATGCAACTAGTGACCTCGTACCAGGCGGCCAAGGGCACAG
















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|88986495|gb|CI033659.1|CI033659
EST:     CACTAAACAATATGTTTGGATATTCAACAGCTCTTCGGTCAATGACACAG                         GGGAAAGGTGAATTTTCGATGGAGTATCTGGAGCACAATACCGTATCGCAG
genomic: CACTAAACAATATGTTTGGATATTCAACAGCTCTTCGGTCAATGACACAGgtcaaatgtt ... tgtcctgcagGGGAAAGGTGAATTTTCGATGGAGTATCTGGAGCACAATACCGTATCGCAG
EST: gi|88366609|gb|CI556393.1|CI556393
EST:     ATATTCAACAGCTCTTCGGTCAATGACACAG                         GGGAAAGGTGAATTTTCGATGGAGTATCTGGAGCACAATACCGTATCGCAG
genomic: ATATTCAACAGCTCTTCGGTCAATGACACAGgtcaaatgtt ... tgtcctgcagGGGAAAGGTGAATTTTCGATGGAGTATCTGGAGCACAATACCGTATCGCAG
EST: gi|89187096|gb|CI047163.1|CI047163
EST:     CACTAAACNATATGTTTGGATATTCAACAGCTCTTCGGTCAATGACACAG                         GGGAAAGGTGAATTTTCGATGGAGTATCTGGAGCACAATACCGTATCGCAG
genomic: CACTAAACAATATGTTTGGATATTCAACAGCTCTTCGGTCAATGACACAGgtcaaatgtt ... tgtcctgcagGGGAAAGGTGAATTTTCGATGGAGTATCTGGAGCACAATACCGTATCGCAG
EST: gi|89164137|gb|CI101225.1|CI101225
EST:     CACTAAACAATATGTTTGGATATTCAACAGCTCTTCGGTCAATGACACAG                         GGGAAAGGTGAATTTTCGATGGAGTATCTGGAGCACAATACCGTATCGCAG
genomic: CACTAAACAATATGTTTGGATATTCAACAGCTCTTCGGTCAATGACACAGgtcaaatgtt ... tgtcctgcagGGGAAAGGTGAATTTTCGATGGAGTATCTGGAGCACAATACCGTATCGCAG
EST: gi|88458930|gb|CI555611.1|CI555611
EST:     TCAATGACACAG                         GGGAAAGGTGAATTTTCGATGGAGTATCTGGAGCACAATACCGTATCGCAG
genomic: TCAATGACACAGgtcaaatgtt ... tgtcctgcagGGGAAAGGTGAATTTTCGATGGAGTATCTGGAGCACAATACCGTATCGCAG
EST: gi|87027719|gb|CI274283.1|CI274283
EST:     CACTAAACAATATGTTTGGATATTCAACAGCTCTTCGGTCAATGACACAG                         GGGAAAGGTGAATTTTCGATGGAGTATCTGGAGCACAATACCGTATCGCAG
genomic: CACTAAACAATATGTTTGGATATTCAACAGCTCTTCGGTCAATGACACAGgtcaaatgtt ... tgtcctgcagGGGAAAGGTGAATTTTCGATGGAGTATCTGGAGCACAATACCGTATCGCAG
EST: gi|86434221|gb|CI094564.1|CI094564
EST:     CACTAAACAATATGTTTGGATATTCAACAGCTCTTCGGTCAATGACACAG                         GGGAAAGGTGAATTTTCGATGGAGTATCTGGAGCACAATACCGTATCGCAG
genomic: CACTAAACAATATGTTTGGATATTCAACAGCTCTTCGGTCAATGACACAGgtcaaatgtt ... tgtcctgcagGGGAAAGGTGAATTTTCGATGGAGTATCTGGAGCACAATACCGTATCGCAG
EST: gi|29670886|gb|CB667161.1|CB667161
EST:     CACTAAACAATATGTTTGGATATTCAACAGCTCTTCGGTCAATGACACAG                         GGGAAAGGTGAATTTTCGATGGAGTATCTGGAGCACAATACCGTATCGCAG
genomic: CACTAAACAATATGTTTGGATATTCAACAGCTCTTCGGTCAATGACACAGgtcaaatgtt ... tgtcctgcagGGGAAAGGTGAATTTTCGATGGAGTATCTGGAGCACAATACCGTATCGCAG
EST: gi|86849356|gb|CI297811.1|CI297811
EST:     CACTAAACAATATGTTTGGATATTCAACAGCTCTTCGGTCAATGACACAG                         GGGAAAGGTGAATTTTCGATGGAGTATCTGGAGCACAATACCGTATCGCAG
genomic: CACTAAACAATATGTTTGGATATTCAACAGCTCTTCGGTCAATGACACAGgtcaaatgtt ... tgtcctgcagGGGAAAGGTGAATTTTCGATGGAGTATCTGGAGCACAATACCGTATCGCAG
EST: gi|89192591|gb|CI049889.1|CI049889
EST:     CACTAAACAATATGTTTGGATATTCAACAGCTCTTCGGTCAATGACACAG                         GGGAAAGGTGAATTTTCGATGGAGTATCTGGAGCACAATACCGTATCGCAG
genomic: CACTAAACAATATGTTTGGATATTCAACAGCTCTTCGGTCAATGACACAGgtcaaatgtt ... tgtcctgcagGGGAAAGGTGAATTTTCGATGGAGTATCTGGAGCACAATACCGTATCGCAG
EST: gi|88965002|gb|CI097870.1|CI097870
EST:     CACTAAACAATATGTTTGGATATTCAACAGCTCTTCGGTCAATGACACAG                         GGGAAAGGTGAATTTTCGATGGAGTATCTGGAGCACAATACCGTATCGCAG
genomic: CACTAAACAATATGTTTGGATATTCAACAGCTCTTCGGTCAATGACACAGgtcaaatgtt ... tgtcctgcagGGGAAAGGTGAATTTTCGATGGAGTATCTGGAGCACAATACCGTATCGCAG
EST: gi|88966342|gb|CI119477.1|CI119477
EST:     CACTAAACAATATGTTTGGATATTCAACAGCTCTTCGGTCAATGACACAG                         GGGAAAGGTGAATTTTCGATGGAGTATCTGGAGCACAATACCGTATCGCAG
genomic: CACTAAACAATATGTTTGGATATTCAACAGCTCTTCGGTCAATGACACAGgtcaaatgtt ... tgtcctgcagGGGAAAGGTGAATTTTCGATGGAGTATCTGGAGCACAATACCGTATCGCAG
EST: gi|88470384|gb|CI407655.1|CI407655
EST:     CACTAAACAATATGTTTGGATATTCAACAGCTCTTCGGTCAATGACACAG                         GGGAAAGGTGAATTTTCGATGGAGTATCTGGAGCACAATACCGTATCGCAG
genomic: CACTAAACAATATGTTTGGATATTCAACAGCTCTTCGGTCAATGACACAGgtcaaatgtt ... tgtcctgcagGGGAAAGGTGAATTTTCGATGGAGTATCTGGAGCACAATACCGTATCGCAG
EST: gi|86255945|gb|CI068394.1|CI068394
EST:     CACTAAACAATATGTTTGGATATTCAACAGCTCTTCGGTCAATGACACAG                         GGGAAAGGTGAATTTTCGATGGAGTATCTGGAGCACAATACCGTATCGCAG
genomic: CACTAAACAATATGTTTGGATATTCAACAGCTCTTCGGTCAATGACACAGgtcaaatgtt ... tgtcctgcagGGGAAAGGTGAATTTTCGATGGAGTATCTGGAGCACAATACCGTATCGCAG
EST: gi|87023356|gb|CI272184.1|CI272184
EST:     CACTAAACAATATGTTTGGATATTCAACAGCTCTTCGGTCAATGACACAG                         GGGAAAGGTGAATTTTCGATGGAGTATCTGGAGCACAATACCGTATCGCAG
genomic: CACTAAACAATATGTTTGGATATTCAACAGCTCTTCGGTCAATGACACAGgtcaaatgtt ... tgtcctgcagGGGAAAGGTGAATTTTCGATGGAGTATCTGGAGCACAATACCGTATCGCAG
EST: gi|58693580|gb|CK082267.1|CK082267
EST:     CACTAAACAATATGTTTGGATATTCAACAGCTCTTCGGTCAATGACACAG                         GGGAAAGGTGAATTTTCGATGGAGTATCTGGAGCACAATACCGTATCGCAG
genomic: CACTAAACAATATGTTTGGATATTCAACAGCTCTTCGGTCAATGACACAGgtcaaatgtt ... tgtcctgcagGGGAAAGGTGAATTTTCGATGGAGTATCTGGAGCACAATACCGTATCGCAG

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: 54 (upstream exon), 62 (downstream exon)
Score: 24

GTTCCACTAAACAATATGTTTGGATATTCAACAGCTCTTCGGTCAATGACACAGgtcaaatgtt ... tgtcctgcagGGGAAAGGTGAATTTTCGATGGAGTATCTGGAGCACAATACCGTATCGCAGGATGTACAGATGCAACTAGTGAATACGTACAAGGCCAGCAGGGGCACAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

accgatgagtgatattttgcgtatttaatttattagttattgttgtgtcctgcagGGGAAAGGTGAATTTTCGATGGAGTATCTGGAGCACAATACCGTATCGCAGGATGTACAGATGCAACTAGTGAATACGTACAAGGCCAGCAGGGGCACAG
                      atttaat  putative branch site (score: 24)
           atattttgcgtattta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttttttttttactcgagagagtacgagtgcctgaaaatagggagaaccgatgagtgatattttgcgtatttaatttattagttattgttgtgtcctgcagGGGAAAGGTGAATTTTCGATGGAGTATCTGGAGCACAATACCGTATCGCAGGATGTACAGATGCAACTAGTGAATACGTACAAGGCCAGCAGGGGCACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - gtgcctg
- - - - - - - - - - - - - - - - -aaaatagg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - attttgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -attgttg