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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaacttctaactctaccatggtaaaacacctttatgcagagcagagtaacattttgtttccttttccttttgtagATATTGTTGGTTGACAAGAAAATTACTGATGCAAGTGAGATTATAAGGATATTGGATAGTGCTGTCAAAGAAGATTATCCATTGTTGATAGTTGCCGAGG

Basic information

species Oryza sativa
transcript 13113.m00214
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: 13113.m00214 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G042253_T01 (Zea mays), 3'ss of exon 4
gtaacttctaactctaccatggtaaaacacctttatgcagagcagag-taacattttgtttccttttcct-tttgtagATATTGTTGGTTGACAAGAAAATTACTGATGCAAGTGAGATTATAAGGATATTGGATAGTGCTGTCAAAGAAGATTATCCATTGTTGATAGTTGCCGAGG
     |     ||||       | | |||   || ||||||  | |  ||| |       | | | |  | |||| ||||| | |||||||||||||||||||| ||||| |||||||||||||||||| |||| ||||||||||||||| | ||||| ||||| ||| | |||||||
----gtgagggctctgttcctcttatacaatgttttgcagaaaaaaaataatagaagaactacatcttgtgtttgcagATACTATTGGTTGACAAGAAAATTACGGATGCTAGTGAGATTATAAGGATACTGGACAGTGCTGTCAAAGAAAACTATCCGTTGTTAATAATCGCCGAGG
















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|58689939|gb|CK078626.1|CK078626
EST:     ATATGT-CGCGGAGTTTACTGACTGTAAG                         ATATTGTTGGTTGACAAGAAAATTACTGATGCAAGTGAGATTATAAGGATA
genomic: ATATGTCCGCGGAGTTTACTGACTGTAAGgtaacttcta ... ccttttgtagATATTGTTGGTTGACAAGAAAATTACTGATGCAAGTGAGATTATAAGGATA
EST: gi|29668864|gb|CB665139.1|CB665139
EST:     ACTTTGTGACTGATTGTACAAATATGTCCGCGGAGTTTACTGACTGTAAG                         ATATTGTTGGTTGACAAGAAAATTACTGATGCAAGTGAGATTATAAGGATA
genomic: ACTTTGTGACTGATTGTACAAATATGTCCGCGGAGTTTACTGACTGTAAGgtaacttcta ... ccttttgtagATATTGTTGGTTGACAAGAAAATTACTGATGCAAGTGAGATTATAAGGATA
EST: gi|58696091|gb|CK084778.1|CK084778
EST:     ACTTTGTGACTGATTGTACAAATATGTCCGCGGAGTTTACTGACTGTAAG                         ATATTGTTGGTTGAC
genomic: ACTTTGTGACTGATTGTACAAATATGTCCGCGGAGTTTACTGACTGTAAGgtaacttcta ... ccttttgtagATATTGTTGGTTGAC
EST: gi|29668478|gb|CB664753.1|CB664753
EST:     ACTTTGTGACTGATTGTACAAATATGTCCGCGGAGTTTACTGACTGTAAG                         ATATTGCTGGTTGACAAGAAAATTACTGATGCAAGTG
genomic: ACTTTGTGACTGATTGTACAAATATGTCCGCGGAGTTTACTGACTGTAAGgtaacttcta ... ccttttgtagATATTGTTGGTTGACAAGAAAATTACTGATGCAAGTG
EST: gi|58692944|gb|CK081631.1|CK081631
EST:     ACTTTGTGACTGATTGTACAAATATGTCCGCGGAGTTTACTGACTGTAAG                         ATATTGTTGGTTGACAAGAAAATTACTGATGCAAGTGAGATTATAAGGATA
genomic: ACTTTGTGACTGATTGTACAAATATGTCCGCGGAGTTTACTGACTGTAAGgtaacttcta ... ccttttgtagATATTGTTGGTTGACAAGAAAATTACTGATGCAAGTGAGATTATAAGGATA
EST: gi|29638632|gb|CB643641.1|CB643641
EST:     ACTTTGTGACTGATTGTACAAATATGTCCGCGGAGTTTACTGACTGTAAG                         ATATTGTTGGTTGACAAGAAAATTACTGATGCAAGTGAGATTATAAGGATA
genomic: ACTTTGTGACTGATTGTACAAATATGTCCGCGGAGTTTACTGACTGTAAGgtaacttcta ... ccttttgtagATATTGTTGGTTGACAAGAAAATTACTGATGCAAGTGAGATTATAAGGATA
EST: gi|58612906|gb|CK040618.1|CK040618
EST:     ACTTTGTGACTGATTGTACAAATATGTCCGCGGAGTTTACTGACTGTAAG                         ATATTGTTGGTTGACAAGAAAATTACTGATGCAAGTGAGATTATAAGGATA
genomic: ACTTTGTGACTGATTGTACAAATATGTCCGCGGAGTTTACTGACTGTAAGgtaacttcta ... ccttttgtagATATTGTTGGTTGACAAGAAAATTACTGATGCAAGTGAGATTATAAGGATA
EST: gi|58587556|gb|CF985864.1|CF985864
EST:     ACTTTGTGACTGATTGTACAAATATGTCCGCGGAGTTTACTGACTGTAAG                         ATATTGTTGGTTGACAAGAAAATTACTGATGCAAGTGAGATTATAAGGATA
genomic: ACTTTGTGACTGATTGTACAAATATGTCCGCGGAGTTTACTGACTGTAAGgtaacttcta ... ccttttgtagATATTGTTGGTTGACAAGAAAATTACTGATGCAAGTGAGATTATAAGGATA
EST: gi|58692874|gb|CK081561.1|CK081561
EST:     ACTTTGTGACTGATTGTACAAATATGTCCGCGGAGTTTACTGACTGTAAG                         ATATTGTTGGTTGACAAGAAAATTACTGATGCAAGTGAGATTATAAGGATA
genomic: ACTTTGTGACTGATTGTACAAATATGTCCGCGGAGTTTACTGACTGTAAGgtaacttcta ... ccttttgtagATATTGTTGGTTGACAAGAAAATTACTGATGCAAGTGAGATTATAAGGATA
EST: gi|29668896|gb|CB665171.1|CB665171
EST:     ACTTTGTGACTGATTGTACAAATATGTCCGCGGAGTTTACTGACTGTAAG                         ATATTGTTGGTTGACAAGAAAATTACTGATGCAAGTGAGATTATAAGGATA
genomic: ACTTTGTGACTGATTGTACAAATATGTCCGCGGAGTTTACTGACTGTAAGgtaacttcta ... ccttttgtagATATTGTTGGTTGACAAGAAAATTACTGATGCAAGTGAGATTATAAGGATA
EST: gi|58691639|gb|CK080326.1|CK080326
EST:     ACTTTGTGACTGATTGTACAAATATGTCCGCGGAGTTTACTGACTGTAAG                         ATATTGTTGGTTGACAAGAAAATTACTGATGCAAGTGAGATTATAAGGATA
genomic: ACTTTGTGACTGATTGTACAAATATGTCCGCGGAGTTTACTGACTGTAAGgtaacttcta ... ccttttgtagATATTGTTGGTTGACAAGAAAATTACTGATGCAAGTGAGATTATAAGGATA
EST: gi|58695949|gb|CK084636.1|CK084636
EST:     ACTTTGTGACTGATTGTACAAATATGTCCGCGGAGTTTACTGACTGTAAG                         ATATTGTTGGTTGACAAGAAAATTACTGATGCAAGTGAGATTATAAGGATA
genomic: ACTTTGTGACTGATTGTACAAATATGTCCGCGGAGTTTACTGACTGTAAGgtaacttcta ... ccttttgtagATATTGTTGGTTGACAAGAAAATTACTGATGCAAGTGAGATTATAAGGATA

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: 47 (upstream exon), 72 (downstream exon)
Score: 11

TCTAGAGATTGTGGAAGGAATGCAATTTGAACGTGGTTACCTCTCACCGTACTTTGTGACTGATTGTACAAATATGTCCGCGGAGTTTACTGACTGTAAGgtaacttcta ... ccttttgtagATATTGTTGGTTGACAAGAAAATTACTGATGCAAGTGAGATTATAAGGATATTGGATAGTGCTGTCAAAGAAGATTATCCATTGTTGATAGTTGCCGAGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtaaaacacctttatgcagagcagagtaacattttgtttccttttccttttgtagATATTGTTGGTTGACAAGAAAATTACTGATGCAAGTGAGATTATAAGGATATTGGATAGTGCTGTCAAAGAAGATTATCCATTGTTGATAGTTGCCGAGG
                       gagtaac  putative branch site (score: 11)
                             cattttgtttcctttt  CT-rich tract
                          taacatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaacttctaactctaccatggtaaaacacctttatgcagagcagagtaacattttgtttccttttccttttgtagATATTGTTGGTTGACAAGAAAATTACTGATGCAAGTGAGATTATAAGGATATTGGATAGTGCTGTCAAAGAAGATTATCCATTGTTGATAGTTGCCGAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG