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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttcagcaaatcagcaatttctctactcggccacactgcagtattgttgatgagcaccttcggttcttacagAGTTACGATGCAACTACTCATTTTGAGACAACGGTGAAGGATGTGCTTGCATTGTACAGCAAGATCACTGGGAAG

Basic information

species Oryza sativa
transcript LOC_Os03g16900.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g16900.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G084440_T01 (Zea mays), 3'ss of exon 10
gtaagttcagcaaatcagcaatttctctactcggccacactgcagtattg------ttgatgagcac------cttcgg-ttcttacagAGTTACGATGCAACTACTCATTTTGAGACAACGGTGAAGGATGTGCTTGCATTGTACAGCAAGATCACTGGGAAG
|||||   |||||||    |      || |      | | ||   |  |       |    || |||      |||||  || ||  |||| || ||  | || || ||||||||||| ||||| ||||||||||| || ||||||| |||||||||||| |||
gtaagccaagcaaatatatagggaacctgcaaatatatattgtgttggtaactaattaagcgaacacaccttccttcgtctttttgtagAGCTATGACTCCACCACCCATTTTGAGACGACGGTCAAGGATGTGCTCGCCTTGTACAACAAGATCACTGGAAAG
















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|86602820|gb|CI357184.1|CI357184
EST:     GATACGAACCTACTAATACCGCTGACGAGGACAACTGCTTCGTGACAAAT                         AGTTACGATGCAACTACTCATTTTGAGACAACGGTGAAGGATGTGCTTGCA
genomic: GATACGAACCTACTAATACCGCTGACGAGGACAACTGCTTCGTGACAAATgtaagttcag ... gttcttacagAGTTACGATGCAACTACTCATTTTGAGACAACGGTGAAGGATGTGCTTGCA
EST: gi|8856777|gb|AU094095.1|AU094095
EST:     GATACGAACCTACTAATACCGCTGACGAGGACAACTGCTTCGTGACAAAT                         AGTTACGATGCAACTACTCATTTTGAGACAACGGTGAAGGATGTGCTTGCA
genomic: GATACGAACCTACTAATACCGCTGACGAGGACAACTGCTTCGTGACAAATgtaagttcag ... gttcttacagAGTTACGATGCAACTACTCATTTTGAGACAACGGTGAAGGATGTGCTTGCA
EST: gi|10109151|gb|AU063867.2|AU063867
EST:     GATACGAACCTACTAATACCGCTGACGAGGACAACTGCTTCGTGACAAAT                         AGTTACGATGCAACTACTCATTTTGAGACAACGGTGAAGGATGTGCTTGCA
genomic: GATACGAACCTACTAATACCGCTGACGAGGACAACTGCTTCGTGACAAATgtaagttcag ... gttcttacagAGTTACGATGCAACTACTCATTTTGAGACAACGGTGAAGGATGTGCTTGCA
EST: gi|88258259|gb|CI360845.1|CI360845
EST:     GATACGAACCTACTAATACCGCTGACGAGGACAACTGCTTCGTGACAAAT                         AGTTACGATGCAACTACTCATTTTGAGACAACGGTGAAGGATGTGCTTGCA
genomic: GATACGAACCTACTAATACCGCTGACGAGGACAACTGCTTCGTGACAAATgtaagttcag ... gttcttacagAGTTACGATGCAACTACTCATTTTGAGACAACGGTGAAGGATGTGCTTGCA
EST: gi|33693913|gb|CF322152.1|CF322152
EST:     GATACGAACCTACTAATACCGCTGACGAGGACAACTGCTTCGTGACAAAT                         AGTTACGATGCAACTACTCATTTTGAGACAACGGTGAAGGATGTGCTTGCA
genomic: GATACGAACCTACTAATACCGCTGACGAGGACAACTGCTTCGTGACAAATgtaagttcag ... gttcttacagAGTTACGATGCAACTACTCATTTTGAGACAACGGTGAAGGATGTGCTTGCA
EST: gi|89197962|gb|CI117440.1|CI117440
EST:     GATACGAACCTACTAATACCGCTGACGAGGACAACTGCTTCGTGACAAAT                         AGTTACGATGCAACTACTCATTTTGAGACAACGGTGAAGGATGTGCTTGCA
genomic: GATACGAACCTACTAATACCGCTGACGAGGACAACTGCTTCGTGACAAATgtaagttcag ... gttcttacagAGTTACGATGCAACTACTCATTTTGAGACAACGGTGAAGGATGTGCTTGCA
EST: gi|88254220|gb|CI352846.1|CI352846
EST:     GATACGAACCTACTAATACCGCTGACGAGGACAACTGCTTCGTGACAAAT                         AGTTACGATGCAACTACTCATTTTGAGACAACGGTGAAGGATGTGCTTGCA
genomic: GATACGAACCTACTAATACCGCTGACGAGGACAACTGCTTCGTGACAAATgtaagttcag ... gttcttacagAGTTACGATGCAACTACTCATTTTGAGACAACGGTGAAGGATGTGCTTGCA
EST: gi|87026816|gb|CI259469.1|CI259469
EST:     GATACGAACCTACTAATACCGCTGACGAGGACAACTGCTTCGTGACAAAT                         AGTTACGATGCAACTACTCATTTTGAGACAACGGTGAAGGATGTGCTTGCA
genomic: GATACGAACCTACTAATACCGCTGACGAGGACAACTGCTTCGTGACAAATgtaagttcag ... gttcttacagAGTTACGATGCAACTACTCATTTTGAGACAACGGTGAAGGATGTGCTTGCA
EST: gi|87026825|gb|CI259478.1|CI259478
EST:     GATACGAACCTACTAATACCGCTGACGAGGACAACTGCTTCGTGACAAAT                         AGTTACGATGCAACTACTCATTTTGAGACAACGGTGAAGGATGTGCTTGCA
genomic: GATACGAACCTACTAATACCGCTGACGAGGACAACTGCTTCGTGACAAATgtaagttcag ... gttcttacagAGTTACGATGCAACTACTCATTTTGAGACAACGGTGAAGGATGTGCTTGCA
EST: gi|88259855|gb|CI364346.1|CI364346
EST:     GATACGAACCTACTAATACCGCTGACGAGGACAACTGCTTCGTGACAAAT                         AGTTACGATGCAACTACTCATTTTGAGACAACGGTGAAGGATGTGCTTGCA
genomic: GATACGAACCTACTAATACCGCTGACGAGGACAACTGCTTCGTGACAAATgtaagttcag ... gttcttacagAGTTACGATGCAACTACTCATTTTGAGACAACGGTGAAGGATGTGCTTGCA
EST: gi|86879928|gb|CI339995.1|CI339995
EST:     GATACGAACCTACTAATACCGCTGACGAGGACAACTGCTTCGTGACAAAT                         AGTTACGATGCAACTACTCA-TTTGAGACAACGGTGAAGGATGTGCTTGCA
genomic: GATACGAACCTACTAATACCGCTGACGAGGACAACTGCTTCGTGACAAATgtaagttcag ... gttcttacagAGTTACGATGCAACTACTCATTTTGAGACAACGGTGAAGGATGTGCTTGCA
EST: gi|11564810|gb|AU165446.1|AU165446
EST:     GATACGAACCTACTAATACCGCTGACGAGGACAACTGCTTCGTGACAAAT                         AGTTACGATGCAACTACTCATTTTGAGACAACGGTGAAGGATGTGCTTGCA
genomic: GATACGAACCTACTAATACCGCTGACGAGGACAACTGCTTCGTGACAAATgtaagttcag ... gttcttacagAGTTACGATGCAACTACTCATTTTGAGACAACGGTGAAGGATGTGCTTGCA
EST: gi|3761371|gb|C98619.1|C98619
EST:     GATACGAACCTACTAATACCGCTGACGAGGACAACTGCTTCGTGACAAAT                         AGTTACGATGCAACTACTCATTTTGAGACAACGGTGAAGGATGTGCTTGCA
genomic: GATACGAACCTACTAATACCGCTGACGAGGACAACTGCTTCGTGACAAATgtaagttcag ... gttcttacagAGTTACGATGCAACTACTCATTTTGAGACAACGGTGAAGGATGTGCTTGCA
EST: gi|89187975|gb|CI115224.1|CI115224
EST:     GATACGAACCTACTAATACCGCTGACGAGGACAACTGCTTCGTGACAAAT                         AGTTACGATGCAACTACTCATTTTGAGACAACGGTGAAGGATGTGCTTGCA
genomic: GATACGAACCTACTAATACCGCTGACGAGGACAACTGCTTCGTGACAAATgtaagttcag ... gttcttacagAGTTACGATGCAACTACTCATTTTGAGACAACGGTGAAGGATGTGCTTGCA
EST: gi|88996545|gb|CI260049.1|CI260049
EST:     GATACGAACCTACTAATACCGCTGACGAGGACAACTGCTTCGTGACAAAT                         AGTTACGATGCAACTACTCATTTTGAGACAACGGTGAAGGATGTGCTTGCA
genomic: GATACGAACCTACTAATACCGCTGACGAGGACAACTGCTTCGTGACAAATgtaagttcag ... gttcttacagAGTTACGATGCAACTACTCATTTTGAGACAACGGTGAAGGATGTGCTTGCA
EST: gi|33693914|gb|CF322153.1|CF322153
EST:     GATACGAACCTACTAATACCGCTGACGAGGACAACTGCTTCGTGACAAAT                         AGTTACGATGCAACTACTCATTTTGAGACAACGGTGAAGGATGTGCTTGCA
genomic: GATACGAACCTACTAATACCGCTGACGAGGACAACTGCTTCGTGACAAATgtaagttcag ... gttcttacagAGTTACGATGCAACTACTCATTTTGAGACAACGGTGAAGGATGTGCTTGCA
EST: gi|86839705|gb|CI343639.1|CI343639
EST:     GATACGAACCTACTAATACCGCTGACGAGGACAACTGCTTCGTGACAAAT                         AGTTACGATGCAACTACTCATTTTGAGACAACGGTGAAGGATGTGCTTGCA
genomic: GATACGAACCTACTAATACCGCTGACGAGGACAACTGCTTCGTGACAAATgtaagttcag ... gttcttacagAGTTACGATGCAACTACTCATTTTGAGACAACGGTGAAGGATGTGCTTGCA

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: 69 (upstream exon), 44 (downstream exon)
Score: 10

GATCGATCTGCTCGGACCTGTAGAGGAAACATTTTTTGACATCTATGACCGATACGAACCTACTAATACCGCTGACGAGGACAACTGCTTCGTGACAAATgtaagttcag ... gttcttacagAGTTACGATGCAACTACTCATTTTGAGACAACGGTGAAGGATGTGCTTGCATTGTACAGCAAGATCACTGGGAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttctctactcggccacactgcagtattgttgatgagcaccttcggttcttacagAGTTACGATGCAACTACTCATTTTGAGACAACGGTGAAGGATGTGCTTGCATTGTACAGCAAGATCACTGGGAAG
                           tgttgat  putative branch site (score: 10)
                                              ttcttac  putative PPT
                        tattgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagttcagcaaatcagcaatttctctactcggccacactgcagtattgttgatgagcaccttcggttcttacagAGTTACGATGCAACTACTCATTTTGAGACAACGGTGAAGGATGTGCTTGCATTGTACAGCAAGATCACTGGGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA