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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtgaccacgataaataacatttcctttataaaagaattgcaaagactgaaaaggcaaagaatatgttgaacatcacttacatcactttactggtatagGCTTTTGCAATGGGGCTTCAGGCTGTTGGAGCAAACCGTCAGTATCTTGGTTCTGCATGTGTATATCTTTCAGTTGGTGGCATTCTGTT

Basic information

species Zea mays
transcript GRMZM2G412899_T04
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G412899_T04 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os02g17500.1 (Oryza sativa), 3'ss of exon 11
gtaagtgaccacgataaataacatttcctttataaaagaattgcaaagactgaaaaggcaaagaatatgttgaacatcacttacatcac---tttactggtatagGCTTTTGCAATGGGGCTTCAGGCTGTTGGAGCAAACCGTCAGTATCTTGGTTCTGCATGTGTATATCTTTCAGTTGGTGGCATTCTGTT
                                  ||   ||  |   || || ||     ||||  ||||||||||| ||| ||  |||   ||||||| ||||||| ||||||||||| |||||||||||||||||||| |||||  | |||||||||||| | ||||||||||||||||||||||| || ||
--------------------------------gtaagctatcactgtgattggaacttggaagataatgttgaacattactcactgcacatctttactgctatagGCCTTTGCAATGGGACTTCAGGCTGTTGGAGCAAATCGTCACCACCTTGGTTCTGCAAGCGTATATCTTTCAGTTGGTGGCATGCTATT
















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|110961485|gb|EE181537.1|EE181537
EST:     TGGACAAGCTAGGTAGAAAAGTGCTTCTTTCAGGGAGTTTTCTTGGGATG                         GCTTTTGCAATGGGGCTTCAGGCTGTTGGAGCAAACCGTCAGTATCTTGGT
genomic: TGGACAAGCTAGGTAGAAAAGTGCTTCTTTCAGGGAGTTTTCTTGGGATGgtaagtgacc ... actggtatagGCTTTTGCAATGGGGCTTCAGGCTGTTGGAGCAAACCGTCAGTATCTTGGT
EST: gi|71321128|gb|DR797263.1|DR797263
EST:     TTCTTGGGATT                         GCTTTTGCAATGGGGCTTCAGGCTGTTGGAGCAAACCGTCAGTATCTTGGT
genomic: TTCTTGGGATGgtaagtgacc ... actggtatagGCTTTTGCAATGGGGCTTCAGGCTGTTGGAGCAAACCGTCAGTATCTTGGT
EST: gi|78110186|gb|DV528601.1|DV528601
EST:     TGGACAAGCTAGGTAGAAAAGTGCTTCTTTCAGGGAGTTTTCTGGGGATG                         GCTTTTGCAATGGGGCTTCAGGCTGTTGGAGCAAACCGTCAGTATCTTGGT
genomic: TGGACAAGCTAGGTAGAAAAGTGCTTCTTTCAGGGAGTTTTCTTGGGATGgtaagtgacc ... actggtatagGCTTTTGCAATGGGGCTTCAGGCTGTTGGAGCAAACCGTCAGTATCTTGGT
EST: gi|148974491|gb|EE025274.2|EE025274
EST:     TGGACAAGCTAGGTAGAAAAGTGCTTCTTTCAGGGAGTTTTCTTGGGATG                         GCTTTTGCAATGGGGCTTCAGGCTGTTGGAGCAAACCGTCAGTATCTTGGT
genomic: TGGACAAGCTAGGTAGAAAAGTGCTTCTTTCAGGGAGTTTTCTTGGGATGgtaagtgacc ... actggtatagGCTTTTGCAATGGGGCTTCAGGCTGTTGGAGCAAACCGTCAGTATCTTGGT
EST: gi|71766867|gb|DR964804.1|DR964804
EST:     TGGACAAGCTAGGTAGAAAAGTGCTTCTTTCAGGGAGTTTTCTTGGGATG                         GCTTTTGCAATGGGGCTTCAGGCTGTTGGAGCAAACCGTCAGTATCTTGGT
genomic: TGGACAAGCTAGGTAGAAAAGTGCTTCTTTCAGGGAGTTTTCTTGGGATGgtaagtgacc ... actggtatagGCTTTTGCAATGGGGCTTCAGGCTGTTGGAGCAAACCGTCAGTATCTTGGT

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 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 45

GATCAATTGTAGCAATGCTTCTAATGGACAAGCTAGGTAGAAAAGTGCTTCTTTCAGGGAGTTTTCTTGGGATGgtaagtgacc ... actggtatagGCTTTTGCAATGGGGCTTCAGGCTGTTGGAGCAAACCGTCAGTATCTTGGTTCTGCATGTGTATATCTTTCAGTTGGTGGCATTCTGTT


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 33

GATCAATTGTAGCAATGCTTCTAATGGACAAGCTAGGTAGAAAAGTGCTTCTTTCAGGGAGTTTTCTTGGGATGgtaagtgacc ... actggtatagGCTTTTGCAATGGGGCTTCAGGCTGTTGGAGCAAACCGTCAGTATCTTGGTTCTGCATGTGTATATCTTTCAGTTGGTGGCATTCTGTT


Block sizes: 46 (upstream exon), 41 (downstream exon)
Score: 27

GATCAATTGTAGCAATGCTTCTAATGGACAAGCTAGGTAGAAAAGTGCTTCTTTCAGGGAGTTTTCTTGGGATGgtaagtgacc ... actggtatagGCTTTTGCAATGGGGCTTCAGGCTGTTGGAGCAAACCGTCAGTATCTTGGTTCTGCATGTGTATATCTTTCAGTTGGTGGCATTCTGTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 71

GATCAATTGTAGCAATGCTTCTAATGGACAAGCTAGGTAGAAAAGTGCTTCTTTCAGGGAGTTTTCTTGGGATGgtaagtgacc ... actggtatagGCTTTTGCAATGGGGCTTCAGGCTGTTGGAGCAAACCGTCAGTATCTTGGTTCTGCATGTGTATATCTTTCAGTTGGTGGCATTCTGTT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gactgaaaaggcaaagaatatgttgaacatcacttacatcactttactggtatagGCTTTTGCAATGGGGCTTCAGGCTGTTGGAGCAAACCGTCAGTATCTTGGTTCTGCATGTGTATATCTTTCAGTTGGTGGCATTCTGTT
                              cacttac  putative branch site (score: 71)
                                         ctttact  putative PPT
            aaagaatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtgaccacgataaataacatttcctttataaaagaattgcaaagactgaaaaggcaaagaatatgttgaacatcacttacatcactttactggtatagGCTTTTGCAATGGGGCTTCAGGCTGTTGGAGCAAACCGTCAGTATCTTGGTTCTGCATGTGTATATCTTTCAGTTGGTGGCATTCTGTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG