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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgagatggtcttgaacttttgttcaatgttgccctctcttttatatggttttggtataatactgtaatatgaaacaaagaatctgatttgtgcctgcagCTTAGAAATTTGGTATGGGCAACGTCCAAGCACGACATCTACCTAGTATCTCATTACTCAATTCGTCACTGGTCAGCATTGAGTGGTGTGGATACTGAAC

Basic information

species Zea mays
transcript GRMZM2G109039_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G109039_T03 (Zea mays), 3'ss of exon 4
lower sequence: AT3G13340.1 (Arabidopsis thaliana), 3'ss of exon 4
-------------------------------------------------------ttgagatggtcttgaacttttgttcaatgttgccctctcttttatatggttttggtataatactgtaa-----tatgaaacaaagaatctgatttgtgcctgcagCTTAGAAATTTGGTATGGGCAACGTCCAAGCACGACATCTACCTAGTATCTCATTACTCAATTCGTCACTGGTCAGCATTGAGTGGTGTGGATACTGAAC
                                                       |     || |        ||| ||   | | ||    |  |  | ||    || || || | ||  ||      ||   |  |||||| |   |||       |||| |||||||||||||||||||| || ||||||||| | || ||  | ||  |||      ||   || |  ||  |  | |    ||   |   |||| 
gttttttttttttaatattgagagctcactaacttggactagttgatagtctttctctttctgattggatttatttattgtgtttggcgtgattgtggacataacatttgtctactgctaaaaacctccatctgatcaagaatttttattggtgtcatagCTGAGAAATTTGGTATGGGCAACTTCTAAGCACGACGTGTATCTTATGTCAAATTTTCTGGTTACACATTATTCTTCTCTAACGTCTGGAAAGCATGAAG
















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|211166255|gb|FL395975.1|FL395975
EST:     AGTTTAGACGAAATACTAGATCGGTTAAATCAACTATTCTACATTTTCAG                         CTTAGAAATTTGGTATGGGCAACGTCCAAGCACGACATCTACCTAGTATCT
genomic: AGTTTAGACGAAATACTAGATCGGTTAAATCAACTATTCTACATTTTCAGgtgagttaac ... gtgcctgcagCTTAGAAATTTGGTATGGGCAACGTCCAAGCACGACATCTACCTAGTATCT
EST: gi|211150113|gb|FL386529.1|FL386529
EST:     AGTTTAGACGAAATACTAGATCGGTTAAATCAACTATTCTACATTTTCAG                         CTTAGAAATTTGGTATGGGCAACGTCCAAGCACGACATCTACCTAGTATCT
genomic: AGTTTAGACGAAATACTAGATCGGTTAAATCAACTATTCTACATTTTCAGgtgagttaac ... gtgcctgcagCTTAGAAATTTGGTATGGGCAACGTCCAAGCACGACATCTACCTAGTATCT
EST: gi|58029875|gb|CX725302.1|CX725302
EST:     AGTTTAGACGAAATACTAGATCGGTTAAATCAACTATTCTACATTTTCAG                         CTTAGAAATTTGGTATGGGCAACGGCCAAGCACGACATCTACCTAGTATCT
genomic: AGTTTAGACGAAATACTAGATCGGTTAAATCAACTATTCTACATTTTCAGgtgagttaac ... gtgcctgcagCTTAGAAATTTGGTATGGGCAACGTCCAAGCACGACATCTACCTAGTATCT
EST: gi|20301188|gb|BQ164131.1|BQ164131
EST:     AGTTTAGACGAAATACTAGATCGGTTAAATCAACTATTCTACATTTTCAG                         CTTAGAAATTTGGTATGGGCAACGTCCAAGCACGACATCTACCTAGTATCT
genomic: AGTTTAGACGAAATACTAGATCGGTTAAATCAACTATTCTACATTTTCAGgtgagttaac ... gtgcctgcagCTTAGAAATTTGGTATGGGCAACGTCCAAGCACGACATCTACCTAGTATCT
EST: gi|20301181|gb|BQ164124.1|BQ164124
EST:     AGTTTAGACGAAATACTAGATCGGTTAAATCAACTATTCTACATTTTCAG                         CTTAGAAATTTGGTATGGGCAACGTCCAAGCACGACATCTACCTAGTATCT
genomic: AGTTTAGACGAAATACTAGATCGGTTAAATCAACTATTCTACATTTTCAGgtgagttaac ... gtgcctgcagCTTAGAAATTTGGTATGGGCAACGTCCAAGCACGACATCTACCTAGTATCT
EST: gi|20300911|gb|BQ163854.1|BQ163854
EST:     AGTTTAGACGAAATACTAGATCGGTTAAATCAACTATTCTACATTTTCAG                         CTTAGAAATTTGGTATGGGCAACGTCCAAGCACGACATCTACCTAGTATCT
genomic: AGTTTAGACGAAATACTAGATCGGTTAAATCAACTATTCTACATTTTCAGgtgagttaac ... gtgcctgcagCTTAGAAATTTGGTATGGGCAACGTCCAAGCACGACATCTACCTAGTATCT
EST: gi|20301275|gb|BQ164218.1|BQ164218
EST:     AGTTTAGACGAAATACTAGATCGG-TAAATCAACTATTCTACATTTTCAG                         CTTAGAAA-TTGGTATGGGCAACGTCCAAGCACGACATCTACCTAGTATCT
genomic: AGTTTAGACGAAATACTAGATCGGTTAAATCAACTATTCTACATTTTCAGgtgagttaac ... gtgcctgcagCTTAGAAATTTGGTATGGGCAACGTCCAAGCACGACATCTACCTAGTATCT
EST: gi|20300918|gb|BQ163861.1|BQ163861
EST:     AGTTTAGACGAAATACTAGATCGGTTAAATCAACTATTCTACATTTTCAG                         CTTAGAAATTTGGTATGGGCAACGTCCAAGCACGACATCTACCTAGTATCT
genomic: AGTTTAGACGAAATACTAGATCGGTTAAATCAACTATTCTACATTTTCAGgtgagttaac ... gtgcctgcagCTTAGAAATTTGGTATGGGCAACGTCCAAGCACGACATCTACCTAGTATCT
EST: gi|26456084|gb|CA827667.1|CA827667
EST:     AGTTTAGACGAAATACTAGATCGGTTAAATCAACTATTCTACATTTTCAG                         CTTAGAAATTTGGTATGGGCAACGTCCAAGCACGACATCTACCTAGTATCT
genomic: AGTTTAGACGAAATACTAGATCGGTTAAATCAACTATTCTACATTTTCAGgtgagttaac ... gtgcctgcagCTTAGAAATTTGGTATGGGCAACGTCCAAGCACGACATCTACCTAGTATCT

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: 478

GATTGCAAACCAACAGAGAAAGGTGGGATATACTATGAGTTTAGACGAAATACTAGATCGGTTAAATCAACTATTCTACATTTTCAGgtgagttaac ... gtgcctgcagCTTAGAAATTTGGTATGGGCAACGTCCAAGCACGACATCTACCTAGTATCTCATTACTCAATTCGTCACTGGTCAGCATTGAGTGGTGTGGATACTGAAC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 596

GATTGCAAACCAACAGAGAAAGGTGGGATATACTATGAGTTTAGACGAAATACTAGATCGGTTAAATCAACTATTCTACATTTTCAGgtgagttaac ... gtgcctgcagCTTAGAAATTTGGTATGGGCAACGTCCAAGCACGACATCTACCTAGTATCTCATTACTCAATTCGTCACTGGTCAGCATTGAGTGGTGTGGATACTGAAC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 778

GATTGCAAACCAACAGAGAAAGGTGGGATATACTATGAGTTTAGACGAAATACTAGATCGGTTAAATCAACTATTCTACATTTTCAGgtgagttaac ... gtgcctgcagCTTAGAAATTTGGTATGGGCAACGTCCAAGCACGACATCTACCTAGTATCTCATTACTCAATTCGTCACTGGTCAGCATTGAGTGGTGTGGATACTGAAC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 663

GATTGCAAACCAACAGAGAAAGGTGGGATATACTATGAGTTTAGACGAAATACTAGATCGGTTAAATCAACTATTCTACATTTTCAGgtgagttaac ... gtgcctgcagCTTAGAAATTTGGTATGGGCAACGTCCAAGCACGACATCTACCTAGTATCTCATTACTCAATTCGTCACTGGTCAGCATTGAGTGGTGTGGATACTGAAC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atggttttggtataatactgtaatatgaaacaaagaatctgatttgtgcctgcagCTTAGAAATTTGGTATGGGCAACGTCCAAGCACGACATCTACCTAGTATCTCATTACTCAATTCGTCACTGGTCAGCATTGAGTGGTGTGGATACTGAAC
                                    atctgat  putative branch site (score: 663)
          tataatactgtaatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgagatggtcttgaacttttgttcaatgttgccctctcttttatatggttttggtataatactgtaatatgaaacaaagaatctgatttgtgcctgcagCTTAGAAATTTGGTATGGGCAACGTCCAAGCACGACATCTACCTAGTATCTCATTACTCAATTCGTCACTGGTCAGCATTGAGTGGTGTGGATACTGAAC

- - - - - - - - -ttttgtt
- - - - - - - - - - - - - -tgttgcc
- - - - - - - - - - - - - - - - - - - - - - - - -ttttggt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaacaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgattt