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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctgggggcaaggcgacaacattttcaggatgaagatgaactaattgataagtttttacgtgaatgttaattaagattaatacttccaattataatttcagGAGAGAGAGATTCCAGTGCTGGTATTTTCTGCAGGACTTGCAGACATAATTGAAGAG

Basic information

species Zea mays
transcript GRMZM2G157310_T02
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G157310_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os03g44660.1 (Oryza sativa), 3'ss of exon 4
-ctgggg--gcaaggcgacaacattttcaggatgaagatgaactaattgataagtttttacgtgaatgttaattaagattaatacttccaattataatttcagGAGAGAGAGATTCCAGTGCTGGTATTTTCTGCAGGACTTGCAGACATAATTGAAGAG
 |||      | ||    || || ||    |   |      |   |     |  |||  | |   | ||    |  ||| ||   |  ||| | ||||||||||||||||| ||||||||  | ||||||||||| |||||||||||||||||||| |||
actgaacttaccagtttgcagcagttatttgggtacttctcatacaccagcatatttgaa-gcagaggtagtct--gataaaacttctcaaatgtaatttcagGAGAGAGATATTCCAGTATTAGTATTTTCTGCTGGACTTGCAGACATAATTGAGGAG
















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|101386461|gb|EB815247.1|EB815247
EST:     CCGCAATTGCTTTCAGAGAGGGTGTGGTGGAGCTCTTTGAGTACTTGGAG                         GAGAGAGAGATTCCAGTGCTGGTATTTTCTGCAGGACTTGCAGACATAATT
genomic: CCGCAATTGCTTTCAGAGAGGGTGTGGTGGAGCTCTTTGAGTACTTGGAGgttttatcaa ... ataatttcagGAGAGAGAGATTCCAGTGCTGGTATTTTCTGCAGGACTTGCAGACATAATT
EST: gi|5268576|gb|AI770540.1|AI770540
EST:     CCGCAATTGCTTTCAGAGAGGGTGTGGTGGAGCTCTTTGAGTACTTGGAG                         GAGAGAGAGATTCCAGTGCTGGTATTTTCTGCAGGACTTGCAGACATAATT
genomic: CCGCAATTGCTTTCAGAGAGGGTGTGGTGGAGCTCTTTGAGTACTTGGAGgttttatcaa ... ataatttcagGAGAGAGAGATTCCAGTGCTGGTATTTTCTGCAGGACTTGCAGACATAATT
EST: gi|76293679|gb|DV033247.1|DV033247
EST:     CCGCAATTGCTTTCAGAGAGGGTGTGGTGGAGCTCTTTGAGTACTTGGAG                         GAGAGAGAGATTCCAGTGCTGGTATTTTCTGCAGGACTTGCAGACATAATT
genomic: CCGCAATTGCTTTCAGAGAGGGTGTGGTGGAGCTCTTTGAGTACTTGGAGgttttatcaa ... ataatttcagGAGAGAGAGATTCCAGTGCTGGTATTTTCTGCAGGACTTGCAGACATAATT
EST: gi|101385767|gb|EB814932.1|EB814932
EST:     CCGCAATTGCTTTCAGAGAGGGTGTGGTGGAGCTCTTTGAGTACTTGGAG                         GAGAGAGAGATTCCAGTGCTGGTATTTTCTGCAGGACTTGCAGACATAATT
genomic: CCGCAATTGCTTTCAGAGAGGGTGTGGTGGAGCTCTTTGAGTACTTGGAGgttttatcaa ... ataatttcagGAGAGAGAGATTCCAGTGCTGGTATTTTCTGCAGGACTTGCAGACATAATT
EST: gi|74242168|gb|DT650082.1|DT650082
EST:     CCGCAATTGCTTTCAGAGAGGGTGTGGTGGAGCTCTTTGAGTACTTGGAG                         GAGAGAGAGATTCCAGTGCTGGTATTTTCTGCAGGACTTGCAGACATAATT
genomic: CCGCAATTGCTTTCAGAGAGGGTGTGGTGGAGCTCTTTGAGTACTTGGAGgttttatcaa ... ataatttcagGAGAGAGAGATTCCAGTGCTGGTATTTTCTGCAGGACTTGCAGACATAATT
EST: gi|78092209|gb|DV520583.1|DV520583
EST:     CCGCAATTGCTTTCAGAGAGGGTGTGGTGGAGCTCTTTGAGTACTTGGAG                         GAGAGAGAGATTCCAGTGCTGGTATTTTCTGCAGGACTTGCAGACATAATT
genomic: CCGCAATTGCTTTCAGAGAGGGTGTGGTGGAGCTCTTTGAGTACTTGGAGgttttatcaa ... ataatttcagGAGAGAGAGATTCCAGTGCTGGTATTTTCTGCAGGACTTGCAGACATAATT
EST: gi|91048046|gb|EB158464.1|EB158464
EST:     CCGCAATTGCTTTCAGAGAGGGTGTGGTGGAGCTCTTTGAGTACTTGGAG                         GAGAGAGAGATTCCAGTGCTGGTATTTTCTGCAGGACTTGC
genomic: CCGCAATTGCTTTCAGAGAGGGTGTGGTGGAGCTCTTTGAGTACTTGGAGgttttatcaa ... ataatttcagGAGAGAGAGATTCCAGTGCTGGTATTTTCTGCAGGACTTGC
EST: gi|91877197|gb|EB407154.1|EB407154
EST:     CCGCAATTGCTTTCAGAGAGGGTGTGGTGGAGCTCTTTGAGTACTTGGAG                         GAGAGAGAGATTCCAGTGCTGGTATTTTCTGCAGGACTTGCAGACATAATT
genomic: CCGCAATTGCTTTCAGAGAGGGTGTGGTGGAGCTCTTTGAGTACTTGGAGgttttatcaa ... ataatttcagGAGAGAGAGATTCCAGTGCTGGTATTTTCTGCAGGACTTGCAGACATAATT
EST: gi|91050984|gb|EB161402.1|EB161402
EST:     CCGCAATTGCTTTCAGAGAGGGTGTGGTGGAGCTCTTTGAGTACTTGGAG                         GAGAGAGAGATTCCAGTGCTGGTATTTTCTGCAGGACTTGCAGACATAATT
genomic: CCGCAATTGCTTTCAGAGAGGGTGTGGTGGAGCTCTTTGAGTACTTGGAGgttttatcaa ... ataatttcagGAGAGAGAGATTCCAGTGCTGGTATTTTCTGCAGGACTTGCAGACATAATT
EST: gi|211118716|gb|FL311656.1|FL311656
EST:     CCGCAATTGCTTTCAGAGAGGGTGTGGTGGAGCTCTTTGAGTACTTGGAG                         GAGAGAGAGATTCCAGTGCTGGTATTTTCTGCAGGACTTGCAGACATAATT
genomic: CCGCAATTGCTTTCAGAGAGGGTGTGGTGGAGCTCTTTGAGTACTTGGAGgttttatcaa ... ataatttcagGAGAGAGAGATTCCAGTGCTGGTATTTTCTGCAGGACTTGCAGACATAATT
EST: gi|31354764|gb|CD439121.1|CD439121
EST:     CCGCAATTGCTTTCAGAGAGGGTGTGGTGGAGCTCTTTGAGTACTTGGAG                         GAGAGAGAGATTCCAGTGCTGGTATTTTCTGCAGGACTTGCAGACATAATT
genomic: CCGCAATTGCTTTCAGAGAGGGTGTGGTGGAGCTCTTTGAGTACTTGGAGgttttatcaa ... ataatttcagGAGAGAGAGATTCCAGTGCTGGTATTTTCTGCAGGACTTGCAGACATAATT
EST: gi|71438827|gb|DR819877.1|DR819877
EST:     CCGCAATTGCTTTCAGAGAGGGTGTGGTGGAGCTCTTTGAGTACTTGGAG                         GAGAGAGAGATTCCAGTGCTGGTATTTTCTGCAGGACTTGCAGACATAATT
genomic: CCGCAATTGCTTTCAGAGAGGGTGTGGTGGAGCTCTTTGAGTACTTGGAGgttttatcaa ... ataatttcagGAGAGAGAGATTCCAGTGCTGGTATTTTCTGCAGGACTTGCAGACATAATT
EST: gi|37400710|gb|CF637712.1|CF637712
EST:     GGTGGAGCTCTTTGAGTACTTGGAG                         GAGAGAGAGATTCCAGTGCTGGTATTTTCTGCAGGACTTGCAGACATAATT
genomic: GGTGGAGCTCTTTGAGTACTTGGAGgttttatcaa ... ataatttcagGAGAGAGAGATTCCAGTGCTGGTATTTTCTGCAGGACTTGCAGACATAATT
EST: gi|50333544|gb|CO528670.1|CO528670
EST:     CCGCAATTGCTTTCAGAGAGGGTGTGGTGGAGCTCTTTGAGTACTTGGAG                         GAGAGAGAGATTCCAGTGCTGGTATTTTCTGCAGGACTTGCAGACATAATT
genomic: CCGCAATTGCTTTCAGAGAGGGTGTGGTGGAGCTCTTTGAGTACTTGGAGgttttatcaa ... ataatttcagGAGAGAGAGATTCCAGTGCTGGTATTTTCTGCAGGACTTGCAGACATAATT
EST: gi|71449422|gb|DR830472.1|DR830472
EST:     CCGCAATTGCTTTCAGAGAGGGTGTGGTGGAGCTCTTTGAGTACTTGGAG                         GAGAGAGAGATTCCAGTGCTGGTATTTTCTGCAGGACTTGCAGACATAATT
genomic: CCGCAATTGCTTTCAGAGAGGGTGTGGTGGAGCTCTTTGAGTACTTGGAGgttttatcaa ... ataatttcagGAGAGAGAGATTCCAGTGCTGGTATTTTCTGCAGGACTTGCAGACATAATT

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: 47 (upstream exon), 49 (downstream exon)
Score: 83

TATTGAAGGCGGTCTTACATACGAAGCTATCACAAAATCTGTCTCTGATGCCGCAATTGCTTTCAGAGAGGGTGTGGTGGAGCTCTTTGAGTACTTGGAGgttttatcaa ... ataatttcagGAGAGAGAGATTCCAGTGCTGGTATTTTCTGCAGGACTTGCAGACATAATTGAAGAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 30

TATTGAAGGCGGTCTTACATACGAAGCTATCACAAAATCTGTCTCTGATGCCGCAATTGCTTTCAGAGAGGGTGTGGTGGAGCTCTTTGAGTACTTGGAGgttttatcaa ... ataatttcagGAGAGAGAGATTCCAGTGCTGGTATTTTCTGCAGGACTTGCAGACATAATTGAAGAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 54

TATTGAAGGCGGTCTTACATACGAAGCTATCACAAAATCTGTCTCTGATGCCGCAATTGCTTTCAGAGAGGGTGTGGTGGAGCTCTTTGAGTACTTGGAGgttttatcaa ... ataatttcagGAGAGAGAGATTCCAGTGCTGGTATTTTCTGCAGGACTTGCAGACATAATTGAAGAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 39

TATTGAAGGCGGTCTTACATACGAAGCTATCACAAAATCTGTCTCTGATGCCGCAATTGCTTTCAGAGAGGGTGTGGTGGAGCTCTTTGAGTACTTGGAGgttttatcaa ... ataatttcagGAGAGAGAGATTCCAGTGCTGGTATTTTCTGCAGGACTTGCAGACATAATTGAAGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gataagtttttacgtgaatgttaattaagattaatacttccaattataatttcagGAGAGAGAGATTCCAGTGCTGGTATTTTCTGCAGGACTTGCAGACATAATTGAAGAG
                            gattaat  putative branch site (score: 39)
                aatgttaattaagatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctgggggcaaggcgacaacattttcaggatgaagatgaactaattgataagtttttacgtgaatgttaattaagattaatacttccaattataatttcagGAGAGAGAGATTCCAGTGCTGGTATTTTCTGCAGGACTTGCAGACATAATTGAAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - -gacaaca
- - - - - - - - - - - - - - - - -gatgaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtgaatg