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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aatgatactactatattatttcccagtgcttcttgctagattatccctgtctacacccttgtgttgaccacgctgtgcctctttcattatttgtctccagGATGCTCTTGACCTTATTAGCGGTTATTATACAGTCAGCCAAGGCAGCTCTTCTCCTTTTCATAATGGTGTTGATTCTTCTTCG

Basic information

species Zea mays
transcript GRMZM2G047894_T02
intron # 17
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G047894_T02 (Zea mays), 3'ss of exon 17
lower sequence: LOC_Os03g18080.2 (Oryza sativa), 3'ss of exon 17
aatgatactactatattatttcccagtgcttcttgctagat-tatccctgtctacacccttgtgttgaccacgctgtgcctct-----ttcattatttgtctccagGATGCTCTTGACCTTATTAGCGGTTATTATACAGTCAGCCAAGGCAGCTCTTCTCCTTTTCATAATGGTG---TTGATTCTTCTTCG
       |  |||| |||    |   |||||  |||    | ||| |      |    ||  || || |  |  |     | |     ||||||| |  ||| ||||||||||| |||||||| |||||||| |||||||||||| |||||| ||||||||||||||| |||||||   |||| ||| |  ||
------ccatctatgttaaaatcttctgcttgctgcagtttatattctacaaaatgtgctcttgctggcttcttttaaattttaatacttcattactcatcttcagGATGCTCTAGACCTTATCAGCGGTTACTATACAGTCAGCAAAGGCATCTCTTCTCCTTTTCAAAATGGTGGATTTGAATCTGCAACG
















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|78021557|gb|DV489944.1|DV489944
EST:     GTGCTCTTTCAAGATATTATTTGAATAATTTTCATGACGGAGTGCGGCAA                         GATGCTCTTGACCTTATTAGCGGTTATTATACAGTCAGCCAAGGCAGCTCT
genomic: GTGCTCTTTCAAGATATTATTTGAATAATTTTCATGACGGAGTGCGGCAAgtaagttctt ... ttgtctccagGATGCTCTTGACCTTATTAGCGGTTATTATACAGTCAGCCAAGGCAGCTCT
EST: gi|71428422|gb|DR809472.1|DR809472
EST:     GTGCTCTTTCAAGATATTATTTGAATAATTTTCATGACGGAGTGCGGCAA                         GATGCTCTTGACCTTATTAGCGGTTATTATACAGTCAGCCAAGGCAGCTCT
genomic: GTGCTCTTTCAAGATATTATTTGAATAATTTTCATGACGGAGTGCGGCAAgtaagttctt ... ttgtctccagGATGCTCTTGACCTTATTAGCGGTTATTATACAGTCAGCCAAGGCAGCTCT
EST: gi|78022411|gb|DV490798.1|DV490798
EST:     GTGCTCTTTCAAGATATTATTTGAATAATTTTCATGACGGAGTGCGGCAA                         GATGCTCTTGACCTTATTAGCGGTTATTATACAGTCAGCCAAGGCAGCTCT
genomic: GTGCTCTTTCAAGATATTATTTGAATAATTTTCATGACGGAGTGCGGCAAgtaagttctt ... ttgtctccagGATGCTCTTGACCTTATTAGCGGTTATTATACAGTCAGCCAAGGCAGCTCT
EST: gi|32934739|gb|CF039551.1|CF039551
EST:     GTGCTCTTTCAAGATATTATTTGAATAATTTTCATGACGGAGTGCGGCAA                         GATGCTCTTGACCTTATTAGCGGTTATTATACAGTCAGCCAAGGCAGCTCT
genomic: GTGCTCTTTCAAGATATTATTTGAATAATTTTCATGACGGAGTGCGGCAAgtaagttctt ... ttgtctccagGATGCTCTTGACCTTATTAGCGGTTATTATACAGTCAGCCAAGGCAGCTCT
EST: gi|37387638|gb|CF631017.1|CF631017
EST:     GTGCTCTTTCAAGATATTATTTGAATAATTTTCATGACGGAGTGCGGCAA                         GATGCTCTTGACCTTATTAGCGGTTATTATACAGTCAGCCAAGGCAGCTCT
genomic: GTGCTCTTTCAAGATATTATTTGAATAATTTTCATGACGGAGTGCGGCAAgtaagttctt ... ttgtctccagGATGCTCTTGACCTTATTAGCGGTTATTATACAGTCAGCCAAGGCAGCTCT
EST: gi|5296286|gb|AI783056.1|AI783056
EST:     GTGCTCTTTCAAGATATTATTTGAATAATTTTCATGACGGAGTGCGGCAA                         GATGCTCTTGACCTTATTAGCGGTTATTATACAGTCAGCCAAGGCAGCTCT
genomic: GTGCTCTTTCAAGATATTATTTGAATAATTTTCATGACGGAGTGCGGCAAgtaagttctt ... ttgtctccagGATGCTCTTGACCTTATTAGCGGTTATTATACAGTCAGCCAAGGCAGCTCT
EST: gi|37391643|gb|CF633065.1|CF633065
EST:     CGGAGTGCGGCAA                         GATGCTCTTGACCTTATTAGCGGTTATTATACAGTCAGCCAAGGCAGCTCT
genomic: CGGAGTGCGGCAAgtaagttctt ... ttgtctccagGATGCTCTTGACCTTATTAGCGGTTATTATACAGTCAGCCAAGGCAGCTCT
EST: gi|31348859|gb|CD433216.1|CD433216
EST:     GTGCTCTTTCAAGATATTATTTGAATAATTTTCATGACGGAGTGCGGCAA                         GATGCTCTTGACCTTATTAGCGGTTATTATACAGTCAGCCAAGGCAGCTCT
genomic: GTGCTCTTTCAAGATATTATTTGAATAATTTTCATGACGGAGTGCGGCAAgtaagttctt ... ttgtctccagGATGCTCTTGACCTTATTAGCGGTTATTATACAGTCAGCCAAGGCAGCTCT
EST: gi|71325384|gb|DR799369.1|DR799369
EST:     GTGCTCTTTCAAGATATTATTTGAATAATTTTCATGACGGAGTGCGGCAA                         GATGCTCTTGACCTTATTAGCGGTTATTATACAGTCAGCCAAGGCAGCTCT
genomic: GTGCTCTTTCAAGATATTATTTGAATAATTTTCATGACGGAGTGCGGCAAgtaagttctt ... ttgtctccagGATGCTCTTGACCTTATTAGCGGTTATTATACAGTCAGCCAAGGCAGCTCT
EST: gi|18385140|gb|BM418339.1|BM418339
EST:     GTGCTCTTTCAAGATATTATTTGAATAATTTTCATGACGGAGTGCGGCAA                         GATGCTCTTGACCTTATTAGCGGTTATTATACAGTCAGCCAAGGCAGCTCT
genomic: GTGCTCTTTCAAGATATTATTTGAATAATTTTCATGACGGAGTGCGGCAAgtaagttctt ... ttgtctccagGATGCTCTTGACCTTATTAGCGGTTATTATACAGTCAGCCAAGGCAGCTCT
EST: gi|17970259|gb|BM277022.1|BM277022
EST:     GTGCTCTTTCAAGATATTATTTGAATAATTTTCATGACGGAGTGCGGCAA                         GATGCTCTTGACCTTATTAGCGGTTATTATACAGTCAGCCAAGGCAGCTCT
genomic: GTGCTCTTTCAAGATATTATTTGAATAATTTTCATGACGGAGTGCGGCAAgtaagttctt ... ttgtctccagGATGCTCTTGACCTTATTAGCGGTTATTATACAGTCAGCCAAGGCAGCTCT
EST: gi|24763373|gb|CA398549.1|CA398549
EST:     GTGCTCTTTCAAGATATTATTTGAATAATTTTCATGACGGAGTGCGGCAA                         GATGCTCTTGCCCTTATTAGCGGTTATTATACAGTCAGCCAAGGCAGCTCT
genomic: GTGCTCTTTCAAGATATTATTTGAATAATTTTCATGACGGAGTGCGGCAAgtaagttctt ... ttgtctccagGATGCTCTTGACCTTATTAGCGGTTATTATACAGTCAGCCAAGGCAGCTCT
EST: gi|12968368|gb|BG265314.1|BG265314
EST:     GTGCTCTTTCAAGATATTATTTGAATAATTTTCATGACGGAGTGCGGCAA                         GATGCTCTTGACCTTATTAGCGGTTATTATACAGTCAGCCAAGGCAGCTCT
genomic: GTGCTCTTTCAAGATATTATTTGAATAATTTTCATGACGGAGTGCGGCAAgtaagttctt ... ttgtctccagGATGCTCTTGACCTTATTAGCGGTTATTATACAGTCAGCCAAGGCAGCTCT
EST: gi|113702249|gb|EE679753.1|EE679753
EST:     GTGCTCTTTCAAGATATTATTTGAATAATTTTCATGACGGAGTGCGGCAA                         GATGCTCTTGACCTTATTAGCGGTTATTATACAGTCAGCCAAGGCAGCTCT
genomic: GTGCTCTTTCAAGATATTATTTGAATAATTTTCATGACGGAGTGCGGCAAgtaagttctt ... ttgtctccagGATGCTCTTGACCTTATTAGCGGTTATTATACAGTCAGCCAAGGCAGCTCT
EST: gi|32850672|gb|CD990353.1|CD990353
EST:     GTGCTCTTTCAAGATATTATTTGAATAATTTTCATGACGGAGTGCGGCAA                         GATGCTCTTGACCTTATTAGCGGTTATTATACAGTCAGCCAAGGCAGCTCT
genomic: GTGCTCTTTCAAGATATTATTTGAATAATTTTCATGACGGAGTGCGGCAAgtaagttctt ... ttgtctccagGATGCTCTTGACCTTATTAGCGGTTATTATACAGTCAGCCAAGGCAGCTCT

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: 127

ATATGGAAGGCAGACATTGCCTGGACTAATTAAAGATGGAATGAGTGCTCTTTCAAGATATTATTTGAATAATTTTCATGACGGAGTGCGGCAAgtaagttctt ... ttgtctccagGATGCTCTTGACCTTATTAGCGGTTATTATACAGTCAGCCAAGGCAGCTCTTCTCCTTTTCATAATGGTGTTGATTCTTCTTCG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 84

ATATGGAAGGCAGACATTGCCTGGACTAATTAAAGATGGAATGAGTGCTCTTTCAAGATATTATTTGAATAATTTTCATGACGGAGTGCGGCAAgtaagttctt ... ttgtctccagGATGCTCTTGACCTTATTAGCGGTTATTATACAGTCAGCCAAGGCAGCTCTTCTCCTTTTCATAATGGTGTTGATTCTTCTTCG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 74

ATATGGAAGGCAGACATTGCCTGGACTAATTAAAGATGGAATGAGTGCTCTTTCAAGATATTATTTGAATAATTTTCATGACGGAGTGCGGCAAgtaagttctt ... ttgtctccagGATGCTCTTGACCTTATTAGCGGTTATTATACAGTCAGCCAAGGCAGCTCTTCTCCTTTTCATAATGGTGTTGATTCTTCTTCG


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 81

ATATGGAAGGCAGACATTGCCTGGACTAATTAAAGATGGAATGAGTGCTCTTTCAAGATATTATTTGAATAATTTTCATGACGGAGTGCGGCAAgtaagttctt ... ttgtctccagGATGCTCTTGACCTTATTAGCGGTTATTATACAGTCAGCCAAGGCAGCTCTTCTCCTTTTCATAATGGTGTTGATTCTTCTTCG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cctgtctacacccttgtgttgaccacgctgtgcctctttcattatttgtctccagGATGCTCTTGACCTTATTAGCGGTTATTATACAGTCAGCCAAGGCAGCTCTTCTCCTTTTCATAATGGTGTTGATTCTTCTTCG
                tgttgac  putative branch site (score: 81)
                                cctctttcattatttg  putative PPT
                                    tttcattattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aatgatactactatattatttcccagtgcttcttgctagattatccctgtctacacccttgtgttgaccacgctgtgcctctttcattatttgtctccagGATGCTCTTGACCTTATTAGCGGTTATTATACAGTCAGCCAAGGCAGCTCTTCTCCTTTTCATAATGGTGTTGATTCTTCTTCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC