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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGACAAGGAGGTGAAAGTAACTGCGACTTGCATACGGGTTCCTGTGATGCGCGCACATGCTGAAAGTGTCAATCTACAGTTTGAAAAGCCACTTGATGAGgttggtattctgcatattatgtgctaactagcattagagcttttctgtacgtgcgaatatgtttctttccttcatactatcctcttttgtctctattagt...

Basic information

species Zea mays
transcript GRMZM2G076885_T01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G076885_T01 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os03g55280.1 (Oryza sativa), 5'ss of exon 5
TGACAAGGAGGTGAAAGTAACTGCGACTTGCATACGGGTTCCTGTGATGCGCGCACATGCTGAAAGTGTCAATCTACAGTTTGAAAAGCCACTTGATGAGgttggtat--------tctgcatattatgtgctaactagcatta--gagcttttctgtacgtgcgaata-tgtttctttccttcatactatcctcttttgtctctattagt
||| || || ||||| |||||||| || |||||||| |||||||||||||| ||||||||||||||||| ||||||||||||||||||||||||||||||||| | ||        |||  ||  ||  | ||   |||||| |   | | ||||||   |||  |||  | |  | ||| ||  |    |  |  | ||           
TGATAAAGATGTGAAGGTAACTGCAACCTGCATACGAGTTCCTGTGATGCGTGCACATGCTGAAAGTGTGAATCTACAGTTTGAAAAGCCACTTGATGAGgttagcataaaatatttcttaatgataaattctggttagcatgaagaatcctttctgcttgtggtaatcctatacccttcttttgttaggtattaatatg-----------

upper sequence: GRMZM2G076885_T01 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA08G05250.1 (Glycine max), 5'ss of exon 5
TGACAAGGAGGTGAAAGTAACTGCGACTTGCATACGGGTTCCTGTGATGCGCGCACATGCTGAAAGTGTCAATCTACAGTTTGAAAAGCCACTTGATGAGgttggt-attctg-catattatgtgctaa--ctagcattagagcttttctgt-acgtgcgaatatgtttctttccttcatactatcctcttttgtctctattagt
| | ||||| || ||||||||||| || |||||||| |||||||| ||||| || |||||||| ||||| ||||| || |||||||  || |||||||||||   | || ||| |||  | |||  | |  | |     | | ||  |   | || |     || ||  |    ||  ||||       |||   ||  |     
TAATAAGGACGTTAAAGTAACTGCCACATGCATACGAGTTCCTGTCATGCGAGCTCATGCTGAGAGTGTGAATCTTCAATTTGAAACACCCCTTGATGAGgtacttcatgctggcatgctgtgtctttatgccattgccaaaactcatagttgacattgctttacgtcccaaaactgaatacagaat--tttaacctagacc---

upper sequence: GRMZM2G076885_T01 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA05G34420.1 (Glycine max), 5'ss of exon 5
TGACAAGGAGGTGAAAGTAACTGCGACTTGCATACGGGTTCCTGTGATGCGCGCACATGCTGAAAGTGTCAATCTACAGTTTGAAAAGCCACTTGATGAGgttggtattctgcatattatgtgcta-actagcattagagcttttctgt-acgtgcgaatatgtttctttccttcatact--atcctcttttgtctctattagt
||||||||| || ||||||||||| || |||||||| |||||  | ||||| || |||||||| ||||| ||||| || |||||||  || |||||||||||     |  ||  | | ||||| ||  | |     | | ||  |   | || |     || ||  |    ||  ||||   ||  |  |      ||| ||  
TGACAAGGATGTTAAAGTAACTGCCACATGCATACGAGTTCCCATCATGCGAGCTCATGCTGAGAGTGTGAATCTTCAATTTGAAAGACCCCTTGATGAGgt--acttcatgt-tgtcatgtgttatgccattgccaaaactcatagttgacattgctttacgtcccaaaactgaatacagaattttaatccagacctagtac-

upper sequence: GRMZM2G076885_T01 (Zea mays), 5'ss of exon 5
lower sequence: AT1G14810.1 (Arabidopsis thaliana), 5'ss of exon 5
TGACAAGGAGGTGAAAGTAACTGCGACTTGCATACGGGTTCCTGTGATGCGCGCACATGCTGAAAGTGTCAATCTACAGTTTGAAAAGCCACTTGATGAGgttggtattctgcatattatgtgctaactagcattagagcttttctgtacgtgcgaatatgtttctttccttcatactatcctcttttgtctctattagt---
|||||  || || |||||||| || || || ||||| ||||| || ||||| || ||||| || ||||| ||||| |||||||| || || |||||||||||   ||     | |   |   | |  |||    |   |  ||  |||     |  ||   ||||  ||  | ||| |  |   ||   ||   ||| |    
TGACACAGAAGTAAAAGTAACAGCAACGTGTATACGTGTTCCAGTTATGCGTGCTCATGCAGAGAGTGTGAATCTTCAGTTTGAGAATCCTCTTGATGAGgt-aataacacacgtcgaacccgatttctactgattctgtgttgttgtgttaccttatg-atttcactcactgata-tgacaatttgaatcataatttgaagt

upper sequence: GRMZM2G076885_T01 (Zea mays), 5'ss of exon 5
lower sequence: Vv01s0011g05860.t01 (Vitis vinifera), 5'ss of exon 5
TGACAAGGAGGTGAAAGTAACTGCGACTTGCATACGGGTTCCTGTGATGCGCGCACATGCTGAAAGTGTCAATCTACAGTTTGAAAAGCCACTTGATGAGgttggtattctgcatattatgtgctaactagcattagagcttttctgtacgtgcgaatatgtttct-ttccttcatactatcctcttttgtctctattagt
||||| | | || ||||| ||||| || ||||||||||| ||||| ||||| || |||||||| ||||| ||||| |||||||| || || |||||||||||               ||   | ||  | || |   |   ||  || ||      || |   ||| ||  |    |  |     |||| |    |  || 
TGACATGAATGTTAAAGTGACTGCCACATGCATACGGGTCCCTGTTATGCGTGCGCATGCTGAGAGTGTTAATCTCCAGTTTGAGAATCCCCTTGATGAGgtacaatgatgatgctataaaagatatattgcttataaaacttggtgcacaattagatgttggtctattgatattcataaaagaatttttttagcacaag-

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|7216942|gb|AW563049.1|AW563049
EST:     GCGCACATGCTGAAAGTGTCAATCTACAGTTTGAAAAGCCACTTGATGAG                         GATACTGCAAGAGAAATTTTGAGAGCAGCTCCTGGTGTTACCATTATTGAT
genomic: GCGCACATGCTGAAAGTGTCAATCTACAGTTTGAAAAGCCACTTGATGAGgttggtattc ... tactctaaagGATACTGCAAGAGAAATTTTGAGAGCAGCTCCTGGTGTTACCATTATTGAT
EST: gi|76292292|gb|DV031860.1|DV031860
EST:     GCGCACATGCTGAAAGTGTCAATCTACAGTTTGAAAAGCCACTTGATGAG                         GATACTGCAAGAGAAATTTTGAGAGCAGCTCCTGGTGTTACCATTATTGAT
genomic: GCGCACATGCTGAAAGTGTCAATCTACAGTTTGAAAAGCCACTTGATGAGgttggtattc ... tactctaaagGATACTGCAAGAGAAATTTTGAGAGCAGCTCCTGGTGTTACCATTATTGAT
EST: gi|5714254|gb|AI944239.1|AI944239
EST:     GCGCACATGCTGAAAGTGTCAATCTACAGTTTGAAAAGCCACTTGATGAG                         GATACTGCAAGAGAAATTTTGAGAGCAGCTCCTGGTGTTACCATTATTGAT
genomic: GCGCACATGCTGAAAGTGTCAATCTACAGTTTGAAAAGCCACTTGATGAGgttggtattc ... tactctaaagGATACTGCAAGAGAAATTTTGAGAGCAGCTCCTGGTGTTACCATTATTGAT
EST: gi|86470660|gb|DY237030.1|DY237030
EST:     GCGCACATGCTGAAAGTGTCAATCTACAGTTTGAAAAGCCACTTGATGAG                         GATACTGCAAGAGAAATTTTGAGAGCAGCTCCTGGTGTTACCATTATTGAT
genomic: GCGCACATGCTGAAAGTGTCAATCTACAGTTTGAAAAGCCACTTGATGAGgttggtattc ... tactctaaagGATACTGCAAGAGAAATTTTGAGAGCAGCTCCTGGTGTTACCATTATTGAT
EST: gi|7216973|gb|AW563095.1|AW563095
EST:     GCGCACATGCTGAAAGTGTCAATCTACAGTTTGAAAAGCCACTTGATGAG                         GATACTGCAAGAGAAATTTTGAGAGCAGCTCCTGGTGTTACCATTATTGAT
genomic: GCGCACATGCTGAAAGTGTCAATCTACAGTTTGAAAAGCCACTTGATGAGgttggtattc ... tactctaaagGATACTGCAAGAGAAATTTTGAGAGCAGCTCCTGGTGTTACCATTATTGAT
EST: gi|76290934|gb|DV030502.1|DV030502
EST:     TTTGAAAAGCCACTTGATGAG                         GATACTGCAAGAGAAATTTTGAGAGCAGCTCCTGGTGTTACCATTATTGAT
genomic: TTTGAAAAGCCACTTGATGAGgttggtattc ... tactctaaagGATACTGCAAGAGAAATTTTGAGAGCAGCTCCTGGTGTTACCATTATTGAT
EST: gi|7227765|gb|AW566406.1|AW566406
EST:     GCGCACATGCTGAAAGTGTCAATCTACAGTTTGAAAAGCCACTTGATGAG                         GATACTGCAAGAGAAATTTTGAGAGCAGCTCCTGGTGTTACCATTATTGAT
genomic: GCGCACATGCTGAAAGTGTCAATCTACAGTTTGAAAAGCCACTTGATGAGgttggtattc ... tactctaaagGATACTGCAAGAGAAATTTTGAGAGCAGCTCCTGGTGTTACCATTATTGAT
EST: gi|78081782|gb|DV510194.1|DV510194
EST:     GCGCACATGCTGAAAGTGTCAATCTACAGTTTGAAAAGCCACTTGATGAG                         GATACTGCAAGAGAAATTTTGAGAGCAGCTCCTGGTGTTACCATTATTGAT
genomic: GCGCACATGCTGAAAGTGTCAATCTACAGTTTGAAAAGCCACTTGATGAGgttggtattc ... tactctaaagGATACTGCAAGAGAAATTTTGAGAGCAGCTCCTGGTGTTACCATTATTGAT
EST: gi|32934711|gb|CF039523.1|CF039523
EST:     GCGCACATGCTGAAAGTGTCAATCTACAGTTTGAAAAGCCACTTGATGAG                         GATACTGCAAGAGAAATTTTGAGAGCAGCTCCTGGTGTTACCATTATTGAT
genomic: GCGCACATGCTGAAAGTGTCAATCTACAGTTTGAAAAGCCACTTGATGAGgttggtattc ... tactctaaagGATACTGCAAGAGAAATTTTGAGAGCAGCTCCTGGTGTTACCATTATTGAT
EST: gi|93011814|gb|EB637334.1|EB637334
EST:     GCGCACATGCTGAAAGTGTCAATCTACAGTTTGAAAAGCCACTTGATGAG                         GATACTGCAAGAGAAATTTTGAGAGCAGCTCCTGGTGTTACCATTATTGAT
genomic: GCGCACATGCTGAAAGTGTCAATCTACAGTTTGAAAAGCCACTTGATGAGgttggtattc ... tactctaaagGATACTGCAAGAGAAATTTTGAGAGCAGCTCCTGGTGTTACCATTATTGAT
EST: gi|211354102|gb|FL202441.1|FL202441
EST:     GCGCACATGCTGAAAGTGTCAATCTACAGTTTGAAAAGCCACTTGATGAG                         GATACTGCAAGAGAAATTTTGAGAGCAGCTCCTGGTGTTACCATTATTGAT
genomic: GCGCACATGCTGAAAGTGTCAATCTACAGTTTGAAAAGCCACTTGATGAGgttggtattc ... tactctaaagGATACTGCAAGAGAAATTTTGAGAGCAGCTCCTGGTGTTACCATTATTGAT
EST: gi|88749457|gb|DY533598.1|DY533598
EST:     GCGCACATGCTGAAAGTGTCAATCTACAGTTTGAAAAGCCACTTGATGAG                         GATACTGCAAGAGAAATTTTGAGAGCAGCTCCTGGTGTTACCATTATTGAT
genomic: GCGCACATGCTGAAAGTGTCAATCTACAGTTTGAAAAGCCACTTGATGAGgttggtattc ... tactctaaagGATACTGCAAGAGAAATTTTGAGAGCAGCTCCTGGTGTTACCATTATTGAT
EST: gi|88757279|gb|DY541420.1|DY541420
EST:     GCGCACATGCTGAAAGTGTCAATCTACAGTTTGAAAAGCCACTTGATGAG                         GATACTGCAAGAGAAATTTTGAGAGCAGCTCCTGGTGTTACCATTATTGAT
genomic: GCGCACATGCTGAAAGTGTCAATCTACAGTTTGAAAAGCCACTTGATGAGgttggtattc ... tactctaaagGATACTGCAAGAGAAATTTTGAGAGCAGCTCCTGGTGTTACCATTATTGAT
EST: gi|78083842|gb|DV512235.1|DV512235
EST:     GCGCACATGCTGAAAGTGTCAATCTACAGTTTGAAAAGCCACTTGATGAG                         GATACTGCAAGAGAAATTTTGAGAGCAGCTCCTGGTGTTACCATTATTGAT
genomic: GCGCACATGCTGAAAGTGTCAATCTACAGTTTGAAAAGCCACTTGATGAGgttggtattc ... tactctaaagGATACTGCAAGAGAAATTTTGAGAGCAGCTCCTGGTGTTACCATTATTGAT

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: 48 (upstream exon), 45 (downstream exon)
Score: 127

TGACAAGGAGGTGAAAGTAACTGCGACTTGCATACGGGTTCCTGTGATGCGCGCACATGCTGAAAGTGTCAATCTACAGTTTGAAAAGCCACTTGATGAGgttggtattc ... tactctaaagGATACTGCAAGAGAAATTTTGAGAGCAGCTCCTGGTGTTACCATTATTGATGACCGAGCTTCCAATCGCTTTCCTACACCTCTGGAG


Block sizes: 48 (upstream exon), 45 (downstream exon)
Score: 109

TGACAAGGAGGTGAAAGTAACTGCGACTTGCATACGGGTTCCTGTGATGCGCGCACATGCTGAAAGTGTCAATCTACAGTTTGAAAAGCCACTTGATGAGgttggtattc ... tactctaaagGATACTGCAAGAGAAATTTTGAGAGCAGCTCCTGGTGTTACCATTATTGATGACCGAGCTTCCAATCGCTTTCCTACACCTCTGGAG


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 108

TGACAAGGAGGTGAAAGTAACTGCGACTTGCATACGGGTTCCTGTGATGCGCGCACATGCTGAAAGTGTCAATCTACAGTTTGAAAAGCCACTTGATGAGgttggtattc ... tactctaaagGATACTGCAAGAGAAATTTTGAGAGCAGCTCCTGGTGTTACCATTATTGATGACCGAGCTTCCAATCGCTTTCCTACACCTCTGGAG


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 93

TGACAAGGAGGTGAAAGTAACTGCGACTTGCATACGGGTTCCTGTGATGCGCGCACATGCTGAAAGTGTCAATCTACAGTTTGAAAAGCCACTTGATGAGgttggtattc ... tactctaaagGATACTGCAAGAGAAATTTTGAGAGCAGCTCCTGGTGTTACCATTATTGATGACCGAGCTTCCAATCGCTTTCCTACACCTCTGGAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGACAAGGAGGTGAAAGTAACTGCGACTTGCATACGGGTTCCTGTGATGCGCGCACATGCTGAAAGTGTCAATCTACAGTTTGAAAAGCCACTTGATGAGgttggtattctgcatattatgtgctaactagcattagagcttttctgtacgtgcgaatatgtttctttccttcatactatcctcttttgtctctattagt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG