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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttcttgttcttttttctgtgtggtagtgtgcatatgcatgtttgacatataatacttagtatttaatgttaaactgttaatggtcacttgtgttttcagAATGAGATGAATGAGCGTGAGTTGTGTGCACTGAAATCTGTCATTAAGTGCATTGAAGATCATAAACTTGAGGAGCAGTACCCTGTGGACCCACTTCAGA

Basic information

species Zea mays
transcript GRMZM2G070054_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G070054_T03 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA03G23740.1 (Glycine max), 3'ss of exon 3
tttcttgttcttttttctgtgtggtagtgtgcatatgcatgtttgacatataatacttagtatttaatgttaaactgttaatggtcacttgtgttt---tcagAATGAGATGAATGAGCGTGAGTTGTGTGCACTGAAATCTGTCATTAAGTGCATTGAAGATCATAAACTTGAGGAGCAGTACCCTGTGGACCCACTTCAGA
     ||  |  |  |||   |  |  |||    ||   |   |    ||||    |   |||||  | |   | | ||  |  | |||||   ||   ||||| |||  | ||||| || ||  ||  |||||| ||| |||| |||||||| ||||||||||| |||||||| || ||||||||| |||| || || ||||
--agatgcccagtgatcttgatcttgatgtttg-ataattaacttgtttatacagatatatattttttctatgaatattcctaattacttgctattgcctcagATTGATGTTAATGATCGAGAACTGATTGCACTTAAAGCTGTAATTAAGTGTATTGAAGATCACAAACTTGATGACCAGTACCCTCTGGATCCTCTCCAGA

upper sequence: GRMZM2G070054_T03 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA16G08590.1 (Glycine max), 3'ss of exon 2
---tttcttgttcttttttctgtgtggtagtgtgcatatgcatgtttgacatataatacttagtatttaatgttaaactgttaatggtcacttgtgttttcagAATGAGATGAATGAGCGTGAGTTGTGTGCACTGAAATCTGTCATTAAGTGCATTGAAGATCATAAACTTGAGGAGCAGTACCCTGTGGACCCACTTCAGA
   ||| |  |  ||| ||        |   |    | ||    | |    | |  || ||  |  ||  | ||||  | |   | ||  ||| ||| | |||| |||| ||||||| || ||| ||   ||||| ||  |||| || |||||||||||||| ||||||||||| |||||||| ||| |||| || || ||||
tgatttttaatagtttcttaaaaagaatttggcttttgtggtaatatactgttttttatttctttctttcttttaa--tatccctagtgtcttttgtct-cagATTGAGGTGAATGAACGAGAGCTGGTCGCACTTAAGGCTGTAATCAAGTGCATTGAAGAACATAAACTTGATGAGCAGTATCCTCTGGATCCTCTCCAGA

upper sequence: GRMZM2G070054_T03 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA03G23760.1 (Glycine max), 3'ss of exon 4
-tttcttgttcttttttctgtgtggtagtgtgcatatgcatgtttgaca-tataatacttagtatttaatgttaaactgttaatggtcacttgtgttttcagAATGAGATGAATGAGCGTGAGTTGTGTGCACTGAAATCTGTCATTAAGTGCATTGAAGATCATAAACTTGAGGAGCAGTACCCTGTGGACCCACTTCAGA
 |   ||| | ||  |  | |     |      ||  || | | ||  | |||| | || | | | |    || || | ||  | ||  ||| ||| | |||| |||| ||||||| || ||| ||  |||||| ||  |||| || |||||||||||||| ||||||||||| |||||||| ||| |||| || || ||||
gtaatttgattttaatagttttcttaaaaagaaattggcttttgtggtaatatactgct-attttctctcttttaaatattcctagtatcttttgtct-cagATTGAGGTGAATGAACGAGAGCTGGTTGCACTTAAGGCTGTAATCAAGTGCATTGAAGAACATAAACTTGATGAGCAGTATCCTCTGGATCCTCTCCAGA

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|60354592|gb|DN221565.1|DN221565
EST:     TTAAGAAACTGTCACATGCCAGGAATGTCAAAATTTCTCCTGGAGCACAG                         AATGAGATGAATGAGCGTGAGTTGTGTGCACTGAAATCTGTCATTAAGTGC
genomic: TTAAGAAACTGTCACATGCCAGGAATGTCAAAATTTCTCCTGGAGCACAGgtacatttta ... gtgttttcagAATGAGATGAATGAGCGTGAGTTGTGTGCACTGAAATCTGTCATTAAGTGC
EST: gi|27575945|gb|CA998639.1|CA998639
EST:     TTAAGAAACTGTCACATGCCAGGAATGTCAAAATTTCTCCTGGAGCACAG                         AATGAGATGAATGAGCGTGAGTTGTGTGCACTGAAATCTGTCATTAAGTGC
genomic: TTAAGAAACTGTCACATGCCAGGAATGTCAAAATTTCTCCTGGAGCACAGgtacatttta ... gtgttttcagAATGAGATGAATGAGCGTGAGTTGTGTGCACTGAAATCTGTCATTAAGTGC
EST: gi|60343207|gb|DN210180.1|DN210180
EST:     TTAAGAAACTGTCACATGCCAGGAATGTCAAAATTTCTCCTGGAGCACAG                         AATGAGATGAATGAGCGTGAGTTGTGTGCACTGAAATCTGTCATTAAGTGC
genomic: TTAAGAAACTGTCACATGCCAGGAATGTCAAAATTTCTCCTGGAGCACAGgtacatttta ... gtgttttcagAATGAGATGAATGAGCGTGAGTTGTGTGCACTGAAATCTGTCATTAAGTGC
EST: gi|31356421|gb|CD440778.1|CD440778
EST:     TTAAGAAACTGTCACATGCCAGGAATGTCAAAATTTCTCCTGGAGCACAG                         AATGAGATGAATGAGCGTGAGTTGTGTGCACTGAAATCTGTC
genomic: TTAAGAAACTGTCACATGCCAGGAATGTCAAAATTTCTCCTGGAGCACAGgtacatttta ... gtgttttcagAATGAGATGAATGAGCGTGAGTTGTGTGCACTGAAATCTGTC
EST: gi|211259144|gb|FL283531.1|FL283531
EST:     TTAAGAAACTGTCACATGCCAGGAATGTCAAAATTTCTCCTGGAGCACAG                         AATGAGATGAATGAGCGTGAGTTGTGTGCACTGAAATCTGTCATTAAGTGC
genomic: TTAAGAAACTGTCACATGCCAGGAATGTCAAAATTTCTCCTGGAGCACAGgtacatttta ... gtgttttcagAATGAGATGAATGAGCGTGAGTTGTGTGCACTGAAATCTGTCATTAAGTGC
EST: gi|14245144|gb|BG873726.1|BG873726
EST:     TTAAGAANCTGTCACATGCCAGGAATGTCAAAATTTCTCCTGGAGCACAG                         AATGAGATGAATGAGCGTGAGTTGTGTGCACTGAAATCTGTCATTAAGTGC
genomic: TTAAGAAACTGTCACATGCCAGGAATGTCAAAATTTCTCCTGGAGCACAGgtacatttta ... gtgttttcagAATGAGATGAATGAGCGTGAGTTGTGTGCACTGAAATCTGTCATTAAGTGC
EST: gi|211256717|gb|FL283528.1|FL283528
EST:     TTAAGAAACTGTCACATGCCAGGAATGTCAAAATTTCTCCTGGAGCACAG                         AATGAGATGAATGAGCGTGAGTTGTGTGCACTGAAATCTGTCATTAAGTGC
genomic: TTAAGAAACTGTCACATGCCAGGAATGTCAAAATTTCTCCTGGAGCACAGgtacatttta ... gtgttttcagAATGAGATGAATGAGCGTGAGTTGTGTGCACTGAAATCTGTCATTAAGTGC
EST: gi|14206613|gb|BG840291.1|BG840291
EST:     TTAAGAAACTGTCACATGCCAGGAATGTCAAAATTTCTCCTGGAGCACAG                         AATGAGATGAATGAGCGTGAGTTGTGTGCACTGAAATCTGTCATTAAGTGC
genomic: TTAAGAAACTGTCACATGCCAGGAATGTCAAAATTTCTCCTGGAGCACAGgtacatttta ... gtgttttcagAATGAGATGAATGAGCGTGAGTTGTGTGCACTGAAATCTGTCATTAAGTGC
EST: gi|9733155|gb|BE511907.1|BE511907
EST:     TTAAGAAACTGTCACATGCCAGGAATGTCAAAATTTCTCCTGGAGCACAG                         AATGAGATGAATGAGCGTGAGTTGTGTGCACTGAAATCTGTCATTAAGTGC
genomic: TTAAGAAACTGTCACATGCCAGGAATGTCAAAATTTCTCCTGGAGCACAGgtacatttta ... gtgttttcagAATGAGATGAATGAGCGTGAGTTGTGTGCACTGAAATCTGTCATTAAGTGC

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: 533

TACTGAACAGTTTGAACCAGTGCAACTGCTTAAAGCATATCTGAGGGATGTTAAGAAACTGTCACATGCCAGGAATGTCAAAATTTCTCCTGGAGCACAGgtacatttta ... gtgttttcagAATGAGATGAATGAGCGTGAGTTGTGTGCACTGAAATCTGTCATTAAGTGCATTGAAGATCATAAACTTGAGGAGCAGTACCCTGTGGACCCACTTCAGA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 194

TACTGAACAGTTTGAACCAGTGCAACTGCTTAAAGCATATCTGAGGGATGTTAAGAAACTGTCACATGCCAGGAATGTCAAAATTTCTCCTGGAGCACAGgtacatttta ... gtgttttcagAATGAGATGAATGAGCGTGAGTTGTGTGCACTGAAATCTGTCATTAAGTGCATTGAAGATCATAAACTTGAGGAGCAGTACCCTGTGGACCCACTTCAGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 294

TACTGAACAGTTTGAACCAGTGCAACTGCTTAAAGCATATCTGAGGGATGTTAAGAAACTGTCACATGCCAGGAATGTCAAAATTTCTCCTGGAGCACAGgtacatttta ... gtgttttcagAATGAGATGAATGAGCGTGAGTTGTGTGCACTGAAATCTGTCATTAAGTGCATTGAAGATCATAAACTTGAGGAGCAGTACCCTGTGGACCCACTTCAGA


Block sizes: 48 (upstream exon), 45 (downstream exon)
Score: 225

TACTGAACAGTTTGAACCAGTGCAACTGCTTAAAGCATATCTGAGGGATGTTAAGAAACTGTCACATGCCAGGAATGTCAAAATTTCTCCTGGAGCACAGgtacatttta ... gtgttttcagAATGAGATGAATGAGCGTGAGTTGTGTGCACTGAAATCTGTCATTAAGTGCATTGAAGATCATAAACTTGAGGAGCAGTACCCTGTGGACCCACTTCAGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acatataatacttagtatttaatgttaaactgttaatggtcacttgtgttttcagAATGAGATGAATGAGCGTGAGTTGTGTGCACTGAAATCTGTCATTAAGTGCATTGAAGATCATAAACTTGAGGAGCAGTACCCTGTGGACCCACTTCAGA
                              tgttaat  putative branch site (score: 225)
                                              tgttttc  putative PPT
     taatacttagtattta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttcttgttcttttttctgtgtggtagtgtgcatatgcatgtttgacatataatacttagtatttaatgttaaactgttaatggtcacttgtgttttcagAATGAGATGAATGAGCGTGAGTTGTGTGCACTGAAATCTGTCATTAAGTGCATTGAAGATCATAAACTTGAGGAGCAGTACCCTGTGGACCCACTTCAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
tttcttg
- - - - - - ttttctg
- - - - - - - - - - - - - - gtgcata
- - - - - - - - - - - - - - - - - -tgcatgt