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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTTATTTCCAAGCTGAACCCCTTTTCGGGGATGAAGCATCTCGATGTGGCTGGTGGAACAGgtaatatctatctccttccctcattgctttcagatgcaccatagaaacaacaaatgcaaatttttactagtatcttaaacattattaattctaccttgat...

Basic information

species Zea mays
transcript GRMZM2G065210_T03
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G065210_T03 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os01g74520.1 (Oryza sativa), 5'ss of exon 3
GCTTATTTCCAAGCTGAACCCCTTTTCGGGGATGAAGCATCTCGATGTGGCTGGTGGAACAGgtaatatctatctccttccctcattgctttcagatgcaccatagaaacaacaaatgcaaatttttactagtatcttaaacattattaattctaccttgat-----
||| || || ||||| || || ||| | |||||||||||||| |||||||||||||||||||||| | |   | || | || |||  || || | || |      |  |      ||||| |  || |||          ||  ||  ||     ||||| |     
GCTCATCTCAAAGCTTAATCCTTTTCCTGGGATGAAGCATCTAGATGTGGCTGGTGGAACAGgtattcttcctttcttaccttca--gcattaacatcctaagatgccatgtaccatgcatagctt-actgacccacccgac--taaaaacatagccttgctagtca

upper sequence: GRMZM2G065210_T03 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os01g74520.2 (Oryza sativa), 5'ss of exon 2
--------------------------------------GCTTATTTCCAAGCTGAACCCCTTTTCGGGGATGAAGCATCTCGATGTGGCTGGTGGAACAGgtaatatctatctccttccctcattgctttcagatgcaccatagaaacaacaaatgcaaatttttactagtatcttaaacattattaattctaccttgat-----
                                      ||| || || ||||| || || ||| | |||||||||||||| |||||||||||||||||||||| | |   | || | || |||  || || | || |      |  |      ||||| |  || |||          ||  ||  ||     ||||| |     
TGTCAGGCTTACCACATTCCTCTTCTCTATTTTTTAAGGCTCATCTCAAAGCTTAATCCTTTTCCTGGGATGAAGCATCTAGATGTGGCTGGTGGAACAGgtattcttcctttcttaccttca--gcattaacatcctaagatgccatgtaccatgcatagctt-actgacccacccgac--taaaaacatagccttgctagtca

upper sequence: GRMZM2G065210_T03 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA08G22890.1 (Glycine max), 5'ss of exon 3
GCTTATTTCCAAGCTGAACCCCTTTTCGGGGATGAAGCATCTCGATGTGGCTGGTGGAACAGgtaatatctatctccttccctcattgctttcagatgcaccatagaaacaacaaatgc-aaatttttacta-gtatcttaaacattattaattctaccttgat----
| |  ||||||||||||| || ||| | || ||||||||||| |||||||||||||||||||||     || | || ||  | |  || |||    ||   | |      |  | ||   | |   || | | |    |||||  | ||  | |||  |   ||    
GTTAGTTTCCAAGCTGAATCCGTTTCCTGGAATGAAGCATCTTGATGTGGCTGGTGGAACAGgt-----ctgtttcattgtcactatgttttatactgtgtcttctgtgtagtagattttagaagattgcaatgcgagttaaat-tgatgcagtctggcaaaatatgt

upper sequence: GRMZM2G065210_T03 (Zea mays), 5'ss of exon 4
lower sequence: Vv16s0039g01590.t01 (Vitis vinifera), 5'ss of exon 4
GCTTATTTCCAAGCTGAACCCCTTTTCGGGGATGAAGCATCTCGATGTGGCTGGTGGAACAGgtaatatctatctccttccctcattgctttcagatgcacca-tagaaacaacaaatgcaaatttttactagtatcttaaacattattaattctaccttgat-
| |  | || ||  || | || ||| | || ||||||||||| ||||||||||||||||||||| |    || ||  | |  | |||   |  ||         | |       |  |  | |   | | |  | |     |  | |  ||   |      |  
GTTGGTCTCTAAATTGCATCCATTTCCTGGAATGAAGCATCTTGATGTGGCTGGTGGAACAGgtta-gcataccttgtacaattattatatgtagtctttttgcttggtgttttaggtagatagggtaaatgat-tgagggagctcaacaaggatggggcaaga

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|32844724|gb|CD984405.1|CD984405
EST:     GCTGAACCCCTTTCCGGCAATGAAGCATCTCGATGTGGCTGGTGGAACAG                         GTGATGTTGCTTTTCGTGTAC
genomic: GCTGAACCCCTTTTCGGGGATGAAGCATCTCGATGTGGCTGGTGGAACAGgtaatatcta ... ttgacttcagGTGATGTTGCTTTTCGTGTAC
EST: gi|32843983|gb|CD983664.1|CD983664
EST:     GCTGAACCCCTTTCCGGGGATGAAGCATCTCGATGTGGCTGGTGGAACAG                         GTGATGTCGCTTTTCGTGTA
genomic: GCTGAACCCCTTTTCGGGGATGAAGCATCTCGATGTGGCTGGTGGAACAGgtaatatcta ... ttgacttcagGTGATGTTGCTTTTCGTGTA

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), 48 (downstream exon)
Score: 126

GCTTATTTCCAAGCTGAACCCCTTTTCGGGGATGAAGCATCTCGATGTGGCTGGTGGAACAGgtaatatcta ... ttgacttcagGTGATGTTGCTTTTCGTGTACTGGAAAGAGTTAAGAGTGTGGGTCACAGAGCTATGCAGGGTACTCTTACTGAAACCGAAGAAGGCACCCACATTTATGT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 86

GCTTATTTCCAAGCTGAACCCCTTTTCGGGGATGAAGCATCTCGATGTGGCTGGTGGAACAGgtaatatcta ... ttgacttcagGTGATGTTGCTTTTCGTGTACTGGAAAGAGTTAAGAGTGTGGGTCACAGAGCTATGCAGGGTACTCTTACTGAAACCGAAGAAGGCACCCACATTTATGT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 96

GCTTATTTCCAAGCTGAACCCCTTTTCGGGGATGAAGCATCTCGATGTGGCTGGTGGAACAGgtaatatcta ... ttgacttcagGTGATGTTGCTTTTCGTGTACTGGAAAGAGTTAAGAGTGTGGGTCACAGAGCTATGCAGGGTACTCTTACTGAAACCGAAGAAGGCACCCACATTTATGT


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 56

GCTTATTTCCAAGCTGAACCCCTTTTCGGGGATGAAGCATCTCGATGTGGCTGGTGGAACAGgtaatatcta ... ttgacttcagGTGATGTTGCTTTTCGTGTACTGGAAAGAGTTAAGAGTGTGGGTCACAGAGCTATGCAGGGTACTCTTACTGAAACCGAAGAAGGCACCCACATTTATGT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCTTATTTCCAAGCTGAACCCCTTTTCGGGGATGAAGCATCTCGATGTGGCTGGTGGAACAGgtaatatctatctccttccctcattgctttcagatgcaccatagaaacaacaaatgcaaatttttactagtatcttaaacattattaattctaccttgat

- - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA