Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgttgtatttgcatcttttttttctatgttttgtggtgcagatctgcagtattttgtactgaactggtttataatttacagGCCTTGATCATAAAGCAATAGATAAGTGTATTGGTGATCCAGATGCAGATGAGGAAAACCATGTTCTGAAAGCTGAACAGGATGCACAG

Basic information

species Zea mays
transcript GRMZM2G347541_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G347541_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os11g02464.1 (Oryza sativa), 3'ss of exon 2
gtatgttgtatttgcatcttttttttctatgttttgtggtgcagatctgcagtattttgtactgaactggtttataatttacagGCCTTGATCATAAAGCAATAGATAAGTGTATTGGTGATCCAGATGCAGATGAGGAAAACCATGTTCTGAAAGCTGAACAGGATGCACAG
||||||||   ||   |  |   |||||||| |||||||||  |   ||||| | || |||||||    ||||| ||| | |||| |||||||| ||||| ||||||||||| ||||||||||||||||| ||| | ||||| | ||| ||||||||||||||||||||||||
gtatgttgctgttttcttatgcctttctatgctttgtggtgagg---tgcagcaatt-gtactgagtatgtttaaaatgtccagGTCTTGATCACAAAGCCATAGATAAGTGCATTGGTGATCCAGATGCTGATAAAGAAAATCCTGTGCTGAAAGCTGAACAGGATGCACAG

upper sequence: GRMZM2G347541_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os12g02390.1 (Oryza sativa), 3'ss of exon 2
gtatgttg-tatttgcat---cttttttttctatgttttgtggtgcagatctgcagtattttgtactgaactggtttataatttacagGCCTTGATCATAAAGCAATAGATAAGTGTATTGGTGATCCAGATGCAGATGAGGAAAACCATGTTCTGAAAGCTGAACAGGATGCACAG
|||||||| | ||| | |   | ||| |||||||| |||||||||  |   ||||| | || |||||||    ||||| |||   |||| |||||||| ||||| ||||||||||| |||| |||||||||||| ||| | ||||| | ||| ||||||||||||||||||||||||
gtatgttgctgttttcttatgcctttctttctatgctttgtggtgagg---tgcagcaatt-gtactgagtatgtttaaaatgcccagGTCTTGATCACAAAGCCATAGATAAGTGCATTGCTGATCCAGATGCTGATAAAGAAAATCCTGTGCTGAAAGCTGAACAGGATGCACAG
















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|71299569|gb|DR785796.1|DR785796
EST:     GGAAAAGAAGTACACAAAGGAGTGTGCCGATGGAGTTATCAAGTCACTTG                         GCCTTGATCATAAAGCAATAGATAAGTGTATTGGTGATCCAGATGCAGATG
genomic: GGAAAAGAAGTACACAAAGGAGTGTGCCGATGGAGTTATCAAGTCACTTGgtatgttgta ... taatttacagGCCTTGATCATAAAGCAATAGATAAGTGTATTGGTGATCCAGATGCAGATG
EST: gi|211315827|gb|FK969310.1|FK969310
EST:     GGAAAAGAAGTACACAAAGGAGTGTGCCGATGGAGTTATCAAGTCACTTG                         GCCTTGATCATAAAGCAATAGATAAGTGTATTGGTGATCCAGATGCAGATG
genomic: GGAAAAGAAGTACACAAAGGAGTGTGCCGATGGAGTTATCAAGTCACTTGgtatgttgta ... taatttacagGCCTTGATCATAAAGCAATAGATAAGTGTATTGGTGATCCAGATGCAGATG
EST: gi|26558897|gb|CA831132.1|CA831132
EST:     GGAAAAGAAGTACACAAAGGAGTGTGCAGATGGAGTTATCAAGTCACTTG                         GCCTTGATCATAAAGCAATAGATAAGTGTATTGGTGATCCAGATGCAGATG
genomic: GGAAAAGAAGTACACAAAGGAGTGTGCCGATGGAGTTATCAAGTCACTTGgtatgttgta ... taatttacagGCCTTGATCATAAAGCAATAGATAAGTGTATTGGTGATCCAGATGCAGATG
EST: gi|67028179|gb|CO456928.1|CO456928
EST:     GGAAAAGAAGTACACAAAGGAGTGTGCCGATGGAGTTATCAAGTCACTTG                         GCCTTGATCATAAAGCAATAGATAAGTGTATTGGTGATCCAGATGCAGATG
genomic: GGAAAAGAAGTACACAAAGGAGTGTGCCGATGGAGTTATCAAGTCACTTGgtatgttgta ... taatttacagGCCTTGATCATAAAGCAATAGATAAGTGTATTGGTGATCCAGATGCAGATG
EST: gi|211315829|gb|FK969312.1|FK969312
EST:     GGAAAAGAAGTACACAAAGGAGTGTGCCGATGGAGTTATCAAGTCACTTG                         GCCTTGATCATAAAGCAATAGATAAGTGTATTGGTGATCCAGATGCAGATG
genomic: GGAAAAGAAGTACACAAAGGAGTGTGCCGATGGAGTTATCAAGTCACTTGgtatgttgta ... taatttacagGCCTTGATCATAAAGCAATAGATAAGTGTATTGGTGATCCAGATGCAGATG
EST: gi|211313818|gb|FK969308.1|FK969308
EST:     GGAAAAGAAGTACACAAAGGAGTGTGCCGATGGAGTTATCAAGTCACTTG                         GCCTTGATCATAAAGCAATAGATAAGTGTATTGGTGATCCAGATGCAGATG
genomic: GGAAAAGAAGTACACAAAGGAGTGTGCCGATGGAGTTATCAAGTCACTTGgtatgttgta ... taatttacagGCCTTGATCATAAAGCAATAGATAAGTGTATTGGTGATCCAGATGCAGATG

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), 49 (downstream exon)
Score: 377

TGGTTATGGTGGGACTACGTTACTGATTTTGCGATTCGGTGCCCGATGAAGGAAAAGAAGTACACAAAGGAGTGTGCCGATGGAGTTATCAAGTCACTTGgtatgttgta ... taatttacagGCCTTGATCATAAAGCAATAGATAAGTGTATTGGTGATCCAGATGCAGATGAGGAAAACCATGTTCTGAAAGCTGAACAGGATGCACAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 171

TGGTTATGGTGGGACTACGTTACTGATTTTGCGATTCGGTGCCCGATGAAGGAAAAGAAGTACACAAAGGAGTGTGCCGATGGAGTTATCAAGTCACTTGgtatgttgta ... taatttacagGCCTTGATCATAAAGCAATAGATAAGTGTATTGGTGATCCAGATGCAGATGAGGAAAACCATGTTCTGAAAGCTGAACAGGATGCACAG


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 154

TGGTTATGGTGGGACTACGTTACTGATTTTGCGATTCGGTGCCCGATGAAGGAAAAGAAGTACACAAAGGAGTGTGCCGATGGAGTTATCAAGTCACTTGgtatgttgta ... taatttacagGCCTTGATCATAAAGCAATAGATAAGTGTATTGGTGATCCAGATGCAGATGAGGAAAACCATGTTCTGAAAGCTGAACAGGATGCACAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 327

TGGTTATGGTGGGACTACGTTACTGATTTTGCGATTCGGTGCCCGATGAAGGAAAAGAAGTACACAAAGGAGTGTGCCGATGGAGTTATCAAGTCACTTGgtatgttgta ... taatttacagGCCTTGATCATAAAGCAATAGATAAGTGTATTGGTGATCCAGATGCAGATGAGGAAAACCATGTTCTGAAAGCTGAACAGGATGCACAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttttgtggtgcagatctgcagtattttgtactgaactggtttataatttacagGCCTTGATCATAAAGCAATAGATAAGTGTATTGGTGATCCAGATGCAGATGAGGAAAACCATGTTCTGAAAGCTGAACAGGATGCACAG
                                         tttataatttaca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgttgtatttgcatcttttttttctatgttttgtggtgcagatctgcagtattttgtactgaactggtttataatttacagGCCTTGATCATAAAGCAATAGATAAGTGTATTGGTGATCCAGATGCAGATGAGGAAAACCATGTTCTGAAAGCTGAACAGGATGCACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG