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'   		12  
 5'  3'   		13  
 5'  3'   		14  
 5'  3'   		15  
 5'  3'   		16  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTTGAGCTACAATCCAATTGGATCAGACGGAGTAAAGGCTTTGTGCGATGTCCTCAAGTTCCATGGGAAGATCCAAACCCTTAAGCTCGGCTGGTGCCAGgtgaccctcagaaccgaatggaattatacgagcagttttgcaccatttaagtgttctcaccagagttgcataacctgcag

Basic information

species Zea mays
transcript GRMZM2G110289_T01
intron # 13
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G110289_T01 (Zea mays), 5'ss of exon 13
lower sequence: LOC_Os06g13050.1 (Oryza sativa), 5'ss of exon 14
TTTGAGCTACAATCCAATTGGATCAGACGGAGTAAAGGCTTTGTGCGATGTCCTCAAGTTCCATGGGAAGATCCAAACCCTTAAGCTCGGCTGGTGCCAGgtgaccctcagaaccgaatggaattatacgagcagttttgcaccatttaagtgttctcaccagagttgcataacctgcag
 |||||||| ||||| |||||  |||| || ||||||||| | || ||||| ||||||||| ||||||| |||||||||||||| || || ||||||||||| | | ||| ||| |||||||||       |||| |||     || |     |  ||| |   ||| ||||   |||||
GTTGAGCTATAATCCGATTGGGCCAGAGGGGGTAAAGGCTCTTTGTGATGTTCTCAAGTTCAATGGGAAAATCCAAACCCTTAAACTTGGTTGGTGCCAGgtaatcttcataactgaatggaatcgcggatgcagatttaagttatat---cctcttcagcctggttacatattttgcag

upper sequence: GRMZM2G110289_T01 (Zea mays), 5'ss of exon 13
lower sequence: GLYMA02G03410.1 (Glycine max), 5'ss of exon 12
TTTGAGCTACAATCCAATTGGATCAGACGGAGTAAAGGCTTTGTGCGATGTCCTCAAGTTCCATGGGAAGATCCAAACCCTTAAGCTCGGCTGGTGCCAGgtgaccctcagaaccgaatggaattatacgagcagttttgcaccatttaagtgttctcaccagagttgcataacct-gcag
  | || || ||||| |||||| |||||||||  ||||| |||   || || |||||||| |||||||| ||  ||||||||||||| || ||||||||||| ||| |   | |   ||| |||||   |   | || |     ||  || | || |    |   ||| ||||| |   ||
ACTTAGTTATAATCCCATTGGACCAGACGGAGCCAAGGCCTTGGCTGAAGTTCTCAAGTTTCATGGGAACATAAAAACCCTTAAGCTTGGTTGGTGCCAGgtaaccttttcacc---atg-aattacctgta-aattatttgtaat--aacttttatttgtaacattgaataactttatag

upper sequence: GRMZM2G110289_T01 (Zea mays), 5'ss of exon 13
lower sequence: GLYMA01G04270.1 (Glycine max), 5'ss of exon 10
TTTGAGCTACAATCCAATTGGATCAGACGGAGTAAAGGCTTTGTGCGATGTCCTCAAGTTCCATGGGAAGATCCAAACCCTTAAGCTCGGCTGGTGCCAGgtgaccctcagaaccgaatggaattatacgagcagttttgcaccatttaagtgttctcaccagagttgcataacct-gcag
  | || || ||||| |||||| |||| ||||  ||||| |||   || || |||||||| |||||||| ||  ||||||||||||| || ||||||||||| ||| |   | |   ||| |||||   |   | || |     ||  || | || |    |   ||| ||||| |   ||
ACTTAGTTATAATCCCATTGGACCAGATGGAGCCAAGGCCTTGGCTGAAGTTCTCAAGTTTCATGGGAACATAAAAACCCTTAAGCTTGGTTGGTGCCAGgtaaccttttcacc---atg-aattacctgta-aattgtttgtaat--aacttttatttgtaacattggataactttatag

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|60354010|gb|DN220983.1|DN220983
EST:     TCCTCAAGTTCCATGGGAAGATCCAAACCCTTAAGCTCGGCTGGTGCCAG                         ATAGGCATGGAAGGTGCAGAGTGTATTGCCGACTGTCTCAAGTACAACACA
genomic: TCCTCAAGTTCCATGGGAAGATCCAAACCCTTAAGCTCGGCTGGTGCCAGgtgaccctca ... taacctgcagATAGGCATGGAAGGTGCAGAGTGTATTGCCGACTGTCTCAAGTACAACACA
EST: gi|67010636|gb|CO439385.1|CO439385
EST:     TCCTCAAGTTCCATGGGAAGATCCAAACCCTTAAGCTCGGCTGGTGCCAG                         ATAGGCGTGGAAGGTGCAGAGTGTATTGCCGACTGTCTCAAGTACAACACA
genomic: TCCTCAAGTTCCATGGGAAGATCCAAACCCTTAAGCTCGGCTGGTGCCAGgtgaccctca ... taacctgcagATAGGCATGGAAGGTGCAGAGTGTATTGCCGACTGTCTCAAGTACAACACA
EST: gi|60346680|gb|DN213653.1|DN213653
EST:     TCCTCAAGTTCCATGGGAAGATCCAAACCCTTAAGCTCGGCTGGTGCCAG                         ATAGGCATGGAAGGTGCAGAGTGTATTGCCGACTGTCTCAAGTACAACACA
genomic: TCCTCAAGTTCCATGGGAAGATCCAAACCCTTAAGCTCGGCTGGTGCCAGgtgaccctca ... taacctgcagATAGGCATGGAAGGTGCAGAGTGTATTGCCGACTGTCTCAAGTACAACACA
EST: gi|71763770|gb|DR961707.1|DR961707
EST:     TCCTCAAGTTCCATGGGAAGATCCAAACCCTTAAGCTCGGCTGGTGCCAG                         ATAGGCATGGAAGGTGCAGAGTGTATTGCCGACTGTCTCAAGTACAACACA
genomic: TCCTCAAGTTCCATGGGAAGATCCAAACCCTTAAGCTCGGCTGGTGCCAGgtgaccctca ... taacctgcagATAGGCATGGAAGGTGCAGAGTGTATTGCCGACTGTCTCAAGTACAACACA
EST: gi|60355903|gb|DN222876.1|DN222876
EST:     TCCTCAAGTTCCATGGGAAGATCCAAACCCTTAAGCTCGGCTGGTGCCAG                         ATAGGCATGGAAGGTGCAGAGTGTATTGCCGACTGTCTCAAGTACAACACA
genomic: TCCTCAAGTTCCATGGGAAGATCCAAACCCTTAAGCTCGGCTGGTGCCAGgtgaccctca ... taacctgcagATAGGCATGGAAGGTGCAGAGTGTATTGCCGACTGTCTCAAGTACAACACA
EST: gi|60341143|gb|DN208116.1|DN208116
EST:     TCCTCAAGTTCCATGGGAAGATCCAAACCCTTAAGCTCGGCTGGTGCCAG                         ATAGGCATGGAAGGTGCAGAGTGTATTGCCGACTGTCTCAAGTACAACACA
genomic: TCCTCAAGTTCCATGGGAAGATCCAAACCCTTAAGCTCGGCTGGTGCCAGgtgaccctca ... taacctgcagATAGGCATGGAAGGTGCAGAGTGTATTGCCGACTGTCTCAAGTACAACACA

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: 133

TTTGAGCTACAATCCAATTGGATCAGACGGAGTAAAGGCTTTGTGCGATGTCCTCAAGTTCCATGGGAAGATCCAAACCCTTAAGCTCGGCTGGTGCCAGgtgaccctca ... taacctgcagATAGGCATGGAAGGTGCAGAGTGTATTGCCGACTGTCTCAAGTACAACACAACGTTATCGACATTGGATCTGCGGGCAAACGGGCTTGGAAACGAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 204

TTTGAGCTACAATCCAATTGGATCAGACGGAGTAAAGGCTTTGTGCGATGTCCTCAAGTTCCATGGGAAGATCCAAACCCTTAAGCTCGGCTGGTGCCAGgtgaccctca ... taacctgcagATAGGCATGGAAGGTGCAGAGTGTATTGCCGACTGTCTCAAGTACAACACAACGTTATCGACATTGGATCTGCGGGCAAACGGGCTTGGAAACGAT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 110

TTTGAGCTACAATCCAATTGGATCAGACGGAGTAAAGGCTTTGTGCGATGTCCTCAAGTTCCATGGGAAGATCCAAACCCTTAAGCTCGGCTGGTGCCAGgtgaccctca ... taacctgcagATAGGCATGGAAGGTGCAGAGTGTATTGCCGACTGTCTCAAGTACAACACAACGTTATCGACATTGGATCTGCGGGCAAACGGGCTTGGAAACGAT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 146

TTTGAGCTACAATCCAATTGGATCAGACGGAGTAAAGGCTTTGTGCGATGTCCTCAAGTTCCATGGGAAGATCCAAACCCTTAAGCTCGGCTGGTGCCAGgtgaccctca ... taacctgcagATAGGCATGGAAGGTGCAGAGTGTATTGCCGACTGTCTCAAGTACAACACAACGTTATCGACATTGGATCTGCGGGCAAACGGGCTTGGAAACGAT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTTGAGCTACAATCCAATTGGATCAGACGGAGTAAAGGCTTTGTGCGATGTCCTCAAGTTCCATGGGAAGATCCAAACCCTTAAGCTCGGCTGGTGCCAGgtgaccctcagaaccgaatggaattatacgagcagttttgcaccatttaagtgttctcaccagagttgcataacctgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA