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'   		17  
 5'  3'   		18  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacatctttttgtgcatgaagttcttcatcatgtgctcattttaggataagtaacacataaaatcttctgaaaaaaagataatagtgcgtgtttttttttcataaaataaattttagcttgcagttagcttcttgttcaacattcatctggttaaattacaatggttaatttgaaatttgttgagagcgcagCTTCGTGAGTCCAAGGGCATGACAACAATCAAACTTCGTCCACACTGTGGGGAG

Basic information

species Zea mays
transcript GRMZM2G134396_T03
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G134396_T03 (Zea mays), 3'ss of exon 13
lower sequence: LOC_Os07g49270.2 (Oryza sativa), 3'ss of exon 14
gtacatctttttgtgcatgaagttcttcatcatgtgctcattttaggataagtaacacataaaatcttctgaaaaaaagataatagtgcgtgtttttttttcataaaataaattttagcttgcag-ttagcttcttgttcaacattcat-------------ctggttaaattacaatggttaatttgaaatttgttgagagcgcagCTTCGTGAGTCCAAGGGCATGACAACAATCAAACTTCGTCCACACTGTGGGGAG
                                                           ||  ||    |       ||||    |   ||  || |  ||||       |||| ||| || ||| |||||||||   |||||||| ||             ||  |     |    ||||| | |||| |||| ||| ||  | ||||||||||||||||||| ||||||||||||||||||||||||||||||||||||
----------------------------------------------------------gtatcattcatttgtccccagatctctgcctgttcttctccttca-------aattctagttttcagattagcttctctctcaacatttatgatgtcctatcccctattggggctctcttggttgacttgagattt-ttgtga-tgtagCTTCGTGAGTCCAAGGGTATGACAACAATCAAACTTCGTCCACACTGTGGGGAG
















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|67028452|gb|CO457201.1|CO457201
EST:     ATGCGTATTATGTGTACTATTGCTATGCCAATCTGTATACACTGAACAAG                         CTTCGTGAGTCCAAGGGCATGACAACAATCAAACTTCGTCCACACTGTGGG
genomic: ATGCGTATTATGTGTACTATTGCTATGCCAATCTGTATACACTGAACAAGgtacatcttt ... gagagcgcagCTTCGTGAGTCCAAGGGCATGACAACAATCAAACTTCGTCCACACTGTGGG
EST: gi|32837964|gb|CD977642.1|CD977642
EST:     ACTATTGCTATGCCAATCTGTATACACTGAACAAG                         CTTCGTGAGTCCAAGGGCATGACAACAATCAAACTTCGTCCACACTGTGGG
genomic: ACTATTGCTATGCCAATCTGTATACACTGAACAAGgtacatcttt ... gagagcgcagCTTCGTGAGTCCAAGGGCATGACAACAATCAAACTTCGTCCACACTGTGGG
EST: gi|21987227|gb|BQ778755.1|BQ778755
EST:     ATGCGTATTATGTGTACTATTGCTATGCCAATCTGTATACACTGAACAAG                         CTTCGTGAGTCCAAGGGCATGACAACAATCAAACTTCGTCCACACTGTGGG
genomic: ATGCGTATTATGTGTACTATTGCTATGCCAATCTGTATACACTGAACAAGgtacatcttt ... gagagcgcagCTTCGTGAGTCCAAGGGCATGACAACAATCAAACTTCGTCCACACTGTGGG
EST: gi|26557914|gb|CA830149.1|CA830149
EST:     ATGCGTATTATGTGTACTATTGCTATGCCAATCTGTATACACTGAACAAG                         CTTCGTGAGTCCAAGGGCATGACAACAATCAAACTTCGTCCACACTGCGGG
genomic: ATGCGTATTATGTGTACTATTGCTATGCCAATCTGTATACACTGAACAAGgtacatcttt ... gagagcgcagCTTCGTGAGTCCAAGGGCATGACAACAATCAAACTTCGTCCACACTGTGGG
EST: gi|32832752|gb|CD972430.1|CD972430
EST:     ACTATTGCTATGCCAATCTGTATACACTGAACAAG                         CTTCGTGAGTCCAAGGGCATGACAACAATCAAACTTCGTCCACACTGTGGG
genomic: ACTATTGCTATGCCAATCTGTATACACTGAACAAGgtacatcttt ... gagagcgcagCTTCGTGAGTCCAAGGGCATGACAACAATCAAACTTCGTCCACACTGTGGG
EST: gi|74237693|gb|DT645607.1|DT645607
EST:     ATGCGTATTATGTGTACTATTGCTATGCCAATCTGTATACACTGAACAAG                         CTTCGTGAGTCCAAGGGCATGACAACAATCAAACTTCGTCCACACTGTGGG
genomic: ATGCGTATTATGTGTACTATTGCTATGCCAATCTGTATACACTGAACAAGgtacatcttt ... gagagcgcagCTTCGTGAGTCCAAGGGCATGACAACAATCAAACTTCGTCCACACTGTGGG
EST: gi|211424036|gb|FL301688.1|FL301688
EST:     ATGCGTATTATGTGTACTATTGCTATGCCAATCTGTATACACTGAACAAG                         CTTCGTGAGTCCAAGGGCATGACAACAATCAAACTTCGTCCACACTGTGGG
genomic: ATGCGTATTATGTGTACTATTGCTATGCCAATCTGTATACACTGAACAAGgtacatcttt ... gagagcgcagCTTCGTGAGTCCAAGGGCATGACAACAATCAAACTTCGTCCACACTGTGGG
EST: gi|71299098|gb|DR785546.1|DR785546
EST:     ATGCGTATTATGTGTACTATTGCTATGCCAATCTGTATACACTGAACAAG                         CTTCGTGAGTCCAAGGGCATGACAACAATCAAACTTCGTCCACACTGTGGG
genomic: ATGCGTATTATGTGTACTATTGCTATGCCAATCTGTATACACTGAACAAGgtacatcttt ... gagagcgcagCTTCGTGAGTCCAAGGGCATGACAACAATCAAACTTCGTCCACACTGTGGG
EST: gi|211424037|gb|FL301689.1|FL301689
EST:     ATGCGTATTATGTGTACTATTGCTATGCCAATCTGTATACACTGAACAAG                         CTTCGTGAGTCCAAGGGCATGACAACAATCAAACTTCGTCCACACTGTGGG
genomic: ATGCGTATTATGTGTACTATTGCTATGCCAATCTGTATACACTGAACAAGgtacatcttt ... gagagcgcagCTTCGTGAGTCCAAGGGCATGACAACAATCAAACTTCGTCCACACTGTGGG
EST: gi|211424038|gb|FL301690.1|FL301690
EST:     ATGCGTATTATGTGTACTATTGCTATGCCAATCTGTATACACTGAACAAG                         CTTCGTGAGTCCAAGGGCATGACAACAATCAAACTTCGTCCACACTGTGGG
genomic: ATGCGTATTATGTGTACTATTGCTATGCCAATCTGTATACACTGAACAAGgtacatcttt ... gagagcgcagCTTCGTGAGTCCAAGGGCATGACAACAATCAAACTTCGTCCACACTGTGGG
EST: gi|78121620|gb|DV540004.1|DV540004
EST:     ATGCGTATTATGTGTACTATTGCTATGCCAATCTGTATACACTGAACAAG                         CTTCGTGAGTCCAAGGGCATGACAACAATCAAACTTCGTCCACACTGTGGG
genomic: ATGCGTATTATGTGTACTATTGCTATGCCAATCTGTATACACTGAACAAGgtacatcttt ... gagagcgcagCTTCGTGAGTCCAAGGGCATGACAACAATCAAACTTCGTCCACACTGTGGG
EST: gi|211424039|gb|FL301691.1|FL301691
EST:     ATGCGTATTATGTGTACTATTGCTATGCCAATCTGTATACACTGAACAAG                         CTTCGTGAGTCCAAGGGCATGACAACAATCAAACTTCGTCCACACTGTGGG
genomic: ATGCGTATTATGTGTACTATTGCTATGCCAATCTGTATACACTGAACAAGgtacatcttt ... gagagcgcagCTTCGTGAGTCCAAGGGCATGACAACAATCAAACTTCGTCCACACTGTGGG

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: 236

AAAACACATGCCAACACCTGAGCAATGGACTAATATTTTCAATCCAGCCTATGCGTATTATGTGTACTATTGCTATGCCAATCTGTATACACTGAACAAGgtacatcttt ... gagagcgcagCTTCGTGAGTCCAAGGGCATGACAACAATCAAACTTCGTCCACACTGTGGGGAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 201

AAAACACATGCCAACACCTGAGCAATGGACTAATATTTTCAATCCAGCCTATGCGTATTATGTGTACTATTGCTATGCCAATCTGTATACACTGAACAAGgtacatcttt ... gagagcgcagCTTCGTGAGTCCAAGGGCATGACAACAATCAAACTTCGTCCACACTGTGGGGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 439

AAAACACATGCCAACACCTGAGCAATGGACTAATATTTTCAATCCAGCCTATGCGTATTATGTGTACTATTGCTATGCCAATCTGTATACACTGAACAAGgtacatcttt ... gagagcgcagCTTCGTGAGTCCAAGGGCATGACAACAATCAAACTTCGTCCACACTGTGGGGAG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 133

AAAACACATGCCAACACCTGAGCAATGGACTAATATTTTCAATCCAGCCTATGCGTATTATGTGTACTATTGCTATGCCAATCTGTATACACTGAACAAGgtacatcttt ... gagagcgcagCTTCGTGAGTCCAAGGGCATGACAACAATCAAACTTCGTCCACACTGTGGGGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caacattcatctggttaaattacaatggttaatttgaaatttgttgagagcgcagCTTCGTGAGTCCAAGGGCATGACAACAATCAAACTTCGTCCACACTGTGGGGAG
                          ggttaat  putative branch site (score: 133)
              ttaaattacaatggtt  TA-rich tract