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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTCTTGCCATGCTACATGAAGCTGATTTCCATGTTGATATTGATGTGAGTGACAGGACAATACAAAAGAAGgtacttcccagttaccatgctcttttaggcttttgcaccgtttattttaatttcttctgtttgtttgttcgtcctttcttatacaaaaattatcaatcat...

Basic information

species Zea mays
transcript GRMZM2G137615_T01
intron # 7
splice site 5'
intron type U2

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|213172391|gb|FM188594.1|FM188594
EST:     CTGATTTCCATGTTGATATTGATGTGAGTGACAGGACAATACAAAAGAAG                         GTACGGGAAGCCCAGGTAGCTCAATTCAACTACATTCTTGTCGTA-GCGCA
genomic: CTGATTTCCATGTTGATATTGATGTGAGTGACAGGACAATACAAAAGAAGgtacttccca ... aatcttgcagGTACGGGAAGCCCAGGTAGCTCAATTCAACTACATTCTTGTCGTAGGCGCA
EST: gi|211198162|gb|FL344190.1|FL344190
EST:     CTGATTTCCATGTTGATATTGATGTGAGTGACAGGACAATACAAAAGAAG                         GTACGGGAAGCCCAGGTAGCTCAATTCAACTACATTCTTGTCGTANGCGCA
genomic: CTGATTTCCATGTTGATATTGATGTGAGTGACAGGACAATACAAAAGAAGgtacttccca ... aatcttgcagGTACGGGAAGCCCAGGTAGCTCAATTCAACTACATTCTTGTCGTAGGCGCA
EST: gi|32911351|gb|CF016163.1|CF016163
EST:     GTTGATATTGATGTGAGTGACAGGACAATACAAAAGAAG                         GTACGGGAAGCCCAGGTAGCTCAATTCAACTACATTCTTGTCGTAGGCGCA
genomic: GTTGATATTGATGTGAGTGACAGGACAATACAAAAGAAGgtacttccca ... aatcttgcagGTACGGGAAGCCCAGGTAGCTCAATTCAACTACATTCTTGTCGTAGGCGCA
EST: gi|5791229|gb|AI978021.1|AI978021
EST:     CTGATTTCCATGTTGATATTGATGTGAGTGACAGGACAATACAAAAGAAG                         GTACGGGAAGCCCAGGTAGCTCAATTCAACTACATTCTTGTCGTAGGCGCA
genomic: CTGATTTCCATGTTGATATTGATGTGAGTGACAGGACAATACAAAAGAAGgtacttccca ... aatcttgcagGTACGGGAAGCCCAGGTAGCTCAATTCAACTACATTCTTGTCGTAGGCGCA
EST: gi|60337159|gb|DN204132.1|DN204132
EST:     CTGATTTCCATGTTGATATTGATGTGAGTGACAGGACAATACAAAAGAAG                         GTACGGGAAGCCCAGGTAGCTCAATTCAACTACATTCTTGTCGTAGGCGCA
genomic: CTGATTTCCATGTTGATATTGATGTGAGTGACAGGACAATACAAAAGAAGgtacttccca ... aatcttgcagGTACGGGAAGCCCAGGTAGCTCAATTCAACTACATTCTTGTCGTAGGCGCA
EST: gi|211513903|gb|FL285080.1|FL285080
EST:     CTGATTTCCATGTTGATATTGATGTGAGTGACAGGACAATACAAAAGAAG                         GTACGGGAAGCCCAGGTAGCTCAATTCAACTACATTCTTGTCGTAGGCGCA
genomic: CTGATTTCCATGTTGATATTGATGTGAGTGACAGGACAATACAAAAGAAGgtacttccca ... aatcttgcagGTACGGGAAGCCCAGGTAGCTCAATTCAACTACATTCTTGTCGTAGGCGCA
EST: gi|30052636|gb|AI065926.2|AI065926
EST:     CTGATTTCCATGTTGATATTGATGTGAGTGACAGGACAATACAAAAGAAG                         GTACGGGAAGCCCAGGTAGCTCAATTCAACTACATTCTTGTCGTAGGCGCA
genomic: CTGATTTCCATGTTGATATTGATGTGAGTGACAGGACAATACAAAAGAAGgtacttccca ... aatcttgcagGTACGGGAAGCCCAGGTAGCTCAATTCAACTACATTCTTGTCGTAGGCGCA
EST: gi|71770369|gb|DR968306.1|DR968306
EST:     CTGATTTCCATGTTGATATTGATGTGAGTGACAGGACAATACAAAAGAAG                         GTACGGGAAGCCCAGGTAGCTCAATTCAACTACATTCTTGTCGTAGGCGCA
genomic: CTGATTTCCATGTTGATATTGATGTGAGTGACAGGACAATACAAAAGAAGgtacttccca ... aatcttgcagGTACGGGAAGCCCAGGTAGCTCAATTCAACTACATTCTTGTCGTAGGCGCA

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), 46 (downstream exon)
Score: 185

GTTCTTGCCATGCTACATGAAGCTGATTTCCATGTTGATATTGATGTGAGTGACAGGACAATACAAAAGAAGgtacttccca ... aatcttgcagGTACGGGAAGCCCAGGTAGCTCAATTCAACTACATTCTTGTCGTAGGCGCACAGGAGGCCGAGACTGGAAAT


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 151

GTTCTTGCCATGCTACATGAAGCTGATTTCCATGTTGATATTGATGTGAGTGACAGGACAATACAAAAGAAGgtacttccca ... aatcttgcagGTACGGGAAGCCCAGGTAGCTCAATTCAACTACATTCTTGTCGTAGGCGCACAGGAGGCCGAGACTGGAAAT


Block sizes: 49 (upstream exon), 33 (downstream exon)
Score: 144

GTTCTTGCCATGCTACATGAAGCTGATTTCCATGTTGATATTGATGTGAGTGACAGGACAATACAAAAGAAGgtacttccca ... aatcttgcagGTACGGGAAGCCCAGGTAGCTCAATTCAACTACATTCTTGTCGTAGGCGCACAGGAGGCCGAGACTGGAAAT


Block sizes: 49 (upstream exon), 33 (downstream exon)
Score: 107

GTTCTTGCCATGCTACATGAAGCTGATTTCCATGTTGATATTGATGTGAGTGACAGGACAATACAAAAGAAGgtacttccca ... aatcttgcagGTACGGGAAGCCCAGGTAGCTCAATTCAACTACATTCTTGTCGTAGGCGCACAGGAGGCCGAGACTGGAAAT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTCTTGCCATGCTACATGAAGCTGATTTCCATGTTGATATTGATGTGAGTGACAGGACAATACAAAAGAAGgtacttcccagttaccatgctcttttaggcttttgcaccgtttattttaatttcttctgtttgtttgttcgtcctttcttatacaaaaattatcaatcat

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - acaaaaat