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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAATTGTCGGATCAGTACTTACAGGCGGTGAGTTTGGCCTTCCCGACTTCAGGGATGCAATCTCTGGTGCTTTCAAGgtctcatcaccccctgccctatctctctgcatgcctcttcttttaagactttaggcatcagcttctccctcccctccttaaattaatttgatataagctagttttacctcacacctactttatcctcctgtctttag

Basic information

species Zea mays
transcript GRMZM2G147587_T01
intron # 2
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|71766303|gb|DR964240.1|DR964240
EST:     GTGAGTTTGGCCTTCCCGACTTCAGGGATGCAATCTCTGGTGCTTTCAAG                         TTCTTGACCAAGAGTGCAAAGCCAGGCAAGGATGGGCCGTCTACCAGCAGT
genomic: GTGAGTTTGGCCTTCCCGACTTCAGGGATGCAATCTCTGGTGCTTTCAAGgtctcatcac ... ctgtctttagTTCTTGACCAAGAGTGCAAAGCCAGGCAAGGATGGGCCGTCTACCAGCAGT
EST: gi|71429464|gb|DR810514.1|DR810514
EST:     GTGAGTTTGGCCTTCCCGACTTCAGGGATGCAATCTCTGGTGCTTTCAAG                         TTCTTGACCAAGAGTGCAAAGCCAGGCAAGGATGGGCCGTCTACCAGCAGT
genomic: GTGAGTTTGGCCTTCCCGACTTCAGGGATGCAATCTCTGGTGCTTTCAAGgtctcatcac ... ctgtctttagTTCTTGACCAAGAGTGCAAAGCCAGGCAAGGATGGGCCGTCTACCAGCAGT
EST: gi|32931585|gb|CF036397.1|CF036397
EST:     GTGAGTTTGGCCTTCCCGACTTCAGGGATGCAATCTCTGGTGCTTTCAAG                         TTCTTGACCAAGAGTGCAAAGCCAGGCAAGGATGGGCCGTCTACCAGCAGT
genomic: GTGAGTTTGGCCTTCCCGACTTCAGGGATGCAATCTCTGGTGCTTTCAAGgtctcatcac ... ctgtctttagTTCTTGACCAAGAGTGCAAAGCCAGGCAAGGATGGGCCGTCTACCAGCAGT

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: 153

GAATTGTCGGATCAGTACTTACAGGCGGTGAGTTTGGCCTTCCCGACTTCAGGGATGCAATCTCTGGTGCTTTCAAGgtctcatcac ... ctgtctttagTTCTTGACCAAGAGTGCAAAGCCAGGCAAGGATGGGCCGTCTACCAGCAGTCCACATACTGCTGAGTTGTTCAGCCAG


Block sizes: 46 (upstream exon), 46 (downstream exon)
Score: 147

GAATTGTCGGATCAGTACTTACAGGCGGTGAGTTTGGCCTTCCCGACTTCAGGGATGCAATCTCTGGTGCTTTCAAGgtctcatcac ... ctgtctttagTTCTTGACCAAGAGTGCAAAGCCAGGCAAGGATGGGCCGTCTACCAGCAGTCCACATACTGCTGAGTTGTTCAGCCAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 129

GAATTGTCGGATCAGTACTTACAGGCGGTGAGTTTGGCCTTCCCGACTTCAGGGATGCAATCTCTGGTGCTTTCAAGgtctcatcac ... ctgtctttagTTCTTGACCAAGAGTGCAAAGCCAGGCAAGGATGGGCCGTCTACCAGCAGTCCACATACTGCTGAGTTGTTCAGCCAG


Block sizes: 46 (upstream exon), 47 (downstream exon)
Score: 138

GAATTGTCGGATCAGTACTTACAGGCGGTGAGTTTGGCCTTCCCGACTTCAGGGATGCAATCTCTGGTGCTTTCAAGgtctcatcac ... ctgtctttagTTCTTGACCAAGAGTGCAAAGCCAGGCAAGGATGGGCCGTCTACCAGCAGTCCACATACTGCTGAGTTGTTCAGCCAG