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

GCAGACCAAGTTGCTCCAGCACACAACCACCATTTACTTGCACCACACTATTGTAGAGTTTGCAGAGGCACTCACCTCCAAAATGCCTGGCAATCTCAAGgtaaaagtaatgtctgtctgggtgcagtcataacacgcaccatttcatttatgtttttggatcctgcag

Basic information

species Zea mays
transcript GRMZM2G124353_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G124353_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os03g07570.1 (Oryza sativa), 5'ss of exon 2
GCAGACCAAGTTGCTCCAGCACACAACCACCATTTACTTGCACCACACTATTGTAGAGTTTGCAGAGGCACTCACCTCCAAAATGCCTGGCAATCTCAAGgtaaaagtaatgtctgtctgggtgcagtcataacacgcac--catttcatttatgtttttggatcctgcag------------------------
|||||||||| ||||||||||||| |||||||| || ||| | ||  | || || ||||||||||| || ||| | ||||| ||||| || ||||||||||| ||||  |  |     | | |   |   |||   | |   ||  ||||| || |   ||||       |                        
GCAGACCAAGCTGCTCCAGCACACGACCACCATATATTTGAATCAACCCATCGTCGAGTTTGCAGAAGCGCTCGCGTCCAAGATGCCAGGAAATCTCAAGgtcaaagatactttgaagtcgatcatgatgtaaattgtaaaacaactcattgatttgcatggaaataattgtttcatatctgaggatgcctgcag
















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|149029600|gb|EE154752.2|EE154752
EST:     TTGTAGAGTTTGCAGAGGCACTCACCTCCAAAATGCCTGGCAATCTCAAG                         GTTGCGTATTTTGTGAATTCTGGGACCGAAGCGAATGAGTTGGCAATGTTG
genomic: TTGTAGAGTTTGCAGAGGCACTCACCTCCAAAATGCCTGGCAATCTCAAGgtaaaagtaa ... gatcctgcagGTTGCGTATTTTGTGAATTCTGGGACCGAAGCGAATGAGTTGGCAATGTTG
EST: gi|67034943|gb|CO463476.1|CO463476
EST:     TTGTAGAGTTTGCAGAGGCACTCACCTCCAAAATGCCTGGCAATCTCAAG                         GTTGCGTATTTTGTGAATTCTGGGACTGAAGCGAATGAGTTGGCAATGTTG
genomic: TTGTAGAGTTTGCAGAGGCACTCACCTCCAAAATGCCTGGCAATCTCAAGgtaaaagtaa ... gatcctgcagGTTGCGTATTTTGTGAATTCTGGGACCGAAGCGAATGAGTTGGCAATGTTG
EST: gi|149042716|gb|EE047231.2|EE047231
EST:     TTGTAGAGTTTGCAGAGGCACTCACCTCCAAAATGCCTGGCAATCTCAAG                         GTTGCGTATTTTGTGAATTCTGGGACCGAAGCGAATGAGTTGGCAATGTTG
genomic: TTGTAGAGTTTGCAGAGGCACTCACCTCCAAAATGCCTGGCAATCTCAAGgtaaaagtaa ... gatcctgcagGTTGCGTATTTTGTGAATTCTGGGACCGAAGCGAATGAGTTGGCAATGTTG
EST: gi|148965746|gb|EE016621.2|EE016621
EST:     TTGTAGAGTTTGCAGAGGCACTCACCTCCAAAATGCCTGGCAATCTCAAG                         GTTGCGTATTTTGTGAATTCTGGGACCGAAGCGAATGAGTTGGCAATGTTG
genomic: TTGTAGAGTTTGCAGAGGCACTCACCTCCAAAATGCCTGGCAATCTCAAGgtaaaagtaa ... gatcctgcagGTTGCGTATTTTGTGAATTCTGGGACCGAAGCGAATGAGTTGGCAATGTTG
EST: gi|6626596|gb|AW258128.1|AW258128
EST:     TTGTAGAGTTTGCAGAGGCACTCACCTCCAAAATGCCTGGCAATCTCAAG                         GTTGCGTATTTTGTGAATTCTGGGACCGAAGCGAATGAGTTGGCAATGTTG
genomic: TTGTAGAGTTTGCAGAGGCACTCACCTCCAAAATGCCTGGCAATCTCAAGgtaaaagtaa ... gatcctgcagGTTGCGTATTTTGTGAATTCTGGGACCGAAGCGAATGAGTTGGCAATGTTG
EST: gi|20811243|gb|BQ295721.1|BQ295721
EST:     TTGTAGAGTTTGCAGAGGCACTCACCTCCAAAATGCCTGGCAATCTCAAG                         GTTGCGTATTTTGTGAATTCTGGGACCGAAGCGAATGAGTTGGCAATGCTG
genomic: TTGTAGAGTTTGCAGAGGCACTCACCTCCAAAATGCCTGGCAATCTCAAGgtaaaagtaa ... gatcctgcagGTTGCGTATTTTGTGAATTCTGGGACCGAAGCGAATGAGTTGGCAATGTTG
EST: gi|94472312|gb|EB701270.1|EB701270
EST:     TTGTAGAGTTTGCAGAGGCACTCACCTCCAAAATGCCTGGCAATCTCAAG                         GTTGCGTATTTTGTGAATTCTGGGACCGAAGCGAATGAGTTGGCAATGTTG
genomic: TTGTAGAGTTTGCAGAGGCACTCACCTCCAAAATGCCTGGCAATCTCAAGgtaaaagtaa ... gatcctgcagGTTGCGTATTTTGTGAATTCTGGGACCGAAGCGAATGAGTTGGCAATGTTG
EST: gi|148955020|gb|EC900523.2|EC900523
EST:     TTGTAGAGTTTGCAGAGGCACTCACCTCCAAAATGCCTGGCAATCTCAAG                         GTTGCGTATTTTGTGAATTCTGGGACCGAAGCGAATGAGTTGGCAATGTTG
genomic: TTGTAGAGTTTGCAGAGGCACTCACCTCCAAAATGCCTGGCAATCTCAAGgtaaaagtaa ... gatcctgcagGTTGCGTATTTTGTGAATTCTGGGACCGAAGCGAATGAGTTGGCAATGTTG
EST: gi|31910697|gb|CD651554.1|CD651554
EST:     TTGTAGAGTTTGCAGAGGCACTCACCTCCAAAATGCCTGGCAATCTCAAG                         GTTGCGTATTTTGTGAATTCTGGGACCGAAGCGAATGAGTTGGCAATGTTG
genomic: TTGTAGAGTTTGCAGAGGCACTCACCTCCAAAATGCCTGGCAATCTCAAGgtaaaagtaa ... gatcctgcagGTTGCGTATTTTGTGAATTCTGGGACCGAAGCGAATGAGTTGGCAATGTTG
EST: gi|5398767|gb|AI812232.1|AI812232
EST:     TTGTAGAGTTTGCAGAGGCACTCACCTCCAAAATGCCTGGCAATCTCAAG                         GTTGCGTATTTTGTGAATTCTGGGACCGAAGCGAATGAGTTGGCAATGTTG
genomic: TTGTAGAGTTTGCAGAGGCACTCACCTCCAAAATGCCTGGCAATCTCAAGgtaaaagtaa ... gatcctgcagGTTGCGTATTTTGTGAATTCTGGGACCGAAGCGAATGAGTTGGCAATGTTG
EST: gi|31350579|gb|CD434936.1|CD434936
EST:     TTGTAGAGTTTGCAGAGGCACTCACCTCCAAAATGCCTGGCAATCTCAAG                         GTTGCGTATTTTGTGAATTCTGGGACCGAAGCGAATGAGTTGGCAATGTTG
genomic: TTGTAGAGTTTGCAGAGGCACTCACCTCCAAAATGCCTGGCAATCTCAAGgtaaaagtaa ... gatcctgcagGTTGCGTATTTTGTGAATTCTGGGACCGAAGCGAATGAGTTGGCAATGTTG
EST: gi|14208236|gb|BG841914.1|BG841914
EST:     TTGTAGAGTTTGCAGAGGCACTCACCTCCAAAATGCCTGGCAATCTCAAG                         GTTGCGTATTTTGTGAATTCTGGGACCGAAGCGAATGAGTTGGCAATGTTG
genomic: TTGTAGAGTTTGCAGAGGCACTCACCTCCAAAATGCCTGGCAATCTCAAGgtaaaagtaa ... gatcctgcagGTTGCGTATTTTGTGAATTCTGGGACCGAAGCGAATGAGTTGGCAATGTTG
EST: gi|24934326|gb|CA452544.1|CA452544
EST:     TTGTAGAGTTTGCAGAGGCACTCACCTCCAAAATGCCTGGCAATCTCAAG                         GTTGCGTATTTTGTGAATTCTGGGACTGAAGCGAATGAGTTGGCAATGTTG
genomic: TTGTAGAGTTTGCAGAGGCACTCACCTCCAAAATGCCTGGCAATCTCAAGgtaaaagtaa ... gatcctgcagGTTGCGTATTTTGTGAATTCTGGGACCGAAGCGAATGAGTTGGCAATGTTG
EST: gi|148929128|gb|EC874538.2|EC874538
EST:     TTGTAGAGTTTGCAGAGGCACTCACCTCCAAAATGCCTGGCAATCTCAAG                         GTTGCGTATTTTGTGAATTCTGGGACCGAAGCGAATGAGTTGGCAATGTTG
genomic: TTGTAGAGTTTGCAGAGGCACTCACCTCCAAAATGCCTGGCAATCTCAAGgtaaaagtaa ... gatcctgcagGTTGCGTATTTTGTGAATTCTGGGACCGAAGCGAATGAGTTGGCAATGTTG

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), 49 (downstream exon)
Score: 505

GCAGACCAAGTTGCTCCAGCACACAACCACCATTTACTTGCACCACACTATTGTAGAGTTTGCAGAGGCACTCACCTCCAAAATGCCTGGCAATCTCAAGgtaaaagtaa ... gatcctgcagGTTGCGTATTTTGTGAATTCTGGGACCGAAGCGAATGAGTTGGCAATGTTGATGGCCCGGCTGTATAGTGGGAATCTCAGTATGGTTGCGCTCAGAAATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 751

GCAGACCAAGTTGCTCCAGCACACAACCACCATTTACTTGCACCACACTATTGTAGAGTTTGCAGAGGCACTCACCTCCAAAATGCCTGGCAATCTCAAGgtaaaagtaa ... gatcctgcagGTTGCGTATTTTGTGAATTCTGGGACCGAAGCGAATGAGTTGGCAATGTTGATGGCCCGGCTGTATAGTGGGAATCTCAGTATGGTTGCGCTCAGAAATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 617

GCAGACCAAGTTGCTCCAGCACACAACCACCATTTACTTGCACCACACTATTGTAGAGTTTGCAGAGGCACTCACCTCCAAAATGCCTGGCAATCTCAAGgtaaaagtaa ... gatcctgcagGTTGCGTATTTTGTGAATTCTGGGACCGAAGCGAATGAGTTGGCAATGTTGATGGCCCGGCTGTATAGTGGGAATCTCAGTATGGTTGCGCTCAGAAATG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 484

GCAGACCAAGTTGCTCCAGCACACAACCACCATTTACTTGCACCACACTATTGTAGAGTTTGCAGAGGCACTCACCTCCAAAATGCCTGGCAATCTCAAGgtaaaagtaa ... gatcctgcagGTTGCGTATTTTGTGAATTCTGGGACCGAAGCGAATGAGTTGGCAATGTTGATGGCCCGGCTGTATAGTGGGAATCTCAGTATGGTTGCGCTCAGAAATG