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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAAAAGATTGGCTGTCACTAGTCGCGGTGCACAGTGATGCTTGGTTGCTGGCTGTGGCCTTTTACTTCGGTGCAAGATTTGGTTTTGACAAAGAATCCAGgtattgtttttgctgctgctctatttctaaggatttcttatgttctggaaacaaatcttgttgttaccatatgctgcttccattatgtttataccagtac...

Basic information

species Zea mays
transcript GRMZM2G008259_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G008259_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os11g14010.2 (Oryza sativa), 5'ss of exon 2
AAAAAGATTGGCTGTCACTAGTCGCGGTGCACAGTGATGCTTGGTTGCTGGCTGTGGCCTTTTACTTCGGTGCAAGATTTGGTTTTGACAAAGAATCCAGgtattgtttttgctgctgc------tctatttctaaggatttcttatgttctggaaacaaatcttgttgttaccatatgctgcttccattatgtttataccagtac
| ||||||||||||||||| || ||||| || |||||| | ||| |||| || || ||||||||||| || |||||||| || |||||||||||||||||||| | | |||| || |        |  | || | |   |   ||   |   |      ||| | ||| |  |  |   ||  ||  | ||| ||  |        
AGAAAGATTGGCTGTCACTTGTTGCGGTTCATAGTGATACCTGGCTGCTAGCAGTAGCCTTTTACTTTGGAGCAAGATTCGGGTTTGACAAAGAATCCAGgtactatatttgttgttctggggcatacaattttgattgtcagttgcttgtggttgttcaatgtggtttt--ctgtcccctatttttaatatattgttcttg----
















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|78544063|gb|DV621561.1|DV621561
EST:     CAAGATTTGGTTTTGACAAAGAATCCAG                         GAAGCGTCTTTTTGTCATGATTAATAACCTCCCTACAATATATGAAGTTGT
genomic: CAAGATTTGGTTTTGACAAAGAATCCAGgtattgtttt ... attgctgcagGAAGCGCCTTTTTGTCATGATTAATAACCTCCCTACAATATATGAAGTTGT
EST: gi|60341456|gb|DN208429.1|DN208429
EST:     GCTGTGGCCTTTTACTTCGGTGCAAGATTTGGTTTTGACAAAGAATCCAG                         GAAGCGCCTTTTTGTCATGATTAATAACCTCCCTACAATATATGAAGTTGT
genomic: GCTGTGGCCTTTTACTTCGGTGCAAGATTTGGTTTTGACAAAGAATCCAGgtattgtttt ... attgctgcagGAAGCGCCTTTTTGTCATGATTAATAACCTCCCTACAATATATGAAGTTGT
EST: gi|19770428|gb|BQ035149.1|BQ035149
EST:     GCTGTGGCCTTTTACTTCGGTGCAAGATTCGGTTTTGACAAAGAATCCAG                         GAAGCGCCTTTTTGTCATGATTAATAACCTCCCTACAATATATGAAGTTGT
genomic: GCTGTGGCCTTTTACTTCGGTGCAAGATTTGGTTTTGACAAAGAATCCAGgtattgtttt ... attgctgcagGAAGCGCCTTTTTGTCATGATTAATAACCTCCCTACAATATATGAAGTTGT
EST: gi|78544023|gb|DV621521.1|DV621521
EST:     GATTTGGTTTTGACAAAGAATCCAG                         GAAGCGTCTTTTTGTCATGATTAATAACCTCCCTACAATATATGAAGTTGT
genomic: GATTTGGTTTTGACAAAGAATCCAGgtattgtttt ... attgctgcagGAAGCGCCTTTTTGTCATGATTAATAACCTCCCTACAATATATGAAGTTGT
EST: gi|27522015|gb|CA989121.1|CA989121
EST:     GCTGTGGCCTTTTACTTCGGTGCAAGATTTGGTTTTGACAAAGAATCCAG                         GAAGCGCCTTTTTGTCATGATTAATAACCTCCCTACAATATATGAAGTTGT
genomic: GCTGTGGCCTTTTACTTCGGTGCAAGATTTGGTTTTGACAAAGAATCCAGgtattgtttt ... attgctgcagGAAGCGCCTTTTTGTCATGATTAATAACCTCCCTACAATATATGAAGTTGT
EST: gi|26455859|gb|CA827442.1|CA827442
EST:     GCTGTGGCCTTTTACTTCGGTGCAAGATTTGGTTTTGACAAAGAATCCAG                         GAAGCGTCTTTTTGTCATGATTAATAACCTCCCTACAATATATGAAGTTGT
genomic: GCTGTGGCCTTTTACTTCGGTGCAAGATTTGGTTTTGACAAAGAATCCAGgtattgtttt ... attgctgcagGAAGCGCCTTTTTGTCATGATTAATAACCTCCCTACAATATATGAAGTTGT
EST: gi|19822278|gb|BQ048302.1|BQ048302
EST:     GCTGTGGCCTTTTACTTCGGTGCAAGATTTGGTTTTGACAAAGAATCCAG                         GAAGCGTCTTTTTGTCATGATTAATAACCTCCCTACAATATATGAAGTTGT
genomic: GCTGTGGCCTTTTACTTCGGTGCAAGATTTGGTTTTGACAAAGAATCCAGgtattgtttt ... attgctgcagGAAGCGCCTTTTTGTCATGATTAATAACCTCCCTACAATATATGAAGTTGT
EST: gi|50337531|gb|CO532657.1|CO532657
EST:     TTTTGACAAAGAATCCAG                         GAAGCGCCTTTTTGTCATGATTAATAACCTCCCTACAATATATGAAGTTGT
genomic: TTTTGACAAAGAATCCAGgtattgtttt ... attgctgcagGAAGCGCCTTTTTGTCATGATTAATAACCTCCCTACAATATATGAAGTTGT
EST: gi|149106606|gb|EE188499.2|EE188499
EST:     GCTGTGGCCTTTTACTTCGGTGCAAGATTTGGTTTTGACAAAGAATCCAG                         GAAGCGCCTTTTTGTCATGATTAATAACCTCCCTACAATATATGAAGTTGT
genomic: GCTGTGGCCTTTTACTTCGGTGCAAGATTTGGTTTTGACAAAGAATCCAGgtattgtttt ... attgctgcagGAAGCGCCTTTTTGTCATGATTAATAACCTCCCTACAATATATGAAGTTGT
EST: gi|211244489|gb|FL128350.1|FL128350
EST:     GCTGTGGCCTTTTACTTCGGTGCAAGATTTGGTTTTGACAAAGAATCCAG                         GAAGCGCCTTTTTGTCATGATTAATAACCTCCCTACAATATATGAAGTTGT
genomic: GCTGTGGCCTTTTACTTCGGTGCAAGATTTGGTTTTGACAAAGAATCCAGgtattgtttt ... attgctgcagGAAGCGCCTTTTTGTCATGATTAATAACCTCCCTACAATATATGAAGTTGT
EST: gi|22546373|gb|BU098684.1|BU098684
EST:     GCCTTTTACTTCGGTGCAAGATTTGGTTTTGACAAAGAATCCAG                         GAAGCGTCTTTTTGTCATGATTAATAACCTCCCTACAATATATGAAGTTGT
genomic: GCCTTTTACTTCGGTGCAAGATTTGGTTTTGACAAAGAATCCAGgtattgtttt ... attgctgcagGAAGCGCCTTTTTGTCATGATTAATAACCTCCCTACAATATATGAAGTTGT

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
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAAAAGATTGGCTGTCACTAGTCGCGGTGCACAGTGATGCTTGGTTGCTGGCTGTGGCCTTTTACTTCGGTGCAAGATTTGGTTTTGACAAAGAATCCAGgtattgtttttgctgctgctctatttctaaggatttcttatgttctggaaacaaatcttgttgttaccatatgctgcttccattatgtttataccagtac

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaaacaaa