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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaagagcgagaccaccctgcccttcccgccccgcgttcccttgacacctctccagcttccaacaccccctcttgtgccggcgcagAAGAAGGACTCCTTTGAGTCGCTGGTGATGGAGCACATCCGCCTCAACGGCGCCTACTGGGGCCTCACCACGCTCGACCTCCTCCACAAGCTCCATGCCG

Basic information

species Zea mays
transcript GRMZM2G124557_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G124557_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os08g40140.1 (Oryza sativa), 3'ss of exon 1
gtaaagagcgagaccaccctgcccttcccgccccgcgttcccttgacacctctccagcttccaacaccccctcttgtgccggcgcagAAGAAGGACTCCTTTGAGTCGCTGGTGATGGAGCACATCCGCCTCAACGGCGCCTACTGGGGCCTCACCACGCTCGACCTCCTCCACAAGCTCCATGCCG
               |  | |||  || | |  | || | |   | |   |    |            | ||  ||    |  ||||| ||||||||| || |||||||||||||||||||||||||| ||||||||||| ||||||||||||||||||||||||||||||||||||||||  ||||
-------------gtaggccgcctctcgctctgctcgatgcagcggctgattctgattggatggtcttcgctgctgctgtgatgcagAGGAAGGACTCGTTCGAGTCGCTGGTGATGGAGCACATCCGGCTCAACGGCGCGTACTGGGGCCTCACCACGCTCGACCTCCTCCACAAGCTCCGCGCCG
















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|74242769|gb|DT650683.1|DT650683
EST:     TGGAGCTTGCTGCGGACCAGCACGTCCGCTACATCGTCACGGTGGAGAAG                         AAGAAGGACTCCTTTGAATCGCTGGTGATGGAGCACATCCGCCTCAACGGC
genomic: TGGAGCTTGCTGCGGACCAGCACGTCCGCTACATCGTCACGGTGGAGAAGgtaaagagcg ... gccggcgcagAAGAAGGACTCCTTTGAGTCGCTGGTGATGGAGCACATCCGCCTCAACGGC
EST: gi|19436989|gb|BM953399.1|BM953399
EST:     CACGTCCGCTACATCGTCACGGTGGAGAAG                         AAGAAGGACTCCTTTGAGTCGCTGGTGATGGAGCACATCCGCCTCAATGGC
genomic: CACGTCCGCTACATCGTCACGGTGGAGAAGgtaaagagcg ... gccggcgcagAAGAAGGACTCCTTTGAGTCGCTGGTGATGGAGCACATCCGCCTCAACGGC
EST: gi|76910998|gb|DV164124.1|DV164124
EST:     TGGAGCTTGCTGCGGACCAGCACGTCCGCTACATCGTCACGGTGGAGAAG                         AAGAAGGACTCCTTTGAGTCGCTGGTGATGGAGCACATCCGCCTCAACGGC
genomic: TGGAGCTTGCTGCGGACCAGCACGTCCGCTACATCGTCACGGTGGAGAAGgtaaagagcg ... gccggcgcagAAGAAGGACTCCTTTGAGTCGCTGGTGATGGAGCACATCCGCCTCAACGGC
EST: gi|78080907|gb|DV509319.1|DV509319
EST:     TGGAGCTTGCTGCGGACCAGCACGTCCGCTACATCGTCACGGTGGAGAAG                         AAGAAGGACTCCTTTGAGTCGCTGGTGATGGAGCACATC
genomic: TGGAGCTTGCTGCGGACCAGCACGTCCGCTACATCGTCACGGTGGAGAAGgtaaagagcg ... gccggcgcagAAGAAGGACTCCTTTGAGTCGCTGGTGATGGAGCACATC
EST: gi|71443999|gb|DR825049.1|DR825049
EST:     TGGAGCTTGCTGCGGACCAGCACGTCCGCTACATCGTCACGGTGGAGAAG                         AAGAAGGACTCCTTTGAGTCGCTGGTGATGGAGCACATCCGCCT
genomic: TGGAGCTTGCTGCGGACCAGCACGTCCGCTACATCGTCACGGTGGAGAAGgtaaagagcg ... gccggcgcagAAGAAGGACTCCTTTGAGTCGCTGGTGATGGAGCACATCCGCCT
EST: gi|78093295|gb|DV521669.1|DV521669
EST:     TGGAGCTTGCTGCGGACCAGCACGTCCGCTACATCGTCACGGTGGAGAAG                         AAGAAGGACTCCTTTGAGTCGCTGGTGATGGAGCACATCTGCCTCAACGGC
genomic: TGGAGCTTGCTGCGGACCAGCACGTCCGCTACATCGTCACGGTGGAGAAGgtaaagagcg ... gccggcgcagAAGAAGGACTCCTTTGAGTCGCTGGTGATGGAGCACATCCGCCTCAACGGC
EST: gi|89762555|gb|DY690082.1|DY690082
EST:     TGGAGCTTGCTGCGGACCAGCACGTCCGCTACATCGTCACGGTGGAGAAG                         AAGAAGGACTCCTTTGAGTCGCTGGTGATGGAGCACATCCGCCTCAACGGC
genomic: TGGAGCTTGCTGCGGACCAGCACGTCCGCTACATCGTCACGGTGGAGAAGgtaaagagcg ... gccggcgcagAAGAAGGACTCCTTTGAGTCGCTGGTGATGGAGCACATCCGCCTCAACGGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccgcgttcccttgacacctctccagcttccaacaccccctcttgtgccggcgcagAAGAAGGACTCCTTTGAGTCGCTGGTGATGGAGCACATCCGCCTCAACGGCGCCTACTGGGGCCTCACCACGCTCGACCTCCTCCACAAGCTCCATGCCG
        ccttgac  putative branch site (score: 4)
                                  ccccctcttgtgcc  putative PPT
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaagagcgagaccaccctgcccttcccgccccgcgttcccttgacacctctccagcttccaacaccccctcttgtgccggcgcagAAGAAGGACTCCTTTGAGTCGCTGGTGATGGAGCACATCCGCCTCAACGGCGCCTACTGGGGCCTCACCACGCTCGACCTCCTCCACAAGCTCCATGCCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT