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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtatgcatctctttatcatttgttattattgtgatatatcatcctcttttgtggaactagatgtgaaactcaagtatagttgaatgtctcttattaagctaaagtttctgtgtgcgaacgtgaaacttgcagATTTCTCCCTGCCCCTGATGATATGTTGGCACTTGACATAGCATATACCATCTACATGAAGTTTGGAGACCTTGCAAGCGCTTTGAGAATTTCTCTGCAG

Basic information

species Zea mays
transcript GRMZM2G155384_T03
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G155384_T01 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os02g05340.1 (Oryza sativa), 3'ss of exon 9
---------------------------------------------------------gtaa-gtatgcatctctttatcat--ttgttattattgtgatatatcat--cctcttttgtggaactagatgtgaaactcaagtatagttgaatgtctctt--attaagctaaagtttctgtgtgcgaacgtgaaacttgcagATTTCTCCCTGCCCCTGATGATATGTTGGCACTTGACATAGCATATACCATCTACATGAAGTTTGGAGACCTTGCAAGCGCTTTGAGAATTTCTCTGCAG
                                                         ||   |||| | | | | |    |   |  | |  |  | || |  ||     || || | | | ||  || |   |||  |||   ||| ||| ||  ||  ||| |  |||    |   | |  ||| || ||||   |||||  |||||||| |||||||| |||||||| |||||||| || |||||||| ||||||||||||| ||||||| |||| |||||| | ||| ||||||  
gtatgtaaacacatttttgttttgttttttgcctccattatatgtctctttttccacgtgttgtatacttttttatgctgtagatcctgtggtcctaatctggcaagatttccttggagtagctgaattttgtactttagt---gttaaatttcaattgaattgaattaatagctgcatctttgaatgtaaaacc-acagATACCTCCCTGCTCCTGATGACATGTTGGCGCTTGACATTGCTTATACCATTTACATGAAGTTTGAAGACCTTACAAGTGCTTTGCGGATTGCTCTGCTC
















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|33093842|gb|CF053836.1|CF053836
EST:     ACCTGACTAGTTCATCCAA                         ATTTCTCCCTGCCCCTGATGATATGTTGGCACTTGACACAGCATATACCAT
genomic: ACCTGACTAGTTCATCCAAgtaagtatgc ... aaacttgcagATTTCTCCCTGCCCCTGATGATATGTTGGCACTTGACATAGCATATACCAT
EST: gi|32832565|gb|CD972243.1|CD972243
EST:     ACCTGACTAGTTCATCCAA                         ATTTCTCCCTGCCCCTGATGATATGTTGGCACTTGACATAGCATATACCAT
genomic: ACCTGACTAGTTCATCCAAgtaagtatgc ... aaacttgcagATTTCTCCCTGCCCCTGATGATATGTTGGCACTTGACATAGCATATACCAT
EST: gi|32834497|gb|CD974175.1|CD974175
EST:     GTACCTGACTAGTTCATCCAA                         ATTTCTCCCTGCCCCTGATGATATGTTGGCACTTGACATAGCATATACCAT
genomic: GTACCTGACTAGTTCATCCAAgtaagtatgc ... aaacttgcagATTTCTCCCTGCCCCTGATGATATGTTGGCACTTGACATAGCATATACCAT
EST: gi|32833976|gb|CD973654.1|CD973654
EST:     ACCTGACTAGTTCATCCAA                         ATTTCTCCCTGCCCCTGATGATATGTTGGCACTTGACATAGCATATACCAT
genomic: ACCTGACTAGTTCATCCAAgtaagtatgc ... aaacttgcagATTTCTCCCTGCCCCTGATGATATGTTGGCACTTGACATAGCATATACCAT
EST: gi|32835155|gb|CD974833.1|CD974833
EST:     GTACCTGACTAGTTCATCCAA                         ATTTCTCCCTGCCCCTGATGATATGTTGGCACTTGACATAGCATATACCAT
genomic: GTACCTGACTAGTTCATCCAAgtaagtatgc ... aaacttgcagATTTCTCCCTGCCCCTGATGATATGTTGGCACTTGACATAGCATATACCAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agttgaatgtctcttattaagctaaagtttctgtgtgcgaacgtgaaacttgcagATTTCTCCCTGCCCCTGATGATATGTTGGCACTTGACATAGCATATACCATCTACATGAAGTTTGGAGACCTTGCAAGCGCTTTGAGAATTTCTCTGCAG
                   agctaaa  putative branch site (score: 3)
           tcttattaa  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtatgcatctctttatcatttgttattattgtgatatatcatcctcttttgtggaactagatgtgaaactcaagtatagttgaatgtctcttattaagctaaagtttctgtgtgcgaacgtgaaacttgcagATTTCTCCCTGCCCCTGATGATATGTTGGCACTTGACATAGCATATACCATCTACATGAAGTTTGGAGACCTTGCAAGCGCTTTGAGAATTTCTCTGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG