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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctatttctcgcccctctctctctcaagttctcattgtgcacaatggatgttatggctgatctccatgtaccttgttgaagGCCGGGTGACACCATTCTTATTGCGGCTGGTGGTTCCCATGTTGCATGTAACATCCAAATAAAGAAGCCTATTTGCATAGTAAGTTTTGCCTACCATGTC

Basic information

species Zea mays
transcript GRMZM2G009021_T03
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G009021_T03 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os07g46555.1 (Oryza sativa), 3'ss of exon 2
-------gtctatttctcgcccctctctctctcaagttctcattgtgcacaatggatgttatggctgatctccatgtaccttgt--tgaagGCCGGGTGACACCATTCTTATTGCGGCTGGTGGTTCCCATGTTGCATGTAACATCCAAATAAAGAAGCCTATTTGCATAGTAAGTTTTGCCTACCATGTC
        ||||| |  |    |  | |   | | ||| | |  | |    |||| | |||||| ||| ||  || | | ||||  | |||||| || || || ||||| ||||| ||||||||  | ||||||||| |||| |||||||||||||||||| | |||||                      
gtccgtgttctatctgactgttcaatgttcattatgttat-agagggggttatgg-tcttatggatgacctttatttgcgttgttttaaagGCCTGGGGATACTATTCTAATTGCTGCTGGTGGCACACATGTTGCACGTAATATCCAAATAAAGAAGCCTCTCTGCATT---------------------
















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|211342147|gb|FL091795.1|FL091795
EST:     ATGGAGCCTGGAGTTTATCCAGATCTCGAGGCTGCTGTTTCTGCTGCTAG                         GCCGGGTGACACCATTCTTATTGCGGCTGGTGGTTCCCATGTTGCATGTAA
genomic: ATGGAGCCTGGAGTTTATCCAGATCTCGAGGCTGCTGTTTCTGCTGCTAGgtctatttct ... cttgttgaagGCCGGGTGACACCATTCTTATTGCGGCTGGTGGTTCCCATGTTGCATGTAA
EST: gi|211116626|gb|FL123093.1|FL123093
EST:     ATGGAGCCTGGAGTTTATCCAGATCTCGAGGCTGCTGTTTCTGCTGCTAG                         GCCGGGTGACACCATTCTTATTGCGGCTGGTGGTTCCCATGTTGCATGTAA
genomic: ATGGAGCCTGGAGTTTATCCAGATCTCGAGGCTGCTGTTTCTGCTGCTAGgtctatttct ... cttgttgaagGCCGGGTGACACCATTCTTATTGCGGCTGGTGGTTCCCATGTTGCATGTAA
EST: gi|211117410|gb|FL123097.1|FL123097
EST:     ATGGAGCCTGGAGTTTATCCAGATCTCGAGGCTGCTGTTTCTGCTGCTAG                         GCCGGGTGACACCATTCTTATTGCGGCTGGTGGTTCCCATGTTGCATGTWA
genomic: ATGGAGCCTGGAGTTTATCCAGATCTCGAGGCTGCTGTTTCTGCTGCTAGgtctatttct ... cttgttgaagGCCGGGTGACACCATTCTTATTGCGGCTGGTGGTTCCCATGTTGCATGTAA
EST: gi|211116627|gb|FL123094.1|FL123094
EST:     ATGGAGCCTGGAGTTTATCCAGATCTCGAGGCTGCTGTTTCTGCTGCTAG                         GCCGGGTGACACCATTCTTATTGCGGCTGGTGGTTCCCATGTTGCATGTAA
genomic: ATGGAGCCTGGAGTTTATCCAGATCTCGAGGCTGCTGTTTCTGCTGCTAGgtctatttct ... cttgttgaagGCCGGGTGACACCATTCTTATTGCGGCTGGTGGTTCCCATGTTGCATGTAA
EST: gi|211117409|gb|FL123096.1|FL123096
EST:     ATGGAGCCTGGAGTTTATCCAGATCTCGARGCTGCTGTTTCTGCTGCTAG                         GCCGGGTGACACCATTCTTATTGCGGCTGGTGGTTCCCATGTTGCATGTAA
genomic: ATGGAGCCTGGAGTTTATCCAGATCTCGAGGCTGCTGTTTCTGCTGCTAGgtctatttct ... cttgttgaagGCCGGGTGACACCATTCTTATTGCGGCTGGTGGTTCCCATGTTGCATGTAA
EST: gi|76286278|gb|DV025846.1|DV025846
EST:     ATGGAGCCTGGAGTTTATCCAGATCTCGAGGCTGCTGTTTCTGCTGCTAG                         GCCGGGTGACACCATTCTTATTGCGGCTGGTGGTTCCCATGTTGCATGTAA
genomic: ATGGAGCCTGGAGTTTATCCAGATCTCGAGGCTGCTGTTTCTGCTGCTAGgtctatttct ... cttgttgaagGCCGGGTGACACCATTCTTATTGCGGCTGGTGGTTCCCATGTTGCATGTAA
EST: gi|211344536|gb|FL091804.1|FL091804
EST:     ATGGASCCTGGAGTTTATCCTGATCTCGAGGCTGCTGTTTCTGCTGCTAG                         GCCGGGGTGACACCATTCTTATTGCGGCTGGTGGTTCCCATGTTGTATGTA
genomic: ATGGAGCCTGGAGTTTATCCAGATCTCGAGGCTGCTGTTTCTGCTGCTAGgtctatttct ... cttgttgaagGCCGGG-TGACACCATTCTTATTGCGGCTGGTGGTTCCCATGTTGCATGTA
EST: gi|211344535|gb|FL091803.1|FL091803
EST:     ATGGAGCCTGGAGTTTATCCTGATCTCGAGGCTGCTGTTTCTGCTGCTAG                         GCCGGGTGACACCATTCTTATTGCGGCTGGTGGTTCCCATGTTGCATGTAA
genomic: ATGGAGCCTGGAGTTTATCCAGATCTCGAGGCTGCTGTTTCTGCTGCTAGgtctatttct ... cttgttgaagGCCGGGTGACACCATTCTTATTGCGGCTGGTGGTTCCCATGTTGCATGTAA
EST: gi|78085122|gb|DV513515.1|DV513515
EST:     ATGGAGCCTGGAGTTTATCCAGATCTCGAGGCTGCTGTTTCTGCTGCTAG                         GCCGGGTGACACCATTCTTATTGCGGCTGGTGGTTCCCATGTTGCATGTAA
genomic: ATGGAGCCTGGAGTTTATCCAGATCTCGAGGCTGCTGTTTCTGCTGCTAGgtctatttct ... cttgttgaagGCCGGGTGACACCATTCTTATTGCGGCTGGTGGTTCCCATGTTGCATGTAA
EST: gi|211344541|gb|FL091809.1|FL091809
EST:     ATGGAGCCTGGAGTTTATCCTGATCTCGAGGCTGCTGTTTCTGCTGCTAG                         GCCGGGTGACACCATTCTTATTGCGGCTGGTGGTTC
genomic: ATGGAGCCTGGAGTTTATCCAGATCTCGAGGCTGCTGTTTCTGCTGCTAGgtctatttct ... cttgttgaagGCCGGGTGACACCATTCTTATTGCGGCTGGTGGTTC
EST: gi|211344537|gb|FL091805.1|FL091805
EST:     ATGGAGCCTGGAGTTTATCCAGATCTCGAGGCTGCTGTTTCTGCTGCTAG                         GCCGGGTGACACCATTCTTATTGCGGCTGGTGGTTCCCATGTTGCATGTAA
genomic: ATGGAGCCTGGAGTTTATCCAGATCTCGAGGCTGCTGTTTCTGCTGCTAGgtctatttct ... cttgttgaagGCCGGGTGACACCATTCTTATTGCGGCTGGTGGTTCCCATGTTGCATGTAA
EST: gi|78108725|gb|DV527143.1|DV527143
EST:     ATGGAGCCTGGAGTTTATCCAGATCTCGAGGCTGCTGTTTCTGCTGCTAG                         GCCGGGTGACACCATTCTTATTGCGGCTGGTGGTTCCCATGTTGCATGTAA
genomic: ATGGAGCCTGGAGTTTATCCAGATCTCGAGGCTGCTGTTTCTGCTGCTAGgtctatttct ... cttgttgaagGCCGGGTGACACCATTCTTATTGCGGCTGGTGGTTCCCATGTTGCATGTAA
EST: gi|211117408|gb|FL123095.1|FL123095
EST:     ATGGAGCCTGGAGTTTATCCAGATCTCGAGGCTGCTGTTTCTGCTGCTAG                         GCCGGGTGACACCATTCTTATTGCGGCTGGTGGTTCCCATGTTGCATGTAA
genomic: ATGGAGCCTGGAGTTTATCCAGATCTCGAGGCTGCTGTTTCTGCTGCTAGgtctatttct ... cttgttgaagGCCGGGTGACACCATTCTTATTGCGGCTGGTGGTTCCCATGTTGCATGTAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agttctcattgtgcacaatggatgttatggctgatctccatgtaccttgttgaagGCCGGGTGACACCATTCTTATTGCGGCTGGTGGTTCCCATGTTGCATGTAACATCCAAATAAAGAAGCCTATTTGCATAGTAAGTTTTGCCTACCATGTC
                            ggctgat  putative branch site (score: 4)
                                            ccttgtt  putative PPT
                     atgttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtctatttctcgcccctctctctctcaagttctcattgtgcacaatggatgttatggctgatctccatgtaccttgttgaagGCCGGGTGACACCATTCTTATTGCGGCTGGTGGTTCCCATGTTGCATGTAACATCCAAATAAAGAAGCCTATTTGCATAGTAAGTTTTGCCTACCATGTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC