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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atctttatctgagcattgattggttcatgggctcatggctattcagtcactttgtgccctttgagactgttagtatacttcctataacctcctctttcagGTTTCACCCTGCTTGCATTGGGATGACAATCAAAGAAGCAAAGAAACTCGAGCATTTTTTCTGCCAGACCTGTACAGCTGAAAATGGTAAGATGGTTGAG

Basic information

species Zea mays
transcript GRMZM2G097726_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G097726_T02 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os07g08880.2 (Oryza sativa), 3'ss of exon 3
atctttatctgagcattgattggttcatgggctcatggctattcagtcactttgt-gccctttgagactgttagtatacttcctataacctcctctttcagGTTTCACCCTGCTTGCATTGGGATGACAATCAAAGAAGCAAAGAAACTCGAGCATTTTTTCTGCCAGACCTGTACAGCTGAAAATGGTAAGATGGTTGAG
|     |  |     ||| || ||   |  |||  |   | | ||   ||||| |   | |||     |   |  | |  ||   |    |    || ||||||||||||| |||||||||| ||||| || ||||| ||||| ||||| ||||||||||||||||||| |||||| || |||||||| ||||||| ||||
aataaaacatttaatttgttttgtct-tctgcttttacttttgcatgaactttcttatcatttttttgtcacaacaaatatctgctgcttttgctttccagGTTTCACCCTTCTTGCATTGGAATGACTATTAAAGATGCAAAAAAACTAGAGCATTTTTTCTGCCAGAGCTGTACTGCGGAAAATGGAAAGATGGCTGAG
















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|18450467|gb|BM428745.1|BM428745
EST:     CCATACAATCCAGATGACCTTATGATCCAATGCGAGGAATGTTCTGACTG                         GNTTCACCCTGCTTGCATTGGGATGACAATCAAAGAAGCAAAGAAACTCGA
genomic: CCATACAATCCAGATGACCTTATGATCCAATGCGAGGAATGTTCTGACTGgtgagcatta ... cctctttcagGTTTCACCCTGCTTGCATTGGGATGACAATCAAAGAAGCAAAGAAACTCGA
EST: gi|78180631|gb|DV550959.1|DV550959
EST:     TCCAATGCGAGGAATGTTCTGACTG                         GTTTCACCCTGCTTGCATTGGGATGACAATCAAAGAAGCAAAGAAACTCGA
genomic: TCCAATGCGAGGAATGTTCTGACTGgtgagcatta ... cctctttcagGTTTCACCCTGCTTGCATTGGGATGACAATCAAAGAAGCAAAGAAACTCGA
EST: gi|19822612|gb|BQ048636.1|BQ048636
EST:     CCATACAATCCAGATGACCTTATGATCCAATGCGAGGAATGTTCTGACTG                         GTTTCACCCTGCTTGCATTGGGATGACAATCAAAGAAGCAAAGAAACTCGA
genomic: CCATACAATCCAGATGACCTTATGATCCAATGCGAGGAATGTTCTGACTGgtgagcatta ... cctctttcagGTTTCACCCTGCTTGCATTGGGATGACAATCAAAGAAGCAAAGAAACTCGA
EST: gi|18648816|gb|BM497635.1|BM497635
EST:     CCATACAATCCAGATGACCTTATGATCCAATGCGAGGAATGTTCTGACTG                         GTTTCACCCTGCTTGCATTGGGATGACAATCAAAGAAGCAAAGAAACTCGA
genomic: CCATACAATCCAGATGACCTTATGATCCAATGCGAGGAATGTTCTGACTGgtgagcatta ... cctctttcagGTTTCACCCTGCTTGCATTGGGATGACAATCAAAGAAGCAAAGAAACTCGA
EST: gi|8551650|gb|BE128821.1|BE128821
EST:     CCATGCAATCCAGATG-CCTTATGATCCAATGCGAGGAATGTTCTGACTG                         GTTTCACCCTGCTTGCATTGGGATGACAATCAAAGAAGCAAAGAAACTCGA
genomic: CCATACAATCCAGATGACCTTATGATCCAATGCGAGGAATGTTCTGACTGgtgagcatta ... cctctttcagGTTTCACCCTGCTTGCATTGGGATGACAATCAAAGAAGCAAAGAAACTCGA
EST: gi|60354816|gb|DN221789.1|DN221789
EST:     CCATACAATCCAGATGACCTTATGATCCAATGCGAGGAATGTTCTGACTG                         GTTTCACCCTGCTTGCATTGGGATGACAATCAAAGAAGCAAAGAAACTCGA
genomic: CCATACAATCCAGATGACCTTATGATCCAATGCGAGGAATGTTCTGACTGgtgagcatta ... cctctttcagGTTTCACCCTGCTTGCATTGGGATGACAATCAAAGAAGCAAAGAAACTCGA
EST: gi|18649546|gb|BM498365.1|BM498365
EST:     CCATACAATCCAGATGACCTTATGATCCAATGCGAGGAATGTTCTGACTG                         GNTTCACCCTGCTTGCATTGGGATGACAATCAAAGAAGCAAAGAAACTCGA
genomic: CCATACAATCCAGATGACCTTATGATCCAATGCGAGGAATGTTCTGACTGgtgagcatta ... cctctttcagGTTTCACCCTGCTTGCATTGGGATGACAATCAAAGAAGCAAAGAAACTCGA
EST: gi|18649399|gb|BM498218.1|BM498218
EST:     CCATACAATCCAGATGACCTTATGATCCAATGCGAGGAATGTTCTGACTG                         GTTTCACCCTGCTTGCATTGGGATGACAATCAAAGAAGCAAAGAAACTCGA
genomic: CCATACAATCCAGATGACCTTATGATCCAATGCGAGGAATGTTCTGACTGgtgagcatta ... cctctttcagGTTTCACCCTGCTTGCATTGGGATGACAATCAAAGAAGCAAAGAAACTCGA
EST: gi|18649290|gb|BM498109.1|BM498109
EST:     CCATACAATCCAGATGACCTTATGATCCAATGCGAGGAATGTTCTGACTG                         GTTTCACCCTGCTTGCATTGGGATGACAATCAAAGAAGCAAAGAAACTCGA
genomic: CCATACAATCCAGATGACCTTATGATCCAATGCGAGGAATGTTCTGACTGgtgagcatta ... cctctttcagGTTTCACCCTGCTTGCATTGGGATGACAATCAAAGAAGCAAAGAAACTCGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtcactttgtgccctttgagactgttagtatacttcctataacctcctctttcagGTTTCACCCTGCTTGCATTGGGATGACAATCAAAGAAGCAAAGAAACTCGAGCATTTTTTCTGCCAGACCTGTACAGCTGAAAATGGTAAGATGGTTGAG
                                    ctataac  putative branch site (score: 3)
                                cttcctataacctcct  CT-rich tract
                        ttagtata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atctttatctgagcattgattggttcatgggctcatggctattcagtcactttgtgccctttgagactgttagtatacttcctataacctcctctttcagGTTTCACCCTGCTTGCATTGGGATGACAATCAAAGAAGCAAAGAAACTCGAGCATTTTTTCTGCCAGACCTGTACAGCTGAAAATGGTAAGATGGTTGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG