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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgatggtcaaatacaaatcacggcctatttctttctctttctatacttgaagttaatgtctctttggcagGTGAATCCTGTGAGAACTAAAGAACTTACAAATATCCGAGCCCCTGGAAAGGATGAAAATGTCCGTTTGTCTCCACCCCGATTG

Basic information

species Zea mays
transcript GRMZM2G128688_T02
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G128688_T01 (Zea mays), 3'ss of exon 16
lower sequence: LOC_Os01g54910.1 (Oryza sativa), 3'ss of exon 16
gtatgatggtcaaatacaaatcacggcctatttctttctctttctatacttgaagttaatgtctctttgg-----cagGTGAATCCTGTGAGAACTAAAGAACTTACAAATATCCGAGCCCCTGGAAAGGATGAAAATGTCCGTTTGTCTCCACCCCGATTG
||| | || | | || |  ||||  |  | |   ||||||||   ||||   || | |||  |||||  |     ||| | ||||||||||||||||||||||||||||| || ||||| || |||||||||||||||||| |  | |||||||| ||||||
gtaagttgattatatgcttatcaatgaat-taggtttctcttctaatacacaaactaaataactcttctgttgttcagATCAATCCTGTGAGAACTAAAGAACTTACAAACATTCGAGCTCCAGGAAAGGATGAAAATGTCAGGCTTTCTCCACCACGATTG

upper sequence: GRMZM2G128688_T01 (Zea mays), 3'ss of exon 16
lower sequence: GLYMA12G14080.1 (Glycine max), 3'ss of exon 16
----gtatgatggtcaaatacaaatcacggcctatttctttctctttctatacttgaagttaatgtctctttggcagGTGAATCCTGTGAGAACTAAAGAACTTACAAATATCCGAGCCCCTGGAAAGGATGAAAATGTCCGTTTGTCTCCACCCCGATTG
    | |  ||  | |  |  ||   |     ||| ||    |   |   |   ||| |   |    | |||  ||||| |||||||||||  |||||||||||||||||||||| ||  ||   || ||||| |||||     || |||| || ||  | 
gtaagaaatattcttagcttgaatcaaattgttatatcaaagttggtgactcactgacgaagactgatattt--cagGTTAATCCTGTGAGGGCTAAAGAACTTACAAATATCCGTGCTGCTACCAAAGATGATAATGTGAAGCTGACTCCCCCGCGCCTT

upper sequence: GRMZM2G128688_T01 (Zea mays), 3'ss of exon 16
lower sequence: GLYMA06G43820.1 (Glycine max), 3'ss of exon 16
----gtatgatggtcaaatacaaatcacggcctatttctttctctttctatacttga--agttaatgtctctttggcagGTGAATCCTGTGAGAACTAAAGAACTTACAAATATCCGAGCCCCTGGAAAGGATGAAAATGTCCGTTTGTCTCCACCCCGATTG
    | |  ||  | |  |  ||   | |   ||| ||        |   |   |||     | || | ||      |||| |||||||| ||  |||||||||||||||||||||| ||  ||   || ||||| |||||     || |||| || ||  | 
gtaagaagtattcttagtttgaatgtaagtgttatatcaaaggtggtgactcgctgacagactgatatttc------agGTCAATCCTGTAAGGGCTAAAGAACTTACAAATATCCGTGCTGCTACCAAAGATGATAATGTGAAGCTGACTCCCCCTCGCCTT

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|71428851|gb|DR809901.1|DR809901
EST:     CATATGAAGGGATGATAGTTGGTGAGCACTCACGTGACAGTGATCTTGAG                         GTGAATCCTGTGAGAACTAAAGAACTTACAAATATCCGAGCCCCTGGAAAG
genomic: CATATGAAGGGATGATAGTTGGTGAGCACTCACGTGACAGTGATCTTGAGgtatgatggt ... tctttggcagGTGAATCCTGTGAGAACTAAAGAACTTACAAATATCCGAGCCCCTGGAAAG
EST: gi|32936632|gb|CF041451.1|CF041451
EST:     CATATGAAGGGATGATAGTTGGTGAGCACTCACGTGACAGTGATCTTGAG                         GTGAATCCTGTGAGAACTAAAGAACTTACAAATATCCGAGCCCCTGGAAAG
genomic: CATATGAAGGGATGATAGTTGGTGAGCACTCACGTGACAGTGATCTTGAGgtatgatggt ... tctttggcagGTGAATCCTGTGAGAACTAAAGAACTTACAAATATCCGAGCCCCTGGAAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatcacggcctatttctttctctttctatacttgaagttaatgtctctttggcagGTGAATCCTGTGAGAACTAAAGAACTTACAAATATCCGAGCCCCTGGAAAGGATGAAAATGTCCGTTTGTCTCCACCCCGATTG
                                   agttaat  putative branch site (score: 4)
                                         tgtctcttt  CT-rich tract
          tatttcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgatggtcaaatacaaatcacggcctatttctttctctttctatacttgaagttaatgtctctttggcagGTGAATCCTGTGAGAACTAAAGAACTTACAAATATCCGAGCCCCTGGAAAGGATGAAAATGTCCGTTTGTCTCCACCCCGATTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG