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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttaaccttttgcaaagacccatgagatgaaattgctattcccaaagtaccactgttcctgtctatatggtttttatagcataatgtgtaattcatgacagGGCCTCTGCGATATTTGTCGGGGTGTATGAGCCAACTAAAAGAAAATTACTGGAAACCCTTCCTGAAAATCTGAGTGCAGTTGCCCATTTT

Basic information

species Zea mays
transcript GRMZM2G042027_T02
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G042027_T05 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os05g29860.1 (Oryza sativa), 3'ss of exon 4
ttaaccttttgcaaagacccatgagatgaaattgctat-tcccaaagtacc---actgttcctgtctatatggtttttatagcataatgtgtaattcatgacagGGCCTCTGCGATATTTGTCGGGGTGTATGAGCCAACTAAAAGAAAATTACTGGAAACCCTTCCTGAAAATCTGAGTGCAGTTGCCCATTTT
     ||   | ||  | || |    | |  ||   |    ||| |  |     |   || |  ||| | |   |  ||| |  |  | | || ||  |   ||||| |||||  ||||||| ||  | || || || || ||||||||| ||||||| ||  ||||||||||| ||||||| ||||||||||||
----tctcaggtaataatccttagcttcactttttcaggctccataacatgggaatcattgcattctctttccatcatattgtttcttctctatttgcttgtagGGCTTCTGCTGTATTTGTGGGAATATACGAACCGACAAAAAGAAAACTACTGGAGACTTTTCCTGAAAATTTGAGTGCTGTTGCCCATTTT
















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|211371111|gb|FL037583.1|FL037583
EST:     TGGAAAGGCTTGTATTCTGGATTAGCTGGAAATCTCACTGGCGTCCTTCC                         GGCCTCTGCGATATTTGTCGGGGTGTATGAGCCAACTAAAAGAAAATTACT
genomic: TGGAAAGGCTTGTATTCTGGATTAGCTGGAAATCTCACTGGCGTCCTTCCgtgagtacac ... ttcatgacagGGCCTCTGCGATATTTGTCGGGGTGTATGAGCCAACTAAAAGAAAATTACT
EST: gi|211373757|gb|FL037585.1|FL037585
EST:     TGGAAAGGCTTGTATTCTGGATTAGCTGGAAATCTCACTGGCGTCCTTCC                         GGCCTCTGCGATATTTGTCGGGGTGTATGAGCCAACTAAAAGAMAATTACT
genomic: TGGAAAGGCTTGTATTCTGGATTAGCTGGAAATCTCACTGGCGTCCTTCCgtgagtacac ... ttcatgacagGGCCTCTGCGATATTTGTCGGGGTGTATGAGCCAACTAAAAGAAAATTACT
EST: gi|50325364|gb|CO520490.1|CO520490
EST:     TGGAAAGGCTTGTATTCTGGATTAGCTGGAAATCTCACTGGCGTCCTTCC                         GGCCTCTGCGATATTTGTCGGGGTGTATGAGCCAACTAAAAGAAAATTACT
genomic: TGGAAAGGCTTGTATTCTGGATTAGCTGGAAATCTCACTGGCGTCCTTCCgtgagtacac ... ttcatgacagGGCCTCTGCGATATTTGTCGGGGTGTATGAGCCAACTAAAAGAAAATTACT
EST: gi|71436673|gb|DR817723.1|DR817723
EST:     TGGAAAGGCTTGTATTCTGGATTAGCTGGAAATCTCACTGGCGTCCTTCC                         GGCCTCTGCGATATTTGTCGGGGTGTATGAGCCAACTAAAAGAAAATTACT
genomic: TGGAAAGGCTTGTATTCTGGATTAGCTGGAAATCTCACTGGCGTCCTTCCgtgagtacac ... ttcatgacagGGCCTCTGCGATATTTGTCGGGGTGTATGAGCCAACTAAAAGAAAATTACT
EST: gi|71302083|gb|DR787129.1|DR787129
EST:     TGGAAAGGCTTGTATTCTGGATTAGCTGGAAATCTCACTGGCGTCCTTCC                         GGCCTCTGCGATATTTGTCGGGGTGTATGAGCCAACTAAAAGAAAATTACT
genomic: TGGAAAGGCTTGTATTCTGGATTAGCTGGAAATCTCACTGGCGTCCTTCCgtgagtacac ... ttcatgacagGGCCTCTGCGATATTTGTCGGGGTGTATGAGCCAACTAAAAGAAAATTACT
EST: gi|91054196|gb|EB164614.1|EB164614
EST:     TGGAAAGGCTTGTATTCTGGATTAGCTGGAAATCTCACTGGCGTCCTTCC                         GGCCTCTGCGATATTTGTCGGGGTGTATGAGCCAACTAAAAGAAAATTACT
genomic: TGGAAAGGCTTGTATTCTGGATTAGCTGGAAATCTCACTGGCGTCCTTCCgtgagtacac ... ttcatgacagGGCCTCTGCGATATTTGTCGGGGTGTATGAGCCAACTAAAAGAAAATTACT
EST: gi|211371112|gb|FL037584.1|FL037584
EST:     TTGAAAGGCTTGTATTCTGGATTAGCTGGAAATCTCACTGGCGTCCTTCC                         GGCCTCTGCGATATTTGTCGGGGTGTATGAGCCAACTAAAAGAAAATTACT
genomic: TGGAAAGGCTTGTATTCTGGATTAGCTGGAAATCTCACTGGCGTCCTTCCgtgagtacac ... ttcatgacagGGCCTCTGCGATATTTGTCGGGGTGTATGAGCCAACTAAAAGAAAATTACT
EST: gi|78083391|gb|DV511784.1|DV511784
EST:     TGGAAAGGCTTGTATTCTGGATTAGCTGGAAATCTCACTGGCGTCCTTCC                         GGCCTCTGCGATATTTGTCGGGGTGTATGAGCCAACTAAAAGAAAATTACT
genomic: TGGAAAGGCTTGTATTCTGGATTAGCTGGAAATCTCACTGGCGTCCTTCCgtgagtacac ... ttcatgacagGGCCTCTGCGATATTTGTCGGGGTGTATGAGCCAACTAAAAGAAAATTACT
EST: gi|60342707|gb|DN209680.1|DN209680
EST:     TGGAAAGGCTTGTATTCTGGATTAGCTGGAAATCTCACTGGCGTCCTTCC                         GGCCTCTGCGATATTTGTCGGGGTGTATGAGCCAACTAAAAGAAAATTACT
genomic: TGGAAAGGCTTGTATTCTGGATTAGCTGGAAATCTCACTGGCGTCCTTCCgtgagtacac ... ttcatgacagGGCCTCTGCGATATTTGTCGGGGTGTATGAGCCAACTAAAAGAAAATTACT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtaccactgttcctgtctatatggtttttatagcataatgtgtaattcatgacagGGCCTCTGCGATATTTGTCGGGGTGTATGAGCCAACTAAAAGAAAATTACTGGAAACCCTTCCTGAAAATCTGAGTGCAGTTGCCCATTTT
                 tatatggtttttata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttaaccttttgcaaagacccatgagatgaaattgctattcccaaagtaccactgttcctgtctatatggtttttatagcataatgtgtaattcatgacagGGCCTCTGCGATATTTGTCGGGGTGTATGAGCCAACTAAAAGAAAATTACTGGAAACCCTTCCTGAAAATCTGAGTGCAGTTGCCCATTTT

- - - ttttgca
- - - - - - - - - ccatgag
- - - - - - - - - - - - - - - - tgctatt
- - - - - - - - - - - - - - - - - - - - - - -gtaccac