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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttggtttgtccagcagaattgtcctactcttctttaagttttgggtaaaagagaactgtacctcatatttgctgcttgcttcagTACCAAGTCGGATGGCAAACTTGCCTCCCTTGACGAGTACATCTCACGGATGAAGTCAGGGCAGAAAGACATCTTCTACATCACGGGAAGCAGCAAAGAG

Basic information

species Zea mays
transcript GRMZM2G141931_T01
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G141931_T02 (Zea mays), 3'ss of exon 12
lower sequence: LOC_Os06g50300.1 (Oryza sativa), 3'ss of exon 12
gttggtttgtccagcagaattgtcctactcttctttaagttttgggtaaaagagaactgtacctcatatttgctgcttgcttcagTACCAAGTCGGATGGCAAACTTGCCTCCCTTGACGAGTACATCTCACGGATGAAGTCAGGGCAGAAAGACATCTTCTACATCACGGGAAGCAGCAAAGAG
||| || | || |    ||| ||||     ||  |  |||| |   |   || ||    ||   |  | ||  |   || ||||||||||||||||| |||||||||||||| ||||| |||||||| ||| |||||||| |||||||||| |||||||| ||||| || ||||||||||| || 
gtttgtct-tctattctaat-gtccactaattgctgtagttatatatgcgaggga-taatagaactgagtttttatctgtttcagTACCAAGTCGGAAGGCAAACTTGCCTCTCTTGATGAGTACATTTCAAGGATGAAGCCAGGGCAGAAGGACATCTTTTACATTACCGGAAGCAGCAAGGAA
















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|60348795|gb|DN215768.1|DN215768
EST:     GAAGACGCGACTAACAGAAACCGCCTTGCGAAGCTTCTTAGATTTGAGAG                         TACCAAGTCGGATGGCAAACTTGCCTCCCTTGACGAGTACATCTCACGGAT
genomic: GAAGACGCGACTAACAGAAACCGCCTTGCGAAGCTTCTTAGATTTGAGAGgttggtttgt ... cttgcttcagTACCAAGTCGGATGGCAAACTTGCCTCCCTTGACGAGTACATCTCACGGAT
EST: gi|7216906|gb|AW563028.1|AW563028
EST:     GAAGACGCGACTAACAGAAACCGCCTTGCGAAGCTTCTTAGATTTGAGAG                         TACCAAGTCGGATGGCAAACTTGCCTCCCTTGACGAGTACATCTCACGGAT
genomic: GAAGACGCGACTAACAGAAACCGCCTTGCGAAGCTTCTTAGATTTGAGAGgttggtttgt ... cttgcttcagTACCAAGTCGGATGGCAAACTTGCCTCCCTTGACGAGTACATCTCACGGAT
EST: gi|211354989|gb|FL245114.1|FL245114
EST:     GAAGACGCGACTAACAGAAACCGCCTTGCGAAGCTTCTTAGATTTGAGAG                         TACCAAGTCGGATGGCAAACTTGCCTCCCTTGACGAGTACATCTCACGGAT
genomic: GAAGACGCGACTAACAGAAACCGCCTTGCGAAGCTTCTTAGATTTGAGAGgttggtttgt ... cttgcttcagTACCAAGTCGGATGGCAAACTTGCCTCCCTTGACGAGTACATCTCACGGAT
EST: gi|211114829|gb|FL096555.1|FL096555
EST:     GAAGACGCGACTAACAGAAACCGCCTTGCGAAGCTTCTTAGATTTGAGAG                         TACCAAGTCGGATGGCAAACTTGCCTCCCTTTACGAGTACATCTCACGGAT
genomic: GAAGACGCGACTAACAGAAACCGCCTTGCGAAGCTTCTTAGATTTGAGAGgttggtttgt ... cttgcttcagTACCAAGTCGGATGGCAAACTTGCCTCCCTTGACGAGTACATCTCACGGAT
EST: gi|14883462|gb|BI273359.1|BI273359
EST:     CTTGCGAAGCTTCTTAGATTTGAGAG                         TACCAAGTCGGATGGCAAACTTGCCTCCCTTGACGAGTACATCTCACGGAT
genomic: CTTGCGAAGCTTCTTAGATTTGAGAGgttggtttgt ... cttgcttcagTACCAAGTCGGATGGCAAACTTGCCTCCCTTGACGAGTACATCTCACGGAT
EST: gi|67040044|gb|CO466299.1|CO466299
EST:     GAAGACGTTACTAACAGAAACCGCCTTGCGAAGCTTCTTAGATTTGAGAG                         TACCAAGTCGGATGTGCAACACTTGCCTCCCTTGACGAGTACATCTCACGG
genomic: GAAGACGCGACTAACAGAAACCGCCTTGCGAAGCTTCTTAGATTTGAGAGgttggtttgt ... cttgcttcagTACCAAGTCGGATG-GCAA-ACTTGCCTCCCTTGACGAGTACATCTCACGG
EST: gi|30306589|gb|CD001262.1|CD001262
EST:     GAAGACGCGACTAACAGAAACCGCCTTGCGAAGCTTCTTAGATTTGAGAG                         TACCAAGTCGGATGGCAAACTTGCCTCCCTTGACGAGTACATCTCACGGAT
genomic: GAAGACGCGACTAACAGAAACCGCCTTGCGAAGCTTCTTAGATTTGAGAGgttggtttgt ... cttgcttcagTACCAAGTCGGATGGCAAACTTGCCTCCCTTGACGAGTACATCTCACGGAT
EST: gi|31354312|gb|CD438669.1|CD438669
EST:     GAAGACGCGACTAACAGAAACCGCCTTGCGAAGCTTCTTAGATTTGAGAG                         TACCAAGTCGGATGGCAAACTTGCCTCCCTTGACGAGTACATCTCACGGAT
genomic: GAAGACGCGACTAACAGAAACCGCCTTGCGAAGCTTCTTAGATTTGAGAGgttggtttgt ... cttgcttcagTACCAAGTCGGATGGCAAACTTGCCTCCCTTGACGAGTACATCTCACGGAT
EST: gi|67017884|gb|CO446633.1|CO446633
EST:     GAAGACGCGACTAACAGAAACCGCCTTGCGAAGCTTCTTAGATTTGAGAG                         TACCAAGTCGGATGGCAAACTTGCCTCCCTTGACGAGTACATCTCACGGAT
genomic: GAAGACGCGACTAACAGAAACCGCCTTGCGAAGCTTCTTAGATTTGAGAGgttggtttgt ... cttgcttcagTACCAAGTCGGATGGCAAACTTGCCTCCCTTGACGAGTACATCTCACGGAT
EST: gi|50339539|gb|CO534665.1|CO534665
EST:     GAAGACGCGACTAACAGAAACCGCCTTGCGAAGCTTCTTAGATTTGAGAG                         TACCAAGTCGGATGGCAAACTTGCCTCCCTTGACGAGTACATCTCACGGAT
genomic: GAAGACGCGACTAACAGAAACCGCCTTGCGAAGCTTCTTAGATTTGAGAGgttggtttgt ... cttgcttcagTACCAAGTCGGATGGCAAACTTGCCTCCCTTGACGAGTACATCTCACGGAT
EST: gi|60344141|gb|DN211114.1|DN211114
EST:     GAAGACGCGACTAACAGAAACCGCCTTGCGAAGCTTCTTAGATTTGAGAG                         TACCAAGTCGGATGGCAAACTTGCCTCCCTTGACGAGTACATCTCACGGAT
genomic: GAAGACGCGACTAACAGAAACCGCCTTGCGAAGCTTCTTAGATTTGAGAGgttggtttgt ... cttgcttcagTACCAAGTCGGATGGCAAACTTGCCTCCCTTGACGAGTACATCTCACGGAT
EST: gi|31356123|gb|CD440480.1|CD440480
EST:     GAAGACGCGACTAACAGAAACCGCCTTGCGAAGCTTCTTAGATTTGAGAG                         TACCAAGTCGGATGGCAAACTTGCCTCCCTTGACGAGTACATCTCACGGAT
genomic: GAAGACGCGACTAACAGAAACCGCCTTGCGAAGCTTCTTAGATTTGAGAGgttggtttgt ... cttgcttcagTACCAAGTCGGATGGCAAACTTGCCTCCCTTGACGAGTACATCTCACGGAT
EST: gi|61118208|gb|DN559169.1|DN559169
EST:     GAAGACGCGACTAACAGAAACCGCCTTGCGAAGCTTCTTAGATTTGAGAG                         TACCAAGTCGGATGGCAAACTTGCCTCCCTTGACGAGTACATCTCACGGAT
genomic: GAAGACGCGACTAACAGAAACCGCCTTGCGAAGCTTCTTAGATTTGAGAGgttggtttgt ... cttgcttcagTACCAAGTCGGATGGCAAACTTGCCTCCCTTGACGAGTACATCTCACGGAT
EST: gi|20208078|gb|BQ134167.1|BQ134167
EST:     GAAGACGCGACTAACAGAAACCGCCTTGCGAAGCTTCTTAGATTTGAGAG                         TACCAAGTCGGATGGCAAACTTGCCTCCCTTGACGAGTACATCTCACGGAT
genomic: GAAGACGCGACTAACAGAAACCGCCTTGCGAAGCTTCTTAGATTTGAGAGgttggtttgt ... cttgcttcagTACCAAGTCGGATGGCAAACTTGCCTCCCTTGACGAGTACATCTCACGGAT
EST: gi|26456287|gb|CA827870.1|CA827870
EST:     GAAGACGCGACTAACAGAAACCGCCTTGCGAAGCTTCTTAGATTTGAGAG                         TACCAAGTCGGATGGCAAACTTGCCTCCCTTGACGAGTACATCTCACGGAT
genomic: GAAGACGCGACTAACAGAAACCGCCTTGCGAAGCTTCTTAGATTTGAGAGgttggtttgt ... cttgcttcagTACCAAGTCGGATGGCAAACTTGCCTCCCTTGACGAGTACATCTCACGGAT
EST: gi|67024193|gb|CO452942.1|CO452942
EST:     GAAGACGCGACTAACAGAAACCGCCTTGCGAAGCTTCTTAGATTTGAGAG                         TACCAAGTCGGATGGCAAACTTGCCTCCCTTGACGAGTACATCTCACGGAT
genomic: GAAGACGCGACTAACAGAAACCGCCTTGCGAAGCTTCTTAGATTTGAGAGgttggtttgt ... cttgcttcagTACCAAGTCGGATGGCAAACTTGCCTCCCTTGACGAGTACATCTCACGGAT
EST: gi|7227450|gb|AW566091.1|AW566091
EST:     GAAGACGCGACTAACAGAAACCGCCTTGCGAAGCTTCTTAGATTTGAGAG                         TACCAAGTCGGATGGCAAACTTGCCTCCCTTGACGAGTACATCTCACGGAT
genomic: GAAGACGCGACTAACAGAAACCGCCTTGCGAAGCTTCTTAGATTTGAGAGgttggtttgt ... cttgcttcagTACCAAGTCGGATGGCAAACTTGCCTCCCTTGACGAGTACATCTCACGGAT
EST: gi|67040100|gb|CO466355.1|CO466355
EST:     GAAGACGCGACTAACAGAAACCGCCTTGCGAAGCTTCTTAGATTTGAGAG                         TACCAAGTCGGATGGCAAACTTGCCCTCCCT-GACGAGTACATCTCACGGA
genomic: GAAGACGCGACTAACAGAAACCGCCTTGCGAAGCTTCTTAGATTTGAGAGgttggtttgt ... cttgcttcagTACCAAGTCGGATGGCAAACTTGCC-TCCCTTGACGAGTACATCTCACGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctttaagttttgggtaaaagagaactgtacctcatatttgctgcttgcttcagTACCAAGTCGGATGGCAAACTTGCCTCCCTTGACGAGTACATCTCACGGATGAAGTCAGGGCAGAAAGACATCTTCTACATCACGGGAAGCAGCAAAGAG
                                             cttgcttc  CT-rich tract
     taagtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttggtttgtccagcagaattgtcctactcttctttaagttttgggtaaaagagaactgtacctcatatttgctgcttgcttcagTACCAAGTCGGATGGCAAACTTGCCTCCCTTGACGAGTACATCTCACGGATGAAGTCAGGGCAGAAAGACATCTTCTACATCACGGGAAGCAGCAAAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG