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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtatacatgttccttgaagagtgaggaatatagttttatatgcaccatccatattgttccttgcactctactcgtgaccagtcgccatctcttattctgttcagGGGTGAGAAATGCAGCCCAGCGCAAACTATTTGATGAGCTGGGAATAGTGGCTGACGAATTACCTGTCGACCAGTTCATTCCGCTTGGGAGGATGCTTTA

Basic information

species Zea mays
transcript GRMZM2G133082_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G133082_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os05g34180.1 (Oryza sativa), 3'ss of exon 4
--gtatgtatacatgttccttgaagag-------tgaggaatatagtttta------tatgcaccatccatattgttccttgcact-ctactcgtgaccagtcgccatctcttattctgttcagGGGTGAGAAATGCAGCCCAGCGCAAACTATTTGATGAGCTGGGAATAGTGGCTGACGAATTACCTGTCGACCAGTTCATTCCGCTTGGGAGGATGCTTTA
    || |||  |  | || ||||  |       |||  || | ||   ||      | |||||  || ||  || ||    |  | |||      || ||| || |  |  ||||    |||||||| ||||||||||| ||||| || ||||| ||||| |||||||||   ||||| ||| ||||||| ||||| |||||||| |||||||||||||||||
gtacatctatctacctgccctgaaatgagaactgtgaaaaacaaagccatacctatctttgcactgtctatgctgctctccaccttactaaataatacaagttgctacgttgtatt----tcagGGGTCAGAAATGCAGCACAGCGGAAGCTATTCGATGAACTGGGAATACAAGCTGAAGAACTACCTGTTGACCAATTCATTCCTCTTGGGAGGATGCTTTA
















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|211304673|gb|FL135311.1|FL135311
EST:     TAGCCATCCTCTCTACCGCGAGTCAGAGTTGATTGAGGAAAATTGTGCAG                         GGGTGAGAAATGCAGCCCAGCGCAAACTATTT
genomic: TAGCCATCCTCTCTACCGCGAGTCAGAGTTGATTGAGGAAAATTGTGCAGgtatgtatac ... ttctgttcagGGGTGAGAAATGCAGCCCAGCGCAAACTATTT
EST: gi|67022742|gb|CO451491.1|CO451491
EST:     TAGCCATCCTCTCTACCGCGAGTCAGAGTTGATTGAGGAAAATTGTGCAG                         GGGTGAGAAATGCAGCCCAGCGCAAACTATTTGATGAGCTGGGAATAGTGG
genomic: TAGCCATCCTCTCTACCGCGAGTCAGAGTTGATTGAGGAAAATTGTGCAGgtatgtatac ... ttctgttcagGGGTGAGAAATGCAGCCCAGCGCAAACTATTTGATGAGCTGGGAATAGTGG
EST: gi|15312900|gb|BI478457.1|BI478457
EST:     TAGCCATCCTCTCTACCGCGAGTCAGAGTTGATTGAGGAAAATTGTGCAG                         GGGTGAGAAATGCAGCCCAGCGCAAACTATTTGATGAGCTGGGAATAGTGG
genomic: TAGCCATCCTCTCTACCGCGAGTCAGAGTTGATTGAGGAAAATTGTGCAGgtatgtatac ... ttctgttcagGGGTGAGAAATGCAGCCCAGCGCAAACTATTTGATGAGCTGGGAATAGTGG
EST: gi|154130380|gb|EC872179.2|EC872179
EST:     TAGCCATCCTCTCTACCGCGAGTCAGAGTTGATTGAGGAAAATTGTGCAG                         GGGTGAGAAATGCAGCCCAGCGCAAACTATTTGATGAGCTGGGAATAGTGG
genomic: TAGCCATCCTCTCTACCGCGAGTCAGAGTTGATTGAGGAAAATTGTGCAGgtatgtatac ... ttctgttcagGGGTGAGAAATGCAGCCCAGCGCAAACTATTTGATGAGCTGGGAATAGTGG
EST: gi|154130466|gb|EC872180.2|EC872180
EST:     TAGCCATCCTCTCTACCGCGAGTCAGAGTTGATTGAGGAAAATTGTGCAG                         GGGTGAGAAATGCAGCCCAGCGCAAACTATTTGATGAGCTGGGAATAGTGG
genomic: TAGCCATCCTCTCTACCGCGAGTCAGAGTTGATTGAGGAAAATTGTGCAGgtatgtatac ... ttctgttcagGGGTGAGAAATGCAGCCCAGCGCAAACTATTTGATGAGCTGGGAATAGTGG
EST: gi|32940743|gb|CF045562.1|CF045562
EST:     TAGCCATCCTCTCTACCGCGAGTCAGAGTTGATTGAGGAAAATTGTGCAG                         GGGTGAGAAATGCAGCCCAGCGCAAACTATTTGATGAGCTGGGAATAGTGG
genomic: TAGCCATCCTCTCTACCGCGAGTCAGAGTTGATTGAGGAAAATTGTGCAGgtatgtatac ... ttctgttcagGGGTGAGAAATGCAGCCCAGCGCAAACTATTTGATGAGCTGGGAATAGTGG
EST: gi|71303304|gb|DR787755.1|DR787755
EST:     AAATTGTGCAG                         GGGTGAGAAATGCAGCCCAGCGCAAACTATTTGATGAGCTGGGAATAGTGG
genomic: AAATTGTGCAGgtatgtatac ... ttctgttcagGGGTGAGAAATGCAGCCCAGCGCAAACTATTTGATGAGCTGGGAATAGTGG
EST: gi|21891394|gb|BQ744607.1|BQ744607
EST:     CTCTCTACCGCGAGTCAGAGTTGATTGAGGAAAATTGTGCCCG                         GGGTGAGAAATGCAGCCCAGCGCAAACTATTTGATGAGCTGGGAATAGTG
genomic: CTCTCTACCGCGAGTCAGAGTTGATTGAGGAAAATTGTG-CAGgtatgtatac ... ttctgttcagGGGTGAGAAATGCAGCCCAGCGCAAACTATTTGATGAGCTGGGAATAGTG
EST: gi|60354876|gb|DN221849.1|DN221849
EST:     TAGCCATCCTCTCTACCGCGAGTCAGAGTTGATTGAGGAAAATTGTGCAG                         GGGTGAGAAATGCAGCCCAGCGCAAACTATTTGATGAGCTGGGAATAGTGG
genomic: TAGCCATCCTCTCTACCGCGAGTCAGAGTTGATTGAGGAAAATTGTGCAGgtatgtatac ... ttctgttcagGGGTGAGAAATGCAGCCCAGCGCAAACTATTTGATGAGCTGGGAATAGTGG
EST: gi|211304672|gb|FL135310.1|FL135310
EST:     GAGCCCTCCTCTCTACCGCGAGTCAAAGTTGATTGAGGAAAATGGGGCAG                         GGGTGAAAAATGCA
genomic: TAGCCATCCTCTCTACCGCGAGTCAGAGTTGATTGAGGAAAATTGTGCAGgtatgtatac ... ttctgttcagGGGTGAGAAATGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catattgttccttgcactctactcgtgaccagtcgccatctcttattctgttcagGGGTGAGAAATGCAGCCCAGCGCAAACTATTTGATGAGCTGGGAATAGTGGCTGACGAATTACCTGTCGACCAGTTCATTCCGCTTGGGAGGATGCTTTA
                                      tctcttattctgttc  CT-rich tract
                                        tcttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtatacatgttccttgaagagtgaggaatatagttttatatgcaccatccatattgttccttgcactctactcgtgaccagtcgccatctcttattctgttcagGGGTGAGAAATGCAGCCCAGCGCAAACTATTTGATGAGCTGGGAATAGTGGCTGACGAATTACCTGTCGACCAGTTCATTCCGCTTGGGAGGATGCTTTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG