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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatatacatgttccttggagagtgagaaaccaatccatactttatagatttgtatgcaccatccatattgttacttgcactctactcatcaccagccacaatcatttattctgttcagGGGTGAGAAATGCAGCCCAACGCAAACTATTTGATGAACTGGGAATAGTTGCTGACGAATTACCTGTTGACCAGTTCATCCTCCTTGGGAGGATGCTTTA

Basic information

species Zea mays
transcript GRMZM2G145029_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G145029_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os05g34180.1 (Oryza sativa), 3'ss of exon 4
----gtatatacatgttccttggagagtgagaaaccaatccatactttatagatttgtatgcaccatccatattgttacttgcact-ctactcatcaccagccacaatcatttattctgttcagGGGTGAGAAATGCAGCCCAACGCAAACTATTTGATGAACTGGGAATAGTTGCTGACGAATTACCTGTTGACCAGTTCATCCTCCTTGGGAGGATGCTTTA
     | |||  |  | || || |  | ||      ||     |    |||  | | | |||||  || ||  || |     |  | |||   |  || ||   | |   | ||||    |||||||| ||||||||||| || || || ||||| |||||||||||||||   ||||| ||| ||||||||||||| ||||| |  |||||||||||||||||
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|60355106|gb|DN222079.1|DN222079
EST:     TAGCCATCCTCTCTACCGCGAGTCAGAGTTGATTGAGGAAAATTGTGCAG                         GGGTGAGAAATGCAGCCCAACGCAAACTATTTGATGAACTGGGAATAGTTG
genomic: TAGCCATCCTCTCTACCGCGAGTCAGAGTTGATTGAGGAAAATTGTGCAGgtatatacat ... ttctgttcagGGGTGAGAAATGCAGCCCAACGCAAACTATTTGATGAACTGGGAATAGTTG
EST: gi|148948633|gb|EC898545.2|EC898545
EST:     TAGCCATCCTCTCTACCGCGAGTCAGAGTTGATTGAGGAAAATTGTGCAG                         GGGTGAGAAATGCAGCCCAACGCAAACTATTTGATGAACTGGGAATAGTTG
genomic: TAGCCATCCTCTCTACCGCGAGTCAGAGTTGATTGAGGAAAATTGTGCAGgtatatacat ... ttctgttcagGGGTGAGAAATGCAGCCCAACGCAAACTATTTGATGAACTGGGAATAGTTG
EST: gi|211523188|gb|FL353428.1|FL353428
EST:     TAGCCATCCTCTCTACCGCGAGTCAGAGTTGATTGAGGAAAATTGTGCAG                         GGGTGAGAAATGCAGCCCAGCGCAAACTATTTGATGAACTGGGAATAGTTG
genomic: TAGCCATCCTCTCTACCGCGAGTCAGAGTTGATTGAGGAAAATTGTGCAGgtatatacat ... ttctgttcagGGGTGAGAAATGCAGCCCAACGCAAACTATTTGATGAACTGGGAATAGTTG
EST: gi|148948634|gb|EC898546.2|EC898546
EST:     TAGCCATCCTCTCTACCGCGAGTCAGAGTTGATTGAGGAAAATTGTGCAG                         GGGTGAGAAATGCAGCCCAACGCAAACTATTTGATGAACTGGGAATAGTTG
genomic: TAGCCATCCTCTCTACCGCGAGTCAGAGTTGATTGAGGAAAATTGTGCAGgtatatacat ... ttctgttcagGGGTGAGAAATGCAGCCCAACGCAAACTATTTGATGAACTGGGAATAGTTG
EST: gi|148930170|gb|EC872550.2|EC872550
EST:     TAGCCATCCTCTCTACCGCGAGTCAGAGTTGATTGAGGAAAATTGTGCAG                         GGGTGAGAAATGCAGCCCAACGCAAACTATTTGATGAACTGGGAATAGTTG
genomic: TAGCCATCCTCTCTACCGCGAGTCAGAGTTGATTGAGGAAAATTGTGCAGgtatatacat ... ttctgttcagGGGTGAGAAATGCAGCCCAACGCAAACTATTTGATGAACTGGGAATAGTTG
EST: gi|8318714|gb|BE025279.1|BE025279
EST:     AGCCATCCTCTCTATTGTTGAGTCAGAGTTGATTGAGGAAAATTGTGCAG                         GGGTGAGAAATGCAGCCCAGCGCAAACTATTTGATGAACTGGGAATAGTTG
genomic: AGCCATCCTCTCTACCG-CGAGTCAGAGTTGATTGAGGAAAATTGTGCAGgtatatacat ... ttctgttcagGGGTGAGAAATGCAGCCCAACGCAAACTATTTGATGAACTGGGAATAGTTG
EST: gi|211035627|gb|FL437931.1|FL437931
EST:     CGCGAGTCAGAGTTGATTGAGGAAAATTGTGCAG                         GGKTGAGAAATGCAGCCCAGCGCAAACTATTTGATGAACTGGGAATAGTTG
genomic: CGCGAGTCAGAGTTGATTGAGGAAAATTGTGCAGgtatatacat ... ttctgttcagGGGTGAGAAATGCAGCCCAACGCAAACTATTTGATGAACTGGGAATAGTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catattgttacttgcactctactcatcaccagccacaatcatttattctgttcagGGGTGAGAAATGCAGCCCAACGCAAACTATTTGATGAACTGGGAATAGTTGCTGACGAATTACCTGTTGACCAGTTCATCCTCCTTGGGAGGATGCTTTA
                                         tttattct  CT-rich tract
                                    aatcatttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatatacatgttccttggagagtgagaaaccaatccatactttatagatttgtatgcaccatccatattgttacttgcactctactcatcaccagccacaatcatttattctgttcagGGGTGAGAAATGCAGCCCAACGCAAACTATTTGATGAACTGGGAATAGTTGCTGACGAATTACCTGTTGACCAGTTCATCCTCCTTGGGAGGATGCTTTA

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