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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgaatgctagatccttacatgccacagtgctagttttctctgtttttcttcccttttgaattcacatggttctctgcatgtatcaagtcacactttctctttatttatgtcggtaacttctgtatagttggagtcacatgatcaccttttgtttccactttggcagGATGTTTTTGACTTGCCCTTTCATATGGCCAGAGATCAGATAGAAGAGAGTTTGCGCACAAAAATGACTTCAATCAAG

Basic information

species Zea mays
transcript GRMZM2G147500_T05
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G147500_T02 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os08g14460.1 (Oryza sativa), 3'ss of exon 10
gtatgaatgctagatccttacatgccacagtgctagttttctctgtttttcttcccttttgaattcacatggttct-ctgcatgtatcaagtcacactttctctttatttatgtcg-gtaacttctgtatagttggagtcacatgatcaccttttgtttccactttgg-----------cagGATGTTTTTGACTTGCCCTTTCATATGGCCAGAGATCAGATAGAAGAGAGTTTGCGCACAAAAATGACTTCAATCAAG
||||| || ||   || | |      |||  | | | | |   | | | |||||   |   | |    ||| || | || ||| |||||| | | | |      || ||  |||||  | |||||     ||||||  ||||||||||||| |||| || |  |  ||           |||||||| ||||| ||||||||||| ||||| ||||| ||||| ||||||||||||||||| |||||| |||| || |||
gtatgcattctcattcttcat----tacatagtttgctcttggtatctgtcttcttctaaaagtcttgatgatttttcttcatttatcaaataataataaaaaatt-ttggtgtcgcatgacttcccctcagttgg--tcacatgatcaccatttgatttctttgcggttccctcctgccagGATGTCTTTGATTTGCCCTTTCACATGGCTAGAGACCAGATTGAAGAGAGTTTGCGCACTAAAATGGCTTCCATAAAG

upper sequence: GRMZM2G147500_T02 (Zea mays), 3'ss of exon 10
lower sequence: GLYMA17G07040.1 (Glycine max), 3'ss of exon 11
gtatgaatgctagatccttacatgccacagtgctagttttctctgtttttcttcccttttgaattcacatggttctctgcatgtatcaagtcacactttctctttatttatgtcggtaacttctgtatagttggagtcacatgatcaccttttgtttccactttggcagGATGTTTTTGACTTGCCCTTTCATATGGCCAGAGATCAGATAGAAGAGAGTTTGCGCACAAAAATGACTTCAATCAAG
                                                                                  ||||  |       ||| |   | || ||     ||     |||  |  ||   ||   |||     ||  ||||     ||| |||||||| |||||| | || ||||| |||||||||||||| |||||||| ||| | ||||  |||||| |||| || |||
----------------------------------------------------------------------------------gtatggaa----ggtttttaaattttcatactt-tattccgtgtcaaactgccttc---tgaaattattgagtttgttacttg-cagGATGTATTTGACCTTCCTTTTCACATGGCCAGAGATCAAATAGAAGAAAGTCTTCGCAACAAAATGGCTTCTATAAAG
















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|74237135|gb|DT645049.1|DT645049
EST:     ATGGAAGACAGGAGTCAGGGTCTCCTCAGTCTCCGCTTGGTGGCAAGACG                         GATGTTTTTGACTTGCCCTTTCATATGGCCAGAGATCAGATAGAAGAGAGT
genomic: ATGGAAGACAGGAGTCAGGGTCTCCTCAGTCTCCGCTTGGTGGCAAGACGgtatgaatgc ... actttggcagGATGTTTTTGACTTGCCCTTTCATATGGCCAGAGATCAGATAGAAGAGAGT
EST: gi|211359662|gb|FL110321.1|FL110321
EST:     ATGGAAGACAGGAGTCAGGGTCTCCTCAGTCTCCGCTTGGTGGCAAGACG                         GATGTNTTTGACTTGCCCTTTCATATGGCCAGAG
genomic: ATGGAAGACAGGAGTCAGGGTCTCCTCAGTCTCCGCTTGGTGGCAAGACGgtatgaatgc ... actttggcagGATGTTTTTGACTTGCCCTTTCATATGGCCAGAG
EST: gi|60347145|gb|DN214118.1|DN214118
EST:     ATGGAAGACAGGAGTCAGGGTCTCCTCAGTCTCCGCTTGGTGGCAAGACG                         GATGTTTTTGACTTGCCCTTT
genomic: ATGGAAGACAGGAGTCAGGGTCTCCTCAGTCTCCGCTTGGTGGCAAGACGgtatgaatgc ... actttggcagGATGTTTTTGACTTGCCCTTT
EST: gi|211359665|gb|FL110324.1|FL110324
EST:     ATGGAAGACAGGAGTCAGGGTCTCCTCAGTCTCCGCTTGGTGGCAAGACG                         GATGTTTTTGACTTGCCCTTTCATATGGCCAGAGATCAGATAGAAGAGAGT
genomic: ATGGAAGACAGGAGTCAGGGTCTCCTCAGTCTCCGCTTGGTGGCAAGACGgtatgaatgc ... actttggcagGATGTTTTTGACTTGCCCTTTCATATGGCCAGAGATCAGATAGAAGAGAGT
EST: gi|24765838|gb|CA400997.1|CA400997
EST:     ATGGAAGACAGGAGTCAGGGTCTCCTCAGTCTCCGCTTGGTGGCAAGACG                         GATGTTTTTGACTTGCCCTTTCATATGGCCAGAGATCAGATAGAAGAGAGT
genomic: ATGGAAGACAGGAGTCAGGGTCTCCTCAGTCTCCGCTTGGTGGCAAGACGgtatgaatgc ... actttggcagGATGTTTTTGACTTGCCCTTTCATATGGCCAGAGATCAGATAGAAGAGAGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggtaacttctgtatagttggagtcacatgatcaccttttgtttccactttggcagGATGTTTTTGACTTGCCCTTTCATATGGCCAGAGATCAGATAGAAGAGAGTTTGCGCACAAAAATGACTTCAATCAAG
 cggtaac  putative branch site (score: 3)
                                 ccttttgtttccactt  putative PPT
                                   ttttgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgaatgctagatccttacatgccacagtgctagttttctctgtttttcttcccttttgaattcacatggttctctgcatgtatcaagtcacactttctctttatttatgtcggtaacttctgtatagttggagtcacatgatcaccttttgtttccactttggcagGATGTTTTTGACTTGCCCTTTCATATGGCCAGAGATCAGATAGAAGAGAGTTTGCGCACAAAAATGACTTCAATCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA