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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttataaagaaaatgaactgctacatgatattatcttttgttttggtcatgccatacatgcatgcccccctttgatgttgatatacttatattattgcagACTGACAAAGGCGACGAAGAACTGTGTAGTGTGTATGTGCCAACAAATCATTTGTACATCGGTGATATATTTCTGGTGAACTCTGAGGAGGTCATAAGAC

Basic information

species Zea mays
transcript GRMZM2G046098_T02
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G046098_T02 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os01g64780.4 (Oryza sativa), 3'ss of exon 4
----------------------------------------------------tttataaagaaaatgaactgctacatg-atattatcttttgttttggtcatgccatacatgcatgc-ccccctttgatgttgatat-acttatatt--attgcagACTGACAAAGGCGACGAAGAACTGTGTAGTGTGTATGTGCCAACAAATCATTTGTACATCGGTGATATATTTCTGGTGAACTCTGAGGAGGTCATAAGAC
                                                    | | | |   |  ||    |  | |   ||   ||    ||| |    | |   |        ||  |    | | |||||  | |   || | ||  || |||||||||||||||||||||||||||||| || || |||||||||||||||||| | ||||| ||||| |||||||||||||||||||||||| | |||||||
gtaattcatgtagggttctatatggaataaatatgagttagattaacaaaaatctgttattgaggtgcttcgtcatagacatgccatgccatgtatgatccgtaataggtgcaactgtgcttgttcttatgttagtcttgtttgtgttctatggcagACTGACAAAGGCGACGAAGAACTGTGCAGCGTTTATGTGCCAACAAATCATCTTTACATTGGTGACATATTTCTGGTGAACTCTGAGGAGATAATAAGAC

upper sequence: GRMZM2G046098_T02 (Zea mays), 3'ss of exon 5
lower sequence: AT1G43130.1 (Arabidopsis thaliana), 3'ss of exon 5
tttataaagaaaatgaactgctacatgatattatcttttgttttggtcatgcca-tacatgcatgcccccctttgatgttgatatacttatattattgcagACTGACAAAGGCGACGAAGAACTGTGTAGTGTGTATGTGCCAACAAATCATTTGTACATCGGTGATATATTTCTGGTGAACTCTGAGGAGGTCATAAGAC
                 | | ||      |  |    | ||      || |  |  | ||   |  |   || | |||    | |  || | || |  ||||||||| | || || |||||  | |||||||||||||| ||||| |||||| ||||||| || ||| | ||||||||||     || ||  ||||||| |
---------------gtcagttattcagcaacaaaactggtaaaacccaagtaagcaaattagttacttgctctcatgc---tttttttttgttgtaacagACTGACCATGGAGAAGAAGAGTTATGTAGTGTGTATGTACCAACGAATCATCTGTACATAGGAGATGTGTTTCTGGTGAGTAGCGAAGAAATCATAAGGC
















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|51871157|gb|CV126041.1|CV126041
EST:     GAATTGGTGAATATGCATTTGGATTCATAACATCAACGGTGGTCCTTCAG                         ACTGACAAAGGCGACGAANAACTGTGTAGTGTGTATGTGCCAACAAATCAT
genomic: GAATTGGTGAATATGCATTTGGATTCATAACATCAACGGTGGTCCTTCAGgtacttgatc ... attattgcagACTGACAAAGGCGACGAAGAACTGTGTAGTGTGTATGTGCCAACAAATCAT
EST: gi|211391866|gb|FL013594.1|FL013594
EST:     ATTGGTGAATATGCATTTGGGAT-CATAACATCAACGGTGGGTC-TTCAG                         ACTGACAA-GGCGACGAAGAACTGTGTAGTGTGTATGTGCCCACAA-TCA
genomic: ATTGGTGAATATGCATTTGG-ATTCATAACATCAACGGTGG-TCCTTCAGgtacttgatc ... attattgcagACTGACAAAGGCGACGAAGAACTGTGTAGTGTGTATGTGCCAACAAATCA
EST: gi|50323815|gb|CO518941.1|CO518941
EST:     GAATTGGTGAATATGCATTTGGATTCATAACATCAACGGTGGTCCTTCAG                         ACTGACAAAGGCGACGAAGAACTGTGTAGTGTGTATGTGCCAACAAATCAT
genomic: GAATTGGTGAATATGCATTTGGATTCATAACATCAACGGTGGTCCTTCAGgtacttgatc ... attattgcagACTGACAAAGGCGACGAAGAACTGTGTAGTGTGTATGTGCCAACAAATCAT
EST: gi|91053372|gb|EB163790.1|EB163790
EST:     GAATTGGTGAATATGCATTTGGATTCATAACATCAACGGTGGTCCTTCAG                         ACTGACAAAGGCGACGAAGAACTGTGTAGTGTGTATGTGCCAACAAATCAT
genomic: GAATTGGTGAATATGCATTTGGATTCATAACATCAACGGTGGTCCTTCAGgtacttgatc ... attattgcagACTGACAAAGGCGACGAAGAACTGTGTAGTGTGTATGTGCCAACAAATCAT
EST: gi|32855801|gb|CD995482.1|CD995482
EST:     GAATTGGTGAATATGCATTTGGATTCATAACATCAACGGTGGTCCTTCAG                         ACTGACAAAGGCGACGAAGAACTGTGTAGTGTGTATGTGCCAACAAATCAT
genomic: GAATTGGTGAATATGCATTTGGATTCATAACATCAACGGTGGTCCTTCAGgtacttgatc ... attattgcagACTGACAAAGGCGACGAAGAACTGTGTAGTGTGTATGTGCCAACAAATCAT
EST: gi|74239462|gb|DT647376.1|DT647376
EST:     GAATTGGTGAATATGCATTTGGATTCATAACATCAACGGTGGTCCTTCAG                         ACTGACAAAGGCGACGAAGAACTGTGTAGTGTGTATGTGCCAACAAATCAT
genomic: GAATTGGTGAATATGCATTTGGATTCATAACATCAACGGTGGTCCTTCAGgtacttgatc ... attattgcagACTGACAAAGGCGACGAAGAACTGTGTAGTGTGTATGTGCCAACAAATCAT
EST: gi|148949550|gb|EC895017.2|EC895017
EST:     GAATTGGTGAATATGCATTTGGATTCATAACATCAACGGTGGTCCTTCAG                         ACTGACAAAGGCGACGAAGAACTGTGTAGTGTGTATGTGCCAACAAATCAT
genomic: GAATTGGTGAATATGCATTTGGATTCATAACATCAACGGTGGTCCTTCAGgtacttgatc ... attattgcagACTGACAAAGGCGACGAAGAACTGTGTAGTGTGTATGTGCCAACAAATCAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtcatgccatacatgcatgcccccctttgatgttgatatacttatattattgcagACTGACAAAGGCGACGAAGAACTGTGTAGTGTGTATGTGCCAACAAATCATTTGTACATCGGTGATATATTTCTGGTGAACTCTGAGGAGGTCATAAGAC
                              tgttgat  putative branch site (score: 4)
                             atgttgatatacttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttataaagaaaatgaactgctacatgatattatcttttgttttggtcatgccatacatgcatgcccccctttgatgttgatatacttatattattgcagACTGACAAAGGCGACGAAGAACTGTGTAGTGTGTATGTGCCAACAAATCATTTGTACATCGGTGATATATTTCTGGTGAACTCTGAGGAGGTCATAAGAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG