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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agggccataactttttgtgaaggaacatttggatcgcgatccattaccacccctaagcacacatgctcctcaacatattcaatttttgttgtttttgtagCTGGGATGAATGGGTTGCAAATGACCGCTTGTTGGAATTGACGGAGGAAAACGTGCGCAAACAACAAGAGCTTGATAAGAATCAGGTAGTTGACAAAACA

Basic information

species Zea mays
transcript GRMZM2G484880_T04
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G484880_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os11g34300.2 (Oryza sativa), 3'ss of exon 3
agggccataactttttgtgaaggaac---atttggatcgcgatcca-ttaccacccctaagcacacatgctcctcaacatattcaatttttgttgtttttgtagCTGGGATGAATGGGTTGCAAATGACCGCTTGTTGGAATTGACGGAGGAAAACGTGCGCAAACAACAAGAGCTTGATAAGAATCAGGTAGTTGACAAAACA
 ||    |  || |   || |   |    |||| | |  |  ||   |  ||      ||| | |||  || || || || || | |||   |   |     |||||||||||||||||  ||||||| |||||  || ||||||| || |||||  | |||||||||||||||||||| ||||  || |||||||||||||  
-ggcttgtttctatcattgcactgatgctatttagttgtctttctgctctcctaattcaagtaaacagtcttcttaatatgtttattttcaatgagt---acagCTGGGATGAATGGGTCACAAATGATCGCTTACTGAAATTGACCGACGAAAATATCCGCAAACAACAAGAGCTTGAAAAGAGCCAAGTAGTTGACAAAAGC
















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|211058544|gb|FK994409.1|FK994409
EST:     TCCATTATCTCGGTTGGAATAAGAA                         CTGGGATGAATGGGTTGCAAATGACCGCTTGTTGGAATTGACGGAGGAAAA
genomic: TCCATTATCTCGGTTGGAATAAGAAgtaagtgttt ... gtttttgtagCTGGGATGAATGGGTTGCAAATGACCGCTTGTTGGAATTGACGGAGGAAAA
EST: gi|211061512|gb|FK994428.1|FK994428
EST:     TCCATTATCTCGGTTGGAATAAGAA                         CTGGGATGAATGGGTTGCAAATGACCGCTTGTTGGAATTGACGGAGGAAAA
genomic: TCCATTATCTCGGTTGGAATAAGAAgtaagtgttt ... gtttttgtagCTGGGATGAATGGGTTGCAAATGACCGCTTGTTGGAATTGACGGAGGAAAA
EST: gi|76912438|gb|DV164732.1|DV164732
EST:     TCCATTATCTCGGTTGGAATAAGAA                         CTGGGATGAATGGGTTGCAAATGACCGCTTGTTGGAATTGACGGAGGAAAA
genomic: TCCATTATCTCGGTTGGAATAAGAAgtaagtgttt ... gtttttgtagCTGGGATGAATGGGTTGCAAATGACCGCTTGTTGGAATTGACGGAGGAAAA
EST: gi|71434326|gb|DR815376.1|DR815376
EST:     TCCATTATCTCGGTTGGAATAAGAA                         CTGGGATGAATGGGTTGCAAATGACCGCTTGTTGGAATTGACGGAGGAAAA
genomic: TCCATTATCTCGGTTGGAATAAGAAgtaagtgttt ... gtttttgtagCTGGGATGAATGGGTTGCAAATGACCGCTTGTTGGAATTGACGGAGGAAAA
EST: gi|211058550|gb|FK994415.1|FK994415
EST:     TCCATTATCTCGGTTGGAATAAGAA                         CTGGGATGAATGGGTTGCAAATGACCGCTTGTTGGAATTGACGGAGGAAAA
genomic: TCCATTATCTCGGTTGGAATAAGAAgtaagtgttt ... gtttttgtagCTGGGATGAATGGGTTGCAAATGACCGCTTGTTGGAATTGACGGAGGAAAA
EST: gi|6031476|gb|AW076378.1|AW076378
EST:     TCCATTATCTCGGTTGGAATAAGAA                         CTGGGATGAATGGGTTGCAAATGACCGCTTGTTGGAATTGACGGAGGAAAA
genomic: TCCATTATCTCGGTTGGAATAAGAAgtaagtgttt ... gtttttgtagCTGGGATGAATGGGTTGCAAATGACCGCTTGTTGGAATTGACGGAGGAAAA
EST: gi|211061507|gb|FK994423.1|FK994423
EST:     TCCATTATCTCGGTTGGAATAAGAA                         CTGGGATGAATGGGTTGCAAATGACCGCTTGTTGGAATTGACGGAGGAAAA
genomic: TCCATTATCTCGGTTGGAATAAGAAgtaagtgttt ... gtttttgtagCTGGGATGAATGGGTTGCAAATGACCGCTTGTTGGAATTGACGGAGGAAAA
EST: gi|211061514|gb|FK994430.1|FK994430
EST:     TCCATTATCTCGGTTGGAATAAGAA                         CTGGGATGAATGGGTTGCAAATGACCGCTTGTTGGAATTGACGGAGGAAAA
genomic: TCCATTATCTCGGTTGGAATAAGAAgtaagtgttt ... gtttttgtagCTGGGATGAATGGGTTGCAAATGACCGCTTGTTGGAATTGACGGAGGAAAA
EST: gi|211058549|gb|FK994414.1|FK994414
EST:     TCCATTATCTCGGTTGGAATAAGAA                         CTGGGATGAATGGGTTGCAAATGACCGCTTGTTGGAATTGACGGAGGAAAA
genomic: TCCATTATCTCGGTTGGAATAAGAAgtaagtgttt ... gtttttgtagCTGGGATGAATGGGTTGCAAATGACCGCTTGTTGGAATTGACGGAGGAAAA
EST: gi|211058545|gb|FK994410.1|FK994410
EST:     TCCATTATCTCGGTTGGAATAAGAA                         CTGGGATGAATGGGTTGCAAATGACCGCTTGTTGGAATTGACGGAGGAAAA
genomic: TCCATTATCTCGGTTGGAATAAGAAgtaagtgttt ... gtttttgtagCTGGGATGAATGGGTTGCAAATGACCGCTTGTTGGAATTGACGGAGGAAAA
EST: gi|93284203|gb|EB676467.1|EB676467
EST:     TCCATTATCTCGGTTGGAATAAGAA                         CTGGGATGAATGGGTTGCAAATGACCGCTTGTTGGAATTGACGGAGGAAAA
genomic: TCCATTATCTCGGTTGGAATAAGAAgtaagtgttt ... gtttttgtagCTGGGATGAATGGGTTGCAAATGACCGCTTGTTGGAATTGACGGAGGAAAA
EST: gi|211058554|gb|FK994419.1|FK994419
EST:     TCCATTATCTCGGTTGGAATAAGAA                         CTGGGATGAATGGGTTGCAAATGACCGCTTGTTGGAATTGACGGAGGAAAA
genomic: TCCATTATCTCGGTTGGAATAAGAAgtaagtgttt ... gtttttgtagCTGGGATGAATGGGTTGCAAATGACCGCTTGTTGGAATTGACGGAGGAAAA
EST: gi|13178287|gb|BG349545.1|BG349545
EST:     TCCATTATCTCGGTTGGAATAAGAA                         CTGGGATGAATGGGTTGCAAATGACCGCTTGTTGGAATTGACGGAGGAAAA
genomic: TCCATTATCTCGGTTGGAATAAGAAgtaagtgttt ... gtttttgtagCTGGGATGAATGGGTTGCAAATGACCGCTTGTTGGAATTGACGGAGGAAAA
EST: gi|211058547|gb|FK994412.1|FK994412
EST:     TCCATTATCTCGGTTGGAATAAGAA                         CTGGGATGAATGGGTTGCAAATGACCGCTTGTTGGAATTGACGGAGGAAAA
genomic: TCCATTATCTCGGTTGGAATAAGAAgtaagtgttt ... gtttttgtagCTGGGATGAATGGGTTGCAAATGACCGCTTGTTGGAATTGACGGAGGAAAA
EST: gi|32913308|gb|CF018120.1|CF018120
EST:     TCCATTATCTCGGTTGGAATAAGAA                         CTGGGATGAATGGGTTGCAAATGACCGCTTGTTGGAATTGACGGAGGAAAA
genomic: TCCATTATCTCGGTTGGAATAAGAAgtaagtgttt ... gtttttgtagCTGGGATGAATGGGTTGCAAATGACCGCTTGTTGGAATTGACGGAGGAAAA
EST: gi|26456042|gb|CA827625.1|CA827625
EST:     TCCATTATCTCGGTTGGAATAAGAA                         CTGGGATGAATGGGTTGCAAATGACCGCTTGTTGGAATTGACGGAGGAAAA
genomic: TCCATTATCTCGGTTGGAATAAGAAgtaagtgttt ... gtttttgtagCTGGGATGAATGGGTTGCAAATGACCGCTTGTTGGAATTGACGGAGGAAAA
EST: gi|211061508|gb|FK994424.1|FK994424
EST:     TCCATTATCTCGGTTGGAATAAGAA                         CTGGGATGAATGGGTTGCAAATGACCGCTTGTTGGAATTGACGGAGGAAAA
genomic: TCCATTATCTCGGTTGGAATAAGAAgtaagtgttt ... gtttttgtagCTGGGATGAATGGGTTGCAAATGACCGCTTGTTGGAATTGACGGAGGAAAA
EST: gi|211061515|gb|FK994431.1|FK994431
EST:     TCCATTATCTCGGTTGGAATAAGAA                         CTGGGATGAATGGGTTGCAAATGACCGCTTGTTGGAATTGACGGAGGAAAA
genomic: TCCATTATCTCGGTTGGAATAAGAAgtaagtgttt ... gtttttgtagCTGGGATGAATGGGTTGCAAATGACCGCTTGTTGGAATTGACGGAGGAAAA
EST: gi|71438521|gb|DR819571.1|DR819571
EST:     TCCATTATCTCGGTTGGAATAAGAA                         CTGGGATGAATGGGTTGCAAATGACCGCTTGTTGGAATTGACGGAGGAAAA
genomic: TCCATTATCTCGGTTGGAATAAGAAgtaagtgttt ... gtttttgtagCTGGGATGAATGGGTTGCAAATGACCGCTTGTTGGAATTGACGGAGGAAAA
EST: gi|211058555|gb|FK994420.1|FK994420
EST:     TCCATTATCTCGGTTGGAATAAGAA                         CTGGGATGAATGGGTTGCAAATGACCGCTTGTTGGAATTGACGGAGGAAAA
genomic: TCCATTATCTCGGTTGGAATAAGAAgtaagtgttt ... gtttttgtagCTGGGATGAATGGGTTGCAAATGACCGCTTGTTGGAATTGACGGAGGAAAA
EST: gi|211061509|gb|FK994425.1|FK994425
EST:     TCCATTATCTCGGTTGGAATAAGAA                         CTGGGATGAATGGGTTGCAAATGACCGCTTGTTGGAATTGACGGAGGAAAA
genomic: TCCATTATCTCGGTTGGAATAAGAAgtaagtgttt ... gtttttgtagCTGGGATGAATGGGTTGCAAATGACCGCTTGTTGGAATTGACGGAGGAAAA
EST: gi|71331879|gb|DR802817.1|DR802817
EST:     TCCATTATCTCGGTTGGAATAAGAA                         CTGGGATGAATGGGTTGCAAATGACCGCTTGTTGGAATTGACGGAGGAAAA
genomic: TCCATTATCTCGGTTGGAATAAGAAgtaagtgttt ... gtttttgtagCTGGGATGAATGGGTTGCAAATGACCGCTTGTTGGAATTGACGGAGGAAAA
EST: gi|32865668|gb|CF005350.1|CF005350
EST:     TCCATTATCTCGGTTGGAATAAGAA                         CTGGGATGAATGGGTTGCAAATGACCGCTTGTTGGAATTGACGGAGGAAAA
genomic: TCCATTATCTCGGTTGGAATAAGAAgtaagtgttt ... gtttttgtagCTGGGATGAATGGGTTGCAAATGACCGCTTGTTGGAATTGACGGAGGAAAA
EST: gi|31997934|gb|CD661839.1|CD661839
EST:     TCCATTATCTCGGTTGGAATAAGAA                         CTGGGATGAATGGGTTGCAAATGACCGCTTGTTGGAATTGACGGAGGAAAA
genomic: TCCATTATCTCGGTTGGAATAAGAAgtaagtgttt ... gtttttgtagCTGGGATGAATGGGTTGCAAATGACCGCTTGTTGGAATTGACGGAGGAAAA
EST: gi|211058548|gb|FK994413.1|FK994413
EST:     TCCATTATCTCGGTTGGAATAAGAA                         CTGGGATGAATGGGTTGCAAATGACCGCTTGTTGGAATTGACGGAGGAAAA
genomic: TCCATTATCTCGGTTGGAATAAGAAgtaagtgttt ... gtttttgtagCTGGGATGAATGGGTTGCAAATGACCGCTTGTTGGAATTGACGGAGGAAAA

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 14 (upstream exon), 49 (downstream exon)
Score: 343

GGTTGGAATAAGAAgtaagtgttt ... gtttttgtagCTGGGATGAATGGGTTGCAAATGACCGCTTGTTGGAATTGACGGAGGAAAACGTGCGCAAACAACAAGAGCTTGATAAGAATCAGGTAGTTGACAAAACA


Block sizes: 14 (upstream exon), 48 (downstream exon)
Score: 167

GGTTGGAATAAGAAgtaagtgttt ... gtttttgtagCTGGGATGAATGGGTTGCAAATGACCGCTTGTTGGAATTGACGGAGGAAAACGTGCGCAAACAACAAGAGCTTGATAAGAATCAGGTAGTTGACAAAACA


Block sizes: 14 (upstream exon), 49 (downstream exon)
Score: 178

GGTTGGAATAAGAAgtaagtgttt ... gtttttgtagCTGGGATGAATGGGTTGCAAATGACCGCTTGTTGGAATTGACGGAGGAAAACGTGCGCAAACAACAAGAGCTTGATAAGAATCAGGTAGTTGACAAAACA


Block sizes: 14 (upstream exon), 48 (downstream exon)
Score: 172

GGTTGGAATAAGAAgtaagtgttt ... gtttttgtagCTGGGATGAATGGGTTGCAAATGACCGCTTGTTGGAATTGACGGAGGAAAACGTGCGCAAACAACAAGAGCTTGATAAGAATCAGGTAGTTGACAAAACA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

accacccctaagcacacatgctcctcaacatattcaatttttgttgtttttgtagCTGGGATGAATGGGTTGCAAATGACCGCTTGTTGGAATTGACGGAGGAAAACGTGCGCAAACAACAAGAGCTTGATAAGAATCAGGTAGTTGACAAAACA
                                     tttttgttgttttt  CT-rich tract
                             atattcaatttttgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agggccataactttttgtgaaggaacatttggatcgcgatccattaccacccctaagcacacatgctcctcaacatattcaatttttgttgtttttgtagCTGGGATGAATGGGTTGCAAATGACCGCTTGTTGGAATTGACGGAGGAAAACGTGCGCAAACAACAAGAGCTTGATAAGAATCAGGTAGTTGACAAAACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT