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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atttgtattgggtttgaaacgagtcactgattagtgtttctgttgtattgctccaaagtttttctgagcaattctttgctgttgcattattgctctgtagGATTATTGCAAGAGCAAGAAGATGGAGATGACTATTAAATACATAG

Basic information

species Zea mays
transcript GRMZM5G879882_T03
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G879882_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os01g53680.1 (Oryza sativa), 3'ss of exon 11
--atttgtattgggtttgaaacgagtcactgattagtgtttctgttgta---ttgctccaaagtttttctgagcaattctttgctgttgcattattgctctgtagGATTATTGCAAGAGCAAGAAGATGGAGATGACTATTAAATACATAG
   | | |  ||| |||  |     ||| | |  | |   |   ||  |   || ||  ||  ||| ||||||  ||| |||  | |||||| | | |  |  ||||||| ||||||| ||| |||||||||||||||||||| || ||||
tagtatcttatggatttccaggatatca-taaccaattaattaattacaagtttccttgaagatttctctgag--atttttt--ttttgcatgaattccttccagGATTACTGCAAGAACAAAAAGATGGAGATGACTATTAAGTATATAG
















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|40334982|gb|CK369052.1|CK369052
EST:     GAAATAAGCTGCTTCTTGATGTTGGTCTCTGGTTGACTCACAAGATTAAG                         GATTATTGCAAGAGCAAGAAGATGGAGATGACTATTAAATACATAG
genomic: GAAATAAGCTGCTTCTTGATGTTGGTCTCTGGTTGACTCACAAGATTAAGgtacattcct ... tgctctgtagGATTATTGCAAGAGCAAGAAGATGGAGATGACTATTAAATACATAG
EST: gi|32858441|gb|CD998122.1|CD998122
EST:     GAAATAAGCTGCTTCTTGATGTTGGTCTCTGGTTGACTCACAAGATTAAG                         GATTATTGCAAGAGCAAGAAGATGGAGATGACTATTAAATACATAG
genomic: GAAATAAGCTGCTTCTTGATGTTGGTCTCTGGTTGACTCACAAGATTAAGgtacattcct ... tgctctgtagGATTATTGCAAGAGCAAGAAGATGGAGATGACTATTAAATACATAG
EST: gi|74238195|gb|DT646109.1|DT646109
EST:     GAAATAAGCTGCTTCTTGATGTTGGTCTCTGGTTGACTCACAAGATTAAG                         GATTATTGCAAGAGCAAGAAGATGGAGATGACTATTAAATACATAG
genomic: GAAATAAGCTGCTTCTTGATGTTGGTCTCTGGTTGACTCACAAGATTAAGgtacattcct ... tgctctgtagGATTATTGCAAGAGCAAGAAGATGGAGATGACTATTAAATACATAG
EST: gi|37401035|gb|CF637880.1|CF637880
EST:     GAAATAAGCTGCTTCTTGATGTTGGTCTCTGGTTGACTCACAAGATTAAG                         GATTATTGCAAGAGCAAGAAGATGGAGATGACTATTAAATACATAG
genomic: GAAATAAGCTGCTTCTTGATGTTGGTCTCTGGTTGACTCACAAGATTAAGgtacattcct ... tgctctgtagGATTATTGCAAGAGCAAGAAGATGGAGATGACTATTAAATACATAG
EST: gi|37382133|gb|CF627993.1|CF627993
EST:     GAAATAAGCTGCTTCTTGATGTTGGTCTCTGGTTGACTCACAAGATTAAG                         GATTATTGCAAGAGCAAGAAGATGGAGATGACTATTAAATACATAG
genomic: GAAATAAGCTGCTTCTTGATGTTGGTCTCTGGTTGACTCACAAGATTAAGgtacattcct ... tgctctgtagGATTATTGCAAGAGCAAGAAGATGGAGATGACTATTAAATACATAG
EST: gi|4967240|gb|AI691913.1|AI691913
EST:     CACAAGATTAAG                         GATTATTGCAAGAGCAAGAAGATGGAGATGACTATTAAATACATAG
genomic: CACAAGATTAAGgtacattcct ... tgctctgtagGATTATTGCAAGAGCAAGAAGATGGAGATGACTATTAAATACATAG
EST: gi|40336088|gb|CK370158.1|CK370158
EST:     TGGTTGACTCACAAGATTATG                         GATTATTGCAAGATCAAGAAGATGGAGATGACTATTAAATACATAG
genomic: TGGTTGACTCACAAGATTAAGgtacattcct ... tgctctgtagGATTATTGCAAGAGCAAGAAGATGGAGATGACTATTAAATACATAG
EST: gi|76286570|gb|DV026138.1|DV026138
EST:     GAAATAAGCTGCTTCTTGATGTTGGTCTCTGGTTGACTCACAAGATTAAG                         GATTATTGCAAGAGCAAGAAGATGGAGATGACTATTAAATACATAG
genomic: GAAATAAGCTGCTTCTTGATGTTGGTCTCTGGTTGACTCACAAGATTAAGgtacattcct ... tgctctgtagGATTATTGCAAGAGCAAGAAGATGGAGATGACTATTAAATACATAG
EST: gi|113703664|gb|EE681168.1|EE681168
EST:     GAAATAAGCTGCTTCTTGATGTTGGTCTCTGGTTGACTCACAAGATTAAG                         GATTATTGCAAGAGCAAGAAGATGGAGATGACTATTAAATACATAG
genomic: GAAATAAGCTGCTTCTTGATGTTGGTCTCTGGTTGACTCACAAGATTAAGgtacattcct ... tgctctgtagGATTATTGCAAGAGCAAGAAGATGGAGATGACTATTAAATACATAG
EST: gi|120480265|gb|EH210787.1|EH210787
EST:     GAAATAAGCTGCTTCTTGATGTTGGTCTCTGGTTGACTCACAAGATTAAG                         GATTATTGCAAGAGCAAGAAGATGGAGATGACTATTAAATACATAG
genomic: GAAATAAGCTGCTTCTTGATGTTGGTCTCTGGTTGACTCACAAGATTAAGgtacattcct ... tgctctgtagGATTATTGCAAGAGCAAGAAGATGGAGATGACTATTAAATACATAG
EST: gi|108954346|gb|EC365109.1|EC365109
EST:     GAAATAAGCTGCTTCTTGATGTTGGTCTCTGGTTGACTCACAAGATTAAG                         GATTATTGCAAGAGCAAGAAGATGGAGATGACTATTAAATACATAG
genomic: GAAATAAGCTGCTTCTTGATGTTGGTCTCTGGTTGACTCACAAGATTAAGgtacattcct ... tgctctgtagGATTATTGCAAGAGCAAGAAGATGGAGATGACTATTAAATACATAG
EST: gi|33942634|gb|CF349234.1|CF349234
EST:     GAAATAAGCTGCTTCTTGATGTTGGTCTCTGGTTGACTCACAAGATTAAG                         GATTATTGCAAGAGCAAGAAGATGGAGATGACTATTAAATACATAG
genomic: GAAATAAGCTGCTTCTTGATGTTGGTCTCTGGTTGACTCACAAGATTAAGgtacattcct ... tgctctgtagGATTATTGCAAGAGCAAGAAGATGGAGATGACTATTAAATACATAG
EST: gi|86474334|gb|DY240704.1|DY240704
EST:     GAAATAAGCTGCTTCTTGATGTTGGTCTCTGGTTGACTCACAAGATTAAG                         GATTATTGCAAGAGCAAGAAGATGGAGATGACTATTAAATACATAG
genomic: GAAATAAGCTGCTTCTTGATGTTGGTCTCTGGTTGACTCACAAGATTAAGgtacattcct ... tgctctgtagGATTATTGCAAGAGCAAGAAGATGGAGATGACTATTAAATACATAG
EST: gi|6540652|gb|AW225314.1|AW225314
EST:     GAAATAAGCTGCTTCTTGATGTTGGTCTCTGGTTGACTCACAAGATTAAG                         GATTATTGCAAGAGCAAGAAGATGGAGATGACTATTAAATACATAG
genomic: GAAATAAGCTGCTTCTTGATGTTGGTCTCTGGTTGACTCACAAGATTAAGgtacattcct ... tgctctgtagGATTATTGCAAGAGCAAGAAGATGGAGATGACTATTAAATACATAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattgctccaaagtttttctgagcaattctttgctgttgcattattgctctgtagGATTATTGCAAGAGCAAGAAGATGGAGATGACTATTAAATACATAG
                                            ttgctct  CT-rich tract
         aaagttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atttgtattgggtttgaaacgagtcactgattagtgtttctgttgtattgctccaaagtttttctgagcaattctttgctgttgcattattgctctgtagGATTATTGCAAGAGCAAGAAGATGGAGATGACTATTAAATACATAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- -tgtattg
- - - - - - - - - - - - -actgatt
- - - - - - - - - - - - - - - - - tgtttct
- - - - - - - - - - - - - - - - - - - - - - - - tgctcca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttttctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttgcatt