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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtgataaaaactaaaatttttacgtctccatatccattgacaaagctagattgcatctatgcttacgccttctatcttttgaataaaagGTTCTTCGCATTCTTGAGGGTGACATGGTCGTGGAATCTGGTGGTTCTGTTACTGGCAGTAGTGATTCTGGGAGCAGAAGCTGGAGGATGCTGAACGAAC

Basic information

species Zea mays
transcript GRMZM2G480607_T04
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G480607_T06 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os01g41870.1 (Oryza sativa), 3'ss of exon 9
-------gttagtgataaaaactaaaatttttacgtctccatatccattgacaaagctagattgcatctatgcttacgcctt---ctatcttttgaataaaagGTTCTTCGCATTCTTGAGGGTGACATGGTCGTGGAATCTGGTGGTTCTGTTACTGGCAGTAGTGATTCTGGGAGCAGAAGCTGGAGGATGCTGAACGAAC
        ||     |   | ||  |||| ||  ||    | |  ||||   | | || |||    |  ||||||   | ||    |||||||||  ||   |||||| ||||| || ||||| |||||||| || || |||||   |  |    |    |||||||||||||||||||| |||||| | |||||||| ||||
gttagttttttccagttctatctgcaattattttgttcttaga--cattagtaca-ctggatcttctaaatgcttttcctttattttatcttttgttta---gGTTCTACGCATACTAGAGGGCGACATGGTTGTCGATTCTGGCTCTGTTTCAGCCCCAAGTAGTGATTCTGGGAGCAGGAGCTGGCGAATGCTGAATGAAC
















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|18661817|gb|BM501594.1|BM501594
EST:     CAAACTTGTGCATAAGACGCGACCCACATTCAAGGCCTCGCATGTCCCAT                         GTTCTTCGCATTCTTGAGGGTGACATGGTCGTGGAATCTGGTGGTTCTGTT
genomic: CAAACTTGTGCATAAGACGCGACCCACATTCAAGGCCTCGCATGTCCCATgttagtgata ... tgaataaaagGTTCTTCGCATTCTTGAGGGTGACATGGTCGTGGAATCTGGTGGTTCTGTT
EST: gi|18963101|gb|BM660240.1|BM660240
EST:     CAAACTTGTGCATAAGACGCGACCCACATTCAAGGCCTCGCATGTCCCAT                         GTTCTTCGCATTCTTGAGGGTGACATGGTCGTGGAATCTGGTGGTTCTGTT
genomic: CAAACTTGTGCATAAGACGCGACCCACATTCAAGGCCTCGCATGTCCCATgttagtgata ... tgaataaaagGTTCTTCGCATTCTTGAGGGTGACATGGTCGTGGAATCTGGTGGTTCTGTT
EST: gi|78023542|gb|DV491929.1|DV491929
EST:     CAAACTTGTGCATAAGACGCGACCCACATTCAAGGCCTCGCATGTCCCAT                         GTTCTTCGCATTCTTGAGGGTGACATGGTCGTGGAATCTGGTGGTTCTGTT
genomic: CAAACTTGTGCATAAGACGCGACCCACATTCAAGGCCTCGCATGTCCCATgttagtgata ... tgaataaaagGTTCTTCGCATTCTTGAGGGTGACATGGTCGTGGAATCTGGTGGTTCTGTT
EST: gi|29129926|gb|CB380630.1|CB380630
EST:     CAAACTTGTGCATAAGACGCGACCCACATTCAAGGCCTCGCATGTCCCAT                         GTTCTTCGCATTCTTGAGGGTGACATGGTCGTGGAATCTGGTGGTTCTGTT
genomic: CAAACTTGTGCATAAGACGCGACCCACATTCAAGGCCTCGCATGTCCCATgttagtgata ... tgaataaaagGTTCTTCGCATTCTTGAGGGTGACATGGTCGTGGAATCTGGTGGTTCTGTT
EST: gi|18655098|gb|BM499903.1|BM499903
EST:     CAAACTTGTGCATAAGACGCGACCCACATTCAAGGCCTCGCATGTCCCAT                         GTTCTTCGCATTCTTGAGGGTGACATGGTCGTGGAATCTGGTGGTTCTGTT
genomic: CAAACTTGTGCATAAGACGCGACCCACATTCAAGGCCTCGCATGTCCCATgttagtgata ... tgaataaaagGTTCTTCGCATTCTTGAGGGTGACATGGTCGTGGAATCTGGTGGTTCTGTT
EST: gi|149095516|gb|EE181172.2|EE181172
EST:     CAAACTTGTGCATAAGACGCGACCCACATTCAAGGCCTCGCATGTCCCAT                         GTTCTTCGCATTCTTGAGGGTGACATGGTCGTGGAATCTGGTGGTTCTGTT
genomic: CAAACTTGTGCATAAGACGCGACCCACATTCAAGGCCTCGCATGTCCCATgttagtgata ... tgaataaaagGTTCTTCGCATTCTTGAGGGTGACATGGTCGTGGAATCTGGTGGTTCTGTT
EST: gi|88750768|gb|DY534909.1|DY534909
EST:     ACTTGTGCATAAGACGCGACCCACATTCAAGGCCTCGCATGTCCCAT                         GTTCTTCGCATTCTTGAGGGTGACATGGTCGTGGAATCTGGTGGTTCTGTT
genomic: ACTTGTGCATAAGACGCGACCCACATTCAAGGCCTCGCATGTCCCATgttagtgata ... tgaataaaagGTTCTTCGCATTCTTGAGGGTGACATGGTCGTGGAATCTGGTGGTTCTGTT
EST: gi|60349296|gb|DN216269.1|DN216269
EST:     CAAACTTGTGCATAAGACGCGACCCACATTCAAGGCCTCGCATGTCCCAT                         GTTCTTCGCATTCTTGAGGGTGACATGGTCGTGGAATCTGGTGGTTCTGTT
genomic: CAAACTTGTGCATAAGACGCGACCCACATTCAAGGCCTCGCATGTCCCATgttagtgata ... tgaataaaagGTTCTTCGCATTCTTGAGGGTGACATGGTCGTGGAATCTGGTGGTTCTGTT
EST: gi|18963177|gb|BM660284.1|BM660284
EST:     CAAACTTGTGCATAAGACGCGACCCACATTCAAGGCCTCGCATGTCCCAT                         GTTCTTCGCATTCTTGAGGGTGACATGGTCGTGGAATCTGGTGGTTCTGTT
genomic: CAAACTTGTGCATAAGACGCGACCCACATTCAAGGCCTCGCATGTCCCATgttagtgata ... tgaataaaagGTTCTTCGCATTCTTGAGGGTGACATGGTCGTGGAATCTGGTGGTTCTGTT
EST: gi|6021797|gb|AW066725.1|AW066725
EST:     CAAACTTGTGCATAAGACGCGACCCACATTCAAGGCCTCGCATGTCCCAT                         GTTCTTCGCATTCTTGAGGGTGACATGGTCGTGGAATCTGGTGGTTCTGTT
genomic: CAAACTTGTGCATAAGACGCGACCCACATTCAAGGCCTCGCATGTCCCATgttagtgata ... tgaataaaagGTTCTTCGCATTCTTGAGGGTGACATGGTCGTGGAATCTGGTGGTTCTGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cattgacaaagctagattgcatctatgcttacgccttctatcttttgaataaaagGTTCTTCGCATTCTTGAGGGTGACATGGTCGTGGAATCTGGTGGTTCTGTTACTGGCAGTAGTGATTCTGGGAGCAGAAGCTGGAGGATGCTGAACGAAC
                         tgcttac  putative branch site (score: 2)
                               cgccttctatctttt  CT-rich tract
                                      tatcttttgaataaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagtgataaaaactaaaatttttacgtctccatatccattgacaaagctagattgcatctatgcttacgccttctatcttttgaataaaagGTTCTTCGCATTCTTGAGGGTGACATGGTCGTGGAATCTGGTGGTTCTGTTACTGGCAGTAGTGATTCTGGGAGCAGAAGCTGGAGGATGCTGAACGAAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG