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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aatttcttatatttttaaggacatgttcagctttgctgcaaatacctagcttcctgtttacatctatgatagaatatagtttgacaaagttgttatccagGTTTGTCTTCTGCATCCTTAGAAATAACTGATGGCGCTTCAGTTGGAGATACTCCATTAACTG

Basic information

species Zea mays
transcript GRMZM2G144716_T02
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G144716_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os01g52720.1 (Oryza sativa), 3'ss of exon 3
----aatttcttatatttttaaggacatgttcagctttgctgcaaatac-ctagcttcctgtttacatctatgatagaatatagtttgacaaagttgttatccagGTTTGTCTTCTGCATCCTTAGAAATAACTGATGGCGCTTCAGTTGGAGATACTCCATTAACTG
    || |||    || |||   | ||  ||     |||   |  |||  | ||||   | || |||||||||  |  || |  ||  |   | ||||||||||||||| || |||||||| || || ||||||||||| | | | | ||| |||||| ||| |||||
attaaacttcactaatatttgttggcacatt-----ttgtaactgataggcaagctctttattcacatctatggaatgatttgattgaaaggaattgttatccagGTTTATCATCTGCATCATTGGAGATAACTGATGGTGGTGCTGGTGGGGATACTTCATCAACTG
















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|12046177|gb|BF728316.1|BF728316
EST:     AAAAGATGAGCTGAAAAGGTGGCATTTGTACTCAGATTCAGAGTATGGAG                         GTTTGTCTTCTGCATCCTTAGAAATAACTGATGGCGCTTCAGTTGGAGATA
genomic: AAAAGATGAGCTGAAAAGGTGGCATTTGTACTCAGATTCAGAGTATGGAGgtattgtatc ... tgttatccagGTTTGTCTTCTGCATCCTTAGAAATAACTGATGGCGCTTCAGTTGGAGATA
EST: gi|71429695|gb|DR810745.1|DR810745
EST:     GGCATTTGTACTCAGATTCAGAGTATGGAG                         GTTTGTCTTCTGCATCCTTAGAAATAACTGATGGCGCTTCAGTTGGAGATA
genomic: GGCATTTGTACTCAGATTCAGAGTATGGAGgtattgtatc ... tgttatccagGTTTGTCTTCTGCATCCTTAGAAATAACTGATGGCGCTTCAGTTGGAGATA
EST: gi|78179752|gb|DV550125.1|DV550125
EST:     AAAAGATGAGCTGAAAAGGTGGCATTTGTACTCAGATTCAGAGTATGGAG                         GTTTGTCTTCTGCATCCTTAGAAATAACTGATGGCGCTTCAGTTGGAGATA
genomic: AAAAGATGAGCTGAAAAGGTGGCATTTGTACTCAGATTCAGAGTATGGAGgtattgtatc ... tgttatccagGTTTGTCTTCTGCATCCTTAGAAATAACTGATGGCGCTTCAGTTGGAGATA
EST: gi|6636927|gb|AW261199.1|AW261199
EST:     AAAAGATGAGCTGAAAAGGTGGCATTTGTACTCAGATTCAGAGTATGGAG                         GTTTGTCTTCTGCATCCTTAGAAATAACTGATGGCGCTTCAGTTGGAGATA
genomic: AAAAGATGAGCTGAAAAGGTGGCATTTGTACTCAGATTCAGAGTATGGAGgtattgtatc ... tgttatccagGTTTGTCTTCTGCATCCTTAGAAATAACTGATGGCGCTTCAGTTGGAGATA
EST: gi|78081291|gb|DV509703.1|DV509703
EST:     AAAAGATGAGCTGAAAAGGTGGCATTTGTACTCAGATTCAGAGTATGGAG                         GTTTGTCTTCTGCATCCTTAGAAATAACTGATGGCGCTTCAGTTGGAGATA
genomic: AAAAGATGAGCTGAAAAGGTGGCATTTGTACTCAGATTCAGAGTATGGAGgtattgtatc ... tgttatccagGTTTGTCTTCTGCATCCTTAGAAATAACTGATGGCGCTTCAGTTGGAGATA
EST: gi|32838973|gb|CD978654.1|CD978654
EST:     ACTCAGATTCAGAGTATGGAG                         GTTTGTCTTCTGCATCCTTAGAAATAACTGATGGCGCTTCAGTTGGAGATA
genomic: ACTCAGATTCAGAGTATGGAGgtattgtatc ... tgttatccagGTTTGTCTTCTGCATCCTTAGAAATAACTGATGGCGCTTCAGTTGGAGATA
EST: gi|6827615|gb|AW331258.1|AW331258
EST:     AAAAGATGAGCTGAAAAGGTGGCATTTGTACTCAGATTCAGAGTATGGAG                         GTTTGTCTTCTGCATCCTTAGAAATAACTGATGGCGCTTCAGTTGGAGATA
genomic: AAAAGATGAGCTGAAAAGGTGGCATTTGTACTCAGATTCAGAGTATGGAGgtattgtatc ... tgttatccagGTTTGTCTTCTGCATCCTTAGAAATAACTGATGGCGCTTCAGTTGGAGATA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctagcttcctgtttacatctatgatagaatatagtttgacaaagttgttatccagGTTTGTCTTCTGCATCCTTAGAAATAACTGATGGCGCTTCAGTTGGAGATACTCCATTAACTG
                                 gtttgac  putative branch site (score: 4)
                   tatgatagaatata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aatttcttatatttttaaggacatgttcagctttgctgcaaatacctagcttcctgtttacatctatgatagaatatagtttgacaaagttgttatccagGTTTGTCTTCTGCATCCTTAGAAATAACTGATGGCGCTTCAGTTGGAGATACTCCATTAACTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT