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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgcattcttcactcttctgaattttcaaattcttgttgcatgatttcttaaaggttaccttgcttgtcgtattatttgtccagGTTCGTCAAGGTACCCAACCTGGAGAGAAGGTCGTCCTCCGGGGCAAAG

Basic information

species Zea mays
transcript GRMZM2G118316_T01
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G118316_T01 (Zea mays), 3'ss of exon 15
lower sequence: LOC_Os12g07060.1 (Oryza sativa), 3'ss of exon 15
-----gtatgcattcttcactcttctgaattttcaaat--tcttgttgcat-gatttcttaaaggttaccttgcttgtcgtattatttgtccagGTTCGTCAAGGTACCCAACCTGGAGAGAAGGTCGTCCTCCGGGGCAAAG
     |  | |||| ||    | |   | |   ||  |  ||  |||   |  ||  ||||    | ||| || |||| |||||   ||  |||||||| |||||||||||||| ||||| ||||| |||||| |||||||||
gtattgatttcatttttgctgcgtgacactaaccatgtaatccagttatttcaatggcttaccaatgaccgtgtttgtggtatttcctgatcagGTTCGCCAAGGTACCCAACCAGGAGAAAAGGTTGTCCTCAGGGGCAAAG
















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|148947432|gb|EC892855.2|EC892855
EST:     TAGGTGGAACTGTCACGGTACCAACCCTCACTGGAAATGTTACAGTCAAG                         GTTCGTCAAGGTACCCAACCTGGAGAGAAGGTCGTCCTCCGGGGCAAAG
genomic: TAGGTGGAACTGTCACGGTACCAACCCTCACTGGAAATGTTACAGTCAAGgtatgcattc ... atttgtccagGTTCGTCAAGGTACCCAACCTGGAGAGAAGGTCGTCCTCCGGGGCAAAG
EST: gi|149101261|gb|EE187373.2|EE187373
EST:     TAGGTGGAACTGTCACGGTACCAACCCTCACTGGAAATGTTACAGTCAAG                         GTTCGTCAAGGTACCCAACCTGGAGAGAAGGTCGTCCTCCGGGGCAAAG
genomic: TAGGTGGAACTGTCACGGTACCAACCCTCACTGGAAATGTTACAGTCAAGgtatgcattc ... atttgtccagGTTCGTCAAGGTACCCAACCTGGAGAGAAGGTCGTCCTCCGGGGCAAAG
EST: gi|60397506|gb|DN230322.1|DN230322
EST:     TAGGTGGAACTGTCACGGTACCAACCCTCACTGGAAATGTTACAGTCAAG                         GTTCGTCAAGGTACCCAACCTGGAGAGAAGGTCGTCCTCCGGGGCAAAG
genomic: TAGGTGGAACTGTCACGGTACCAACCCTCACTGGAAATGTTACAGTCAAGgtatgcattc ... atttgtccagGTTCGTCAAGGTACCCAACCTGGAGAGAAGGTCGTCCTCCGGGGCAAAG
EST: gi|93017255|gb|EB642775.1|EB642775
EST:     TAGGTGGAACTGTCACGGTACCAACCCTCACTGGAAATGTTACAGTCAAG                         GTTCGTCAAGGTACCCAACCTGGAGAGAAGGTCGTCCTCCGGGGCAAAG
genomic: TAGGTGGAACTGTCACGGTACCAACCCTCACTGGAAATGTTACAGTCAAGgtatgcattc ... atttgtccagGTTCGTCAAGGTACCCAACCTGGAGAGAAGGTCGTCCTCCGGGGCAAAG
EST: gi|71757144|gb|DR955081.1|DR955081
EST:     TAGGTGGAACTGTCACGGTACCAACCCTCACTGGAAATGTTACAGTCAAG                         GTTCGTCAAGGTACCCAACCTGGAGAGAAGGTCGTCCTCCGGGGCAAAG
genomic: TAGGTGGAACTGTCACGGTACCAACCCTCACTGGAAATGTTACAGTCAAGgtatgcattc ... atttgtccagGTTCGTCAAGGTACCCAACCTGGAGAGAAGGTCGTCCTCCGGGGCAAAG
EST: gi|211267316|gb|FL091730.1|FL091730
EST:     TAGGTGGAACTGTCACGGTACCAACCCTCACTGGAAATGTTACAGTCAAG                         GTTCGTCAAGGTACCCAACCTGGAGAGAAGGTCGTCCTCCGGGGCAAAG
genomic: TAGGTGGAACTGTCACGGTACCAACCCTCACTGGAAATGTTACAGTCAAGgtatgcattc ... atttgtccagGTTCGTCAAGGTACCCAACCTGGAGAGAAGGTCGTCCTCCGGGGCAAAG
EST: gi|76922540|gb|DV169051.1|DV169051
EST:     TAGGTGGAACTGTCACGGTACCAACCCTCACTGGAAATGTTACAGTCAAG                         GTTCGTCAAGGTACCCAACCTGGAGAGAAGGTCGTCCTCCGGGGCAAAG
genomic: TAGGTGGAACTGTCACGGTACCAACCCTCACTGGAAATGTTACAGTCAAGgtatgcattc ... atttgtccagGTTCGTCAAGGTACCCAACCTGGAGAGAAGGTCGTCCTCCGGGGCAAAG
EST: gi|17929416|gb|BM266376.1|BM266376
EST:     TAGGTGGAACTGTCACGGTACCAACCCTCACTGGAAATGTTACAGTCAAG                         GTTCGTCAAGGTACCCAACCTGGAGAGAAGGTCGTCCTCCGGGGCAAAG
genomic: TAGGTGGAACTGTCACGGTACCAACCCTCACTGGAAATGTTACAGTCAAGgtatgcattc ... atttgtccagGTTCGTCAAGGTACCCAACCTGGAGAGAAGGTCGTCCTCCGGGGCAAAG
EST: gi|86469547|gb|DY235917.1|DY235917
EST:     TAGGTGGAACTGTCACGGTACCAACCCTCACTGGAAATGTTACAGTCAAG                         GTTCGTCAAGGTACCCAACCTGGAGAGAAGGTCGTCCTCCGGGGCAAAG
genomic: TAGGTGGAACTGTCACGGTACCAACCCTCACTGGAAATGTTACAGTCAAGgtatgcattc ... atttgtccagGTTCGTCAAGGTACCCAACCTGGAGAGAAGGTCGTCCTCCGGGGCAAAG
EST: gi|60398827|gb|DN231643.1|DN231643
EST:     TAGGTGGAACTGTCACGGTACCAACCCTCACTGGAAATGTTACAGTCAAG                         GTTCGTCAAGGTACCCAACCTGGAGAGAAGGTCGTCCTCCGGGGCAAAG
genomic: TAGGTGGAACTGTCACGGTACCAACCCTCACTGGAAATGTTACAGTCAAGgtatgcattc ... atttgtccagGTTCGTCAAGGTACCCAACCTGGAGAGAAGGTCGTCCTCCGGGGCAAAG
EST: gi|211267317|gb|FL091731.1|FL091731
EST:     TAGGTGGAACTGTCACGGTACCAACCCTCACTGGAAATGTTACAGTCAAG                         GTTCGTCAAGGTACCCAACCTGGAGAGAAGGTCGTCCTCCGGGGCAAAG
genomic: TAGGTGGAACTGTCACGGTACCAACCCTCACTGGAAATGTTACAGTCAAGgtatgcattc ... atttgtccagGTTCGTCAAGGTACCCAACCTGGAGAGAAGGTCGTCCTCCGGGGCAAAG
EST: gi|71769071|gb|DR967008.1|DR967008
EST:     TAGGTGGAACTGTCACGGTACCAACCCTCACTGGAAATGTTACAGTCAAG                         GTTCGTCAAGGTACCCAACCTGGAGAGAAGGTCGTCCTCCGGGGCAAAG
genomic: TAGGTGGAACTGTCACGGTACCAACCCTCACTGGAAATGTTACAGTCAAGgtatgcattc ... atttgtccagGTTCGTCAAGGTACCCAACCTGGAGAGAAGGTCGTCCTCCGGGGCAAAG
EST: gi|71427930|gb|DR808980.1|DR808980
EST:     TAGGTGGAACTGTCACGGTACCAACCCTCACTGGAAATGTTACAGTCAAG                         GTTCGTCAAGGTACCCAACCTGGAGAGAAGGTCGTCCTCCGGGGCAAAG
genomic: TAGGTGGAACTGTCACGGTACCAACCCTCACTGGAAATGTTACAGTCAAGgtatgcattc ... atttgtccagGTTCGTCAAGGTACCCAACCTGGAGAGAAGGTCGTCCTCCGGGGCAAAG
EST: gi|211435107|gb|FL442358.1|FL442358
EST:     TAGGTGGAACTGTCACGGTACCAACCCTCACTGGAAATGTTACAGTCAAG                         GTTCGTCAAGGTACCCAACCTGGAGAGAAGGTCGTCCTCCGGGGCAAAG
genomic: TAGGTGGAACTGTCACGGTACCAACCCTCACTGGAAATGTTACAGTCAAGgtatgcattc ... atttgtccagGTTCGTCAAGGTACCCAACCTGGAGAGAAGGTCGTCCTCCGGGGCAAAG
EST: gi|6022509|gb|AW067542.1|AW067542
EST:     TAGGTGGAACTGTCACTGTACCAACCCTCACTGGAAATGTTACAGNCAAG                         GTTCGTCAAGGTACCCAACCTGGAGAGAAGGTGGTCCTCCGGGGCAAAG
genomic: TAGGTGGAACTGTCACGGTACCAACCCTCACTGGAAATGTTACAGTCAAGgtatgcattc ... atttgtccagGTTCGTCAAGGTACCCAACCTGGAGAGAAGGTCGTCCTCCGGGGCAAAG
EST: gi|37397730|gb|CF636173.1|CF636173
EST:     TAGGTGGAACTGTCACGGTACCAACCCTCACTGGAAATGTTACAGTCAAG                         GTTCGTCAAGGTACCCAGCCTGGAGAGAAGGTGGTCCTACGGGGCAAAG
genomic: TAGGTGGAACTGTCACGGTACCAACCCTCACTGGAAATGTTACAGTCAAGgtatgcattc ... atttgtccagGTTCGTCAAGGTACCCAACCTGGAGAGAAGGTCGTCCTCCGGGGCAAAG
EST: gi|67040336|gb|CO466591.1|CO466591
EST:     TAGGTGGAACTGTCACGGTACCAACCCTCACTGGAAATGTTACAGTCAAG                         GTTCGTCAAGGTACCCAACCTGGAGAGAAGGTGGTCCTCCGGGGCAAAG
genomic: TAGGTGGAACTGTCACGGTACCAACCCTCACTGGAAATGTTACAGTCAAGgtatgcattc ... atttgtccagGTTCGTCAAGGTACCCAACCTGGAGAGAAGGTCGTCCTCCGGGGCAAAG
EST: gi|40337178|gb|CK371248.1|CK371248
EST:     TAGGTGGAACTGTCACGGTACCAACCCTCACTGGAAATGTTACAGTCAAG                         GTTCGTCAAGGTACCCAGCCTGGAGAGAAGGTGGTCCTACGGGGCAAAG
genomic: TAGGTGGAACTGTCACGGTACCAACCCTCACTGGAAATGTTACAGTCAAGgtatgcattc ... atttgtccagGTTCGTCAAGGTACCCAACCTGGAGAGAAGGTCGTCCTCCGGGGCAAAG

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: 47 (upstream exon), 49 (downstream exon)
Score: 273

GCTGTCCTAGGTGGAACTGTCACGGTACCAACCCTCACTGGAAATGTTACAGTCAAGgtatgcattc ... atttgtccagGTTCGTCAAGGTACCCAACCTGGAGAGAAGGTCGTCCTCCGGGGCAAAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 209

GCTGTCCTAGGTGGAACTGTCACGGTACCAACCCTCACTGGAAATGTTACAGTCAAGgtatgcattc ... atttgtccagGTTCGTCAAGGTACCCAACCTGGAGAGAAGGTCGTCCTCCGGGGCAAAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 185

GCTGTCCTAGGTGGAACTGTCACGGTACCAACCCTCACTGGAAATGTTACAGTCAAGgtatgcattc ... atttgtccagGTTCGTCAAGGTACCCAACCTGGAGAGAAGGTCGTCCTCCGGGGCAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 274

GCTGTCCTAGGTGGAACTGTCACGGTACCAACCCTCACTGGAAATGTTACAGTCAAGgtatgcattc ... atttgtccagGTTCGTCAAGGTACCCAACCTGGAGAGAAGGTCGTCCTCCGGGGCAAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attcttgttgcatgatttcttaaaggttaccttgcttgtcgtattatttgtccagGTTCGTCAAGGTACCCAACCTGGAGAGAAGGTCGTCCTCCGGGGCAAAG
                                              tttgtcc  CT-rich tract
              atttcttaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgcattcttcactcttctgaattttcaaattcttgttgcatgatttcttaaaggttaccttgcttgtcgtattatttgtccagGTTCGTCAAGGTACCCAACCTGGAGAGAAGGTCGTCCTCCGGGGCAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG