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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGAAACTGAAGGCCAGTGCATCTGTTAAGCACCTTGCTCTTCCTTGTAACAAGGCAGCAAGGGCACAACTTATTCCAGATATTATCCGATGTTACAGCCAgtatgtactacccataaatggttgtcttttttcagtatgccatttgattttcgttgactttgctaaacttttctttgcttcag

Basic information

species Zea mays
transcript GRMZM2G164956_T02
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G164956_T02 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os09g34910.1 (Oryza sativa), 5'ss of exon 6
AGAAACTGAAGGCCAGTGCATCTGTTAAGCACCTTGCTCTTCCTTGTAACAAGGCAGCAAGGGCACAACTTATTCCAGATATTATCCGATGTTACAGCCAgtatgtactacccataaatggttgtcttttttcagtatgccatttgattttcgttgactttgctaaacttttctttg-cttcag
||||| |||| || ||||||||||||| ||| ||||||||||||||||||   || |||||||| ||| |||||||||| || |||||||| || |||| || ||||| |||||  ||   ||||| || |        |  |||  |  |   | ||||  |     || | |||| ||||||
AGAAATTGAAAGCTAGTGCATCTGTTAGGCATCTTGCTCTTCCTTGTAACCGTGCTGCAAGGGCTCAAGTTATTCCAGACATCATCCGATGCTATAGCCGgtgtgtac-acccaccaa--attgtccttgtgagaataactttttagtcatttcttacttaccc---tttatatttgtcttcag
















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|22491136|gb|BU051059.1|BU051059
EST:     AAGGCAGCAAGGGCACAACTTATTCCAGATATTATCCGATGTTACAGCCA                         TGGAGGCCGAACCATTATCTTCACTGAGACGAAGGATTCTGCATCAGAGCT
genomic: AAGGCAGCAAGGGCACAACTTATTCCAGATATTATCCGATGTTACAGCCAgtatgtacta ... tttgcttcagTGGAGGCCGAACCATTATCTTCACTGAGACGAAGGATTCTGCATCAGAGCT
EST: gi|18964493|gb|BM661037.1|BM661037
EST:     AAGGCAGCAAGGGCACAACTTATTCCAGATATTATCCGATGTTACAGCCA                         TGGAGGCCGAACCATTATCTTCACTGAGGCCGGAGGGTTTCTGCATCAGAG
genomic: AAGGCAGCAAGGGCACAACTTATTCCAGATATTATCCGATGTTACAGCCAgtatgtacta ... tttgcttcagTGGAGGCCGAACCATTATCTTCACTGAGAC-GAAGGATT-CTGCATCAGAG
EST: gi|32802153|gb|CD954389.1|CD954389
EST:     GGGCAGCAAGGGCACCAACTTATTCCAGATATTATCCGATGTTACAGCCA                         TGGAGGCCGAACCATTATCTTCACTGAGACGAAGGATTCTGCATCAGAGCT
genomic: -GGCAGCAAGGGCA-CAACTTATTCCAGATATTATCCGATGTTACAGCCAgtatgtacta ... tttgcttcagTGGAGGCCGAACCATTATCTTCACTGAGACGAAGGATTCTGCATCAGAGCT
EST: gi|32928427|gb|CF033239.1|CF033239
EST:     AAGGCAGCAAGGGCACAACTTATTCCAGATATTATCCGATGTTACAGCCA                         TGGAGGCCGAACCATTATCTTCACTGAGACGAAGGATTCTGCATCAGAGCT
genomic: AAGGCAGCAAGGGCACAACTTATTCCAGATATTATCCGATGTTACAGCCAgtatgtacta ... tttgcttcagTGGAGGCCGAACCATTATCTTCACTGAGACGAAGGATTCTGCATCAGAGCT
EST: gi|32846981|gb|CD986662.1|CD986662
EST:     AAGGCAGCAAGGGCACAACTTATTCCAGATATTATCCGATGTTACAGCCA                         TGGAGGCCGAACCATTATCTTCACTGAGACGAAGGATTCTGCATCCAGAGC
genomic: AAGGCAGCAAGGGCACAACTTATTCCAGATATTATCCGATGTTACAGCCAgtatgtacta ... tttgcttcagTGGAGGCCGAACCATTATCTTCACTGAGACGAAGGATTCTGCATC-AGAGC
EST: gi|19272557|gb|BM888813.1|BM888813
EST:     AAGGCAGCAAGGGCACAACTTATTCCAGATATTATCCGATGTTACAGCCA                         TGGAGGCCGAACCATTATCTTCACTGAGACGAAGGATTCTGCATCAGAGCT
genomic: AAGGCAGCAAGGGCACAACTTATTCCAGATATTATCCGATGTTACAGCCAgtatgtacta ... tttgcttcagTGGAGGCCGAACCATTATCTTCACTGAGACGAAGGATTCTGCATCAGAGCT
EST: gi|32929175|gb|CF033987.1|CF033987
EST:     AAGGCAGCAAGGGCACAACTTATTCCAGATATTATCCGATGTTACAGCCA                         TGGAGGCCGAACCATTATCTTCGCTGAGACGAAGGATTCTGCATCAGAGCT
genomic: AAGGCAGCAAGGGCACAACTTATTCCAGATATTATCCGATGTTACAGCCAgtatgtacta ... tttgcttcagTGGAGGCCGAACCATTATCTTCACTGAGACGAAGGATTCTGCATCAGAGCT
EST: gi|161407373|gb|DW042376.1|DW042376
EST:     TAGGCAGCAAGGGCACTACTTATTCCAGATATTATCCGATGTTACAGCCA                         TGGAGGCCGAACCATTATCTTCACTGAGACGAAGGATTCTGCATCAGAGCT
genomic: AAGGCAGCAAGGGCACAACTTATTCCAGATATTATCCGATGTTACAGCCAgtatgtacta ... tttgcttcagTGGAGGCCGAACCATTATCTTCACTGAGACGAAGGATTCTGCATCAGAGCT
EST: gi|87153206|gb|DY397995.1|DY397995
EST:     AAGGCAGCAAGGGCACAACTTATTCCAGATATTATCCGATGTTACAGCCA                         TGGAGGCCGAACCATTATCTTCACTGAGACGAAGGATTCTGCATCAGAGCT
genomic: AAGGCAGCAAGGGCACAACTTATTCCAGATATTATCCGATGTTACAGCCAgtatgtacta ... tttgcttcagTGGAGGCCGAACCATTATCTTCACTGAGACGAAGGATTCTGCATCAGAGCT
EST: gi|32928455|gb|CF033267.1|CF033267
EST:     AAGGCAGCAAGGGCACAACTTATTCCAGATATTATCCGATGTTACAGCCA                         TGGAGGCCGAACCATTATCTTCACTGAGACGAAGGATTCTGCATCAGAGCT
genomic: AAGGCAGCAAGGGCACAACTTATTCCAGATATTATCCGATGTTACAGCCAgtatgtacta ... tttgcttcagTGGAGGCCGAACCATTATCTTCACTGAGACGAAGGATTCTGCATCAGAGCT

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: 49 (upstream exon), 49 (downstream exon)
Score: 398

AGAAACTGAAGGCCAGTGCATCTGTTAAGCACCTTGCTCTTCCTTGTAACAAGGCAGCAAGGGCACAACTTATTCCAGATATTATCCGATGTTACAGCCAgtatgtacta ... tttgcttcagTGGAGGCCGAACCATTATCTTCACTGAGACGAAGGATTCTGCATCAGAGCTTTCTGGTTTGATTCCTGGATCCCGTGCCTTGCATGGAGATGTTGTGCAA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 237

AGAAACTGAAGGCCAGTGCATCTGTTAAGCACCTTGCTCTTCCTTGTAACAAGGCAGCAAGGGCACAACTTATTCCAGATATTATCCGATGTTACAGCCAgtatgtacta ... tttgcttcagTGGAGGCCGAACCATTATCTTCACTGAGACGAAGGATTCTGCATCAGAGCTTTCTGGTTTGATTCCTGGATCCCGTGCCTTGCATGGAGATGTTGTGCAA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 273

AGAAACTGAAGGCCAGTGCATCTGTTAAGCACCTTGCTCTTCCTTGTAACAAGGCAGCAAGGGCACAACTTATTCCAGATATTATCCGATGTTACAGCCAgtatgtacta ... tttgcttcagTGGAGGCCGAACCATTATCTTCACTGAGACGAAGGATTCTGCATCAGAGCTTTCTGGTTTGATTCCTGGATCCCGTGCCTTGCATGGAGATGTTGTGCAA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 103

AGAAACTGAAGGCCAGTGCATCTGTTAAGCACCTTGCTCTTCCTTGTAACAAGGCAGCAAGGGCACAACTTATTCCAGATATTATCCGATGTTACAGCCAgtatgtacta ... tttgcttcagTGGAGGCCGAACCATTATCTTCACTGAGACGAAGGATTCTGCATCAGAGCTTTCTGGTTTGATTCCTGGATCCCGTGCCTTGCATGGAGATGTTGTGCAA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGAAACTGAAGGCCAGTGCATCTGTTAAGCACCTTGCTCTTCCTTGTAACAAGGCAGCAAGGGCACAACTTATTCCAGATATTATCCGATGTTACAGCCAgtatgtactacccataaatggttgtcttttttcagtatgccatttgattttcgttgactttgctaaacttttctttgcttcag

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