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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGTTGATGAGCAGAAGCGTTTTGTTAAGACCTACCTGAACATTTCTGgtaattctgagctcactgttggtttaatggttctgtattgtagttcagtgctgcataactgtacgtaaattttcatcaggggtacgtacagaacgcatca...

Basic information

species Zea mays
transcript GRMZM2G425249_T01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G425249_T01 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os01g51920.1 (Oryza sativa), 5'ss of exon 5
ATGTTGATGAGCAGAAGCGTTTTGTTAAGACCTACCTGAACATTTCTGgtaattctgagctcactgttggtttaat-------ggttctgtattgtagttcagtg-ctgcataactgtacgtaaattttcatcaggggtacgtacagaacgcatca----------------------------------------------------------------------
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ACACTGATGAGCAGAAGCGTTTTGTGAAGACGTACCTAAGCAATTCTGgtaagtgcaaattcatttctcgtttcattatctgaagatttctttggcactaccatgattatttgactgcaaccattctttttggaggaatatttctgttacaaattcgaattcagcttccattgaatactacttttttcacaataactagctaagatatgctcctaattttgtttag
















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|32831253|gb|CD970931.1|CD970931
EST:     ATGTTGACGAGCAGAAGCGTTTTGTTAAGACCTACCTGAACATTTCTG                         GTGAGGAACCTGATGCGGAAGTTGTGGAGAACCTGCTCCAAAGCATTGAGA
genomic: ATGTTGATGAGCAGAAGCGTTTTGTTAAGACCTACCTGAACATTTCTGgtaattctga ... tacctttcagGTGAGGAACCTGATGCGGAAGTTGTGGAGAACCTGCTCCAAAGCATTGAGA
EST: gi|32831274|gb|CD970952.1|CD970952
EST:     ATGTTGACGAGCAGAAGCGTTTTGTTAAGACCTACCTGAACATTTCTG                         GTGAGGAACCTGATGCGGAAGTTGTGGAGAACCTGCTCCAAAGCATTGAGA
genomic: ATGTTGATGAGCAGAAGCGTTTTGTTAAGACCTACCTGAACATTTCTGgtaattctga ... tacctttcagGTGAGGAACCTGATGCGGAAGTTGTGGAGAACCTGCTCCAAAGCATTGAGA
EST: gi|37422901|gb|CF649166.1|CF649166
EST:     ATGTTGATGAGCAGAAGCGTTTTGTTAAGACCTACCTGAACATTTCTG                         GTGAGGAACCTGATGCGGAAGTTGTGGAGAACCTGCTCCAAAGCATTGAG
genomic: ATGTTGATGAGCAGAAGCGTTTTGTTAAGACCTACCTGAACATTTCTGgtaattctga ... tacctttcagGTGAGGAACCTGATGCGGAAGTTGTGGAGAACCTGCTCCAAAGCATTGAG
EST: gi|84970221|gb|DW468571.1|DW468571
EST:     ATGTTGATGAGCAGAAGCGTTTTTGTTAAGACCTACCTGAACATTTCTG                         GTGAGGAACCTGATGCGGAAGTTGTGGAGAACCTGCTCCAAAGCATTGAGA
genomic: ATGTTGATGAGCAGAAGCG-TTTTGTTAAGACCTACCTGAACATTTCTGgtaattctga ... tacctttcagGTGAGGAACCTGATGCGGAAGTTGTGGAGAACCTGCTCCAAAGCATTGAGA
EST: gi|7135750|gb|AW498246.1|AW498246
EST:     ATGTTGATGAGCAGAAGCGTTTTGTTAAGACCTACCTGAACATTTCTG                         GTGAGGAACCTGATGCGGAAGTTGTG
genomic: ATGTTGATGAGCAGAAGCGTTTTGTTAAGACCTACCTGAACATTTCTGgtaattctga ... tacctttcagGTGAGGAACCTGATGCGGAAGTTGTG
EST: gi|32830339|gb|CD970017.1|CD970017
EST:     ATGTTGACGAGCAGAAGCGTTTTGTTAAGACCTACCTGAACATTTCTG                         GTGAGGAACCTGATGCGGAAGTTGTGGAGAACCTGCTCCAAAGCATTGAGA
genomic: ATGTTGATGAGCAGAAGCGTTTTGTTAAGACCTACCTGAACATTTCTGgtaattctga ... tacctttcagGTGAGGAACCTGATGCGGAAGTTGTGGAGAACCTGCTCCAAAGCATTGAGA
EST: gi|5895683|gb|AW036929.1|AW036929
EST:     CCTGAACATTTCTG                         GTGAGGAACCTGATGCGGAAGTTGTGGAGAACCTGCTCCAAAGCATTGAGA
genomic: CCTGAACATTTCTGgtaattctga ... tacctttcagGTGAGGAACCTGATGCGGAAGTTGTGGAGAACCTGCTCCAAAGCATTGAGA
EST: gi|60347369|gb|DN214342.1|DN214342
EST:     ATGTTGATGAGCAGAAGCGTTTTGTTAAGACCTACCTGAACATTTCTG                         GTGAGGAACCTGATGCGGAAGTTGTGGAGAACCTGCTCCAAAGCATTGAGA
genomic: ATGTTGATGAGCAGAAGCGTTTTGTTAAGACCTACCTGAACATTTCTGgtaattctga ... tacctttcagGTGAGGAACCTGATGCGGAAGTTGTGGAGAACCTGCTCCAAAGCATTGAGA
EST: gi|71321225|gb|DR797321.1|DR797321
EST:     ATGTTGATGAGCAGAAGCGTTTTGTTAAGACCTACCTGAACATTTCTG                         GTGAGGAACCTGATGCGGAAGTTGTGGAGAACCTGCTCCAAAGCATTGAGA
genomic: ATGTTGATGAGCAGAAGCGTTTTGTTAAGACCTACCTGAACATTTCTGgtaattctga ... tacctttcagGTGAGGAACCTGATGCGGAAGTTGTGGAGAACCTGCTCCAAAGCATTGAGA
EST: gi|89762412|gb|DY690008.1|DY690008
EST:     ATGTTGATGAGCAGAAGCGTTTTGTTAAGACCTACCTGAACATTTCTG                         GTGAGGAACCTGATGC
genomic: ATGTTGATGAGCAGAAGCGTTTTGTTAAGACCTACCTGAACATTTCTGgtaattctga ... tacctttcagGTGAGGAACCTGATGC
EST: gi|32830652|gb|CD970330.1|CD970330
EST:     ATGTTGACGAGCAGAAGCGTTTTGTTAAGACCTACCCTGA-CATTTCTG                         GTGAGGAAC-TGATGCGGAAGT
genomic: ATGTTGATGAGCAGAAGCGTTTTGTTAAGACCTACC-TGAACATTTCTGgtaattctga ... tacctttcagGTGAGGAACCTGATGCGGAAGT

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: 23 (upstream exon), 27 (downstream exon)
Score: 1

ATGTTGATGAGCAGAAGCGTTTTGTTAAGACCTACCTGAACATTTCTGgtaattctga ... tacctttcagGTGAGGAACCTGATGCGGAAGTTGTGGAGAACCTGCTCCAAAGCATTGAGAAGCACACGCTCGCCAGCCATCTAGTATGGGGCCTCTGGGGAATAATTTC


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 86

ATGTTGATGAGCAGAAGCGTTTTGTTAAGACCTACCTGAACATTTCTGgtaattctga ... tacctttcagGTGAGGAACCTGATGCGGAAGTTGTGGAGAACCTGCTCCAAAGCATTGAGAAGCACACGCTCGCCAGCCATCTAGTATGGGGCCTCTGGGGAATAATTTC


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 22

ATGTTGATGAGCAGAAGCGTTTTGTTAAGACCTACCTGAACATTTCTGgtaattctga ... tacctttcagGTGAGGAACCTGATGCGGAAGTTGTGGAGAACCTGCTCCAAAGCATTGAGAAGCACACGCTCGCCAGCCATCTAGTATGGGGCCTCTGGGGAATAATTTC


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 113

ATGTTGATGAGCAGAAGCGTTTTGTTAAGACCTACCTGAACATTTCTGgtaattctga ... tacctttcagGTGAGGAACCTGATGCGGAAGTTGTGGAGAACCTGCTCCAAAGCATTGAGAAGCACACGCTCGCCAGCCATCTAGTATGGGGCCTCTGGGGAATAATTTC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATGTTGATGAGCAGAAGCGTTTTGTTAAGACCTACCTGAACATTTCTGgtaattctgagctcactgttggtttaatggttctgtattgtagttcagtgctgcataactgtacgtaaattttcatcaggggtacgtacagaacgcatca

- - - - GAGCAG
- - - - - - AGAAGC