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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacctattgactctcttatgtctttgtggtgaccattatatttcattatcattgttcattcctttgttctgttcatgcagATGTTTCTAAAACTTCCTGGGTTTACTGATAACGTTTTTACGCATCTTTTAGCTGGACTTGGTGCTGGGTTTTTTGCTGTTTGCATTGGCTCTCCGGTGG

Basic information

species Zea mays
transcript GRMZM5G852877_T02
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G852877_T02 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os01g74640.3 (Oryza sativa), 3'ss of exon 5
gtacctattgactctcttatgtctt--tgtggtgaccattatatttcattatcattgttcattcctttgttctgttcatgcagATGTTTCTAAAACTTCCTGGGTTTACTGATAACGTTTTTACGCATCTTTTAGCTGGACTTGGTGCTGGGTTTTTTGCTGTTTGCATTGGCTCTCCGGTGG
|| ||| |||| ||| | |  |  |  | | ||| ||| | | | |   | | | |||||||  ||||||||||||  |||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||| |||||||||||||||||||||||||| ||||
gtgccttttgattctttcaccttgtattcttgtggccactttctatgtgtgttactgttcatcactttgttctgtttgtgcagATGTTTCTAAAACTTCCTGGGTTTACTGATAACGTTTTTACCCATCTTTTAGCTGGACTTGGTGCTGGATTTTTTGCTGTTTGCATTGGCTCTCCAGTGG
















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|88748458|gb|DY532599.1|DY532599
EST:     ATGCCATAATTAACGCTGCCGAGTTGGCCAGCTATGATCAGTTCAAACAG                         ATGTTTCTAAAACTTCCTGGGTTTACTGATAACGTTTTTACGCATCTTTTA
genomic: ATGCCATAATTAACGCTGCCGAGTTGGCCAGCTATGATCAGTTCAAACAGgtacctattg ... gttcatgcagATGTTTCTAAAACTTCCTGGGTTTACTGATAACGTTTTTACGCATCTTTTA
EST: gi|89762468|gb|DY690033.1|DY690033
EST:     ATGCCATAATTAACGCTGCCGAGTTGGCCAGCTATGATCAGTTCAAACAG                         ATGTTTCTAAAACTTCCTGGGTTTACTGATAACGTTTTTACGCATCTTTTA
genomic: ATGCCATAATTAACGCTGCCGAGTTGGCCAGCTATGATCAGTTCAAACAGgtacctattg ... gttcatgcagATGTTTCTAAAACTTCCTGGGTTTACTGATAACGTTTTTACGCATCTTTTA
EST: gi|93017381|gb|EB642901.1|EB642901
EST:     ATGCCATAATTAACGCTGCCGAGTTGGCCAGCTATGATCAGTTCAAACAG                         ATGTTTCTAAAACTTCCTGGGTTTACTGATAACGTTTTTACGCATCTTTTA
genomic: ATGCCATAATTAACGCTGCCGAGTTGGCCAGCTATGATCAGTTCAAACAGgtacctattg ... gttcatgcagATGTTTCTAAAACTTCCTGGGTTTACTGATAACGTTTTTACGCATCTTTTA
EST: gi|89250280|gb|DY622066.1|DY622066
EST:     ATGCCATAATTAACGCTGCCGAGTTGGCCAGCTATGATCAGTTCAAACAG                         ATGTTTCTAAAACTTCCTGGGTTTACTGATAACGTTTTTACGCATCTTTTA
genomic: ATGCCATAATTAACGCTGCCGAGTTGGCCAGCTATGATCAGTTCAAACAGgtacctattg ... gttcatgcagATGTTTCTAAAACTTCCTGGGTTTACTGATAACGTTTTTACGCATCTTTTA
EST: gi|78084604|gb|DV512997.1|DV512997
EST:     ATGCCATAATTAACGCTGCCGAGTTGGCCAGCTATGATCAGTTCAAACAG                         ATGTTTCTAAAACTTCCTGGGTTTACTGATAACGTTTTTACGCATCCTTTT
genomic: ATGCCATAATTAACGCTGCCGAGTTGGCCAGCTATGATCAGTTCAAACAGgtacctattg ... gttcatgcagATGTTTCTAAAACTTCCTGGGTTTACTGATAACGTTTTTACGCATC-TTTT
EST: gi|84980856|gb|DW531205.1|DW531205
EST:     ATGCCATAATTAACGCTGCCGAGTTGGCCAGCTATGATCAGTTCAAACAG                         ATGTTTCTAAAACTTCCTGGGTTTACTGATAACGTTTTTACGCATCTT
genomic: ATGCCATAATTAACGCTGCCGAGTTGGCCAGCTATGATCAGTTCAAACAGgtacctattg ... gttcatgcagATGTTTCTAAAACTTCCTGGGTTTACTGATAACGTTTTTACGCATCTT
EST: gi|6527113|gb|AW216323.1|AW216323
EST:     ATGCCATAATTAACGCTGCCGAGTTGGCCAGCTATGATCAGTTCAAACAG                         ATGTTTCTAAAACTTCCTGGGTTTACTGATAACGTTTTTACGCATCTTTTA
genomic: ATGCCATAATTAACGCTGCCGAGTTGGCCAGCTATGATCAGTTCAAACAGgtacctattg ... gttcatgcagATGTTTCTAAAACTTCCTGGGTTTACTGATAACGTTTTTACGCATCTTTTA
EST: gi|93017382|gb|EB642902.1|EB642902
EST:     ATGCCATAATTAACGCTGCCGAGTTGGCCAGCTATGATCAGTTCAAACAG                         ATGTTTCTAAAACTTCCTGGGTTTACTGATAACGTTTTTACGCATCTTTTA
genomic: ATGCCATAATTAACGCTGCCGAGTTGGCCAGCTATGATCAGTTCAAACAGgtacctattg ... gttcatgcagATGTTTCTAAAACTTCCTGGGTTTACTGATAACGTTTTTACGCATCTTTTA
EST: gi|60354253|gb|DN221226.1|DN221226
EST:     ATGCCATAATTAACGCTGCCGAGTTGGCCAGCTATGATCAGTTCAAACAG                         ATGTTTCTAAAACTTCCTGGGTTTACTGATAACGTTTTTAC
genomic: ATGCCATAATTAACGCTGCCGAGTTGGCCAGCTATGATCAGTTCAAACAGgtacctattg ... gttcatgcagATGTTTCTAAAACTTCCTGGGTTTACTGATAACGTTTTTAC
EST: gi|60401298|gb|DN234105.1|DN234105
EST:     ATGCCATAATTAACGCTGCCGAGTTGGCCAGCTATGATCAGTTCAAACAG                         ATGTTTCTAAAACTTCCTGGGTTTACTGATAACGTTTTTACGCATCTTTTA
genomic: ATGCCATAATTAACGCTGCCGAGTTGGCCAGCTATGATCAGTTCAAACAGgtacctattg ... gttcatgcagATGTTTCTAAAACTTCCTGGGTTTACTGATAACGTTTTTACGCATCTTTTA
EST: gi|101399785|gb|EB821739.1|EB821739
EST:     ATGCCATAATTAACGCTGCCGAGTTGGCCAGCTATGATCAGTTCAAACAG                         ATGTTTCTAAAACTTCCTGGGTTTACTGATAACGTTTTTACGCATCTTTTA
genomic: ATGCCATAATTAACGCTGCCGAGTTGGCCAGCTATGATCAGTTCAAACAGgtacctattg ... gttcatgcagATGTTTCTAAAACTTCCTGGGTTTACTGATAACGTTTTTACGCATCTTTTA

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: 42 (upstream exon), 47 (downstream exon)
Score: 47

GAAGGTATTGGAGCTTTGTGGACTGGCCTTGGTCCAAATGTCGCACGCAATGCCATAATTAACGCTGCCGAGTTGGCCAGCTATGATCAGTTCAAACAGgtacctattg ... gttcatgcagATGTTTCTAAAACTTCCTGGGTTTACTGATAACGTTTTTACGCATCTTTTAGCTGGACTTGGTGCTGGGTTTTTTGCTGTTTGCATTGGCTCTCCGGTGG


Block sizes: 33 (upstream exon), 46 (downstream exon)
Score: 18

GAAGGTATTGGAGCTTTGTGGACTGGCCTTGGTCCAAATGTCGCACGCAATGCCATAATTAACGCTGCCGAGTTGGCCAGCTATGATCAGTTCAAACAGgtacctattg ... gttcatgcagATGTTTCTAAAACTTCCTGGGTTTACTGATAACGTTTTTACGCATCTTTTAGCTGGACTTGGTGCTGGGTTTTTTGCTGTTTGCATTGGCTCTCCGGTGG


Block sizes: 48 (upstream exon), 41 (downstream exon)
Score: 31

GAAGGTATTGGAGCTTTGTGGACTGGCCTTGGTCCAAATGTCGCACGCAATGCCATAATTAACGCTGCCGAGTTGGCCAGCTATGATCAGTTCAAACAGgtacctattg ... gttcatgcagATGTTTCTAAAACTTCCTGGGTTTACTGATAACGTTTTTACGCATCTTTTAGCTGGACTTGGTGCTGGGTTTTTTGCTGTTTGCATTGGCTCTCCGGTGG


Block sizes: 48 (upstream exon), 41 (downstream exon)
Score: 25

GAAGGTATTGGAGCTTTGTGGACTGGCCTTGGTCCAAATGTCGCACGCAATGCCATAATTAACGCTGCCGAGTTGGCCAGCTATGATCAGTTCAAACAGgtacctattg ... gttcatgcagATGTTTCTAAAACTTCCTGGGTTTACTGATAACGTTTTTACGCATCTTTTAGCTGGACTTGGTGCTGGGTTTTTTGCTGTTTGCATTGGCTCTCCGGTGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtggtgaccattatatttcattatcattgttcattcctttgttctgttcatgcagATGTTTCTAAAACTTCCTGGGTTTACTGATAACGTTTTTACGCATCTTTTAGCTGGACTTGGTGCTGGGTTTTTTGCTGTTTGCATTGGCTCTCCGGTGG
                                 ttcctttgttctgttc  CT-rich tract
         attatatttcattatc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacctattgactctcttatgtctttgtggtgaccattatatttcattatcattgttcattcctttgttctgttcatgcagATGTTTCTAAAACTTCCTGGGTTTACTGATAACGTTTTTACGCATCTTTTAGCTGGACTTGGTGCTGGGTTTTTTGCTGTTTGCATTGGCTCTCCGGTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT