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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgcgctgctagctgcagccacacacagcacgctctcatattccttcctccttcctttgtggttctgtgcatgtcttcggtggagtcactcccatgtgaatgccctcgggtgtgttcttgcgcgtctcgcttagGATCCTGGCATGGGAGGACGGGTTCTGCAACTTCGCGGCGGCCAGCAGCTCTGCCGCCGCGTCCGCGTGCGGCCAAGAGGGGGCAGCGGCAGCTGCGGCG

Basic information

species Zea mays
transcript GRMZM2G136831_T03
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G136831_T03 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os06g12740.1 (Oryza sativa), 3'ss of exon 2
gtacgcgctgctagctgcagccacacacagcacgctctcatattccttcctccttcctttgtggttctgtgcatgtcttcggtggagtcactcccatgtgaatgc-cctcgggtgtgttcttgcgcgtctcgcttagGATCCTGGCATGGGAGGACGGGTTCTGCAACTTCGCGGCGGCCAGCAGCTCTGCCGCCGCGTCCGCGTGCGGCCAAG--AGGGGGCAGCGGCAGCTGCGGCG
                                   |  |  |   || |  |  | || ||        |   ||   | | |      ||||   |     ||   |||   ||    |         |||| ||||||| |||| |||||||||||||||||||||||||||||  ||  |  | |  | || ||| | ||| |  | |     | | ||| |||| |   | || |
----------------------------------gtaactgaagtctactccactactctgcttcgtcttctttgctcttgctactactactctactagctttgtgtctcatttgcaaacaaaaaaaaatcgcctagGATCTTGGCGTGGGAGGACGGGTTCTGCAACTTCGCGGCCACCTCCGCCGC--CTGCGGCGACGGCGCGGCGGCGGCTTACGCGGCCGCGGAATGCGAGGAG
















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|101386485|gb|EB815259.1|EB815259
EST:     GATCTCCCTGGCGCCGCGTACGACAGGACCCGAGGGAACAGGAGGAACTG                         GATCCTGGCATGGGAGGACGGGTTCTGCAACTTCGCGGCGGCCAGCAGCTC
genomic: GATCTCCCTGGCGCCGCGTACGACAGGACCCGAGGGAACAGGAGGAACTGgtacgcgctg ... tctcgcttagGATCCTGGCATGGGAGGACGGGTTCTGCAACTTCGCGGCGGCCAGCAGCTC
EST: gi|149070786|gb|EE159197.2|EE159197
EST:     GATCTCCCTGGCGCCGCGTACGACAGGACCCGAGGGAACAGGAGGAACTG                         GATCCTGGCATGGGAGGACGGGTTCTGCAACTTCGCGGCGGCCAGCAGCTC
genomic: GATCTCCCTGGCGCCGCGTACGACAGGACCCGAGGGAACAGGAGGAACTGgtacgcgctg ... tctcgcttagGATCCTGGCATGGGAGGACGGGTTCTGCAACTTCGCGGCGGCCAGCAGCTC
EST: gi|74238082|gb|DT645996.1|DT645996
EST:     GATCTCCCTGGCGCCGCGTACGACAGGACCCGAGGGAACAGGAGGAACTG                         GATCCTGGCATGGGAGGACGGGTTCTGCAACTTCGCGGCGGCCAGCAGCTC
genomic: GATCTCCCTGGCGCCGCGTACGACAGGACCCGAGGGAACAGGAGGAACTGgtacgcgctg ... tctcgcttagGATCCTGGCATGGGAGGACGGGTTCTGCAACTTCGCGGCGGCCAGCAGCTC
EST: gi|148980599|gb|EE027224.2|EE027224
EST:     GATCTCCCTGGCGCCGCGTACGACAGGACCCGAGGGAACAGGAGGAACTG                         GATCCTGGCATGGGAGGACGGGTTCTGCAACTTCGCGGCGGCCAGCAGCTC
genomic: GATCTCCCTGGCGCCGCGTACGACAGGACCCGAGGGAACAGGAGGAACTGgtacgcgctg ... tctcgcttagGATCCTGGCATGGGAGGACGGGTTCTGCAACTTCGCGGCGGCCAGCAGCTC
EST: gi|71435285|gb|DR816335.1|DR816335
EST:     GATCTCCCTGGCGCCGCGTACGACAGGACCCGAGGGAACAGGAGGAACTG                         GATCCTGGCATGGGAGGACGGGTTCTGCAACTTCGCGGCGGGCAGCAGCTC
genomic: GATCTCCCTGGCGCCGCGTACGACAGGACCCGAGGGAACAGGAGGAACTGgtacgcgctg ... tctcgcttagGATCCTGGCATGGGAGGACGGGTTCTGCAACTTCGCGGCGGCCAGCAGCTC
EST: gi|71429782|gb|DR810832.1|DR810832
EST:     GATCTCCCTGGCGCCGCGTACGACAGGACCCGAGGGAACAGGAGGAACTG                         GATCCTGGCATGGGAGGACGGGTTCTGCAACTTCGCGGCGGCCAGCAGCTC
genomic: GATCTCCCTGGCGCCGCGTACGACAGGACCCGAGGGAACAGGAGGAACTGgtacgcgctg ... tctcgcttagGATCCTGGCATGGGAGGACGGGTTCTGCAACTTCGCGGCGGCCAGCAGCTC
EST: gi|76287078|gb|DV026646.1|DV026646
EST:     GATCTCCCTGGCGCCGCGTACGACAGGACCCGAGGGAACAGGAGGAACTG                         GATCCTGGCATGGGAGGACGGGTTCTGCAACTTCGCGGCGGCCAGCAGCTC
genomic: GATCTCCCTGGCGCCGCGTACGACAGGACCCGAGGGAACAGGAGGAACTGgtacgcgctg ... tctcgcttagGATCCTGGCATGGGAGGACGGGTTCTGCAACTTCGCGGCGGCCAGCAGCTC
EST: gi|149104906|gb|EE290376.2|EE290376
EST:     GATCTCCCTGGCGCCGCGTACGACAGGACCCGAGGGAACAGGAGGAACTG                         GATCCTGGCATGGGAGGACGGGTTCTGCAACTTCGCGGCGGCCAGCAGCTC
genomic: GATCTCCCTGGCGCCGCGTACGACAGGACCCGAGGGAACAGGAGGAACTGgtacgcgctg ... tctcgcttagGATCCTGGCATGGGAGGACGGGTTCTGCAACTTCGCGGCGGCCAGCAGCTC
EST: gi|78119598|gb|DV537982.1|DV537982
EST:     GATCTCCCTGGCGCCGCGTACGACAGGACCCGAGGGAACAGGAGGAACTG                         GATCCTGGCATGGGAGGGCGGGTTCTGCAACTTTCGCGGCGGCCAG
genomic: GATCTCCCTGGCGCCGCGTACGACAGGACCCGAGGGAACAGGAGGAACTGgtacgcgctg ... tctcgcttagGATCCTGGCATGGGAGGACGGGTTCTGCAACTT-CGCGGCGGCCAG
EST: gi|94477121|gb|EB706079.1|EB706079
EST:     GATCTCCCTGGCGCCGCGTACGACAGGACCCGAGGGAACAGGAGGAACTG                         GATCCTGGCATGGGAGGACGGGTTCTGCAACTTCGCGGCGGCCAGCAGCTC
genomic: GATCTCCCTGGCGCCGCGTACGACAGGACCCGAGGGAACAGGAGGAACTGgtacgcgctg ... tctcgcttagGATCCTGGCATGGGAGGACGGGTTCTGCAACTTCGCGGCGGCCAGCAGCTC
EST: gi|78111427|gb|DV529824.1|DV529824
EST:     GATCTCCCTGGCGCCGCGTACGACAGGACCCGAGGGAACAGGAGGAACTG                         GATCCTGGCATGGGAGGACGGGTTCTGCAACTTCGCGGCGGCCAGCAGCTC
genomic: GATCTCCCTGGCGCCGCGTACGACAGGACCCGAGGGAACAGGAGGAACTGgtacgcgctg ... tctcgcttagGATCCTGGCATGGGAGGACGGGTTCTGCAACTTCGCGGCGGCCAGCAGCTC

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: 46 (upstream exon), 48 (downstream exon)
Score: 61

ATGGGATCTCCCTGGCGCCGCGTACGACAGGACCCGAGGGAACAGGAGGAACTGgtacgcgctg ... tctcgcttagGATCCTGGCATGGGAGGACGGGTTCTGCAACTTCGCGGCGGCCAGCAGCTCTGCCGCCGCGTCCGCGTGCGGCCAAGAGGGGGCAGCGGCAGCTGCGGCG


Block sizes: 42 (upstream exon), 47 (downstream exon)
Score: 18

ATGGGATCTCCCTGGCGCCGCGTACGACAGGACCCGAGGGAACAGGAGGAACTGgtacgcgctg ... tctcgcttagGATCCTGGCATGGGAGGACGGGTTCTGCAACTTCGCGGCGGCCAGCAGCTCTGCCGCCGCGTCCGCGTGCGGCCAAGAGGGGGCAGCGGCAGCTGCGGCG


Block sizes: 42 (upstream exon), 48 (downstream exon)
Score: 15

ATGGGATCTCCCTGGCGCCGCGTACGACAGGACCCGAGGGAACAGGAGGAACTGgtacgcgctg ... tctcgcttagGATCCTGGCATGGGAGGACGGGTTCTGCAACTTCGCGGCGGCCAGCAGCTCTGCCGCCGCGTCCGCGTGCGGCCAAGAGGGGGCAGCGGCAGCTGCGGCG


Block sizes: 44 (upstream exon), 36 (downstream exon)
Score: 6

ATGGGATCTCCCTGGCGCCGCGTACGACAGGACCCGAGGGAACAGGAGGAACTGgtacgcgctg ... tctcgcttagGATCCTGGCATGGGAGGACGGGTTCTGCAACTTCGCGGCGGCCAGCAGCTCTGCCGCCGCGTCCGCGTGCGGCCAAGAGGGGGCAGCGGCAGCTGCGGCG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtggagtcactcccatgtgaatgccctcgggtgtgttcttgcgcgtctcgcttagGATCCTGGCATGGGAGGACGGGTTCTGCAACTTCGCGGCGGCCAGCAGCTCTGCCGCCGCGTCCGCGTGCGGCCAAGAGGGGGCAGCGGCAGCTGCGGCG
                                             tctcgctt  CT-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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgcgctgctagctgcagccacacacagcacgctctcatattccttcctccttcctttgtggttctgtgcatgtcttcggtggagtcactcccatgtgaatgccctcgggtgtgttcttgcgcgtctcgcttagGATCCTGGCATGGGAGGACGGGTTCTGCAACTTCGCGGCGGCCAGCAGCTCTGCCGCCGCGTCCGCGTGCGGCCAAGAGGGGGCAGCGGCAGCTGCGGCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC