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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagagacggtattatcatttgtttttgaagatgttaacccactttctagctctgatttacatctatttattcatgacgcacatgttcctttagGAAATGAAAGAGCTTACTACGAGAGATCACCAATCAACTTTGTCAACCAGTTTACTTGTCCAGTCATTTTGTTTCAAGGGTTGGAGGATAAG

Basic information

species Zea mays
transcript GRMZM2G120302_T01
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G120302_T02 (Zea mays), 3'ss of exon 15
lower sequence: LOC_Os06g11180.1 (Oryza sativa), 3'ss of exon 15
gtaaga----gacggtattatcatt--tgtttt--tgaagatgtt-aacccactttctagctctgatttacatctatttattcatgacgcacatgttcctttagGAAATGAAAGAGCTTACTACGAGAGATCACCAATCAACTTTGTCAACCAGTTTACTTGTCCAGTCATTTTGTTTCAAGGGTTGGAGGATAAG
||||||     |  || | |  |||  || |||  | ||  | || || |||     ||  ||  || ||    || | |    |  |  ||||    ||| |||||||||||  |||||||| ||||||||||| |||||||||||  || | ||||| |||||||| |||||||||||||| ||||| ||||||
gtaagaccataagagtctcactatttctgctttggtaaaagtattcaatccaacccgtatgtccaatgtaa---tagtcaccttttgc-tacattgctcttcagGAAATGAAAATGCTTACTATGAGAGATCACCGATCAACTTTGTTGACAAATTTACATGTCCAGTTATTTTGTTTCAAGGCTTGGATGATAAG
















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|113757246|gb|DW880471.1|DW880471
EST:     GCGGAGACGCACAAATTTGAGTCTCATTATATGGACAAATCTTGTAG                         GAAATGAAAGAGCTTACTACGAGAGATCACCAATCAACTT-GTCAACCAGT
genomic: GCGGAGACGCACAAATTTGAGTCTCATTATATGGAC-AATCTTGTAGgtaagagacg ... gttcctttagGAAATGAAAGAGCTTACTACGAGAGATCACCAATCAACTTTGTCAACCAGT
EST: gi|33091583|gb|CF051577.1|CF051577
EST:     GAGAGCGGAGACGCACAAATTTGAGTCTCATTATATGGACAATCTTGTAG                         GAAATGAAAGAGCTTACTACGAGAGATCACCAATCAACTTTGTCAACCAGT
genomic: GAGAGCGGAGACGCACAAATTTGAGTCTCATTATATGGACAATCTTGTAGgtaagagacg ... gttcctttagGAAATGAAAGAGCTTACTACGAGAGATCACCAATCAACTTTGTCAACCAGT
EST: gi|5847476|gb|AW000555.1|AW000555
EST:     GAGAGCGGAGACACACAAATTTGAGTCTCATTATATGGACAATCTTGTAG                         GAAATGAAAGAGCTTACTACGAGAGATCACCAATCAACTTTGTCAACCAGT
genomic: GAGAGCGGAGACGCACAAATTTGAGTCTCATTATATGGACAATCTTGTAGgtaagagacg ... gttcctttagGAAATGAAAGAGCTTACTACGAGAGATCACCAATCAACTTTGTCAACCAGT
EST: gi|6031233|gb|AW076135.1|AW076135
EST:     GAGAGCGGAGACACACAAATTTGAGTCTCATTATATGGACAATCTTGTAG                         GAAAAGAAAGAGCTTACT
genomic: GAGAGCGGAGACGCACAAATTTGAGTCTCATTATATGGACAATCTTGTAGgtaagagacg ... gttcctttagGAAATGAAAGAGCTTACT
EST: gi|148972938|gb|EE023964.2|EE023964
EST:     GAGAGCGGAGACGCACAAATTTGAGTCTCATTATATGGACAATCTTGTAG                         GAAATGAAAGAGCTTACTACGAGAGATCACCAATCAACTTTGTCAACCAGT
genomic: GAGAGCGGAGACGCACAAATTTGAGTCTCATTATATGGACAATCTTGTAGgtaagagacg ... gttcctttagGAAATGAAAGAGCTTACTACGAGAGATCACCAATCAACTTTGTCAACCAGT
EST: gi|148961815|gb|EE012596.2|EE012596
EST:     GAGAGCGGAGACGCACAAATTTGAGTCTCATTATATGGACAATCTTGTAG                         GAAATGAAAGAGCTTACTACGAGAGATCACCAATCAACTTTGTCAACCAGT
genomic: GAGAGCGGAGACGCACAAATTTGAGTCTCATTATATGGACAATCTTGTAGgtaagagacg ... gttcctttagGAAATGAAAGAGCTTACTACGAGAGATCACCAATCAACTTTGTCAACCAGT
EST: gi|32935186|gb|CF039998.1|CF039998
EST:     GAGAGCGGAGACGCACAAATTTGAGTCTCATTATATGGACAATCTTGTAG                         GAAATGAAAGAGCTTACTACGAGAGATCACCAACCAACTTTGTCAACCAGT
genomic: GAGAGCGGAGACGCACAAATTTGAGTCTCATTATATGGACAATCTTGTAGgtaagagacg ... gttcctttagGAAATGAAAGAGCTTACTACGAGAGATCACCAATCAACTTTGTCAACCAGT
EST: gi|32934798|gb|CF039610.1|CF039610
EST:     GAGAGCGGAGACGCACAAATTTGAGTCTCATTATATGGACAATCTTGTAG                         GAAATGAAAGAGCTTACTACGAGAGATCACCAATCAACTTTGTCAACCAGT
genomic: GAGAGCGGAGACGCACAAATTTGAGTCTCATTATATGGACAATCTTGTAGgtaagagacg ... gttcctttagGAAATGAAAGAGCTTACTACGAGAGATCACCAATCAACTTTGTCAACCAGT
EST: gi|148964887|gb|EE015749.2|EE015749
EST:     GAGAGCGGAGACGCACAAATTTGAGTCTCATTATATGGACAATCTTGTAG                         GAAATGAAAGAGCTTACTACGAGAGATCACCAATCAACTTTGTCAACCAGT
genomic: GAGAGCGGAGACGCACAAATTTGAGTCTCATTATATGGACAATCTTGTAGgtaagagacg ... gttcctttagGAAATGAAAGAGCTTACTACGAGAGATCACCAATCAACTTTGTCAACCAGT
EST: gi|211128689|gb|FL442064.1|FL442064
EST:     TTTGAGTCTCATTATATGGACAATCTTGTAG                         GAAATGAAAGAGCTTACTACGAGAGATCACCAATCAACTTTGTCAACCAGT
genomic: TTTGAGTCTCATTATATGGACAATCTTGTAGgtaagagacg ... gttcctttagGAAATGAAAGAGCTTACTACGAGAGATCACCAATCAACTTTGTCAACCAGT
EST: gi|78023231|gb|DV491618.1|DV491618
EST:     GAGAGCGGAGACACACAAATTTGAGTCTCATTATATGGACAATCTTGTAG                         GAAATGAAAGAGCTTACTACGAGAGATCACCAATCAACTTTGTCAACCAGT
genomic: GAGAGCGGAGACGCACAAATTTGAGTCTCATTATATGGACAATCTTGTAGgtaagagacg ... gttcctttagGAAATGAAAGAGCTTACTACGAGAGATCACCAATCAACTTTGTCAACCAGT

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: 155

GTTGGGGACTTGACTCTGTTGAGAGCGGAGACGCACAAATTTGAGTCTCATTATATGGACAATCTTGTAGgtaagagacg ... gttcctttagGAAATGAAAGAGCTTACTACGAGAGATCACCAATCAACTTTGTCAACCAGTTTACTTGTCCAGTCATTTTGTTTCAAGGGTTGGAGGATAAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 126

GTTGGGGACTTGACTCTGTTGAGAGCGGAGACGCACAAATTTGAGTCTCATTATATGGACAATCTTGTAGgtaagagacg ... gttcctttagGAAATGAAAGAGCTTACTACGAGAGATCACCAATCAACTTTGTCAACCAGTTTACTTGTCCAGTCATTTTGTTTCAAGGGTTGGAGGATAAG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 139

GTTGGGGACTTGACTCTGTTGAGAGCGGAGACGCACAAATTTGAGTCTCATTATATGGACAATCTTGTAGgtaagagacg ... gttcctttagGAAATGAAAGAGCTTACTACGAGAGATCACCAATCAACTTTGTCAACCAGTTTACTTGTCCAGTCATTTTGTTTCAAGGGTTGGAGGATAAG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 131

GTTGGGGACTTGACTCTGTTGAGAGCGGAGACGCACAAATTTGAGTCTCATTATATGGACAATCTTGTAGgtaagagacg ... gttcctttagGAAATGAAAGAGCTTACTACGAGAGATCACCAATCAACTTTGTCAACCAGTTTACTTGTCCAGTCATTTTGTTTCAAGGGTTGGAGGATAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccactttctagctctgatttacatctatttattcatgacgcacatgttcctttagGAAATGAAAGAGCTTACTACGAGAGATCACCAATCAACTTTGTCAACCAGTTTACTTGTCCAGTCATTTTGTTTCAAGGGTTGGAGGATAAG
           ctctgat  putative branch site (score: 131)
                                            tgttccttt  putative PPT
                atttacatctatttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagagacggtattatcatttgtttttgaagatgttaacccactttctagctctgatttacatctatttattcatgacgcacatgttcctttagGAAATGAAAGAGCTTACTACGAGAGATCACCAATCAACTTTGTCAACCAGTTTACTTGTCCAGTCATTTTGTTTCAAGGGTTGGAGGATAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT