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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGAAAGAAGTTGCAGCAATGCGTGCCAGTAAAGAACAAGAAATCAGAGCCAAGCGGCTTGGTACGAAAGGCTCTGGTAGTTCACAACTGCTTCCTGGAAGgtacattttcaggaatgcaacaatattttgtattagaagtttgagcttctcattattgaaatgctcaatgctttaggatgctgtttgattagaagtcgct...

Basic information

species Zea mays
transcript GRMZM2G008556_T01
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G008556_T01 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os06g14080.1 (Oryza sativa), 5'ss of exon 10
AGAAAGAAGTTGCAGCAATGCGTGCCAGTAAAGAACAAGAAATCAGAGCCAAGCGGCTTGGTA---CGAAAGGCTCTGGTAGTTCACAACTGCTTCCTGGAAGgtacattttcaggaatgcaacaatatt-ttgtattagaagtttgagcttctcattattgaaatgctcaatgc---tttaggatgctgtttgattagaagtcgct
   ||||||||||||| |||||||    ||| ||||||||| ||| ||||| |||||||||||   | |||||  |||| ||||| ||| ||||| ||||||||||||| |||| |     || | | || ||| ||| ||  |||    || | |   |  |  |  | |  ||   ||||| ||| || ||||| |  ||| || 
---AAGAAGTTGCAGCTATGCGTGTTGATAAGGAACAAGAAGTCAAAGCCAGGCGGCTTGGTAGTTCTAAAGGGACTGGAAGTTCTCAAGTGCTTTCTGGAAGgtacatcttcaagtgctgaagagttttattgaatttgatattt----ttattaccgtcaagttcttaagggcacatttagaatgttggttgatcattagtagca
















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|211220744|gb|FL455240.1|FL455240
EST:     CTCTGGTAGTTCACAACTGCTTCCTGGAAG                         AAACGCCACCACGAAGTGGGTCCATGCGCAACTTCCAATGATGGCAGCACT
genomic: CTCTGGTAGTTCACAACTGCTTCCTGGAAGgtacattttc ... atgcctgcagAAACG-CACCACGAAGTGGGTCCATGCGCAACTTCCAATGATGGCAGCACT
EST: gi|60355070|gb|DN222043.1|DN222043
EST:     AAGCGGCTTGGTACGAAAGGCTCTGGTAGTTCACAACTGCTTCCTGGAAG                         AAACGCACCACGAAGTGGGTCCATGCGCAACTTCCAATGATGGCAGCACTA
genomic: AAGCGGCTTGGTACGAAAGGCTCTGGTAGTTCACAACTGCTTCCTGGAAGgtacattttc ... atgcctgcagAAACGCACCACGAAGTGGGTCCATGCGCAACTTCCAATGATGGCAGCACTA
EST: gi|21809904|gb|BQ668222.1|BQ668222
EST:     AAGCGGCTTGGTACGAAAGGCTCTGGTAGTTCACAACTGCTTCCTGGAAG                         AAACCCCCCACGAAGTGGGTCCATGCGCAACTTACAATGATGGCAGCACTA
genomic: AAGCGGCTTGGTACGAAAGGCTCTGGTAGTTCACAACTGCTTCCTGGAAGgtacattttc ... atgcctgcagAAACGCACCACGAAGTGGGTCCATGCGCAACTTCCAATGATGGCAGCACTA
EST: gi|71759732|gb|DR957669.1|DR957669
EST:     GGCTTGGTACGAAAGGCTCTGGTAGTTCACAACTGCTTCCTGGAAG                         AAACGCACCACGAAGTGGGTCCATGCGCAACTTCCAATGATGGCAGCACTA
genomic: GGCTTGGTACGAAAGGCTCTGGTAGTTCACAACTGCTTCCTGGAAGgtacattttc ... atgcctgcagAAACGCACCACGAAGTGGGTCCATGCGCAACTTCCAATGATGGCAGCACTA
EST: gi|71426784|gb|DR807834.1|DR807834
EST:     AAGCGGCTTGGTACGAAAGGCTCTGGTAGTTCACAACTGCTTCCTGGAAG                         AAACGCACCACGAAGTGGGTCCATGCGCAACTTCCAATGATGGCAGCACTA
genomic: AAGCGGCTTGGTACGAAAGGCTCTGGTAGTTCACAACTGCTTCCTGGAAGgtacattttc ... atgcctgcagAAACGCACCACGAAGTGGGTCCATGCGCAACTTCCAATGATGGCAGCACTA
EST: gi|113703080|gb|EE680584.1|EE680584
EST:     AAGCGGCTTGGTACGAAAGGCTCTGGTAGTTCACAACTGCTTCCTGGAAG                         AAACGCACCACGAAGTGGGTCCATGCGCAACTTACAATGATGGCAGCACTA
genomic: AAGCGGCTTGGTACGAAAGGCTCTGGTAGTTCACAACTGCTTCCTGGAAGgtacattttc ... atgcctgcagAAACGCACCACGAAGTGGGTCCATGCGCAACTTCCAATGATGGCAGCACTA
EST: gi|33091801|gb|CF051795.1|CF051795
EST:     ACGAAAGGCTCTGGTAGTTCACAACTGCTTCCTGGAAG                         AAACGCACCACGAAGTGGGTCCATGCGCAACTTCCAATGATGGCAGCACTA
genomic: ACGAAAGGCTCTGGTAGTTCACAACTGCTTCCTGGAAGgtacattttc ... atgcctgcagAAACGCACCACGAAGTGGGTCCATGCGCAACTTCCAATGATGGCAGCACTA
EST: gi|71762835|gb|DR960772.1|DR960772
EST:     AAGCGGCTTGGTACGAAAGGCTCTGGTAGTTCACAACTGCTTCCTGGAAG                         AAACGCACCACGAAGTGGGTCCATGCGCAACTTCCAATGATGGCAGCACTA
genomic: AAGCGGCTTGGTACGAAAGGCTCTGGTAGTTCACAACTGCTTCCTGGAAGgtacattttc ... atgcctgcagAAACGCACCACGAAGTGGGTCCATGCGCAACTTCCAATGATGGCAGCACTA
EST: gi|5739791|gb|AI947367.1|AI947367
EST:     AAGCGGCTTGGTACGAAAGGCTCTGGTAGTTCACAACTGCTTCCTGGAAG                         AAACGCACCACGAAGTGGGTCCATGCGCAACTTCCAATGATGGCAGCACTA
genomic: AAGCGGCTTGGTACGAAAGGCTCTGGTAGTTCACAACTGCTTCCTGGAAGgtacattttc ... atgcctgcagAAACGCACCACGAAGTGGGTCCATGCGCAACTTCCAATGATGGCAGCACTA
EST: gi|88754494|gb|DY538635.1|DY538635
EST:     AAGCGGCTTGGTACGAAAGGCTCTGGTAGTTCACAACTGCTTCCTGGAAG                         AAACGCACCACGAAGTGGGTCCATGCGCAACTTCCAATGATGGCAGCACTA
genomic: AAGCGGCTTGGTACGAAAGGCTCTGGTAGTTCACAACTGCTTCCTGGAAGgtacattttc ... atgcctgcagAAACGCACCACGAAGTGGGTCCATGCGCAACTTCCAATGATGGCAGCACTA
EST: gi|211220743|gb|FL455239.1|FL455239
EST:     AAGCGGCTTGGTACGAAAGGCTCTGGTAGTTCACAACTGCTTCCTGGAAG                         AAACGCACCACGAAGTGGGTCCATGCGCAACTTCCAATGATGGCAGCACTA
genomic: AAGCGGCTTGGTACGAAAGGCTCTGGTAGTTCACAACTGCTTCCTGGAAGgtacattttc ... atgcctgcagAAACGCACCACGAAGTGGGTCCATGCGCAACTTCCAATGATGGCAGCACTA
EST: gi|6021554|gb|AW066482.1|AW066482
EST:     AAGCGGCTTGGTACGAAAGGCTCTGGTAGTTCACAACTGCTTCCTGGAAG                         AAACGCACCACGAAGTGGGTCCATGCGCAACTTACAATGATGGCAGCAC
genomic: AAGCGGCTTGGTACGAAAGGCTCTGGTAGTTCACAACTGCTTCCTGGAAGgtacattttc ... atgcctgcagAAACGCACCACGAAGTGGGTCCATGCGCAACTTCCAATGATGGCAGCAC
EST: gi|32935029|gb|CF039841.1|CF039841
EST:     GCGGCTTGGTACGAAAGGCTCTGGTAGTTCACAACTGCTTCCTGGAAG                         AAACGCACCACGAAGTGGGTCCATGCGCAACTTCCAATGATGGCAGCACTA
genomic: GCGGCTTGGTACGAAAGGCTCTGGTAGTTCACAACTGCTTCCTGGAAGgtacattttc ... atgcctgcagAAACGCACCACGAAGTGGGTCCATGCGCAACTTCCAATGATGGCAGCACTA

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), 48 (downstream exon)
Score: 486

AGAAAGAAGTTGCAGCAATGCGTGCCAGTAAAGAACAAGAAATCAGAGCCAAGCGGCTTGGTACGAAAGGCTCTGGTAGTTCACAACTGCTTCCTGGAAGgtacattttc ... atgcctgcagAAACGCACCACGAAGTGGGTCCATGCGCAACTTCCAATGATGGCAGCACTAACACCAAGCAGCATTCTTGGATAGGTCCTCTGTTCCACCATTTGTTCTG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 109

AGAAAGAAGTTGCAGCAATGCGTGCCAGTAAAGAACAAGAAATCAGAGCCAAGCGGCTTGGTACGAAAGGCTCTGGTAGTTCACAACTGCTTCCTGGAAGgtacattttc ... atgcctgcagAAACGCACCACGAAGTGGGTCCATGCGCAACTTCCAATGATGGCAGCACTAACACCAAGCAGCATTCTTGGATAGGTCCTCTGTTCCACCATTTGTTCTG


Block sizes: 46 (upstream exon), 48 (downstream exon)
Score: 73

AGAAAGAAGTTGCAGCAATGCGTGCCAGTAAAGAACAAGAAATCAGAGCCAAGCGGCTTGGTACGAAAGGCTCTGGTAGTTCACAACTGCTTCCTGGAAGgtacattttc ... atgcctgcagAAACGCACCACGAAGTGGGTCCATGCGCAACTTCCAATGATGGCAGCACTAACACCAAGCAGCATTCTTGGATAGGTCCTCTGTTCCACCATTTGTTCTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 220

AGAAAGAAGTTGCAGCAATGCGTGCCAGTAAAGAACAAGAAATCAGAGCCAAGCGGCTTGGTACGAAAGGCTCTGGTAGTTCACAACTGCTTCCTGGAAGgtacattttc ... atgcctgcagAAACGCACCACGAAGTGGGTCCATGCGCAACTTCCAATGATGGCAGCACTAACACCAAGCAGCATTCTTGGATAGGTCCTCTGTTCCACCATTTGTTCTG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGAAAGAAGTTGCAGCAATGCGTGCCAGTAAAGAACAAGAAATCAGAGCCAAGCGGCTTGGTACGAAAGGCTCTGGTAGTTCACAACTGCTTCCTGGAAGgtacattttcaggaatgcaacaatattttgtattagaagtttgagcttctcattattgaaatgctcaatgctttaggatgctgtttgattagaagtcgct

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG