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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGGTCCCTTGGTGCTATTATGTATGAAATGCTAGTTGGTTACCCTCCATTTTATTCAGAGGACCCAATGTCTACTTGCAGAAAGgtacatgtggtatccacaggatatatgtgtgtgcatactattctatattcattgtcatcctatgcaaacttcatgaacattcattagtaggataactaca...

Basic information

species Zea mays
transcript GRMZM2G375904_T01
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G375904_T01 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os05g43570.1 (Oryza sativa), 5'ss of exon 8
GTGGTCCCTTGGTGCTATTATGTATGAAATGCTAGTTGGTTACCCTCCATTTTATTCAGAGGACCCAATGTCTACTTGCAGAAAGgtacatgtggtatccacaggatatatgtgtgtgcatactattctatattcatt-gtcatcctatgcaaacttcatgaacattcattagtaggataactaca
||||||||||||||| ||||||||||||||||| |||||||| |||||||| ||||| ||||| |||||||| || |||||||||| |  |    |  ||||||  | | |   | ||    |||     || |  || |  ||  | |  |  |    | | ||  | | |      |  | |  
GTGGTCCCTTGGTGCAATTATGTATGAAATGCTTGTTGGTTATCCTCCATTCTATTCGGAGGATCCAATGTCAACCTGCAGAAAGgcatgtactttgcccacagttttttttaatttgttatctagagggtaattgtttggaattttctatattcagtctaagcaaacctcacccaacttgcaag-

upper sequence: GRMZM2G375904_T01 (Zea mays), 5'ss of exon 7
lower sequence: Vv10s0003g05720.t01 (Vitis vinifera), 5'ss of exon 8
GTGGTCCCTTGGTGCTATTATGTATGAAATGCTAGTTGGTTACCCTCCATTTTATTCAGAGGACCCAATGTCTACTTGCAGAAAGgtacatgtggtatccacaggatat--atgtgtgtgcatactattctatattcattgtcatcctatgcaaacttcatgaacattcattagtaggataactaca-
|||||| ||||| || ||||||||||| ||||| || || || || || |||||||| ||||| |||||||| || |||||||||||| ||||| |  |      ||    || | |   |||  |||| ||| ||  || | |   | ||  ||    ||   ||  |   ||    || ||||   
GTGGTCTCTTGGGGCAATTATGTATGAGATGCTTGTGGGATATCCACCTTTTTATTCTGAGGAACCAATGTCAACATGCAGAAAGgtatatgtgttgactttgttattccaattttttatcattttattttattttatttttgaaaatctgggaaaaatat---cacaccagaggtttatcactatga

upper sequence: GRMZM2G375904_T01 (Zea mays), 5'ss of exon 7
lower sequence: PP1S86_100V6.1 (Physcomitrella patens), 5'ss of exon 7
GTGGTCCCTTGGTGCTATTATGTATGAAATGCTAGTTGGTTACCCTCCATTTTATTCAGAGGACCCAATGTCTACTTGCAGAAAGgtacatg-tggtatccacaggatatatgtgtgtgcatac---tattctatattcattgtcatcctatgcaaacttcatgaacattcattagtaggataactaca
|||||| ||||| || || ||||| || ||||||||||| |||||||||||||| || || || || ||| | |||||  | |||||           |  ||   || ||  || || ||| |   | ||| | |  |  | | |    |||      |  |     | ||    |  | |   |   
GTGGTCACTTGGAGCAATCATGTACGAGATGCTAGTTGGCTACCCTCCATTTTACTCTGACGAACCTATGACAACTTGTCGCAAGgtgtgcaacaacctttactc-atttacatgggttcattcattttttccaaaagctctataaatggatgtggtgcttttagttttgcaaatctcaggtttgt---

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|213171755|gb|FM196253.1|FM196253
EST:     TTGGTTACCCTCCATTTTATTCAGAGGACCCAATGTCTACTTGCAGAAAG                         ATTGTGAACTGGAGAAGTCACTTGAAATTCCCTGAAGNNNCNAAGCTTCCT
genomic: TTGGTTACCCTCCATTTTATTCAGAGGACCCAATGTCTACTTGCAGAAAGgtacatgtgg ... gttcatgtagATTGTGAACTGGAGAAGTCACTTGAAATTCCCTGAAGAGGCAAAGCTTCCT
EST: gi|28187719|gb|CB179329.1|CB179329
EST:     TTGGTTACCCTCCATTTTATTCAGAGGACCCAATGTCTACTTGCAGAAAG                         ATTGTGAACTGGAGAAGTCACTTGAAATTCCCTGAAGAGGCAAAGTTTCCT
genomic: TTGGTTACCCTCCATTTTATTCAGAGGACCCAATGTCTACTTGCAGAAAGgtacatgtgg ... gttcatgtagATTGTGAACTGGAGAAGTCACTTGAAATTCCCTGAAGAGGCAAAGCTTCCT
EST: gi|5901099|gb|AW042199.1|AW042199
EST:     GAGGACCCAATGTCTACTTGCAGAAAG                         ATTGTGAACTGGAGAAGTCACTTGAAATTCCCTGAAGAGGCAAAGCTTCCT
genomic: GAGGACCCAATGTCTACTTGCAGAAAGgtacatgtgg ... gttcatgtagATTGTGAACTGGAGAAGTCACTTGAAATTCCCTGAAGAGGCAAAGCTTCCT
EST: gi|33285627|gb|CF075422.1|CF075422
EST:     TTGGTTACCCTCCATTTTATTCAGAGGACCCAATGTCTACTTGCAGAAAG                         ATTGTGAACTGGAGAAGTCACTTGAAATTCCCTGAAGAGGCAAAGCTTCCT
genomic: TTGGTTACCCTCCATTTTATTCAGAGGACCCAATGTCTACTTGCAGAAAGgtacatgtgg ... gttcatgtagATTGTGAACTGGAGAAGTCACTTGAAATTCCCTGAAGAGGCAAAGCTTCCT
EST: gi|211195854|gb|FL001022.1|FL001022
EST:     TTGGTTACCCTCCATTTTATTCAGAGGACCCAATGTCTACTTGCAGAAAG                         ATTGTGAACTGGAGAAGTCACTTGAAATTCCCTGAAGAGGCAAAGCTTCCT
genomic: TTGGTTACCCTCCATTTTATTCAGAGGACCCAATGTCTACTTGCAGAAAGgtacatgtgg ... gttcatgtagATTGTGAACTGGAGAAGTCACTTGAAATTCCCTGAAGAGGCAAAGCTTCCT
EST: gi|31628455|gb|CD526616.1|CD526616
EST:     TTGGTTACCCTCCATTTTATTCAGAGGACCCAATGTCTACTTGCAGAAAG                         ATTGTGAACTGGAGAAGTCACTTGAAATTCCCTGAAGAGGCAAAGCTTCCT
genomic: TTGGTTACCCTCCATTTTATTCAGAGGACCCAATGTCTACTTGCAGAAAGgtacatgtgg ... gttcatgtagATTGTGAACTGGAGAAGTCACTTGAAATTCCCTGAAGAGGCAAAGCTTCCT
EST: gi|32870336|gb|CF010018.1|CF010018
EST:     TTGGTTACCCTCCATTTTATTCAGAGGACCCAATGTCTACTTGCAGAAAG                         ATTGTGAACTGGAGAAGTCACTTGAAATTCCCTGAAGAGGCAAAGCTTCCT
genomic: TTGGTTACCCTCCATTTTATTCAGAGGACCCAATGTCTACTTGCAGAAAGgtacatgtgg ... gttcatgtagATTGTGAACTGGAGAAGTCACTTGAAATTCCCTGAAGAGGCAAAGCTTCCT
EST: gi|211127917|gb|FL461340.1|FL461340
EST:     TTGGTTACCCTCCATTTTATTCAGAGGACCCAATGTCTACTTGCAGAAAG                         ATTGTGAACTGG
genomic: TTGGTTACCCTCCATTTTATTCAGAGGACCCAATGTCTACTTGCAGAAAGgtacatgtgg ... gttcatgtagATTGTGAACTGG

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: 48 (upstream exon), 47 (downstream exon)
Score: 248

GTGGTCCCTTGGTGCTATTATGTATGAAATGCTAGTTGGTTACCCTCCATTTTATTCAGAGGACCCAATGTCTACTTGCAGAAAGgtacatgtgg ... gttcatgtagATTGTGAACTGGAGAAGTCACTTGAAATTCCCTGAAGAGGCAAAGCTTCCTCCTGAAGCTAAGGCTCTCATCAGCAAGCTTTTGTGTAATGTTGAGCATC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 426

GTGGTCCCTTGGTGCTATTATGTATGAAATGCTAGTTGGTTACCCTCCATTTTATTCAGAGGACCCAATGTCTACTTGCAGAAAGgtacatgtgg ... gttcatgtagATTGTGAACTGGAGAAGTCACTTGAAATTCCCTGAAGAGGCAAAGCTTCCTCCTGAAGCTAAGGCTCTCATCAGCAAGCTTTTGTGTAATGTTGAGCATC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 485

GTGGTCCCTTGGTGCTATTATGTATGAAATGCTAGTTGGTTACCCTCCATTTTATTCAGAGGACCCAATGTCTACTTGCAGAAAGgtacatgtgg ... gttcatgtagATTGTGAACTGGAGAAGTCACTTGAAATTCCCTGAAGAGGCAAAGCTTCCTCCTGAAGCTAAGGCTCTCATCAGCAAGCTTTTGTGTAATGTTGAGCATC


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 448

GTGGTCCCTTGGTGCTATTATGTATGAAATGCTAGTTGGTTACCCTCCATTTTATTCAGAGGACCCAATGTCTACTTGCAGAAAGgtacatgtgg ... gttcatgtagATTGTGAACTGGAGAAGTCACTTGAAATTCCCTGAAGAGGCAAAGCTTCCTCCTGAAGCTAAGGCTCTCATCAGCAAGCTTTTGTGTAATGTTGAGCATC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGGTCCCTTGGTGCTATTATGTATGAAATGCTAGTTGGTTACCCTCCATTTTATTCAGAGGACCCAATGTCTACTTGCAGAAAGgtacatgtggtatccacaggatatatgtgtgtgcatactattctatattcattgtcatcctatgcaaacttcatgaacattcattagtaggataactaca

- - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA