Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGAAATAATTTCCCTGCTCTCAATGCCAGAATTTAGTCGCAGCGATCTTGCCGATTTACTGAAGGGTGTTCAAGCACATGAGAAAGAGAAGTTGCATTTGgtaagttagcttgggctcttgggcgtgttgtattgccatatgggccatgaaatagtgcttccttaaaataactagattttgtttaagagcggaaacttat...

Basic information

species Zea mays
transcript GRMZM2G138097_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G138097_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os01g16080.1 (Oryza sativa), 5'ss of exon 3
TGAAATAATTTCCCTGCTCTCAATGCCAGAATTTAGTCGCAGCGATCTTGCCGATTTACTGAAGGGTGTTCAAGCACATGAGAAAGAGAAGTTGCATTTGgtaagttagcttgggctcttgggcgt-gttgt--attgccatatgggcca---tgaaatagtgcttccttaaaataactagattttgtttaagagcggaaacttat
 |||||  |  |||| || |||| ||||||| || ||||  ||||||||||| | |||||||||| ||| || ||||| |||||||||||||||||| ||||||  |  ||  | |||    | || ||| |  | |   | ||||  ||   | |     |  || |     | ||||   ||   || || | |  ||      
CGAAATGGTAGCCCTCCTATCAACGCCAGAAATTTGTCGTGGCGATCTTGCCAACTTACTGAAGGATGTGCAGGCACACGAGAAAGAGAAGTTGCATCTGgtaacctgtctatgactccattgtgttgttatgaaatttgacatggttcagccttatgctttattttcaactgaaaactgatttcctttcaaaaaccaaa------
















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|87157280|gb|DY402069.1|DY402069
EST:     CCGATTTACTGAAGGGTGTTCAAGCACATGAGAAAGAGAAGTTGCATTTG                         ACAGCTAAGATTCAGGTGCTGAAGAAAGCCGGCAGGCCTTCAGAGCGCCTG
genomic: CCGATTTACTGAAGGGTGTTCAAGCACATGAGAAAGAGAAGTTGCATTTGgtaagttagc ... atttctgaagACAGCTAAGATTCAGGTGCTGAAGAAAGCCGGCAGGCCTTCAGAGCGCCTG
EST: gi|26558850|gb|CA831085.1|CA831085
EST:     CCGATTTACTGAAGGGTGTTCAAGCACATGAGAAAGAGAAGTTGCATTTG                         ACAGCTAAGATTCAGGTGCTGAAGAAAGCCGGCAGGCCTTCAGAGCGCCTG
genomic: CCGATTTACTGAAGGGTGTTCAAGCACATGAGAAAGAGAAGTTGCATTTGgtaagttagc ... atttctgaagACAGCTAAGATTCAGGTGCTGAAGAAAGCCGGCAGGCCTTCAGAGCGCCTG
EST: gi|32919596|gb|CF024408.1|CF024408
EST:     CCGATTTACTGAAGGGTGTTCAAGCACATGAGAAAGAGAAGTTGCATTTG                         ACAGCTAAGATTCAGGTGCTGAAGAAAGCCGGCAGGCCTTCAGAGCGCCTG
genomic: CCGATTTACTGAAGGGTGTTCAAGCACATGAGAAAGAGAAGTTGCATTTGgtaagttagc ... atttctgaagACAGCTAAGATTCAGGTGCTGAAGAAAGCCGGCAGGCCTTCAGAGCGCCTG
EST: gi|22546690|gb|BU099001.1|BU099001
EST:     CCGATTTACTGAAGGGTGTTCAAGCACATGAGAAAGAGAAGTTGCATTTG                         ACAGCTAAGATTCAGGTGCTGAAGAAAGCCGGCAGGCCTTCAGAGCGCCTG
genomic: CCGATTTACTGAAGGGTGTTCAAGCACATGAGAAAGAGAAGTTGCATTTGgtaagttagc ... atttctgaagACAGCTAAGATTCAGGTGCTGAAGAAAGCCGGCAGGCCTTCAGAGCGCCTG
EST: gi|211279941|gb|FL459046.1|FL459046
EST:     CCGATTTACTGAAGGGTGTTCAAGCACATGAGAAAGAGAAGTTGCATTTG                         ACAGCTAAGATTCAGGTGCTGAAGAAAGCCGGCAGGCCTTCAGAGCGCCTG
genomic: CCGATTTACTGAAGGGTGTTCAAGCACATGAGAAAGAGAAGTTGCATTTGgtaagttagc ... atttctgaagACAGCTAAGATTCAGGTGCTGAAGAAAGCCGGCAGGCCTTCAGAGCGCCTG
EST: gi|18179124|gb|BM380334.1|BM380334
EST:     CCGATTTACTGAAGGGTGTTCAAGCACATGAGAAAGAGAAGTTGCATTTG                         ACAGCTAAGATTCAGGTGCTGAAGAAAGCCGGCAGGCCTTCAGAGCGCCTG
genomic: CCGATTTACTGAAGGGTGTTCAAGCACATGAGAAAGAGAAGTTGCATTTGgtaagttagc ... atttctgaagACAGCTAAGATTCAGGTGCTGAAGAAAGCCGGCAGGCCTTCAGAGCGCCTG
EST: gi|113700937|gb|EE678441.1|EE678441
EST:     CCGATTTACTGAAGGGTGTTCAAGCACATGAGAAAGAGAAGTTGCATTTG                         ACAGCTAAGATTCAGGTGCTGAAGAAAGCCGGCAGGCCTTCAGAGCGCCTG
genomic: CCGATTTACTGAAGGGTGTTCAAGCACATGAGAAAGAGAAGTTGCATTTGgtaagttagc ... atttctgaagACAGCTAAGATTCAGGTGCTGAAGAAAGCCGGCAGGCCTTCAGAGCGCCTG
EST: gi|87155516|gb|DY400305.1|DY400305
EST:     CCGATTTACTGAAGGGTGTTCAAGCACATGAGAAAGAGAAGTTGCATTTG                         ACAGCTAAGATTCAGGTGCTGAAGAAAGCCGGCAGGCCTTCAGAGCGCCTG
genomic: CCGATTTACTGAAGGGTGTTCAAGCACATGAGAAAGAGAAGTTGCATTTGgtaagttagc ... atttctgaagACAGCTAAGATTCAGGTGCTGAAGAAAGCCGGCAGGCCTTCAGAGCGCCTG
EST: gi|211158371|gb|FL410891.1|FL410891
EST:     CCGATTTACTGAAGGGTGTTCAAGCACATGAGAAAGAGAAGTTGCATTT-                         ---GCTAAGATCCAGGTGCTGAAGAAAGCCGGCAGGCCTTCAGAGCGCCTG
genomic: CCGATTTACTGAAGGGTGTTCAAGCACATGAGAAAGAGAAGTTGCATTTGgtaagttagc ... atttctgaagACAGCTAAGATTCAGGTGCTGAAGAAAGCCGGCAGGCCTTCAGAGCGCCTG
EST: gi|211410847|gb|FL397563.1|FL397563
EST:     CGATTTACTGAAGGGGTGT-CAAGCACATGAGAAAGAGAAGTTGCATTTG                         ACAGCTAAGAATTCNGGTGCTGGAGGAAGCCGGCAGGGCTTCAGAGCGGCT
genomic: CGATTTACTGAAGGG-TGTTCAAGCACATGAGAAAGAGAAGTTGCATTTGgtaagttagc ... atttctgaagACAGCTAAGA-TTCAGGTGCTGAAGAAAGCCGGCAGGCCTTCAGAGCGCCT
EST: gi|87157593|gb|DY402382.1|DY402382
EST:     CCGATTTACTGAAGGGTGTTCAAGCACATGAGAAAGAGAAGTTGCATTTG                         ACAGCTAAGATTCAGGTGCTGAAGAAAGCCGGCAGGCCTTCAGAGCGCCTG
genomic: CCGATTTACTGAAGGGTGTTCAAGCACATGAGAAAGAGAAGTTGCATTTGgtaagttagc ... atttctgaagACAGCTAAGATTCAGGTGCTGAAGAAAGCCGGCAGGCCTTCAGAGCGCCTG
EST: gi|211505115|gb|FL432445.1|FL432445
EST:     CCGATTTACTGAAGGGTGTTCAAGCACATGAGAAAGAGAAGTTGCATTTG                         ACAGCTAATATTCAGGTGCTGAAGAAAGCCGGCAGGCCTTCAGAGCGCCTG
genomic: CCGATTTACTGAAGGGTGTTCAAGCACATGAGAAAGAGAAGTTGCATTTGgtaagttagc ... atttctgaagACAGCTAAGATTCAGGTGCTGAAGAAAGCCGGCAGGCCTTCAGAGCGCCTG
EST: gi|21987675|gb|BQ779203.1|BQ779203
EST:     CCGATTTACTGAAGGGTGTTCAAGCACATGAGAAAGAGAAGTTGCATTTG                         ACAGCTAAGATTCAGGTGCTGAAGAAAGCCGGCAGGCCTTCAGAGCGCCTG
genomic: CCGATTTACTGAAGGGTGTTCAAGCACATGAGAAAGAGAAGTTGCATTTGgtaagttagc ... atttctgaagACAGCTAAGATTCAGGTGCTGAAGAAAGCCGGCAGGCCTTCAGAGCGCCTG
EST: gi|26559457|gb|CA831692.1|CA831692
EST:     CCGATTTACTGAAGGGTGTTCAAGCACATGAGAAAGAGAAGTTGCATTTG                         ACAGCTAAGATTCAGGTGCTGAAGAAAGCCGGCAGGCCTTCAGAGCGCCTG
genomic: CCGATTTACTGAAGGGTGTTCAAGCACATGAGAAAGAGAAGTTGCATTTGgtaagttagc ... atttctgaagACAGCTAAGATTCAGGTGCTGAAGAAAGCCGGCAGGCCTTCAGAGCGCCTG
EST: gi|22472818|gb|BU037298.1|BU037298
EST:     CCGATTTACTGAAGGGTGTTCAAGCACATGAGAAAGAGAAGTTGCATTTG                         ACAGCTAAGATTCAGGTGCTGAAGAAAGCCGGCAGGCCTTCAGAGCGCCTG
genomic: CCGATTTACTGAAGGGTGTTCAAGCACATGAGAAAGAGAAGTTGCATTTGgtaagttagc ... atttctgaagACAGCTAAGATTCAGGTGCTGAAGAAAGCCGGCAGGCCTTCAGAGCGCCTG

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), 41 (downstream exon)
Score: 16

TGAAATAATTTCCCTGCTCTCAATGCCAGAATTTAGTCGCAGCGATCTTGCCGATTTACTGAAGGGTGTTCAAGCACATGAGAAAGAGAAGTTGCATTTGgtaagttagc ... atttctgaagACAGCTAAGATTCAGGTGCTGAAGAAAGCCGGCAGGCCTTCAGAGCGCCTGGTGAACCACGCAGACTGCAGGTCGCGCAGCATGGCCCAGCACGTGTGCG


Block sizes: 48 (upstream exon), 46 (downstream exon)
Score: 24

TGAAATAATTTCCCTGCTCTCAATGCCAGAATTTAGTCGCAGCGATCTTGCCGATTTACTGAAGGGTGTTCAAGCACATGAGAAAGAGAAGTTGCATTTGgtaagttagc ... atttctgaagACAGCTAAGATTCAGGTGCTGAAGAAAGCCGGCAGGCCTTCAGAGCGCCTGGTGAACCACGCAGACTGCAGGTCGCGCAGCATGGCCCAGCACGTGTGCG


Block sizes: 49 (upstream exon), 43 (downstream exon)
Score: 19

TGAAATAATTTCCCTGCTCTCAATGCCAGAATTTAGTCGCAGCGATCTTGCCGATTTACTGAAGGGTGTTCAAGCACATGAGAAAGAGAAGTTGCATTTGgtaagttagc ... atttctgaagACAGCTAAGATTCAGGTGCTGAAGAAAGCCGGCAGGCCTTCAGAGCGCCTGGTGAACCACGCAGACTGCAGGTCGCGCAGCATGGCCCAGCACGTGTGCG


Block sizes: 48 (upstream exon), 42 (downstream exon)
Score: 18

TGAAATAATTTCCCTGCTCTCAATGCCAGAATTTAGTCGCAGCGATCTTGCCGATTTACTGAAGGGTGTTCAAGCACATGAGAAAGAGAAGTTGCATTTGgtaagttagc ... atttctgaagACAGCTAAGATTCAGGTGCTGAAGAAAGCCGGCAGGCCTTCAGAGCGCCTGGTGAACCACGCAGACTGCAGGTCGCGCAGCATGGCCCAGCACGTGTGCG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGAAATAATTTCCCTGCTCTCAATGCCAGAATTTAGTCGCAGCGATCTTGCCGATTTACTGAAGGGTGTTCAAGCACATGAGAAAGAGAAGTTGCATTTGgtaagttagcttgggctcttgggcgtgttgtattgccatatgggccatgaaatagtgcttccttaaaataactagattttgtttaagagcggaaacttat

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaataac