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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAAATCATGTCCTTTATAAGATCATATGTTGTGCCCGAAGGCTTTCCAGATAGTGTCACACCTTCATATGTTCCATACATGACATGGAGAGCATTGAAGgtatattttcattacaatatatttgggttccatgatctactggatagatgcatttatttagattttcctttaattttctcttgccag

Basic information

species Zea mays
transcript GRMZM5G833124_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G833124_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os05g34650.1 (Oryza sativa), 5'ss of exon 2
GAAATCATGTCCTTTATAAGATCATATGTTGTGCCCGAAGGCTTTCCAGATAGTGTCACACCTTCATATGTTCCATACATGACATGGAGAGCATTGAAGgtatattttcattacaatatatttgggttccatgatctactggatagatgcatttatttagattttcctttaattttctcttgccag
||||| |||||||| || || ||||||||||| || ||||||||||| ||||||||||| ||||||||||| ||||||||||||||||||||||||||||| |||||||   |||  |   |||| ||  || ||| ||||  |   || |||   ||      ||| |    ||||||||   ||
GAAATAATGTCCTTCATTAGGTCATATGTTGTACCTGAAGGCTTTCCGGATAGTGTCACTCCTTCATATGTCCCATACATGACATGGAGAGCATTGAAGgtgtattttctggacatgac--ttggatt--attatc-actgt-tgactgtattatcttgctaaatccctactatttctctttttag

upper sequence: GRMZM5G833124_T01 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA07G40210.1 (Glycine max), 5'ss of exon 2
GAAATCATGTCCTTTATAAGATCATATGTTGTGCCCGAAGGCTTTCCAGATAGTGTCACACCTTCATATGTTCCATACATGACATGGAGAGCATTGAAGgtatattttcattacaatatatttgggttccatgatctactggatagatgcatttatttagattttcctttaattttctcttgccag
||| || | || ||  | | ||| |||||||| |||||||| || || |||||||| || ||||| ||||| || |||||||||||||| ||  | |||||||  |||  |     | | ||    ||  |    |  ||   |   ||| || ||| || |    | | | |||    |||    
GAAGTCCTCTCTTTCGTTACATCCTATGTTGTCCCCGAAGGTTTCCCTGATAGTGTTACTCCTTCTTATGTCCCCTACATGACATGGAGGGCTCTTAAGgtatccttttgtc----tttcttctacttttacacacacctacctg--tgccttcattcagctccatcatca-tttgtaattgtag-

upper sequence: GRMZM5G833124_T01 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA17G00580.1 (Glycine max), 5'ss of exon 1
-GAAATCATGTCCTTTATAAGATCATATGTTGTGCCCGAAGGCTTTCCAGATAGTGTCACACCTTCATATGTTCCATACATGACATGGAGAGCATTGAAGgtatattttcattacaatatatttgggttccatgatctactggatagatgcatttatttagattttcctttaattttctc-ttgccag---------------
 ||| || |  | ||  | | ||| |||||||| |||||||| ||||| |||||||| |  ||||| ||||| || |||||||||||||| ||  | ||||||| |         ||||| | ||   |  ||  | ||||   |  |  |||| |  |      ||| | |   |  || |   ||                
TGAAGTCCTCGCTTTCGTTACATCCTATGTTGTCCCCGAAGGTTTTCCTGATAGTGTTATTCCTTCCTATGTCCCCTACATGACATGGAGGGCTCTTAAGgtatgt---------aatatgtatgttgtttatcttgtactacttttacacattcagctcttaactccatcatcatcatcatcatcatcatttgtaattgtag

upper sequence: GRMZM5G833124_T01 (Zea mays), 5'ss of exon 2
lower sequence: Vv12s0035g01870.t01 (Vitis vinifera), 5'ss of exon 2
GAAATCATGTCCTTTATAAGATCATATGTTGTGCCCGAAGGCTTTCCAGATAGTGTCACACCTTCATATGTTCCATACATGACATGGAGAGCATTGAAGgtatattttcat-----------tacaatatatttgggttccatgatctactggatagatgcatttatttagattttcctttaattttc--tcttgccag-----------------------------------------------------------------------------
||  | ||||| || |||||||| ||||| |||||||| || || || |||||||| || ||||||||||| ||||||||| |||||||||| || |||||||  | | |            ||| ||| |   ||| |   | |   | ||        |   ||||| ||     |    ||| |   | || | |                                                                              
GAGTTGATGTCATTCATAAGATCCTATGTGGTGCCCGAGGGATTCCCGGATAGTGTTACTCCTTCATATGTGCCATACATGTCATGGAGAGCTTTAAAGgtattctcttacgtttggtgctataccataaaggcgggcttttttaggaaatgagagccatctcatatttggagaacacggatattatgaatattacaaaacattctacgtctaatttatgtgaagtggggttgctgccctaaaatacaatactgatgaatttcatgttcattgtag

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|211214593|gb|FL385234.1|FL385234
EST:     ATAGTGTCACACCTTCATATGTTCCATACATGACATGGAGAGCATTGAAG                         CATTTCTTTGGTGGAGCAATGGGGTGTGTTTACAACAAGGACCTTGCTCAA
genomic: ATAGTGTCACACCTTCATATGTTCCATACATGACATGGAGAGCATTGAAGgtatattttc ... ctcttgccagCATTTCTTTGGTGGAGCAATGGG-TGTGTTTACAACAAGGACCTTGCTCAA
EST: gi|19822663|gb|BQ048687.1|BQ048687
EST:     ATAGTGTCACACCTTCATATGTTCCATACATGACATGGAGAGCATTGAAG                         CATTTCTTTGGTGGAGCAATGGGTGTGTTTACAACAAGGACCTTGCTCAAC
genomic: ATAGTGTCACACCTTCATATGTTCCATACATGACATGGAGAGCATTGAAGgtatattttc ... ctcttgccagCATTTCTTTGGTGGAGCAATGGGTGTGTTTACAACAAGGACCTTGCTCAAC
EST: gi|211217885|gb|FL417136.1|FL417136
EST:     ATAGTGTCACACCTTCATATGTTCCATACATGACATGGAGAGCATTGAAG                         CATTTCTTTGGTGGAGCAATGGGTGTGTTTACAACAAGGACCTTGCTCAAC
genomic: ATAGTGTCACACCTTCATATGTTCCATACATGACATGGAGAGCATTGAAGgtatattttc ... ctcttgccagCATTTCTTTGGTGGAGCAATGGGTGTGTTTACAACAAGGACCTTGCTCAAC
EST: gi|18450494|gb|BM428772.1|BM428772
EST:     ATAGTGTCACACCTTCATATGTTCCATACATGACATGGAGAGCATTGAAG                         CATTTCTTTGGTGGAGCAATGGGTGTGTTTACAACAAGGACCTTGCTCAAC
genomic: ATAGTGTCACACCTTCATATGTTCCATACATGACATGGAGAGCATTGAAGgtatattttc ... ctcttgccagCATTTCTTTGGTGGAGCAATGGGTGTGTTTACAACAAGGACCTTGCTCAAC
EST: gi|91876063|gb|EB406020.1|EB406020
EST:     ATAGTGTCACACCTTCATATGTTCCATACATGACATGGAGAGCATTGAAG                         CATTTCTTTGGTGGAGCAATGGGTGTGTTTACAACAAGGACCTTGCTCAAC
genomic: ATAGTGTCACACCTTCATATGTTCCATACATGACATGGAGAGCATTGAAGgtatattttc ... ctcttgccagCATTTCTTTGGTGGAGCAATGGGTGTGTTTACAACAAGGACCTTGCTCAAC
EST: gi|19822664|gb|BQ048688.1|BQ048688
EST:     ATAGTGTCACACCTTCATATGTTCCATACATGACATGGAGAGCATTGAAG                         CATTTCTTTGGTGGAGCAATGGGTGTGTTTACAACAAGGACCTTGCTCAAC
genomic: ATAGTGTCACACCTTCATATGTTCCATACATGACATGGAGAGCATTGAAGgtatattttc ... ctcttgccagCATTTCTTTGGTGGAGCAATGGGTGTGTTTACAACAAGGACCTTGCTCAAC
EST: gi|87153939|gb|DY398728.1|DY398728
EST:     ATAGTGTCACACCTTCATATGTTCCATACATGACATGGAGAGCATTGAAG                         CATTTCTTTGGTGGAGCAATGGGTGTGTTTACAACAAGGACCTTGCTCAAC
genomic: ATAGTGTCACACCTTCATATGTTCCATACATGACATGGAGAGCATTGAAGgtatattttc ... ctcttgccagCATTTCTTTGGTGGAGCAATGGGTGTGTTTACAACAAGGACCTTGCTCAAC
EST: gi|71440154|gb|DR821204.1|DR821204
EST:     ATAGTGTCACACCTTCATATGTTCCATACATGACATGGAGAGCATTGAAG                         CATTTCTTTGGTGGAGCAATGGGTGTGTTTACAACAAGGACCTTGCTCAAC
genomic: ATAGTGTCACACCTTCATATGTTCCATACATGACATGGAGAGCATTGAAGgtatattttc ... ctcttgccagCATTTCTTTGGTGGAGCAATGGGTGTGTTTACAACAAGGACCTTGCTCAAC
EST: gi|93281685|gb|EB673949.1|EB673949
EST:     ATAGTGTCACACCTTCATATGTTCCATACATGACATGGAGAGCATTGAAG                         CATTTCTTTGGTGGAGCAATGGGTGTGTTTACAACAAGGACCTTGCTCAAC
genomic: ATAGTGTCACACCTTCATATGTTCCATACATGACATGGAGAGCATTGAAGgtatattttc ... ctcttgccagCATTTCTTTGGTGGAGCAATGGGTGTGTTTACAACAAGGACCTTGCTCAAC

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), 49 (downstream exon)
Score: 131

GAAATCATGTCCTTTATAAGATCATATGTTGTGCCCGAAGGCTTTCCAGATAGTGTCACACCTTCATATGTTCCATACATGACATGGAGAGCATTGAAGgtatattttc ... ctcttgccagCATTTCTTTGGTGGAGCAATGGGTGTGTTTACAACAAGGACCTTGCTCAACTCTGTTGGAGTCTCCCAAAGCAGGGCTGCATCTGGTGCTGTGGCTATCA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 294

GAAATCATGTCCTTTATAAGATCATATGTTGTGCCCGAAGGCTTTCCAGATAGTGTCACACCTTCATATGTTCCATACATGACATGGAGAGCATTGAAGgtatattttc ... ctcttgccagCATTTCTTTGGTGGAGCAATGGGTGTGTTTACAACAAGGACCTTGCTCAACTCTGTTGGAGTCTCCCAAAGCAGGGCTGCATCTGGTGCTGTGGCTATCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 361

GAAATCATGTCCTTTATAAGATCATATGTTGTGCCCGAAGGCTTTCCAGATAGTGTCACACCTTCATATGTTCCATACATGACATGGAGAGCATTGAAGgtatattttc ... ctcttgccagCATTTCTTTGGTGGAGCAATGGGTGTGTTTACAACAAGGACCTTGCTCAACTCTGTTGGAGTCTCCCAAAGCAGGGCTGCATCTGGTGCTGTGGCTATCA


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 243

GAAATCATGTCCTTTATAAGATCATATGTTGTGCCCGAAGGCTTTCCAGATAGTGTCACACCTTCATATGTTCCATACATGACATGGAGAGCATTGAAGgtatattttc ... ctcttgccagCATTTCTTTGGTGGAGCAATGGGTGTGTTTACAACAAGGACCTTGCTCAACTCTGTTGGAGTCTCCCAAAGCAGGGCTGCATCTGGTGCTGTGGCTATCA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAAATCATGTCCTTTATAAGATCATATGTTGTGCCCGAAGGCTTTCCAGATAGTGTCACACCTTCATATGTTCCATACATGACATGGAGAGCATTGAAGgtatattttcattacaatatatttgggttccatgatctactggatagatgcatttatttagattttcctttaattttctcttgccag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG