Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATGGGTGTACTATACTTGTCCATGGGTATTCCAGAGTAGTACTGGAAGTTCTAAAGCTTGCTGCATCCAATCGCAAGCTCTTCCGGGTACTATGCACAGgtacaatgatttagttgcaagatgtgataatctgtttctacaaagatagcttgcctgtggcaaatatgtcatacacatacatggcatttagtgatatatt...

Basic information

species Zea mays
transcript GRMZM2G084647_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G084647_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os12g31380.1 (Oryza sativa), 5'ss of exon 3
GATGGGTGTACTATACTTGTCCATGGGTATTCCAGAGTAGTACTGGAAGTTCTAAAGCTTGCTGCATCCAATCGCAAGCTCTTCCGGGTACTATGCACAGgtacaatgatttagttgcaagatgtgata-atctgtttctacaaagat-agcttgcctgtggcaaatatgtcatacacatacatggcatttagtgatatatt
||||| |||||||| || || ||||| ||||||||||| ||  |||||||||||||||| |||||||| || ||||| |||||| ||||||| |||||||||| | ||||  |||||||        |  ||||   | | ||||  | | |     ||   |||   | |  |||||| ||| |     |  || |  |  
GATGGTTGTACTATTCTGGTACATGGTTATTCCAGAGTTGTTTTGGAAGTTCTAAAGCTAGCTGCATCAAACCGCAAACTCTTCAGGGTACTTTGCACAGgtaaattgatcaagttgcatttgaaactgcatctacattttcaaattttatcaaagatgcaacaacattattctacacagaca-gcttggtgatggtgaac-
















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|87152207|gb|DY396996.1|DY396996
EST:     TCTAAAGCTTGCTGCATCCAATCGCAAGCTCTTCCGGGTACTATGCACAG                         AGGGCAGGCCAGACAGAACTGGTTTAAGGATGTCAAATGAACTTGCAGCAT
genomic: TCTAAAGCTTGCTGCATCCAATCGCAAGCTCTTCCGGGTACTATGCACAGgtacaatgat ... tggaccgcagAGGGCAGGCCAGACAGAACTGGTTTAAGGATGTCAAATGAACTTGCAGCAT
EST: gi|32928780|gb|CF033592.1|CF033592
EST:     ACTATGCACAG                         AGGGCAGGCCAGACAGAACTGGTTTAAGGATGTCAAATGAACTTGCAGCAT
genomic: ACTATGCACAGgtacaatgat ... tggaccgcagAGGGCAGGCCAGACAGAACTGGTTTAAGGATGTCAAATGAACTTGCAGCAT
EST: gi|71328055|gb|DR800674.1|DR800674
EST:     TCTAAAGCTTGCTGCATCCAATCGCAAGCTCTTCCGGGTACTATGCACAG                         AGGGCAGGCCAGACAGAACTGGTTTAAGGATGTCAAATGAACTTGCAGCAT
genomic: TCTAAAGCTTGCTGCATCCAATCGCAAGCTCTTCCGGGTACTATGCACAGgtacaatgat ... tggaccgcagAGGGCAGGCCAGACAGAACTGGTTTAAGGATGTCAAATGAACTTGCAGCAT
EST: gi|76282990|gb|DV022558.1|DV022558
EST:     TCTAAAGCTTGCTGCATCCAATCGCAAGCTCTTCCGGGTACTATGCACAG                         AGGGCAGGCCAGACAGAACTGGTTTAAGGATGTCAAATGAACTTGCAGCAT
genomic: TCTAAAGCTTGCTGCATCCAATCGCAAGCTCTTCCGGGTACTATGCACAGgtacaatgat ... tggaccgcagAGGGCAGGCCAGACAGAACTGGTTTAAGGATGTCAAATGAACTTGCAGCAT
EST: gi|71758051|gb|DR955988.1|DR955988
EST:     TCTAAAGCTTGCTGCATCCAATCGCAAGCTCTTCCGGGTACTATGCACAG                         AGGGCAGGCCAGACAGAACTGGTTTAAGGATGTCAAATGAACTTGCAGCAT
genomic: TCTAAAGCTTGCTGCATCCAATCGCAAGCTCTTCCGGGTACTATGCACAGgtacaatgat ... tggaccgcagAGGGCAGGCCAGACAGAACTGGTTTAAGGATGTCAAATGAACTTGCAGCAT
EST: gi|78118155|gb|DV536542.1|DV536542
EST:     TCTAAAGCTTGCTGCATCCAATCGCAAGCTCTTCCGGGTACTATGCACAG                         AGGGCAGGCCAGACAGAACTGGTTTAAGGATGTCAAATGAACTTGCAGCAT
genomic: TCTAAAGCTTGCTGCATCCAATCGCAAGCTCTTCCGGGTACTATGCACAGgtacaatgat ... tggaccgcagAGGGCAGGCCAGACAGAACTGGTTTAAGGATGTCAAATGAACTTGCAGCAT
EST: gi|76928321|gb|DV171574.1|DV171574
EST:     TCTAAAGCTTGCTGCATCCAATCGCAAGCTCTTCCGGGTACTATGCACAG                         AGGGCAGGCCAGACAGAACTGGTTTAAGGATGTCAAATGAACTTGCAGCAT
genomic: TCTAAAGCTTGCTGCATCCAATCGCAAGCTCTTCCGGGTACTATGCACAGgtacaatgat ... tggaccgcagAGGGCAGGCCAGACAGAACTGGTTTAAGGATGTCAAATGAACTTGCAGCAT
EST: gi|71762540|gb|DR960477.1|DR960477
EST:     TCTAAAGCTTGCTGCATCCAATCGCAAGCTCTTCCGGGTACTATGCACAG                         AGGGCAGGCCAGACAGAACTGGTTTAAGGATGTCAAATGAACTTGCAGCAT
genomic: TCTAAAGCTTGCTGCATCCAATCGCAAGCTCTTCCGGGTACTATGCACAGgtacaatgat ... tggaccgcagAGGGCAGGCCAGACAGAACTGGTTTAAGGATGTCAAATGAACTTGCAGCAT
EST: gi|18965102|gb|BM661393.1|BM661393
EST:     TCTAAAGCTTGCTGCATCCAATCGCAAGCTCTTCCGGGTACTATGCACAG                         AGGGCAGGCCAGACAGAACTGGTTTAAGGATGTCAAATGAACTTGCAGCAT
genomic: TCTAAAGCTTGCTGCATCCAATCGCAAGCTCTTCCGGGTACTATGCACAGgtacaatgat ... tggaccgcagAGGGCAGGCCAGACAGAACTGGTTTAAGGATGTCAAATGAACTTGCAGCAT
EST: gi|78105935|gb|DV524353.1|DV524353
EST:     TCTAAAGCTTGCTGCATCCAATCGCAAGCTCTTCCGGGTACTATGCACAG                         AGGGCAGGCCAGACAGAACTGGTTTAAGGATGTCAAATGAACTTGCAGCAT
genomic: TCTAAAGCTTGCTGCATCCAATCGCAAGCTCTTCCGGGTACTATGCACAGgtacaatgat ... tggaccgcagAGGGCAGGCCAGACAGAACTGGTTTAAGGATGTCAAATGAACTTGCAGCAT
EST: gi|211260422|gb|FL227455.1|FL227455
EST:     TCTAAAGCTTGCTGCATCCAATCGCAAGCTCTTCCGGGTACTATGCACAG                         AGGGCAGGCCAGACAGAACTGG
genomic: TCTAAAGCTTGCTGCATCCAATCGCAAGCTCTTCCGGGTACTATGCACAGgtacaatgat ... tggaccgcagAGGGCAGGCCAGACAGAACTGG
EST: gi|50337597|gb|CO532723.1|CO532723
EST:     TCTAAAGCTTGCTGCATCCAATCGCAAGCTCTTCCGGGTACTATGCACAG                         AGGGCAGGCCAGACAGAACTGGTTTAAGGATGTCAAATGAACTTGCAGCAT
genomic: TCTAAAGCTTGCTGCATCCAATCGCAAGCTCTTCCGGGTACTATGCACAGgtacaatgat ... tggaccgcagAGGGCAGGCCAGACAGAACTGGTTTAAGGATGTCAAATGAACTTGCAGCAT
EST: gi|71769908|gb|DR967845.1|DR967845
EST:     TCTAAAGCTTGCTGCATCCAATCGCAAGCTCTTCCGGGTACTATGCACAG                         AGGGCAGGCCAGACAGAACTGGTTTAAGGATGTCAAATGAACTTGCAGCAT
genomic: TCTAAAGCTTGCTGCATCCAATCGCAAGCTCTTCCGGGTACTATGCACAGgtacaatgat ... tggaccgcagAGGGCAGGCCAGACAGAACTGGTTTAAGGATGTCAAATGAACTTGCAGCAT
EST: gi|71764897|gb|DR962834.1|DR962834
EST:     TCTAAAGCTTGCTGCATCCAATCGCAAGCTCTTCCGGGTACTATGCACAG                         AGGGCAGGCCAGACAGAACTGGTTTAAGGATGTCAAATGAACTTGCAGCAT
genomic: TCTAAAGCTTGCTGCATCCAATCGCAAGCTCTTCCGGGTACTATGCACAGgtacaatgat ... tggaccgcagAGGGCAGGCCAGACAGAACTGGTTTAAGGATGTCAAATGAACTTGCAGCAT
EST: gi|60348428|gb|DN215401.1|DN215401
EST:     TCTAAAGCTTGCTGCATCCAATCGCAAGCTCTTCCGGGTACTATGCACAG                         AGGGCAGGCCAGACAGAACTGGTTTAAGGATGTCAAATGAACTTGCAGCAT
genomic: TCTAAAGCTTGCTGCATCCAATCGCAAGCTCTTCCGGGTACTATGCACAGgtacaatgat ... tggaccgcagAGGGCAGGCCAGACAGAACTGGTTTAAGGATGTCAAATGAACTTGCAGCAT
EST: gi|19351346|gb|BM895878.1|BM895878
EST:     TCTAAAGCTTGCTGCATCCAATCGCAAGCTCTTCCGGGTACTATGCACAG                         AGGGCAGGCCAGACAGAACTGGTTTAAGGATGTCAAATGAACTTGCAGCAT
genomic: TCTAAAGCTTGCTGCATCCAATCGCAAGCTCTTCCGGGTACTATGCACAGgtacaatgat ... tggaccgcagAGGGCAGGCCAGACAGAACTGGTTTAAGGATGTCAAATGAACTTGCAGCAT
EST: gi|22490267|gb|BU050190.1|BU050190
EST:     TCTAAAGCTTGCTGCATCCAATCGCAAGCTCTTCCGGGTACTATGCACAG                         AGGGCAGGCCAGACAGAACTGGTTTAAGGATGTCAAATGAACTTGCAGCAT
genomic: TCTAAAGCTTGCTGCATCCAATCGCAAGCTCTTCCGGGTACTATGCACAGgtacaatgat ... tggaccgcagAGGGCAGGCCAGACAGAACTGGTTTAAGGATGTCAAATGAACTTGCAGCAT
EST: gi|19272520|gb|BM888776.1|BM888776
EST:     TCTAAAGCTTGCTGCATCCAATCGCAAGCTCTTCCGGGTACTATGCACAG                         AGGGCAGGCCAGACAGAACTGGTTTAAGGATGTCAAATGAACTTGCAGCAT
genomic: TCTAAAGCTTGCTGCATCCAATCGCAAGCTCTTCCGGGTACTATGCACAGgtacaatgat ... tggaccgcagAGGGCAGGCCAGACAGAACTGGTTTAAGGATGTCAAATGAACTTGCAGCAT
EST: gi|31360905|gb|CD445262.1|CD445262
EST:     CATCCAATCGCAAGCTCTTCCGGGTACTATGCACAG                         AGGGCAGGCCAGACAGAACTGGTTTAAGGATGTCAAATGAACTTGCAGCAT
genomic: CATCCAATCGCAAGCTCTTCCGGGTACTATGCACAGgtacaatgat ... tggaccgcagAGGGCAGGCCAGACAGAACTGGTTTAAGGATGTCAAATGAACTTGCAGCAT

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), 49 (downstream exon)
Score: 109

GATGGGTGTACTATACTTGTCCATGGGTATTCCAGAGTAGTACTGGAAGTTCTAAAGCTTGCTGCATCCAATCGCAAGCTCTTCCGGGTACTATGCACAGgtacaatgat ... tggaccgcagAGGGCAGGCCAGACAGAACTGGTTTAAGGATGTCAAATGAACTTGCAGCATTAGGGATCCCTGTTAAGGTTCTAATTGATTCAGCTGTTGCTTATTCCAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 84

GATGGGTGTACTATACTTGTCCATGGGTATTCCAGAGTAGTACTGGAAGTTCTAAAGCTTGCTGCATCCAATCGCAAGCTCTTCCGGGTACTATGCACAGgtacaatgat ... tggaccgcagAGGGCAGGCCAGACAGAACTGGTTTAAGGATGTCAAATGAACTTGCAGCATTAGGGATCCCTGTTAAGGTTCTAATTGATTCAGCTGTTGCTTATTCCAT


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 81

GATGGGTGTACTATACTTGTCCATGGGTATTCCAGAGTAGTACTGGAAGTTCTAAAGCTTGCTGCATCCAATCGCAAGCTCTTCCGGGTACTATGCACAGgtacaatgat ... tggaccgcagAGGGCAGGCCAGACAGAACTGGTTTAAGGATGTCAAATGAACTTGCAGCATTAGGGATCCCTGTTAAGGTTCTAATTGATTCAGCTGTTGCTTATTCCAT


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 79

GATGGGTGTACTATACTTGTCCATGGGTATTCCAGAGTAGTACTGGAAGTTCTAAAGCTTGCTGCATCCAATCGCAAGCTCTTCCGGGTACTATGCACAGgtacaatgat ... tggaccgcagAGGGCAGGCCAGACAGAACTGGTTTAAGGATGTCAAATGAACTTGCAGCATTAGGGATCCCTGTTAAGGTTCTAATTGATTCAGCTGTTGCTTATTCCAT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GATGGGTGTACTATACTTGTCCATGGGTATTCCAGAGTAGTACTGGAAGTTCTAAAGCTTGCTGCATCCAATCGCAAGCTCTTCCGGGTACTATGCACAGgtacaatgatttagttgcaagatgtgataatctgtttctacaaagatagcttgcctgtggcaaatatgtcatacacatacatggcatttagtgatatatt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaagatag