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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCACCGAGGATAATAGCAGCACGATTTTGGAACTGGCGCAGCTGCTCGACGTTTACGATCATCTCTACCCCGGAAAGgtgagatcttgcttcccatttgtgttggaatggagtgattgctcgagaaagtaagagatgtatgtaatagtgcttgaacttgttacattttag

Basic information

species Zea mays
transcript GRMZM2G054706_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G054706_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os02g04260.1 (Oryza sativa), 5'ss of exon 2
---GCACCGAGGATAATAGCAGCACGATTTTGGAACTGGCGCAGCTGCTCGACGTTTACGATCATCTCTACCCCGGAAAGgtgagatcttgcttccc---atttgtgttggaatggagtgattgctcgagaaagtaagagatgtatgtaatagtgcttgaacttgttacattttag
   |    ||| |   |  |||||||||| | || || ||||||||||||||||| |||||| |||||| ||| |  |||||||||||||||||||     || |   |     ||  ||||||  ||||||  ||      ||| ||| |  || ||| | || || | |  |||
GTGGGGAGGAGAAGCGTGACAGCACGATTCTTGAGCTCGCGCAGCTGCTCGACGTGTACGATGATCTCTTCCCTGCTAAGgtgagatcttgcttccaccggttcgcacttaggagggttgattgtgcgagaatttaga----gtaggtagtgctgattgtaatttttgcgtgatag
















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|18649042|gb|BM497861.1|BM497861
EST:     TGGAACTGGCGCAGCTGCTCGACGTTTACGATCATCTCTACCCCGGAAAG                         AATGCGGAAAGTGGTCAAGAAGTTGCCCAAGTGGATCCACAGGAGCTCGTG
genomic: TGGAACTGGCGCAGCTGCTCGACGTTTACGATCATCTCTACCCCGGAAAGgtgagatctt ... tacattttagAATGAGGAAAGTGGTCAAGAAGTTGCCCAAGTGGATCCACAGGAGCTCGTG
EST: gi|211331853|gb|FL370139.1|FL370139
EST:     TGGAACTGGCGCAGCTGCTCGACGTTTACGATCATCTCTACCCCGGAAAG                         AATGCGGAAAGTGGTCAAGAAGTTGCCCAAGTGGATCCACAGGAGCTCGTG
genomic: TGGAACTGGCGCAGCTGCTCGACGTTTACGATCATCTCTACCCCGGAAAGgtgagatctt ... tacattttagAATGAGGAAAGTGGTCAAGAAGTTGCCCAAGTGGATCCACAGGAGCTCGTG
EST: gi|74236590|gb|DT644504.1|DT644504
EST:     TGGAACTGGCGCAGCTGCTCGACGTTTACGATCATCTCTACCCCGGAAAG                         AATGAGGAAAGTGGTCAAGAAGTTGCCCAAGTGGATCCACAGGAGCTCGTG
genomic: TGGAACTGGCGCAGCTGCTCGACGTTTACGATCATCTCTACCCCGGAAAGgtgagatctt ... tacattttagAATGAGGAAAGTGGTCAAGAAGTTGCCCAAGTGGATCCACAGGAGCTCGTG
EST: gi|88752193|gb|DY536334.1|DY536334
EST:     TGGAACTGGCGCAGCTGCTCGACGTTTACGATCATCTCTACCCCGGAAAG                         AATGAGGAAAGTGGTCAAGAAGTTGCCCAAGTGGATCCACAGGAGCTCGTG
genomic: TGGAACTGGCGCAGCTGCTCGACGTTTACGATCATCTCTACCCCGGAAAGgtgagatctt ... tacattttagAATGAGGAAAGTGGTCAAGAAGTTGCCCAAGTGGATCCACAGGAGCTCGTG
EST: gi|71326892|gb|DR800103.1|DR800103
EST:     TGGAACTGGCGCAGCTGCTCGACGTTTACGATCATCTCTACCCCGGAAAG                         AATGAGGAAAGTGGTCAAGAAGTTGCCCAAGTGGATCCACAGGAGCTCGTG
genomic: TGGAACTGGCGCAGCTGCTCGACGTTTACGATCATCTCTACCCCGGAAAGgtgagatctt ... tacattttagAATGAGGAAAGTGGTCAAGAAGTTGCCCAAGTGGATCCACAGGAGCTCGTG
EST: gi|76931669|gb|DV172797.1|DV172797
EST:     TGGAACTGGCGCAGCTGCTCGACGTTTACGATCATCTCTACCCCGGAAAG                         AATGAGGAAAGTGGTCAAGAAGTTGCCCAAGTGGATCCACAGGAGCTCGTG
genomic: TGGAACTGGCGCAGCTGCTCGACGTTTACGATCATCTCTACCCCGGAAAGgtgagatctt ... tacattttagAATGAGGAAAGTGGTCAAGAAGTTGCCCAAGTGGATCCACAGGAGCTCGTG
EST: gi|89757721|gb|DY687204.1|DY687204
EST:     TGGAACTGGCGCAGCTGCTCGACGTTTACGATCATCTCTACCCCGGAAAG                         AATGAGGAAAGTGGTCAAGAAGTTGCCCAAGTGGATCCACAGGAGCTCGTG
genomic: TGGAACTGGCGCAGCTGCTCGACGTTTACGATCATCTCTACCCCGGAAAGgtgagatctt ... tacattttagAATGAGGAAAGTGGTCAAGAAGTTGCCCAAGTGGATCCACAGGAGCTCGTG
EST: gi|88752231|gb|DY536372.1|DY536372
EST:     TGGAACTGGCGCAGCTGCTCGACGTTTACGATCATCTCTACCCCGGAAAG                         AATGAGGAAAGTGGTCAAGAAGTTGCCCAAGTGGATCCACAGGAGCTCGTG
genomic: TGGAACTGGCGCAGCTGCTCGACGTTTACGATCATCTCTACCCCGGAAAGgtgagatctt ... tacattttagAATGAGGAAAGTGGTCAAGAAGTTGCCCAAGTGGATCCACAGGAGCTCGTG
EST: gi|50324552|gb|CO519678.1|CO519678
EST:     TGGAACTGGCGCAGCTGCTCGACGTTTACGATCATCTCTACCCCGGAAAG                         AATGAGGAAAGTGGTCAAGAAGTTGCCCAAGTGGATCCACAGGAGCTCGTG
genomic: TGGAACTGGCGCAGCTGCTCGACGTTTACGATCATCTCTACCCCGGAAAGgtgagatctt ... tacattttagAATGAGGAAAGTGGTCAAGAAGTTGCCCAAGTGGATCCACAGGAGCTCGTG
EST: gi|211447325|gb|FL371185.1|FL371185
EST:     TGGAACTGGCGCAGCTGCTCGACGTTTACGATCATCTCTACCCCGGAWAG                         AATGCGGAAAGTGGTCAAGAAGTTGCCCAAGTGGATCCACAGGAGCTCGTG
genomic: TGGAACTGGCGCAGCTGCTCGACGTTTACGATCATCTCTACCCCGGAAAGgtgagatctt ... tacattttagAATGAGGAAAGTGGTCAAGAAGTTGCCCAAGTGGATCCACAGGAGCTCGTG
EST: gi|93015545|gb|EB641065.1|EB641065
EST:     TGGAACTGGCGCAGCTGCTCGACGTTTACGATCATCTCTACCCCGGAAAG                         AATGAGGAAAGTGGTCAAGAAGTTGCCCAAGTGGATCCACAGGAGCTCGTG
genomic: TGGAACTGGCGCAGCTGCTCGACGTTTACGATCATCTCTACCCCGGAAAGgtgagatctt ... tacattttagAATGAGGAAAGTGGTCAAGAAGTTGCCCAAGTGGATCCACAGGAGCTCGTG
EST: gi|60399511|gb|DN232323.1|DN232323
EST:     TGGAACTGGCGCAGCTGCTCGACGTTTACGATCATCTCTACCCCGGAAAG                         AATGAGGAAAGTGGTCAAGAAGTTGCCCAAGTGGATCCACAGGAGCTCGTG
genomic: TGGAACTGGCGCAGCTGCTCGACGTTTACGATCATCTCTACCCCGGAAAGgtgagatctt ... tacattttagAATGAGGAAAGTGGTCAAGAAGTTGCCCAAGTGGATCCACAGGAGCTCGTG
EST: gi|211042074|gb|FL383254.1|FL383254
EST:     TGGAACTGGCGCAGCTGCTCGACGTTTACGATCATCTCTACCCCGGAAAG                         AATGCGGAAAGTGGTCAAGAAGTTGCCCAAGTGGATCCACAGGAGCTCGTG
genomic: TGGAACTGGCGCAGCTGCTCGACGTTTACGATCATCTCTACCCCGGAAAGgtgagatctt ... tacattttagAATGAGGAAAGTGGTCAAGAAGTTGCCCAAGTGGATCCACAGGAGCTCGTG
EST: gi|71769763|gb|DR967700.1|DR967700
EST:     TGGAACTGGCGCAGCTGCTCGACGTTTACGATCATCTCTACCCCGGAAAG                         AATGAGGAAAGTGGTCAAGAAGTTGCCCAAGTGGATCCACAGGAGCTCGTG
genomic: TGGAACTGGCGCAGCTGCTCGACGTTTACGATCATCTCTACCCCGGAAAGgtgagatctt ... tacattttagAATGAGGAAAGTGGTCAAGAAGTTGCCCAAGTGGATCCACAGGAGCTCGTG
EST: gi|18654773|gb|BM499578.1|BM499578
EST:     TGGAACTGGCGCAGCTGCTCGACGTTTACGATCATCTCTACCCCGGAAAG                         AATGCGGAAAGTGGTCAAGAAGTTGCCCAAGTGGATCCACAGGAGCTCGTG
genomic: TGGAACTGGCGCAGCTGCTCGACGTTTACGATCATCTCTACCCCGGAAAGgtgagatctt ... tacattttagAATGAGGAAAGTGGTCAAGAAGTTGCCCAAGTGGATCCACAGGAGCTCGTG
EST: gi|93015602|gb|EB641122.1|EB641122
EST:     TGGAACTGGCGCAGCTGCTCGACGTTTACGATCATCTCTACCCCGGAAAG                         AATGAGGAAAGTGGTCAAGAAGTTGCCCAAGTGGATCCACAGGAGCTCGTG
genomic: TGGAACTGGCGCAGCTGCTCGACGTTTACGATCATCTCTACCCCGGAAAGgtgagatctt ... tacattttagAATGAGGAAAGTGGTCAAGAAGTTGCCCAAGTGGATCCACAGGAGCTCGTG
EST: gi|211434257|gb|FL404589.1|FL404589
EST:     TGGAACTGGCGCAGCTGCTCGACGTTTACGATCATCTCTACCCCGGAAAG                         AATGCGGAAAGTGGTCAAGAAGTTGCCCAAGTGGATCCACAGGAGCTCGTG
genomic: TGGAACTGGCGCAGCTGCTCGACGTTTACGATCATCTCTACCCCGGAAAGgtgagatctt ... tacattttagAATGAGGAAAGTGGTCAAGAAGTTGCCCAAGTGGATCCACAGGAGCTCGTG
EST: gi|71436328|gb|DR817378.1|DR817378
EST:     TGGAACTGGCGCAGCTGCTCGACGTTTACGATCATCTCTACCCCGGAAAG                         AATGAGGAAAGTGGTCAAGAAGTTGCCCAAGTGGATCCACAGGAGCTCGTG
genomic: TGGAACTGGCGCAGCTGCTCGACGTTTACGATCATCTCTACCCCGGAAAGgtgagatctt ... tacattttagAATGAGGAAAGTGGTCAAGAAGTTGCCCAAGTGGATCCACAGGAGCTCGTG
EST: gi|76923536|gb|DV169535.1|DV169535
EST:     TGGAACTGGCGCAGCTGCTCGACGTTTACGATCATCTCTACCCCGGAAAG                         AATGAGGAAAGTGGTCAAGAAGTTGCCCAAGTGGATCCACAGGAGCTCGTG
genomic: TGGAACTGGCGCAGCTGCTCGACGTTTACGATCATCTCTACCCCGGAAAGgtgagatctt ... tacattttagAATGAGGAAAGTGGTCAAGAAGTTGCCCAAGTGGATCCACAGGAGCTCGTG
EST: gi|71428269|gb|DR809319.1|DR809319
EST:     TGGAACTGGCGCAGCTGCTCGACGTTTACGATCATCTCTACCCCGGAAAG                         AATGAGGAAAGTGGTCAAGAAGTTGCCCAAGTGGATCCACAGGAGCTCGTG
genomic: TGGAACTGGCGCAGCTGCTCGACGTTTACGATCATCTCTACCCCGGAAAGgtgagatctt ... tacattttagAATGAGGAAAGTGGTCAAGAAGTTGCCCAAGTGGATCCACAGGAGCTCGTG
EST: gi|37418625|gb|CF646983.1|CF646983
EST:     TGGAACTGGCGCAGCTGCTCGACGTTTACGATCATCTCTACCCCGGAAAG                         AATGAGGAAAGTGGTCAAGAAGTTGCCCAAGTGGATCCACAGGAGCTCGTG
genomic: TGGAACTGGCGCAGCTGCTCGACGTTTACGATCATCTCTACCCCGGAAAGgtgagatctt ... tacattttagAATGAGGAAAGTGGTCAAGAAGTTGCCCAAGTGGATCCACAGGAGCTCGTG
EST: gi|211301339|gb|FL414902.1|FL414902
EST:     TGGAACTGGCGCAGCTGCTCGACGTTTACGATCATCTCTACCCCGGAAAG                         AATGCGGAAAGTGGTCAAGAAGTTGCCCAAGTGGATCCACAGGAGCTCGTG
genomic: TGGAACTGGCGCAGCTGCTCGACGTTTACGATCATCTCTACCCCGGAAAGgtgagatctt ... tacattttagAATGAGGAAAGTGGTCAAGAAGTTGCCCAAGTGGATCCACAGGAGCTCGTG
EST: gi|149044689|gb|EE047662.2|EE047662
EST:     TGGAACTGGCGCAGCTGCTCGACGTTTACGATCATCTCTACCCCGGAAAG                         AATGAGGAAAGTGGTCAAGAAGTTGCCCAAGTGGATCCACAGGAGCTCGTG
genomic: TGGAACTGGCGCAGCTGCTCGACGTTTACGATCATCTCTACCCCGGAAAGgtgagatctt ... tacattttagAATGAGGAAAGTGGTCAAGAAGTTGCCCAAGTGGATCCACAGGAGCTCGTG
EST: gi|76283964|gb|DV023532.1|DV023532
EST:     TGGAACTGGCGCAGCTGCTCGACGTTTACGATCATCTCTACCCCGGAAAG                         AATGAGGAAAGTGGTCAAGAAGTTGCCCAAGTGGATCCACAGGAGCTCGTG
genomic: TGGAACTGGCGCAGCTGCTCGACGTTTACGATCATCTCTACCCCGGAAAGgtgagatctt ... tacattttagAATGAGGAAAGTGGTCAAGAAGTTGCCCAAGTGGATCCACAGGAGCTCGTG
EST: gi|93013386|gb|EB638906.1|EB638906
EST:     TGGAACTGGCGCAGCTGCTCGACGTTTACGATCATCTCTACCCCGGAAAG                         AATGAGGAAAGTGGTCAAGAAGTTGCCCAAGTGGATCCACAGGAGCTCGTG
genomic: TGGAACTGGCGCAGCTGCTCGACGTTTACGATCATCTCTACCCCGGAAAGgtgagatctt ... tacattttagAATGAGGAAAGTGGTCAAGAAGTTGCCCAAGTGGATCCACAGGAGCTCGTG
EST: gi|21390005|gb|BQ528054.1|BQ528054
EST:     TGGAACTGGCGCAGCTGCTCGACGTTTACGATCATCTCTACCCCGGAAAG                         AATGCGGAAAGTGGTCAAGAAGTTGCCCAAGTGGATCCACAGGAGCTCGTG
genomic: TGGAACTGGCGCAGCTGCTCGACGTTTACGATCATCTCTACCCCGGAAAGgtgagatctt ... tacattttagAATGAGGAAAGTGGTCAAGAAGTTGCCCAAGTGGATCCACAGGAGCTCGTG
EST: gi|78081498|gb|DV509910.1|DV509910
EST:     TGGAACTGGCGCAGCTGCTCGACGTTTACGATCATCTCTACCCCGGAAAG                         AATGAGGAAAGTGGTCAAGAAGTTGCCCAAGTGGATCCACAGGAGCTCGTG
genomic: TGGAACTGGCGCAGCTGCTCGACGTTTACGATCATCTCTACCCCGGAAAGgtgagatctt ... tacattttagAATGAGGAAAGTGGTCAAGAAGTTGCCCAAGTGGATCCACAGGAGCTCGTG
EST: gi|211217744|gb|FL411417.1|FL411417
EST:     TGGAACTGGCGCAGCTGCTCGACGTTTACGATCATCTCTACCCCGGAAAG                         AATGCGGAAAGTGGTCAAGAAGTTGCCCAAGTGGATCCACAGGAGCTCGTG
genomic: TGGAACTGGCGCAGCTGCTCGACGTTTACGATCATCTCTACCCCGGAAAGgtgagatctt ... tacattttagAATGAGGAAAGTGGTCAAGAAGTTGCCCAAGTGGATCCACAGGAGCTCGTG

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: 109

GCACCGAGGATAATAGCAGCACGATTTTGGAACTGGCGCAGCTGCTCGACGTTTACGATCATCTCTACCCCGGAAAGgtgagatctt ... tacattttagAATGAGGAAAGTGGTCAAGAAGTTGCCCAAGTGGATCCACAGGAGCTCGTGGTTCCCAAGCTGTTTGAGAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 85

GCACCGAGGATAATAGCAGCACGATTTTGGAACTGGCGCAGCTGCTCGACGTTTACGATCATCTCTACCCCGGAAAGgtgagatctt ... tacattttagAATGAGGAAAGTGGTCAAGAAGTTGCCCAAGTGGATCCACAGGAGCTCGTGGTTCCCAAGCTGTTTGAGAG


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 90

GCACCGAGGATAATAGCAGCACGATTTTGGAACTGGCGCAGCTGCTCGACGTTTACGATCATCTCTACCCCGGAAAGgtgagatctt ... tacattttagAATGAGGAAAGTGGTCAAGAAGTTGCCCAAGTGGATCCACAGGAGCTCGTGGTTCCCAAGCTGTTTGAGAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 70

GCACCGAGGATAATAGCAGCACGATTTTGGAACTGGCGCAGCTGCTCGACGTTTACGATCATCTCTACCCCGGAAAGgtgagatctt ... tacattttagAATGAGGAAAGTGGTCAAGAAGTTGCCCAAGTGGATCCACAGGAGCTCGTGGTTCCCAAGCTGTTTGAGAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCACCGAGGATAATAGCAGCACGATTTTGGAACTGGCGCAGCTGCTCGACGTTTACGATCATCTCTACCCCGGAAAGgtgagatcttgcttcccatttgtgttggaatggagtgattgctcgagaaagtaagagatgtatgtaatagtgcttgaacttgttacattttag

- - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - GCTGCT