Skip to another splice site:
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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tctgtagctaagtttcatcaggaaacaagtcaccttgtgatgtttttttaacttccatgtaacatgataagttgtttgacatatgcctccatttgtttagGGAGAAGGTCATGACAATGCCCAGGAAGCAAACACAGCGTGATCTCCGGAGAATGGAGAAAGCTGAAAGGGCTGCTCAACTAGAAAGG

Basic information

species Zea mays
transcript GRMZM2G461793_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G461793_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os07g16950.5 (Oryza sativa), 3'ss of exon 4
tctgtag-ctaagtttcatcaggaaaca-agtcaccttgtgatgtttttttaacttccatgtaacatgataagttgtttga-catatgcctc-catttgtttagGGAGAAGGTCATGACAATGCCCAGGAAGCAAACACAGCGTGATCTCCGGAGAATGGAGAAAGCTGAAAGGGCTGCTCAACTAGAAAGG
    ||  || | || | |   ||   | | ||   ||||||  ||| |     |  | | | |    ||     | || | ||||| |||| |   |  | || |||||||| |||||||||||||||||| | || |||||  ||||| | |||||||| |||||||||| ||| |||||  | |||| |
---ataatctgatttgcttgttgatgtatactctttttgtgaactttctgctgttctc-tctgatgcaatggaaagattaatcatattcctctccccttatcagAGAGAAGGTGATGACAATGCCCAGGAAGGAGACTCAGCGCCATCTCAGAAGAATGGATAAAGCTGAAAAGGCCGCTCAGTTGGAAAAG
















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|93012902|gb|EB638422.1|EB638422
EST:     AAAATGACTCAATATCGTATAAGAATGAGGAAACTTCAACTGAAAGTGAG                         GGAGAAGGTCATGACAATGCCCAGGAAGCAAACACAGCGTGATCTCCGGAG
genomic: AAAATGACTCAATATCGTATAAGAATGAGGAAACTTCAACTGAAAGTGAGgtaggcactt ... atttgtttagGGAGAAGGTCATGACAATGCCCAGGAAGCAAACACAGCGTGATCTCCGGAG
EST: gi|71330256|gb|DR801876.1|DR801876
EST:     AAAATGACTCAATATCGTATAAGAATGAGGAAACTTCAACTGAAAGTGAG                         GGAGAAGGTCATGACAATGCCCAGGAAGCAAACACAGCGTGATCTCCGGAG
genomic: AAAATGACTCAATATCGTATAAGAATGAGGAAACTTCAACTGAAAGTGAGgtaggcactt ... atttgtttagGGAGAAGGTCATGACAATGCCCAGGAAGCAAACACAGCGTGATCTCCGGAG
EST: gi|148939429|gb|EC883983.2|EC883983
EST:     AAAATGACTCAATATCGTATAAGAATGAGGAAACTTCAACTGAAAGTGAG                         GGAGAAGGTCATGACAATGCCCAGGAAGCAAACACAGCGTGATCTCCGGAG
genomic: AAAATGACTCAATATCGTATAAGAATGAGGAAACTTCAACTGAAAGTGAGgtaggcactt ... atttgtttagGGAGAAGGTCATGACAATGCCCAGGAAGCAAACACAGCGTGATCTCCGGAG
EST: gi|33468206|gb|CF245255.1|CF245255
EST:     TATAAGAATGAGGAAACTTCAACTGAAAGTGAG                         GGAGAAGGTCATGACAATGCCCAGGAAGCAAACACAGCGTGATCTCCGGAG
genomic: TATAAGAATGAGGAAACTTCAACTGAAAGTGAGgtaggcactt ... atttgtttagGGAGAAGGTCATGACAATGCCCAGGAAGCAAACACAGCGTGATCTCCGGAG
EST: gi|211374387|gb|FK951695.1|FK951695
EST:     GAGGAAACTTCAACTGAAAGTGAG                         GGAGAAGGTCATGACAATGCCCAGGAAGCAAACACAGCGTGATCTCCGGAG
genomic: GAGGAAACTTCAACTGAAAGTGAGgtaggcactt ... atttgtttagGGAGAAGGTCATGACAATGCCCAGGAAGCAAACACAGCGTGATCTCCGGAG
EST: gi|31355775|gb|CD440132.1|CD440132
EST:     AAAATGACTCAATATCGTATAAGAATGAGGAAACTTCAACTGAAAGTGAG                         GGAGAAGGTCATGACAATGCCCAGGAAGCAAACACAGCGTGATCTCCGGAG
genomic: AAAATGACTCAATATCGTATAAGAATGAGGAAACTTCAACTGAAAGTGAGgtaggcactt ... atttgtttagGGAGAAGGTCATGACAATGCCCAGGAAGCAAACACAGCGTGATCTCCGGAG
EST: gi|76932105|gb|DV172945.1|DV172945
EST:     AAAATGACTCAATATCGTATAAGAATGAGGAAACTTCAACTGAAAGTGAG                         GGAGAAGGTCATGACAATGCCCAGGAAGCAAACACAGCGTGATCTCCGGAG
genomic: AAAATGACTCAATATCGTATAAGAATGAGGAAACTTCAACTGAAAGTGAGgtaggcactt ... atttgtttagGGAGAAGGTCATGACAATGCCCAGGAAGCAAACACAGCGTGATCTCCGGAG
EST: gi|148946083|gb|EC891379.2|EC891379
EST:     AAAATGACTCAATATCGTATAAGAATGAGGAAACTTCAACTGAAAGTGAG                         GGAGAAGGTCATGACAATGCCCAGGAAGCAAACACAGCGTGATCTCCGGAG
genomic: AAAATGACTCAATATCGTATAAGAATGAGGAAACTTCAACTGAAAGTGAGgtaggcactt ... atttgtttagGGAGAAGGTCATGACAATGCCCAGGAAGCAAACACAGCGTGATCTCCGGAG
EST: gi|211374386|gb|FK951694.1|FK951694
EST:     ATGACTCAATATCGTATAAGAATGAGGAAACTTCAACTGAAAGTGAG                         GGAGAAGGTCATGACAATGCCCAGGAAGCAAACACAGCGTGATCTCCAGGA
genomic: ATGACTCAATATCGTATAAGAATGAGGAAACTTCAACTGAAAGTGAGgtaggcactt ... atttgtttagGGAGAAGGTCATGACAATGCCCAGGAAGCAAACACAGCGTGATCTCC-GGA
EST: gi|91872818|gb|EB402775.1|EB402775
EST:     AAAATGACTCAATATCGTATAAGAATGAGGAAACTTCAACTGAAAGTGAG                         GGAGAAGGTCATGACAATGCCCAGGAAGCAAACACAGCGTGATCTCCGGAG
genomic: AAAATGACTCAATATCGTATAAGAATGAGGAAACTTCAACTGAAAGTGAGgtaggcactt ... atttgtttagGGAGAAGGTCATGACAATGCCCAGGAAGCAAACACAGCGTGATCTCCGGAG
EST: gi|148987550|gb|EE031415.2|EE031415
EST:     AAAATGACTCAATATCGTATAAGAATGAGGAAACTTCAACTGAAAGTGAG                         GGAGAAGGTCATGACAATGCCCAGGAAGCAAACACAGCGTGATCTCCGGAG
genomic: AAAATGACTCAATATCGTATAAGAATGAGGAAACTTCAACTGAAAGTGAGgtaggcactt ... atttgtttagGGAGAAGGTCATGACAATGCCCAGGAAGCAAACACAGCGTGATCTCCGGAG
EST: gi|94477914|gb|EB706872.1|EB706872
EST:     AAAATGACTCAATATCGTATAAGAATGAGGAAACTTCAACTGAAAGTGAG                         GGAGAAGGTCATGACAATGCCCAGGAAGCAAACACAGCGTGATCTCCGGAG
genomic: AAAATGACTCAATATCGTATAAGAATGAGGAAACTTCAACTGAAAGTGAGgtaggcactt ... atttgtttagGGAGAAGGTCATGACAATGCCCAGGAAGCAAACACAGCGTGATCTCCGGAG
EST: gi|211360103|gb|FL362300.1|FL362300
EST:     AAAATGACTCAATATCGTATAAGAATGAGGAAACTTCAACTGAAAGTGAG                         GGAGAAGGTCATGACAATGCCCAGGAAGCAAACACAGCGTGATCTCCGGAG
genomic: AAAATGACTCAATATCGTATAAGAATGAGGAAACTTCAACTGAAAGTGAGgtaggcactt ... atttgtttagGGAGAAGGTCATGACAATGCCCAGGAAGCAAACACAGCGTGATCTCCGGAG
EST: gi|60395012|gb|DN227881.1|DN227881
EST:     TATCGTATAAGAATGAGGAAACTTCAACTGAAAGTGAG                         GGAGAAGGTCATGACAATGCCCAGGAAGCAAACACAGCGTGATCTCCGGAG
genomic: TATCGTATAAGAATGAGGAAACTTCAACTGAAAGTGAGgtaggcactt ... atttgtttagGGAGAAGGTCATGACAATGCCCAGGAAGCAAACACAGCGTGATCTCCGGAG
EST: gi|71322072|gb|DR797726.1|DR797726
EST:     AAAATGACTCAATATCGTATAAGAATGAGGAAACTTCAACTGAAAGTGAG                         GGAGAAGGTCATGACAATGCCCAGGAAGCAAACACAGCGTGATCTCCGGAG
genomic: AAAATGACTCAATATCGTATAAGAATGAGGAAACTTCAACTGAAAGTGAGgtaggcactt ... atttgtttagGGAGAAGGTCATGACAATGCCCAGGAAGCAAACACAGCGTGATCTCCGGAG
EST: gi|31355774|gb|CD440131.1|CD440131
EST:     AAAATGACTCAATATCGTATAAGAATGAGGAAACTTCAACTGAAAGTGAG                         GGAGAAGGTCATGACAATGCCCAGGAAGCAAACACAGCGTGATCTCCGGAG
genomic: AAAATGACTCAATATCGTATAAGAATGAGGAAACTTCAACTGAAAGTGAGgtaggcactt ... atttgtttagGGAGAAGGTCATGACAATGCCCAGGAAGCAAACACAGCGTGATCTCCGGAG
EST: gi|148953458|gb|EE152961.2|EE152961
EST:     AAAATGACTCAATATCGTATAAGAATGAGGAAACTTCAACTGAAAGTGAG                         GGAGAAGGTCATGACAATGCCCAGGAAGCAAACACAGCGTGATCTCCGGAG
genomic: AAAATGACTCAATATCGTATAAGAATGAGGAAACTTCAACTGAAAGTGAGgtaggcactt ... atttgtttagGGAGAAGGTCATGACAATGCCCAGGAAGCAAACACAGCGTGATCTCCGGAG

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: 239

GAATTTTGGCCTAAGCTACTTGTGCACAAGATCAAACAGCGGCTGACAAAAATGACTCAATATCGTATAAGAATGAGGAAACTTCAACTGAAAGTGAGgtaggcactt ... atttgtttagGGAGAAGGTCATGACAATGCCCAGGAAGCAAACACAGCGTGATCTCCGGAGAATGGAGAAAGCTGAAAGGGCTGCTCAACTAGAAAGG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 97

GAATTTTGGCCTAAGCTACTTGTGCACAAGATCAAACAGCGGCTGACAAAAATGACTCAATATCGTATAAGAATGAGGAAACTTCAACTGAAAGTGAGgtaggcactt ... atttgtttagGGAGAAGGTCATGACAATGCCCAGGAAGCAAACACAGCGTGATCTCCGGAGAATGGAGAAAGCTGAAAGGGCTGCTCAACTAGAAAGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 150

GAATTTTGGCCTAAGCTACTTGTGCACAAGATCAAACAGCGGCTGACAAAAATGACTCAATATCGTATAAGAATGAGGAAACTTCAACTGAAAGTGAGgtaggcactt ... atttgtttagGGAGAAGGTCATGACAATGCCCAGGAAGCAAACACAGCGTGATCTCCGGAGAATGGAGAAAGCTGAAAGGGCTGCTCAACTAGAAAGG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 176

GAATTTTGGCCTAAGCTACTTGTGCACAAGATCAAACAGCGGCTGACAAAAATGACTCAATATCGTATAAGAATGAGGAAACTTCAACTGAAAGTGAGgtaggcactt ... atttgtttagGGAGAAGGTCATGACAATGCCCAGGAAGCAAACACAGCGTGATCTCCGGAGAATGGAGAAAGCTGAAAGGGCTGCTCAACTAGAAAGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttaacttccatgtaacatgataagttgtttgacatatgcctccatttgtttagGGAGAAGGTCATGACAATGCCCAGGAAGCAAACACAGCGTGATCTCCGGAGAATGGAGAAAGCTGAAAGGGCTGCTCAACTAGAAAGG
                                        cctccattt  CT-rich tract
                                             atttgttta  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tctgtagctaagtttcatcaggaaacaagtcaccttgtgatgtttttttaacttccatgtaacatgataagttgtttgacatatgcctccatttgtttagGGAGAAGGTCATGACAATGCCCAGGAAGCAAACACAGCGTGATCTCCGGAGAATGGAGAAAGCTGAAAGGGCTGCTCAACTAGAAAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
-ctgtagc
- - - - - - - - - - - aaacaag
- - - - - - - - - - - - - - - - - -tgtgatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttgtttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcctcc