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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCAGCAGAACAAGAATATGAAAAGGAAAAGCTCAATGAGAGGATAGCGAAGCTTGCTGGCGGTGTTGCTGTCATTCAGgtaatgtgaagtccacgggtcgcaatgtgttatttgttcaatgttcttttcatcgattcaatgttgcaggtatggtggataaccataattcatgtatggcgttgcttgacag

Basic information

species Zea mays
transcript GRMZM2G083716_T04
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G083716_T04 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os06g02380.2 (Oryza sativa), 5'ss of exon 9
GCAGCAGAACAAGAATATGAAAAGGAAAAGCTCAATGAGAGGATAGCGAAGCTTGCTGGCGGTGTTGCTGTCATTCAGgta--atgtgaagtccacgggtcgcaatgtgttatttgttcaatgttcttttcatcgattcaatgtt-----------gcaggtatggtg--gataaccataattcatgtatggcgttgcttgacag
|| || ||||||||||| || ||||||||||||||||||||||| || ||||||||||| |||||||| ||||||||||||  ||  ||| |  ||     || ||||  ||| |||    |||||||||  | | |||  ||||             || | ||||   |     | |||| || || | |      |||| ||
GCTGCCGAACAAGAATACGAGAAGGAAAAGCTCAATGAGAGGATTGCAAAGCTTGCTGGTGGTGTTGCAGTCATTCAGgtataataagaaatggacaaaatgccatgt--tatctgtatc-tgttctttttcttggttctttgtttggaaagatagatagatgtggttatgtgggtcgtaatccaagttttgttacttttgatag

upper sequence: GRMZM2G083716_T04 (Zea mays), 5'ss of exon 8
lower sequence: AT5G56500.2 (Arabidopsis thaliana), 5'ss of exon 9
GCAGCAGAACAAGAATATGAAAAGGAAAAGCTCAATGAGAGGATAGCGAAGCTTGCTGGCGGTGTTGCTGTCATTCAGgtaatgtgaagtccacgggtcgcaatgtgttatttgttcaatgttcttttcatcgattcaatgttgcaggtatggtggataaccataattcatgtatggcgttgcttgacag
|| || |||||||| ||||||||||||||||| |||||||| || || ||  |  | |||||||||||||| |||||||| |  |     | | |   |  |     | ||      |  ||             | || ||      || |  | |||| | |||   | || |    ||  ||     
GCTGCTGAACAAGACTATGAAAAGGAAAAGCTTAATGAGAGAATTGCTAAATTATCAGGCGGTGTTGCTGTAATTCAGgtgagata----ctaagaaacaaatcacatgatgcaaaaagcgt----------agcttaaggt----aataagaagaataatc-taa---acgttttatattctttag---

upper sequence: GRMZM2G083716_T04 (Zea mays), 5'ss of exon 8
lower sequence: Vv09s0002g03930.t01 (Vitis vinifera), 5'ss of exon 8
GCAGCAGAACAAGAATATGAAAAGGAAAAGCTCAATGAGAGGATAGCGAAGCTTGCTGGCGGTGTTGCTGTCATTCAGgtaatgtgaagtccacg-ggtcgcaatgt-gttatttgttcaatgttcttttcatcgattcaatgttgcaggtatggtggataaccataattcatgtatggcgttgcttgacag
|||||||| || || |||||||| || ||||| ||||| || || || || ||| | || ||||||||||||||||||||||| |    |   |       |||||| | | || ||| |  | |    |  |  |   | ||||     |       |  |   |||||  ||| | ||       |    
GCAGCAGATCAGGACTATGAAAAAGAGAAGCTTAATGAAAGAATTGCAAAACTTTCAGGTGGTGTTGCTGTCATTCAGgtaatttttttttttcttaaatacaatgtagctgttggttgatagatggaattctgaaagtattgttctt--ttctacccactattttaatttttgtgttgcacattcag----

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|211283747|gb|FL354677.1|FL354677
EST:     AGCTCAATGAGAGGATAGCGAAGCTTGCTGGCGGTGTTGCTGTCATTCAG                         GTGGGAGCACAAACAGAAACTGAACTAAAAGAGAAGAAGTTGAGAGTTGAG
genomic: AGCTCAATGAGAGGATAGCGAAGCTTGCTGGCGGTGTTGCTGTCATTCAGgtaatgtgaa ... tgcttgacagGTGGGAGCACAAACAGAAACTGAACTAAAAGAGAAGAAGTTGAGAGTTGAG
EST: gi|33094001|gb|CF053995.1|CF053995
EST:     AGCTCAATGAGAGGATAGCGAAGCTTGCTGGTGGTGTTGCTGTCATTCAG                         GTGGGAGCACAAACAGAAACTGAACTAAAAGAGAAGAAGTTGAGAGTTGAG
genomic: AGCTCAATGAGAGGATAGCGAAGCTTGCTGGCGGTGTTGCTGTCATTCAGgtaatgtgaa ... tgcttgacagGTGGGAGCACAAACAGAAACTGAACTAAAAGAGAAGAAGTTGAGAGTTGAG
EST: gi|22545503|gb|BU097862.1|BU097862
EST:     AGCTCAATGAGAGGATAGCGAAGCTTGCTGGCGGTGTTGCTGTCATTCAG                         GTGGGAGCACAAACAGAAACTGAACTAAAAGAGAAGAAGTTGAGAGTTGAG
genomic: AGCTCAATGAGAGGATAGCGAAGCTTGCTGGCGGTGTTGCTGTCATTCAGgtaatgtgaa ... tgcttgacagGTGGGAGCACAAACAGAAACTGAACTAAAAGAGAAGAAGTTGAGAGTTGAG
EST: gi|87156784|gb|DY401573.1|DY401573
EST:     AGCTCAATGAGAGGATAGCGAAGCTTGCTGGCGGTGTTGCTGTCATTCAG                         GTGGGAGCACAAACAGAAACTGAACTAAAAGAGAAGAAGTTGAGAGTTGAG
genomic: AGCTCAATGAGAGGATAGCGAAGCTTGCTGGCGGTGTTGCTGTCATTCAGgtaatgtgaa ... tgcttgacagGTGGGAGCACAAACAGAAACTGAACTAAAAGAGAAGAAGTTGAGAGTTGAG
EST: gi|24934364|gb|CA452582.1|CA452582
EST:     AGCTCAATGAGAGGATAGCGAAGCTTGCTGGCGGTGTTGCTGTCATTCAG                         GTGGGAGCACAAACAGAAACTGAACTAAAAGAGAAGAAGTTGAGAATTGAG
genomic: AGCTCAATGAGAGGATAGCGAAGCTTGCTGGCGGTGTTGCTGTCATTCAGgtaatgtgaa ... tgcttgacagGTGGGAGCACAAACAGAAACTGAACTAAAAGAGAAGAAGTTGAGAGTTGAG
EST: gi|23357758|gb|BU645407.1|BU645407
EST:     AGCTCAATGAGAGGATAGCGAAGCTTGCTGGCGGTGTTGCTGTCATTCAG                         GTGGGAGCACAAACAGAAACTGAACTAAAAGAGAAGAAGTTGAGAGTTGAG
genomic: AGCTCAATGAGAGGATAGCGAAGCTTGCTGGCGGTGTTGCTGTCATTCAGgtaatgtgaa ... tgcttgacagGTGGGAGCACAAACAGAAACTGAACTAAAAGAGAAGAAGTTGAGAGTTGAG
EST: gi|32837828|gb|CD977506.1|CD977506
EST:     AGCTCAATGAGAGGATAGCGAAGCTTGCTGGTGGTGTTGCTGTCATTCAG                         GTGGGAGCACAAACAGAAACTGAACTAAAAGAGAAGAAGTTGAGAGTTGAG
genomic: AGCTCAATGAGAGGATAGCGAAGCTTGCTGGCGGTGTTGCTGTCATTCAGgtaatgtgaa ... tgcttgacagGTGGGAGCACAAACAGAAACTGAACTAAAAGAGAAGAAGTTGAGAGTTGAG
EST: gi|211268071|gb|FL357474.1|FL357474
EST:     AGCTCAATGAGAGGATAGCGAAGCTTGCTGGTGGTGTTGCTGTCATTCAG                         GTGGGAGCACAAACAGAAACTGAACTAAAAGAGAAGAAGTTGAGAGTTGAG
genomic: AGCTCAATGAGAGGATAGCGAAGCTTGCTGGCGGTGTTGCTGTCATTCAGgtaatgtgaa ... tgcttgacagGTGGGAGCACAAACAGAAACTGAACTAAAAGAGAAGAAGTTGAGAGTTGAG
EST: gi|26558604|gb|CA830839.1|CA830839
EST:     AGCTCAATGAGAGGATAGCGAAGCTTGCTGGCGGTGTTGCTGTCATTCAG                         GTGGGAGCACAAACAGAAACTGAACTAAAAGAGAAGAAGTTGAGAGTTGAG
genomic: AGCTCAATGAGAGGATAGCGAAGCTTGCTGGCGGTGTTGCTGTCATTCAGgtaatgtgaa ... tgcttgacagGTGGGAGCACAAACAGAAACTGAACTAAAAGAGAAGAAGTTGAGAGTTGAG
EST: gi|22545873|gb|BU098247.1|BU098247
EST:     AGCTCAATGAGAGGATAGCGAAGCTTGCTGGCGGTGTTGCTGTCATTCAG                         GTGGGAGCACAAACAGAAACTGAACTAAAAGAGAAGAAGTTGAGAGTTGAG
genomic: AGCTCAATGAGAGGATAGCGAAGCTTGCTGGCGGTGTTGCTGTCATTCAGgtaatgtgaa ... tgcttgacagGTGGGAGCACAAACAGAAACTGAACTAAAAGAGAAGAAGTTGAGAGTTGAG
EST: gi|120480889|gb|EH211078.1|EH211078
EST:     AGCTCAATGAGAGGATAGCGAAGCTTGCTGGCGGTGTTGCTGTCATTCAG                         GTGGGAGCACAAACAGAAACTGAACTAAAAGAGAAGAAGTTGAGAGTTGAG
genomic: AGCTCAATGAGAGGATAGCGAAGCTTGCTGGCGGTGTTGCTGTCATTCAGgtaatgtgaa ... tgcttgacagGTGGGAGCACAAACAGAAACTGAACTAAAAGAGAAGAAGTTGAGAGTTGAG

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: 39 (upstream exon), 49 (downstream exon)
Score: 348

GCAGCAGAACAAGAATATGAAAAGGAAAAGCTCAATGAGAGGATAGCGAAGCTTGCTGGCGGTGTTGCTGTCATTCAGgtaatgtgaa ... tgcttgacagGTGGGAGCACAAACAGAAACTGAACTAAAAGAGAAGAAGTTGAGAGTTGAGGATGCCCTAAATGCAACTAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1708

GCAGCAGAACAAGAATATGAAAAGGAAAAGCTCAATGAGAGGATAGCGAAGCTTGCTGGCGGTGTTGCTGTCATTCAGgtaatgtgaa ... tgcttgacagGTGGGAGCACAAACAGAAACTGAACTAAAAGAGAAGAAGTTGAGAGTTGAGGATGCCCTAAATGCAACTAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 182

GCAGCAGAACAAGAATATGAAAAGGAAAAGCTCAATGAGAGGATAGCGAAGCTTGCTGGCGGTGTTGCTGTCATTCAGgtaatgtgaa ... tgcttgacagGTGGGAGCACAAACAGAAACTGAACTAAAAGAGAAGAAGTTGAGAGTTGAGGATGCCCTAAATGCAACTAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 538

GCAGCAGAACAAGAATATGAAAAGGAAAAGCTCAATGAGAGGATAGCGAAGCTTGCTGGCGGTGTTGCTGTCATTCAGgtaatgtgaa ... tgcttgacagGTGGGAGCACAAACAGAAACTGAACTAAAAGAGAAGAAGTTGAGAGTTGAGGATGCCCTAAATGCAACTAAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCAGCAGAACAAGAATATGAAAAGGAAAAGCTCAATGAGAGGATAGCGAAGCTTGCTGGCGGTGTTGCTGTCATTCAGgtaatgtgaagtccacgggtcgcaatgtgttatttgttcaatgttcttttcatcgattcaatgttgcaggtatggtggataaccataattcatgtatggcgttgcttgacag

- - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - GAGGAT