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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAGTGTTCTCGAAGCTGATATTGTTATTGTTGGCGTCGGCGGCAGGCCATTGACGCGTCTCTTCATAGGCCAAGCTGCTGACGAGAAAGGTGGACTCAAGgtcagttcacttcttgcttttcttctcaaaaaaagaagaaatgttcgagtctcgatgagcttctgtgtcttgcctgatattgtgctaacgtttttgttatgtcag

Basic information

species Zea mays
transcript GRMZM2G134708_T01
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G134708_T01 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os08g44340.1 (Oryza sativa), 5'ss of exon 8
AAGTGTTCTCGAAGCTGATATTGTTATTGTTGGCGTCGGCGGCAGGCCATTGACGCGTCTCTTCATAGGCCAAGCTGCTGACGAGAAAGGTGGACTCAAGgtcagttcacttcttgcttttcttctcaaaaaaagaagaaatgttcgagtctcgatgagcttctgtgtcttgcctgatattgtgctaacgtttttgttatgtcag--------------------------------------------------------------------------------
||  || || |||||||| ||||||||||| || ||||| ||||||||| |||| | ||||||||  || |||| ||| || ||||| |||||| |||||||  || |  ||  || |  ||||    |         |  || |  | |      | | |  | ||| || |  | |||||| |    |  |        | ||                                                                                
AAACGTGCTGGAAGCTGACATTGTTATTGTCGGTGTCGGTGGCAGGCCACTGACTCATCTCTTCAAGGGTCAAGTTGCAGAGGAGAAGGGTGGAATCAAGgtttgtccggtttctgttcatctttcagattctgctctatctgctacatttgttgcgtgatgat-tgtatttcaggctattgtccatttgagtcaccctaattagcaactgaaccttctttcgagcttgttcttgcttataccttcgaattagctgaacatttcaaatctgcatgtgtcttccag
















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|32921847|gb|CF026659.1|CF026659
EST:     TGACGCGTCTCTTCATAGGCCAAGCTGCTGACGAGAAAGGTGGACTCAAG                         ACCGATGCATTCTTCGAAACAAGCGTAGCCGGGGTATACGCGATCGGCGAC
genomic: TGACGCGTCTCTTCATAGGCCAAGCTGCTGACGAGAAAGGTGGACTCAAGgtcagttcac ... gttatgtcagACCGATGCATTCTTCGAAACAAGTGTAGCCGGGGTATACGCGATCGGCGAC
EST: gi|32922844|gb|CF027656.1|CF027656
EST:     TGACGCGTCTCTTCATAGGCCAAGCTGCTGACGAGAAAGGTGGACTCAAG                         ACCGATGCATTCTTCGAAACAAGCGTAGCCGGGGTATACGCGATCGGCGAC
genomic: TGACGCGTCTCTTCATAGGCCAAGCTGCTGACGAGAAAGGTGGACTCAAGgtcagttcac ... gttatgtcagACCGATGCATTCTTCGAAACAAGTGTAGCCGGGGTATACGCGATCGGCGAC
EST: gi|40334658|gb|CK368728.1|CK368728
EST:     TGACGCGTCTCTTCATAGGCCAAGCTGCTGACGAGAAAGGTGGACTCAAG                         ACCGATGCATTCTTCGAAACAAGTGTAGCCGGGGTATACGCGATCGGCGAC
genomic: TGACGCGTCTCTTCATAGGCCAAGCTGCTGACGAGAAAGGTGGACTCAAGgtcagttcac ... gttatgtcagACCGATGCATTCTTCGAAACAAGTGTAGCCGGGGTATACGCGATCGGCGAC
EST: gi|32836981|gb|CD976659.1|CD976659
EST:     TGACGCGTCTCTTCATAGGCCAAGCTGCTGACGAGAAAGGTGGACTCAAG                         ACCGATGCATTCTTCGAAACAAGTGTAGCCGGGGTATACGCGATCGGCGAC
genomic: TGACGCGTCTCTTCATAGGCCAAGCTGCTGACGAGAAAGGTGGACTCAAGgtcagttcac ... gttatgtcagACCGATGCATTCTTCGAAACAAGTGTAGCCGGGGTATACGCGATCGGCGAC
EST: gi|32923140|gb|CF027952.1|CF027952
EST:     TGACGCGTCTCTTCATAGGCCAAGCTGCTGACGAGAAAGGTGGACTCAAG                         ACCGATGCATTCTTCGAAACAAGCGTAGCCGGGGTATACGCGATCGGCGAC
genomic: TGACGCGTCTCTTCATAGGCCAAGCTGCTGACGAGAAAGGTGGACTCAAGgtcagttcac ... gttatgtcagACCGATGCATTCTTCGAAACAAGTGTAGCCGGGGTATACGCGATCGGCGAC
EST: gi|44682264|gb|CK787312.1|CK787312
EST:     TGACGCGTCTCTTCATAGGCCAAGCTGCTGACGAGAAAGGTGGACTCAAG                         ACCGATGCATTCTTCGAAACAAGTGTAGCCGGGGTATACGCGATCGGCGAC
genomic: TGACGCGTCTCTTCATAGGCCAAGCTGCTGACGAGAAAGGTGGACTCAAGgtcagttcac ... gttatgtcagACCGATGCATTCTTCGAAACAAGTGTAGCCGGGGTATACGCGATCGGCGAC
EST: gi|32847254|gb|CD986935.1|CD986935
EST:     TGACGCGTCTCTTTATAGGCCAAGCTGCTGACGAGAAAGGTGGACTCAAG                         ACCGATGCATTCTTCGAAACAAGTGTAGCCGGGGTATACGCGATCGGCGAC
genomic: TGACGCGTCTCTTCATAGGCCAAGCTGCTGACGAGAAAGGTGGACTCAAGgtcagttcac ... gttatgtcagACCGATGCATTCTTCGAAACAAGTGTAGCCGGGGTATACGCGATCGGCGAC
EST: gi|32922493|gb|CF027305.1|CF027305
EST:     TGACGCGTCTCTTCATAGGCCAAGCTGCTGACGAGAAAGGTGGACTCAAG                         ACCGATGCATTCTTCGAAACAAGCGTAGCCGGGGTATACGCGATCGGCGAC
genomic: TGACGCGTCTCTTCATAGGCCAAGCTGCTGACGAGAAAGGTGGACTCAAGgtcagttcac ... gttatgtcagACCGATGCATTCTTCGAAACAAGTGTAGCCGGGGTATACGCGATCGGCGAC
EST: gi|32921861|gb|CF026673.1|CF026673
EST:     TGACGCGTCTCTTCATAGGCCAAGCTGCTGACGAGAAAGGTGGACTCAAG                         ACCGATGCATTCTTCGAAACAAGCGTAGCCGGGGTATACGCGATCGGCGAC
genomic: TGACGCGTCTCTTCATAGGCCAAGCTGCTGACGAGAAAGGTGGACTCAAGgtcagttcac ... gttatgtcagACCGATGCATTCTTCGAAACAAGTGTAGCCGGGGTATACGCGATCGGCGAC
EST: gi|32920363|gb|CF025175.1|CF025175
EST:     TGACGCGTCTCTTCATAGGCCAAGCTGCTGACGAGAAAGGTGGACTCAAG                         ACCGATGCATTCTTCGAAACAAGCGTAGCCGGGGTATACGCGATCGGCGAC
genomic: TGACGCGTCTCTTCATAGGCCAAGCTGCTGACGAGAAAGGTGGACTCAAGgtcagttcac ... gttatgtcagACCGATGCATTCTTCGAAACAAGTGTAGCCGGGGTATACGCGATCGGCGAC
EST: gi|32921955|gb|CF026767.1|CF026767
EST:     TGACGCGTCTCTTCATAGGCCAAGCTGCTGACGAGAAAGGTGGACTCAAG                         ACCGATGCATTCTTCGAAACAAGCGTAGCCGGGGTATACGCGATCGGCGAC
genomic: TGACGCGTCTCTTCATAGGCCAAGCTGCTGACGAGAAAGGTGGACTCAAGgtcagttcac ... gttatgtcagACCGATGCATTCTTCGAAACAAGTGTAGCCGGGGTATACGCGATCGGCGAC
EST: gi|32922296|gb|CF027108.1|CF027108
EST:     TGACGCGTCTCTTCATAGGCCAAGCTGCTGACGAGAAAGGTGGACTCAAG                         ACCGATGCATTCTTCGAAACAAGCGTAGCCGGGGTATACGCGATCGGCGAC
genomic: TGACGCGTCTCTTCATAGGCCAAGCTGCTGACGAGAAAGGTGGACTCAAGgtcagttcac ... gttatgtcagACCGATGCATTCTTCGAAACAAGTGTAGCCGGGGTATACGCGATCGGCGAC
EST: gi|32923579|gb|CF028391.1|CF028391
EST:     TGACGCGTCTCTTCATAGGCCAAGCTGCTGACGAGAAAGGTGGACTCAAG                         ACCGATGCATTCTTCGAAACAAGCGTAGCCGGGGTATACGCGATCGGCGAC
genomic: TGACGCGTCTCTTCATAGGCCAAGCTGCTGACGAGAAAGGTGGACTCAAGgtcagttcac ... gttatgtcagACCGATGCATTCTTCGAAACAAGTGTAGCCGGGGTATACGCGATCGGCGAC
EST: gi|67014083|gb|CO442832.1|CO442832
EST:     TGACGCGTCTCTTCATAGGCCAAGCTGCTGACGAGAAAGGTGGACTCAAG                         ACCGATGCATTCTTCGAAACAAGTGTAGCCGGGGTATACGCGATCGGCGAC
genomic: TGACGCGTCTCTTCATAGGCCAAGCTGCTGACGAGAAAGGTGGACTCAAGgtcagttcac ... gttatgtcagACCGATGCATTCTTCGAAACAAGTGTAGCCGGGGTATACGCGATCGGCGAC
EST: gi|32839119|gb|CD978800.1|CD978800
EST:     TGACGCGTCTCTTCATAGGCCAAGCTGCTGACGAGAAAGGTGGACTCAAG                         ACCGATGCATTCTTCGAAACAAGTGTAGCCGGGGTATACGCGATCGGCGAC
genomic: TGACGCGTCTCTTCATAGGCCAAGCTGCTGACGAGAAAGGTGGACTCAAGgtcagttcac ... gttatgtcagACCGATGCATTCTTCGAAACAAGTGTAGCCGGGGTATACGCGATCGGCGAC
EST: gi|6918570|gb|AW400100.1|AW400100
EST:     TGACGCGTCTCTTCATAGGCCAAGCTGCTGACGAGAAAGGTGGACTCAAG                         ACCGATGCATTCTTCGAAACAAGTGTAGCCGGGGTATACGCGATCGGCGAC
genomic: TGACGCGTCTCTTCATAGGCCAAGCTGCTGACGAGAAAGGTGGACTCAAGgtcagttcac ... gttatgtcagACCGATGCATTCTTCGAAACAAGTGTAGCCGGGGTATACGCGATCGGCGAC
EST: gi|113703090|gb|EE680594.1|EE680594
EST:     TGACGCGTCTCTTCATAGGCCAAGCTGCTGACGAGAAAGGTGGACTCAAG                         ACCGATGCATTCTTCGAAACAAGTGTAGCCGGGGTATACGCGATCGGCGAC
genomic: TGACGCGTCTCTTCATAGGCCAAGCTGCTGACGAGAAAGGTGGACTCAAGgtcagttcac ... gttatgtcagACCGATGCATTCTTCGAAACAAGTGTAGCCGGGGTATACGCGATCGGCGAC
EST: gi|32923589|gb|CF028401.1|CF028401
EST:     TGACGCGTCTCTTCATAGGCCAAGCTGCTGACGAGAAAGGTGGACTCAAG                         ACCGATGCATTCTTCGAAACAAGCGTAGCCGGGGTATACGCGATCGGCGAC
genomic: TGACGCGTCTCTTCATAGGCCAAGCTGCTGACGAGAAAGGTGGACTCAAGgtcagttcac ... gttatgtcagACCGATGCATTCTTCGAAACAAGTGTAGCCGGGGTATACGCGATCGGCGAC
EST: gi|32837202|gb|CD976880.1|CD976880
EST:     TGACGCGTCTCTTCATAGGCCAAGCTGCTGACGAGAAAGGTGGACTCAAG                         ACCGATGCATTCTTCGAAACAAGTGTAGCCGGGGTATACGCGATCGGCGAC
genomic: TGACGCGTCTCTTCATAGGCCAAGCTGCTGACGAGAAAGGTGGACTCAAGgtcagttcac ... gttatgtcagACCGATGCATTCTTCGAAACAAGTGTAGCCGGGGTATACGCGATCGGCGAC
EST: gi|76931160|gb|DV172671.1|DV172671
EST:     ATAGGCCAAGCTGCTGACGAGAAAGGTGGACTCAAG                         ACCGATGCATTCTTCGAAACAAGTGTAGCCGGGGTATACGCGATCGGCGAC
genomic: ATAGGCCAAGCTGCTGACGAGAAAGGTGGACTCAAGgtcagttcac ... gttatgtcagACCGATGCATTCTTCGAAACAAGTGTAGCCGGGGTATACGCGATCGGCGAC
EST: gi|32922893|gb|CF027705.1|CF027705
EST:     TGACGCGTCTCTTCATAGGCCAAGCTGCTGACGAGAAAGGTGGACTCAAG                         ACCGATGCATTCTTCGAAACAAGCGTAGCCGGGGTATACGCGATCGGCGAC
genomic: TGACGCGTCTCTTCATAGGCCAAGCTGCTGACGAGAAAGGTGGACTCAAGgtcagttcac ... gttatgtcagACCGATGCATTCTTCGAAACAAGTGTAGCCGGGGTATACGCGATCGGCGAC
EST: gi|32836497|gb|CD976175.1|CD976175
EST:     TGACGCGTCTCTTCATAGGCCAAGCTGCTGACGAGAAAGGTGGACTCAAG                         ACCGATGCATTCTTCGAAACAAGTGTAGCCGGGGTATACGCGATCGGCGAC
genomic: TGACGCGTCTCTTCATAGGCCAAGCTGCTGACGAGAAAGGTGGACTCAAGgtcagttcac ... gttatgtcagACCGATGCATTCTTCGAAACAAGTGTAGCCGGGGTATACGCGATCGGCGAC
EST: gi|91056173|gb|EB166591.1|EB166591
EST:     TGACGCGTCTCTTCATAGGCCAAGCTGCTGACGAGAAAGGTGGACTCAAG                         ACCGATGCATTCTTCGAAACAAGTGTAGCCGGGGTATACGCGATCGGCGAC
genomic: TGACGCGTCTCTTCATAGGCCAAGCTGCTGACGAGAAAGGTGGACTCAAGgtcagttcac ... gttatgtcagACCGATGCATTCTTCGAAACAAGTGTAGCCGGGGTATACGCGATCGGCGAC
EST: gi|32922583|gb|CF027395.1|CF027395
EST:     TGGCGCGTCTCTTCATAGGCCAAGCTGCTGACGAGAAAGGTGGACTCAAG                         ACCGATGCATTCTTCGAAACAAGCGTAGCCGGGGTATACGCGATCGGCGAC
genomic: TGACGCGTCTCTTCATAGGCCAAGCTGCTGACGAGAAAGGTGGACTCAAGgtcagttcac ... gttatgtcagACCGATGCATTCTTCGAAACAAGTGTAGCCGGGGTATACGCGATCGGCGAC
EST: gi|32920371|gb|CF025183.1|CF025183
EST:     TGACGCGTCTCTTCATAGGCCAAGCTGCTGACGAGAAAGGTGGACTCAAG                         ACCGATGCATTCTTCGAAACAAGCGTAGCCGGGGTATACGCGATCGGCGAC
genomic: TGACGCGTCTCTTCATAGGCCAAGCTGCTGACGAGAAAGGTGGACTCAAGgtcagttcac ... gttatgtcagACCGATGCATTCTTCGAAACAAGTGTAGCCGGGGTATACGCGATCGGCGAC
EST: gi|24934486|gb|CA452704.1|CA452704
EST:     TGACGCGTCTCTTCATAGGCCAAGCTGCTGACGAGAAAGGTGGACTCAAG                         ACCGATGCATTCTTCGAAACAAGTGTAGCCGGGGTATACGCGATCGGCGAC
genomic: TGACGCGTCTCTTCATAGGCCAAGCTGCTGACGAGAAAGGTGGACTCAAGgtcagttcac ... gttatgtcagACCGATGCATTCTTCGAAACAAGTGTAGCCGGGGTATACGCGATCGGCGAC
EST: gi|32920307|gb|CF025119.1|CF025119
EST:     TGACGCGTCTCTTCATAGGCCAAGCTGCTGACGAGAAAGGTGGACTCAAG                         ACCGATGCATTCTTCGAAACAAGCGTAGCCGGGGTATACGCGATC
genomic: TGACGCGTCTCTTCATAGGCCAAGCTGCTGACGAGAAAGGTGGACTCAAGgtcagttcac ... gttatgtcagACCGATGCATTCTTCGAAACAAGTGTAGCCGGGGTATACGCGATC
EST: gi|32923404|gb|CF028216.1|CF028216
EST:     TGACGCGTCTCTTCATAGGCCAAGCTGCTGACGAGAAAGGTGGACTCAAG                         ACCGATGCATTCTTCGAAACAAGCGTAGCCGGGGTATACGCGATCGGCGCC
genomic: TGACGCGTCTCTTCATAGGCCAAGCTGCTGACGAGAAAGGTGGACTCAAGgtcagttcac ... gttatgtcagACCGATGCATTCTTCGAAACAAGTGTAGCCGGGGTATACGCGATCGGCGAC

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: 46 (upstream exon), 46 (downstream exon)
Score: 30

AAGTGTTCTCGAAGCTGATATTGTTATTGTTGGCGTCGGCGGCAGGCCATTGACGCGTCTCTTCATAGGCCAAGCTGCTGACGAGAAAGGTGGACTCAAGgtcagttcac ... gttatgtcagACCGATGCATTCTTCGAAACAAGTGTAGCCGGGGTATACGCGATCGGCGACGTGGCCACCTTCCCTCTGAAGCTCTACAACGAGCAGAGGAGAGTTGAGC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 167

AAGTGTTCTCGAAGCTGATATTGTTATTGTTGGCGTCGGCGGCAGGCCATTGACGCGTCTCTTCATAGGCCAAGCTGCTGACGAGAAAGGTGGACTCAAGgtcagttcac ... gttatgtcagACCGATGCATTCTTCGAAACAAGTGTAGCCGGGGTATACGCGATCGGCGACGTGGCCACCTTCCCTCTGAAGCTCTACAACGAGCAGAGGAGAGTTGAGC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 94

AAGTGTTCTCGAAGCTGATATTGTTATTGTTGGCGTCGGCGGCAGGCCATTGACGCGTCTCTTCATAGGCCAAGCTGCTGACGAGAAAGGTGGACTCAAGgtcagttcac ... gttatgtcagACCGATGCATTCTTCGAAACAAGTGTAGCCGGGGTATACGCGATCGGCGACGTGGCCACCTTCCCTCTGAAGCTCTACAACGAGCAGAGGAGAGTTGAGC


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 86

AAGTGTTCTCGAAGCTGATATTGTTATTGTTGGCGTCGGCGGCAGGCCATTGACGCGTCTCTTCATAGGCCAAGCTGCTGACGAGAAAGGTGGACTCAAGgtcagttcac ... gttatgtcagACCGATGCATTCTTCGAAACAAGTGTAGCCGGGGTATACGCGATCGGCGACGTGGCCACCTTCCCTCTGAAGCTCTACAACGAGCAGAGGAGAGTTGAGC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAGTGTTCTCGAAGCTGATATTGTTATTGTTGGCGTCGGCGGCAGGCCATTGACGCGTCTCTTCATAGGCCAAGCTGCTGACGAGAAAGGTGGACTCAAGgtcagttcacttcttgcttttcttctcaaaaaaagaagaaatgttcgagtctcgatgagcttctgtgtcttgcctgatattgtgctaacgtttttgttatgtcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA