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 5'  3'   		2  
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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTCATACGGTTATGGAGAGGAGCAGCCCAAGTATCAGAGTGGCGGGTATGAGAGGCCGAGCTATGGTGGGGGAGAGGGGTACTATGGCCGCAAGAAAGATgtaagatcctttctccctctttggtttacctatgtgaatgtgaattcatttactttatagtggttgaataactgcttatccttctaatccttgaatagga...

Basic information

species Zea mays
transcript GRMZM2G701082_T04
intron # 2
splice site 5'
intron type U2

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|51592776|gb|CV071922.1|CV071922
EST:     AGAGGCCGAGCTATGGTGGGGGAGAGGGGTACTATGGCCGCAAGAAAGAT                         GATGACGACTCGGATGATGAGAAGAAGCGGCGTCATTCTAAGCACCACCAC
genomic: AGAGGCCGAGCTATGGTGGGGGAGAGGGGTACTATGGCCGCAAGAAAGATgtaagatcct ... tcttgtgtagGATGACGACTCGGATGATGAGAAGAAGCGGCGTCATTCTAAGCACCACCAC
EST: gi|18181291|gb|BM382501.1|BM382501
EST:     AGAGGCCGAGCTATGGTGGGGGAGAGGGGTACTATGGCCGCAAGAAAGAT                         GATGACGACTCGGATGATGAGAAGAAGCGGCGTCATTATAAGCACCACCAC
genomic: AGAGGCCGAGCTATGGTGGGGGAGAGGGGTACTATGGCCGCAAGAAAGATgtaagatcct ... tcttgtgtagGATGACGACTCGGATGATGAGAAGAAGCGGCGTCATTCTAAGCACCACCAC
EST: gi|148983084|gb|EE029000.2|EE029000
EST:     AGAGGCCGAGCTATGGTGGGGGAGAGGGGTACTATGGCCGCAAGAAAGAT                         GATGACGACTCGGATGATGAGAAGAAGCGGCGTCATTTTAAGCACCACCAC
genomic: AGAGGCCGAGCTATGGTGGGGGAGAGGGGTACTATGGCCGCAAGAAAGATgtaagatcct ... tcttgtgtagGATGACGACTCGGATGATGAGAAGAAGCGGCGTCATTCTAAGCACCACCAC
EST: gi|32847709|gb|CD987390.1|CD987390
EST:     GGTACTATGGCCGCAAGAAAGAT                         GATGACGACTCGGATGATGAGAAGAAGCGGCGTCATTCTAAGCACCACCAC
genomic: GGTACTATGGCCGCAAGAAAGATgtaagatcct ... tcttgtgtagGATGACGACTCGGATGATGAGAAGAAGCGGCGTCATTCTAAGCACCACCAC
EST: gi|76915921|gb|DV166168.1|DV166168
EST:     AGAGGCCGAGCTATGGTGGGGGAGAGGGGTACTATGGCCGCAAGAAAGAT                         GATGACGACTCGGATGATGAGAAGAAGCGGCGTCATTTTAAGCACCACCCC
genomic: AGAGGCCGAGCTATGGTGGGGGAGAGGGGTACTATGGCCGCAAGAAAGATgtaagatcct ... tcttgtgtagGATGACGACTCGGATGATGAGAAGAAGCGGCGTCATTCTAAGCACCACCAC
EST: gi|149112698|gb|EE295531.2|EE295531
EST:     AGAGGCCGAGCTATGGTGGGGGAGAGGGGTACTATGGCCGCAAGAAAGAT                         GATGACGACTCGGATGATGAGAAGAAGGGGGGTCATTTTAAGCACCACCCC
genomic: AGAGGCCGAGCTATGGTGGGGGAGAGGGGTACTATGGCCGCAAGAAAGATgtaagatcct ... tcttgtgtagGATGACGACTCGGATGATGAGAAGAAGCGGCGTCATTCTAAGCACCACCAC
EST: gi|116822898|gb|EC866366.1|EC866366
EST:     GGGGTACTATGGCCGCAAGAAAGAT                         GATGACGACTCGGATGATGAGAAGAAGCGGCGTCATTCTAAGCACCA-CAC
genomic: GGGGTACTATGGCCGCAAGAAAGATgtaagatcct ... tcttgtgtagGATGACGACTCGGATGATGAGAAGAAGCGGCGTCATTCTAAGCACCACCAC
EST: gi|149101324|gb|EE187441.2|EE187441
EST:     AGAGGCCGAGCTATGGTGGGGGAGAGGGGTACTATGGCCGCAAGAAAGAT                         GATGACGACTCGGATGATGAGAAGAAGCGGCGTCATTTTAAGCACCACCCC
genomic: AGAGGCCGAGCTATGGTGGGGGAGAGGGGTACTATGGCCGCAAGAAAGATgtaagatcct ... tcttgtgtagGATGACGACTCGGATGATGAGAAGAAGCGGCGTCATTCTAAGCACCACCAC
EST: gi|47962343|gb|CN845052.1|CN845052
EST:     AGAGGCCGAGCTATGGTGGGGGAGAGGGGTACTATGGCCGCAAGAAAGAT                         GATGACGACTCGGATGATGAGAAGAAGCGGCGTCATTCTAAGCACCACCAC
genomic: AGAGGCCGAGCTATGGTGGGGGAGAGGGGTACTATGGCCGCAAGAAAGATgtaagatcct ... tcttgtgtagGATGACGACTCGGATGATGAGAAGAAGCGGCGTCATTCTAAGCACCACCAC
EST: gi|110506424|gb|EE017972.1|EE017972
EST:     AGAGGCCGAGCTATGGTGGGGGAGAGGGGTACTATGGCCGCAAGAAAGAT                         GATGACGACTCGGATGATGAGAAGAAGCGGCGTCATTTTAAGCACCACCCC
genomic: AGAGGCCGAGCTATGGTGGGGGAGAGGGGTACTATGGCCGCAAGAAAGATgtaagatcct ... tcttgtgtagGATGACGACTCGGATGATGAGAAGAAGCGGCGTCATTCTAAGCACCACCAC
EST: gi|113701985|gb|EE679489.1|EE679489
EST:     AGAGGCCGAGCTATGGTGGGGGAGAGGGGTACTATGGCCGCAAGAAAGAT                         GATGACGACTCGGATGATGAGAAGAAGCGGCGTCATTCTAAGCACCACCAC
genomic: AGAGGCCGAGCTATGGTGGGGGAGAGGGGTACTATGGCCGCAAGAAAGATgtaagatcct ... tcttgtgtagGATGACGACTCGGATGATGAGAAGAAGCGGCGTCATTCTAAGCACCACCAC
EST: gi|32857936|gb|CD997617.1|CD997617
EST:     AGAGACCGAGCTATGGTGGGGGAGAGGGGTACTATGGCCGCAAGGAAGAT                         GATGACGACTCGGATGATGAGAAGAAGCGGCGTCATTCTAAGCACCACCAC
genomic: AGAGGCCGAGCTATGGTGGGGGAGAGGGGTACTATGGCCGCAAGAAAGATgtaagatcct ... tcttgtgtagGATGACGACTCGGATGATGAGAAGAAGCGGCGTCATTCTAAGCACCACCAC
EST: gi|32849926|gb|CD989607.1|CD989607
EST:     ACTATGGCCGCAAGAAAGAT                         GATGACGACTCGGATGATGAGAAGAAGCGGCGTCATTCTAAGCACCACCAC
genomic: ACTATGGCCGCAAGAAAGATgtaagatcct ... tcttgtgtagGATGACGACTCGGATGATGAGAAGAAGCGGCGTCATTCTAAGCACCACCAC
EST: gi|149045876|gb|EE047874.2|EE047874
EST:     AGAGGCCGAGCTATGGTGGGGGAGAGGGGTACTATGGCCGCAAGAAAGAT                         GATGACGACTCGGATGATGAGAAGAAGGGGGGTCATTTTAAGCACCACCCC
genomic: AGAGGCCGAGCTATGGTGGGGGAGAGGGGTACTATGGCCGCAAGAAAGATgtaagatcct ... tcttgtgtagGATGACGACTCGGATGATGAGAAGAAGCGGCGTCATTCTAAGCACCACCAC
EST: gi|110540719|gb|EE044639.1|EE044639
EST:     AGAGGCCGAGCTATGGTGGGGGAGAGGGGTACTATGGCCGCAAGAAAGAT                         GATGACGACTCGGATGATGAGAAGAAGGGGGGTCATTTTAAGCACCACCCC
genomic: AGAGGCCGAGCTATGGTGGGGGAGAGGGGTACTATGGCCGCAAGAAAGATgtaagatcct ... tcttgtgtagGATGACGACTCGGATGATGAGAAGAAGCGGCGTCATTCTAAGCACCACCAC
EST: gi|91048543|gb|EB158961.1|EB158961
EST:     AGAGGCCGAGCTATGGTGGGGGAGAGGGGTACTATGGCCGCAAGAAAGAT                         GATGACGACTCGGATGATGAGAAGAAGCGGCGTCATTTTAAGCACCACCAC
genomic: AGAGGCCGAGCTATGGTGGGGGAGAGGGGTACTATGGCCGCAAGAAAGATgtaagatcct ... tcttgtgtagGATGACGACTCGGATGATGAGAAGAAGCGGCGTCATTCTAAGCACCACCAC
EST: gi|78087593|gb|DV515986.1|DV515986
EST:     AGAGGCCGAGCTATGGTGGGGGAGAGGGGTACTATGGCCGCAAGAAAGAT                         GATGACGACTCGGATGATGAGAAGAAGCGGCGTCATTTTAAGCACCACCAC
genomic: AGAGGCCGAGCTATGGTGGGGGAGAGGGGTACTATGGCCGCAAGAAAGATgtaagatcct ... tcttgtgtagGATGACGACTCGGATGATGAGAAGAAGCGGCGTCATTCTAAGCACCACCAC
EST: gi|32844054|gb|CD983735.1|CD983735
EST:     ACTATGGCCGCAAGAAAGAT                         GATGACGACTCGGATGATGAGAAGAAGCGGCGTCATTCTAAGCACCACCAC
genomic: ACTATGGCCGCAAGAAAGATgtaagatcct ... tcttgtgtagGATGACGACTCGGATGATGAGAAGAAGCGGCGTCATTCTAAGCACCACCAC
EST: gi|211077645|gb|FL084272.1|FL084272
EST:     AGAGACCGAGCTATGGTGGGGGAGAGGGGTACTATGGCCGCAAGAAAGAT                         GATGACGACTCGGATGATGAGAAGAAGCGGCGTCATTCTAAGCACCACCAC
genomic: AGAGGCCGAGCTATGGTGGGGGAGAGGGGTACTATGGCCGCAAGAAAGATgtaagatcct ... tcttgtgtagGATGACGACTCGGATGATGAGAAGAAGCGGCGTCATTCTAAGCACCACCAC
EST: gi|37378476|gb|CF625928.1|CF625928
EST:     AGAGACCGAGCTATGGTGGGGGAGAGGGGTACTATGGCCGCAAGAAAGAT                         GATGACGACTCGGATGATGAGAAGAAGCGGCGTCATTCTAAGCACCACCAC
genomic: AGAGGCCGAGCTATGGTGGGGGAGAGGGGTACTATGGCCGCAAGAAAGATgtaagatcct ... tcttgtgtagGATGACGACTCGGATGATGAGAAGAAGCGGCGTCATTCTAAGCACCACCAC
EST: gi|37384116|gb|CF629105.1|CF629105
EST:     TACTATGGCCGCAAGAAAGAT                         GATGACGACTCGGATGATGAGAAGAAGCGGCGTCATTCTAAGCACCACCAC
genomic: TACTATGGCCGCAAGAAAGATgtaagatcct ... tcttgtgtagGATGACGACTCGGATGATGAGAAGAAGCGGCGTCATTCTAAGCACCACCAC
EST: gi|32929263|gb|CF034075.1|CF034075
EST:     ACTATGGCCGCAAGAAAGAT                         GATGACGACTCGGATGATGAGAAGAAGCGGCGTCATTCTAAGCACCACCAC
genomic: ACTATGGCCGCAAGAAAGATgtaagatcct ... tcttgtgtagGATGACGACTCGGATGATGAGAAGAAGCGGCGTCATTCTAAGCACCACCAC
EST: gi|78023510|gb|DV491897.1|DV491897
EST:     AGAGGCCGAGCTATGGTGGGGGAGAGGGGTACTATGGCCGCAAGAAAGAT                         GATGACGACTCGGATGATGAGAAGAAGCGGCGTCATTCTAAGCACCACCAC
genomic: AGAGGCCGAGCTATGGTGGGGGAGAGGGGTACTATGGCCGCAAGAAAGATgtaagatcct ... tcttgtgtagGATGACGACTCGGATGATGAGAAGAAGCGGCGTCATTCTAAGCACCACCAC
EST: gi|76019977|gb|DT947147.1|DT947147
EST:     AGAGGCCGAGCTATGGTGGGGGAGAGGGGTACTATGGCCGCAAGAAAGAT                         GATGACGACTCGGATGATGAGAAGAAGCGGCGTCATTTTAAGCACCACCCC
genomic: AGAGGCCGAGCTATGGTGGGGGAGAGGGGTACTATGGCCGCAAGAAAGATgtaagatcct ... tcttgtgtagGATGACGACTCGGATGATGAGAAGAAGCGGCGTCATTCTAAGCACCACCAC
EST: gi|71763026|gb|DR960963.1|DR960963
EST:     AGAGGCCGAGCTATGGTGGGGGAGAGGGGTACTATGGCCGCAAGAAAGAT                         GATGACGACTCGGATGATGAGAAGAAGCGGCGTCATTTTAAGCACCACCAC
genomic: AGAGGCCGAGCTATGGTGGGGGAGAGGGGTACTATGGCCGCAAGAAAGATgtaagatcct ... tcttgtgtagGATGACGACTCGGATGATGAGAAGAAGCGGCGTCATTCTAAGCACCACCAC
EST: gi|37378721|gb|CF626066.1|CF626066
EST:     AGAGGCCGAGCTATGGTGGGGGAGAGGGGTACTATGGCCGCAAGAAAGAT                         GATGACGACTCGGATGATGAGAAGAAGCGGCGTCATTCTAAGCACCACCAC
genomic: AGAGGCCGAGCTATGGTGGGGGAGAGGGGTACTATGGCCGCAAGAAAGATgtaagatcct ... tcttgtgtagGATGACGACTCGGATGATGAGAAGAAGCGGCGTCATTCTAAGCACCACCAC
EST: gi|32928424|gb|CF033236.1|CF033236
EST:     ACTATGGCCGCAAGAAAGAT                         GATGACGACTCGGATGATGAGAAGAAGCGGCGTCATTTTAAGCACCACCAC
genomic: ACTATGGCCGCAAGAAAGATgtaagatcct ... tcttgtgtagGATGACGACTCGGATGATGAGAAGAAGCGGCGTCATTCTAAGCACCACCAC
EST: gi|14202914|gb|BG836591.1|BG836591
EST:     AGAGGCCGAGCTATGGTGGGGGAGAGGGGTACTATGGCCGCAAGAAAGAT                         GATGACGACTCGGATGATGAGAAGAAGCGGCGTCATTCTAAGCACCACCAC
genomic: AGAGGCCGAGCTATGGTGGGGGAGAGGGGTACTATGGCCGCAAGAAAGATgtaagatcct ... tcttgtgtagGATGACGACTCGGATGATGAGAAGAAGCGGCGTCATTCTAAGCACCACCAC
EST: gi|89247251|gb|DY619037.1|DY619037
EST:     AGAGGCCGAGCTATGGTGGGGGAGAGGGGTACTATGGCCGCAAGAAAGAT                         GATGACGACTCGGATGATGAGAAGAAGCGGCGTCATTTTAAGCACCACCCC
genomic: AGAGGCCGAGCTATGGTGGGGGAGAGGGGTACTATGGCCGCAAGAAAGATgtaagatcct ... tcttgtgtagGATGACGACTCGGATGATGAGAAGAAGCGGCGTCATTCTAAGCACCACCAC
EST: gi|71441598|gb|DR822648.1|DR822648
EST:     AGAGGCCGAGCTATGGTGGGGGAGAGGGGTACTATGGCCGCAAGAAAGAT                         GATGACGACTCGGATGATGAGAAGAAGCGGCGTCATTTTAAGCACCACCAC
genomic: AGAGGCCGAGCTATGGTGGGGGAGAGGGGTACTATGGCCGCAAGAAAGATgtaagatcct ... tcttgtgtagGATGACGACTCGGATGATGAGAAGAAGCGGCGTCATTCTAAGCACCACCAC
EST: gi|148973727|gb|EE024858.2|EE024858
EST:     AGAGGCCGAGCTATGGTGGGGGAGAGGGGTACTATGGCCGCAAGAAAGAT                         GATGACGACTCGGATGATGAGAAGAAGCGGCGTCATTCTAAGCACCACCAC
genomic: AGAGGCCGAGCTATGGTGGGGGAGAGGGGTACTATGGCCGCAAGAAAGATgtaagatcct ... tcttgtgtagGATGACGACTCGGATGATGAGAAGAAGCGGCGTCATTCTAAGCACCACCAC
EST: gi|116826742|gb|EC870563.1|EC870563
EST:     TGGGGGAGAGGGGTA-TCTGGCCGCAAGAAAGAT                         GATGACGACTCGGATGATGAGAAGAAGCGGCGTCATTCTAAGCACCAGCAC
genomic: TGGGGGAGAGGGGTACTATGGCCGCAAGAAAGATgtaagatcct ... tcttgtgtagGATGACGACTCGGATGATGAGAAGAAGCGGCGTCATTCTAAGCACCACCAC
EST: gi|32863305|gb|CF002987.1|CF002987
EST:     AGA-GCCGAGCTATGGTGGGGGAGAGGGGTACTATGGCCGCAAGAAAGAT                         GATGACGACTCGGATGATGAGAAGAAGCGGCGTCATTCTAAGCACCACCAC
genomic: AGAGGCCGAGCTATGGTGGGGGAGAGGGGTACTATGGCCGCAAGAAAGATgtaagatcct ... tcttgtgtagGATGACGACTCGGATGATGAGAAGAAGCGGCGTCATTCTAAGCACCACCAC

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 2 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 11

TTCATACGGTTATGGAGAGGAGCAGCCCAAGTATCAGAGTGGCGGGTATGAGAGGCCGAGCTATGGTGGGGGAGAGGGGTACTATGGCCGCAAGAAAGATgtaagatcct ... tcttgtgtagGATGACGACTCGGATGATGAGAAGAAGCGGCGTCATTCTAAGCACCACCACCATGGCCACCACTACGATGACTAAGCACCAGTGCCTTCTGCTGGGCGTT


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 21

TTCATACGGTTATGGAGAGGAGCAGCCCAAGTATCAGAGTGGCGGGTATGAGAGGCCGAGCTATGGTGGGGGAGAGGGGTACTATGGCCGCAAGAAAGATgtaagatcct ... tcttgtgtagGATGACGACTCGGATGATGAGAAGAAGCGGCGTCATTCTAAGCACCACCACCATGGCCACCACTACGATGACTAAGCACCAGTGCCTTCTGCTGGGCGTT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTCATACGGTTATGGAGAGGAGCAGCCCAAGTATCAGAGTGGCGGGTATGAGAGGCCGAGCTATGGTGGGGGAGAGGGGTACTATGGCCGCAAGAAAGATgtaagatcctttctccctctttggtttacctatgtgaatgtgaattcatttactttatagtggttgaataactgcttatccttctaatccttgaatagga

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA