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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagaaactaaactaaacaagctacatatagctcactcattcttccctgctcctccagattcagttctgaaggcacacctgtatctaactaagaatggttctgtcctacagCTGATGGGAGCAGTCAATTCTGAAACTTTACTAGGAGG

Basic information

species Zea mays
transcript GRMZM2G111954_T03
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G111954_T03 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os07g04990.1 (Oryza sativa), 3'ss of exon 2
gtaagaaactaaactaaacaagctacat-atagctcactcattcttccctgctcctccagattcagttctgaaggcacacctgtatctaactaagaatggttctgtcctacagCTGATGGGAGCAGTCAATTCTGAAACTTTACTAGGAGG
||||||||||| |      || || ||| ||  ||| |||||  || |||  | |  || |     |||||||||  ||  |     ||  |       |||||||||| ||||||||||||||||| |||||||||| |||||| |||||
gtaagaaactagaa-----aaacttcatgattcctcgctcatattttcct--tgcgtcaaa----attctgaaggttcatttaaccttagtt-------gttctgtccttcagCTGATGGGAGCAGTAAATTCTGAAAGTTTACTCGGAGG
















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|76281356|gb|DV020924.1|DV020924
EST:     TCGATAACGGGATGACCTTCTTCGATACTGCAGAAGTTTACGGTACAGCA                         CTGATGGGAGCAGTCAATTCTGAAACTTTACTAGGAGG
genomic: TCGATAACGGGATGACCTTCTTCGATACTGCAGAAGTTTACGGTACAGCAgtaagaaact ... tgtcctacagCTGATGGGAGCAGTCAATTCTGAAACTTTACTAGGAGG
EST: gi|149077171|gb|EE165834.2|EE165834
EST:     TCGATAACGGGATGACCTTCTTCGATACTGCAGAAGTTTACGGTACAGCA                         CTGATGGGAGCAGTCAATTCTGAAACTTTACTAGGAGG
genomic: TCGATAACGGGATGACCTTCTTCGATACTGCAGAAGTTTACGGTACAGCAgtaagaaact ... tgtcctacagCTGATGGGAGCAGTCAATTCTGAAACTTTACTAGGAGG
EST: gi|148931921|gb|EC875135.2|EC875135
EST:     TCGATAACGGGATGACCTTCTTCGATACTGCAGAAGTTTACGGTACAGCA                         CTGATGGGAGCAGTCAATTCTGAAACTTTACTAGGAGG
genomic: TCGATAACGGGATGACCTTCTTCGATACTGCAGAAGTTTACGGTACAGCAgtaagaaact ... tgtcctacagCTGATGGGAGCAGTCAATTCTGAAACTTTACTAGGAGG
EST: gi|148935240|gb|EC879277.2|EC879277
EST:     TCGATAACGGGATGACCTTCTTCGATACTGCAGAAGTTTACGGTACAGCA                         CTGATGGGAGCAGTCAATTCTGAAACTTTACTAGGAGG
genomic: TCGATAACGGGATGACCTTCTTCGATACTGCAGAAGTTTACGGTACAGCAgtaagaaact ... tgtcctacagCTGATGGGAGCAGTCAATTCTGAAACTTTACTAGGAGG
EST: gi|149063769|gb|EE157636.2|EE157636
EST:     TCGATAACGGGATGACCTTCTTCGATACTGCAGAAGTTTACGGTACAGCA                         CTGATGGGAGCAGTCAATTCTGAAACTTTACTAGGAGG
genomic: TCGATAACGGGATGACCTTCTTCGATACTGCAGAAGTTTACGGTACAGCAgtaagaaact ... tgtcctacagCTGATGGGAGCAGTCAATTCTGAAACTTTACTAGGAGG
EST: gi|149013468|gb|EE042982.2|EE042982
EST:     TCGATAACGGGATGACCTTCTTCGATACTGCAGAAGTTTACGGTACAGCA                         CTGATGGGAGCAGTCAATTCTGAAACTTTACTAGGAGG
genomic: TCGATAACGGGATGACCTTCTTCGATACTGCAGAAGTTTACGGTACAGCAgtaagaaact ... tgtcctacagCTGATGGGAGCAGTCAATTCTGAAACTTTACTAGGAGG
EST: gi|148972626|gb|EE023587.2|EE023587
EST:     TCGATAACGGGATGACCTTCTTCGATACTGCAGAAGTTTACGGTACAGCA                         CTGATGGGAGCAGTCAATTCTGAAACTTTACTAGGAGG
genomic: TCGATAACGGGATGACCTTCTTCGATACTGCAGAAGTTTACGGTACAGCAgtaagaaact ... tgtcctacagCTGATGGGAGCAGTCAATTCTGAAACTTTACTAGGAGG
EST: gi|148982464|gb|EE028329.2|EE028329
EST:     TCGATAACGGGATGACCTTCTTCGATACTGCAGAAGTTTACGGTACAGCA                         CTGATGGGAGCAGTCAATTCTGAAACTTTACTAGGAGG
genomic: TCGATAACGGGATGACCTTCTTCGATACTGCAGAAGTTTACGGTACAGCAgtaagaaact ... tgtcctacagCTGATGGGAGCAGTCAATTCTGAAACTTTACTAGGAGG
EST: gi|148936271|gb|EC880349.2|EC880349
EST:     TCGATAACGGGATGACCTTCTTCGATACTGCAGAAGTTTACGGTACAGCA                         CTGATGGGAGCAGTCAATTCTGAAACTTTACTAGGAGG
genomic: TCGATAACGGGATGACCTTCTTCGATACTGCAGAAGTTTACGGTACAGCAgtaagaaact ... tgtcctacagCTGATGGGAGCAGTCAATTCTGAAACTTTACTAGGAGG
EST: gi|149111659|gb|EE190803.2|EE190803
EST:     TCGATAACGGGATGACCTTCTTCGATACTGCAGAAGTTTACGGTACAGCA                         CTGATGGGAGCAGTCAATTCTGAAACTTTACTAGGAGG
genomic: TCGATAACGGGATGACCTTCTTCGATACTGCAGAAGTTTACGGTACAGCAgtaagaaact ... tgtcctacagCTGATGGGAGCAGTCAATTCTGAAACTTTACTAGGAGG

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 1 RNA-Seqlibrary.


Block sizes: 33 (upstream exon), 39 (downstream exon)
Score: 5

ACAGGAGACTGAGGGAAGCACAGGACGCGTTCGATGCGAGCATCGATAACGGGATGACCTTCTTCGATACTGCAGAAGTTTACGGTACAGCAgtaagaaact ... tgtcctacagCTGATGGGAGCAGTCAATTCTGAAACTTTACTAGGAGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agattcagttctgaaggcacacctgtatctaactaagaatggttctgtcctacagCTGATGGGAGCAGTCAATTCTGAAACTTTACTAGGAGG
                          atctaac  putative branch site (score: 5)
                                          ttctgtcct  putative PPT
                         tatctaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagaaactaaactaaacaagctacatatagctcactcattcttccctgctcctccagattcagttctgaaggcacacctgtatctaactaagaatggttctgtcctacagCTGATGGGAGCAGTCAATTCTGAAACTTTACTAGGAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG