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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cagttagtttttaaaattatcttcatggtatgctttcacccatggttttttttgggtttcagtatatgtcattaagtagccaacttgctttcatatgcagGTGAAGCAACTGAATTTTCAAGGGTATGAGGTGATTCTGGTAACCTCAGGAGCTGTTGGTGTTGGGAGGCAGAGGCTCCAATACCGTAAACTTATCCATA

Basic information

species Zea mays
transcript GRMZM2G028535_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G028535_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os01g62900.1 (Oryza sativa), 3'ss of exon 2
cagttagtttttaaaatta-tcttcatggtatgctttcacccatggttttttttgggtttcagtatatgtcattaagtagccaacttgctttcatatgcagGTGAAGCAACTGAATTTTCAAGGGTATGAGGTGATTCTGGTAACCTCAGGAGCTGTTGGTGTTGGGAGGCAGAGGCTCCAATACCGTAAACTTATCCATA
  || |  |||       | | ||  |   |    || |  |   |         | ||    ||       | |  || ||    || |    |   ||||||||||| || |||||| | ||||| |||||||||||||| ||||| || ||||||||||||||||||||||||||| | ||||| || ||  || |||
--gtaaactttccccccaaatttttttaccagaggttaatgctctgaccaaccgagcttgtgctaatcagtgtcagttaaccggtgtgataaatttcccagGTGAAGCAGCTAAATTTTGAGGGGTACGAGGTGATTCTGGTCACCTCTGGTGCTGTTGGTGTTGGGAGGCAGAGGCTCAAGTACCGGAAGCTCGTCAATA
















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|211510200|gb|FL110015.1|FL110015
EST:     GCATGAATGGCCGATTGGCCATGGGGAGGCTCGGTTCTCTCTGTGAACAG                         GTGAAGCAACTGAATTTTCAAGGGTATG
genomic: GCATGAATGGCCGATTGGCCATGGGGAGGCTCGGTTCTCTCTGTGAACAGgtacaatacg ... tcatatgcagGTGAAGCAACTGAATTTTCAAGGGTATG
EST: gi|74239241|gb|DT647155.1|DT647155
EST:     GCATGAATGGCCGATTGGCCATGGGGAGGCTCGGTTCTCTCTGTGAACAG                         GTGAAGCAACTGAATTTTCAAGGGGATGAGGTGATTCTGGTAACCTCAGGA
genomic: GCATGAATGGCCGATTGGCCATGGGGAGGCTCGGTTCTCTCTGTGAACAGgtacaatacg ... tcatatgcagGTGAAGCAACTGAATTTTCAAGGGTATGAGGTGATTCTGGTAACCTCAGGA
EST: gi|88755722|gb|DY539863.1|DY539863
EST:     GCATGAATGGCCGATTGGCCATGGGGAGGCTCGGTTCTCTCTGTGAACAG                         GTGAAGCAACTGAATTTTCAAGGGTATGAGGTGATTCTGGTAACCTCAGGA
genomic: GCATGAATGGCCGATTGGCCATGGGGAGGCTCGGTTCTCTCTGTGAACAGgtacaatacg ... tcatatgcagGTGAAGCAACTGAATTTTCAAGGGTATGAGGTGATTCTGGTAACCTCAGGA
EST: gi|6021065|gb|AW065993.1|AW065993
EST:     GCATGAATGGCCGATTGGCCATGGGGAGGCTCGGTTCTCTCTGTGAACAG                         GTGAAGCAACTGAATTTTCAAGGGTATGAGGTGATTCTGGTAACCTCAGGA
genomic: GCATGAATGGCCGATTGGCCATGGGGAGGCTCGGTTCTCTCTGTGAACAGgtacaatacg ... tcatatgcagGTGAAGCAACTGAATTTTCAAGGGTATGAGGTGATTCTGGTAACCTCAGGA
EST: gi|149066720|gb|EE286861.2|EE286861
EST:     GCATGAATGGCCGATTGGCCATGGGGAGGCTCGGTTCTCTCTGTGAACAG                         GTGAAGCAACTGAATTTTCAAGGGTATGAGGTGATTCTGGTAACCTCAGGA
genomic: GCATGAATGGCCGATTGGCCATGGGGAGGCTCGGTTCTCTCTGTGAACAGgtacaatacg ... tcatatgcagGTGAAGCAACTGAATTTTCAAGGGTATGAGGTGATTCTGGTAACCTCAGGA
EST: gi|74245732|gb|DT653646.1|DT653646
EST:     GCATGAATGGCCGATTGGCCATGGGGAGGCTCGGTTCTCTCTGTGAACAG                         GTGAAGCAACTGAATTTTCAAGGGTATGAGGTGATTCTGGTAACCTCAGGA
genomic: GCATGAATGGCCGATTGGCCATGGGGAGGCTCGGTTCTCTCTGTGAACAGgtacaatacg ... tcatatgcagGTGAAGCAACTGAATTTTCAAGGGTATGAGGTGATTCTGGTAACCTCAGGA
EST: gi|101391687|gb|EB817780.1|EB817780
EST:     GCATGAATGGCCGATTGGCCATGGGGAGGCTCGGTTCTCTCTGTGAACAG                         GTGAAGCAACTGAATTTTCAAGGGTATGAGGTGATTCTGGTAACCTCAGGA
genomic: GCATGAATGGCCGATTGGCCATGGGGAGGCTCGGTTCTCTCTGTGAACAGgtacaatacg ... tcatatgcagGTGAAGCAACTGAATTTTCAAGGGTATGAGGTGATTCTGGTAACCTCAGGA

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), 49 (downstream exon)
Score: 131

GTGGGCACGGCTGTTGTCACTGGCATGAATGGCCGATTGGCCATGGGGAGGCTCGGTTCTCTCTGTGAACAGgtacaatacg ... tcatatgcagGTGAAGCAACTGAATTTTCAAGGGTATGAGGTGATTCTGGTAACCTCAGGAGCTGTTGGTGTTGGGAGGCAGAGGCTCCAATACCGTAAACTTATCCATA


Block sizes: 31 (upstream exon), 49 (downstream exon)
Score: 9

GTGGGCACGGCTGTTGTCACTGGCATGAATGGCCGATTGGCCATGGGGAGGCTCGGTTCTCTCTGTGAACAGgtacaatacg ... tcatatgcagGTGAAGCAACTGAATTTTCAAGGGTATGAGGTGATTCTGGTAACCTCAGGAGCTGTTGGTGTTGGGAGGCAGAGGCTCCAATACCGTAAACTTATCCATA


Block sizes: 49 (upstream exon), 39 (downstream exon)
Score: 21

GTGGGCACGGCTGTTGTCACTGGCATGAATGGCCGATTGGCCATGGGGAGGCTCGGTTCTCTCTGTGAACAGgtacaatacg ... tcatatgcagGTGAAGCAACTGAATTTTCAAGGGTATGAGGTGATTCTGGTAACCTCAGGAGCTGTTGGTGTTGGGAGGCAGAGGCTCCAATACCGTAAACTTATCCATA


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 449

GTGGGCACGGCTGTTGTCACTGGCATGAATGGCCGATTGGCCATGGGGAGGCTCGGTTCTCTCTGTGAACAGgtacaatacg ... tcatatgcagGTGAAGCAACTGAATTTTCAAGGGTATGAGGTGATTCTGGTAACCTCAGGAGCTGTTGGTGTTGGGAGGCAGAGGCTCCAATACCGTAAACTTATCCATA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttttttgggtttcagtatatgtcattaagtagccaacttgctttcatatgcagGTGAAGCAACTGAATTTTCAAGGGTATGAGGTGATTCTGGTAACCTCAGGAGCTGTTGGTGTTGGGAGGCAGAGGCTCCAATACCGTAAACTTATCCATA
                                      cttgctttc  CT-rich tract
                         attaagta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cagttagtttttaaaattatcttcatggtatgctttcacccatggttttttttgggtttcagtatatgtcattaagtagccaacttgctttcatatgcagGTGAAGCAACTGAATTTTCAAGGGTATGAGGTGATTCTGGTAACCTCAGGAGCTGTTGGTGTTGGGAGGCAGAGGCTCCAATACCGTAAACTTATCCATA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT
- - - - - - - - - - cttcatg
- - - - - - - - - - - - - - - tgctttc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtagcca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cttgctt