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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAAAAGTTGATTCTGAACACGCTGCAGTTCAACATGTCTGTTCCAACACCTTATGTCTTCATGAAGAGGTTTCTGAAAGCTGCAGATGCAGATAAACAGgtgaaatatcactacactagctcaagctcaagatgcagatgatccgtgttttgtctacttggataaacaaaacacctgtagcagtgatcttttggttttatgattgacactgccccactgttgtatctcgcag

Basic information

species Zea mays
transcript GRMZM2G138886_T01
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G138886_T01 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os04g47580.1 (Oryza sativa), 5'ss of exon 8
GAAAAGTTGATTCTGAACACGCTGCAGTTCAACATGTCTGTTCCAACACCTTATGTCTTCATGAAGAGGTTTCTGAAAGCTGCAGATGCAGATAAACAGgtgaaatatcactacactagctcaagctcaagatgcagatgatccgtgttttgtctacttggataaacaaaacacctgtagcagtgatcttttggttttatgattgacactgccccactgttgtatctcgcag
||||||||||| || ||||| || ||||||||||||||||| ||||||||||| || || ||||   |||||||||| || ||  |  | || || |||||||  ||||   ||| ||   |||  |||               || |||  || ||||| ||||  ||    ||   |||    ||  |    | || | | | |||                        
GAAAAGTTGATCCTAAACACACTCCAGTTCAACATGTCTGTACCAACACCTTACGTTTTTATGAGACGGTTTCTGAAGGCAGCTCAGTCTGACAAGCAGgtgatttatcctaacatta---caaaatcag-------------tgtttttcatc-acttgaataacaaagctcccaacagccaatataatgca-tgttgtcaatcacag-----------------------
















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|78124436|gb|DV542820.1|DV542820
EST:     CTTATGTCTTCATGAAGAGGTTTTTGAAAGCTGCAGATGCAGATAAACAG                         CTTGAGCTAGCGTCATTTTTCATGCTGGAGCTCTGCTTGGTAGAATACCAA
genomic: CTTATGTCTTCATGAAGAGGTTTCTGAAAGCTGCAGATGCAGATAAACAGgtgaaatatc ... tatctcgcagCTTGAGCTAGCGTCATTTTTCATGCTGGAGCTCTGCTTGGTAGAATACCAA
EST: gi|71760161|gb|DR958098.1|DR958098
EST:     CTTATGTCTTCATGAAGAGGTTTCTGAAAGCTGCAGATGCAGATAAACAG                         CTTGAGCTAGCGTCATTTTTCATGCTGGAGCTCTGCTTGGTAGAATACCAA
genomic: CTTATGTCTTCATGAAGAGGTTTCTGAAAGCTGCAGATGCAGATAAACAGgtgaaatatc ... tatctcgcagCTTGAGCTAGCGTCATTTTTCATGCTGGAGCTCTGCTTGGTAGAATACCAA
EST: gi|9951959|gb|BE638542.1|BE638542
EST:     CTTATGTCTTCATGAAGAGGTTTCTGAAAGCTGCAGATGCAGATAAACAG                         CTTGAGCTAGCGTCATTTTTCATGCTGGAGCTCTGCTTGGTAGAATACCAA
genomic: CTTATGTCTTCATGAAGAGGTTTCTGAAAGCTGCAGATGCAGATAAACAGgtgaaatatc ... tatctcgcagCTTGAGCTAGCGTCATTTTTCATGCTGGAGCTCTGCTTGGTAGAATACCAA
EST: gi|12973190|gb|BG268357.1|BG268357
EST:     CTTATGTCTTCATGAAGAGGTTTCTGAAAGCTGCAGATACAGATAAACAG                         CTTGAGCTAGCGTCATTTTTCATGCTGGAGCTCTGCTTGGTAGAATACCAA
genomic: CTTATGTCTTCATGAAGAGGTTTCTGAAAGCTGCAGATGCAGATAAACAGgtgaaatatc ... tatctcgcagCTTGAGCTAGCGTCATTTTTCATGCTGGAGCTCTGCTTGGTAGAATACCAA
EST: gi|50324449|gb|CO519575.1|CO519575
EST:     CTTATGTCTTCATGAAGAGGTTTCTGAAAGCTGCAGATGCAGATAAACAG                         CTTGAGCTAGCGTCATTTTTCATGCTGGAGCTCTGCTTGGTAGAATACCAA
genomic: CTTATGTCTTCATGAAGAGGTTTCTGAAAGCTGCAGATGCAGATAAACAGgtgaaatatc ... tatctcgcagCTTGAGCTAGCGTCATTTTTCATGCTGGAGCTCTGCTTGGTAGAATACCAA
EST: gi|76283025|gb|DV022593.1|DV022593
EST:     CTTATGTCTTCATGAAGAGGTTTCTGAAAGCTGCAGATGCAGATAAACAG                         CTTGAGCTAGCGTCATTTTTCATGCTGGAGCTCTGCTTGGTAGAATACCAA
genomic: CTTATGTCTTCATGAAGAGGTTTCTGAAAGCTGCAGATGCAGATAAACAGgtgaaatatc ... tatctcgcagCTTGAGCTAGCGTCATTTTTCATGCTGGAGCTCTGCTTGGTAGAATACCAA
EST: gi|211247237|gb|FL156677.1|FL156677
EST:     CTTATGTCTTCATGAAGAGGTTTCTGAAAGCTGCAGATGCAGATAAACAG                         CTTGAGCTAGCGTCATTTTTCATGCTGGAGCTCTGCTTGGTAGAATACCAA
genomic: CTTATGTCTTCATGAAGAGGTTTCTGAAAGCTGCAGATGCAGATAAACAGgtgaaatatc ... tatctcgcagCTTGAGCTAGCGTCATTTTTCATGCTGGAGCTCTGCTTGGTAGAATACCAA
EST: gi|211247239|gb|FL156679.1|FL156679
EST:     CTTATGTCTTCATGAAGAGGTTTCTGAAAGCTGC-GATGCAGATWAACAG                         CTTGAGCTAGCGTCATTTT-CATGCTGGA
genomic: CTTATGTCTTCATGAAGAGGTTTCTGAAAGCTGCAGATGCAGATAAACAGgtgaaatatc ... tatctcgcagCTTGAGCTAGCGTCATTTTTCATGCTGGA
EST: gi|61118386|gb|DN559347.1|DN559347
EST:     CTTATGTCTTCATGAAGAGGTTTCTGAAAGCTGCAGATGCAGATAAACAG                         CTTGAGCTAGCGTCATTTTTCATGCTGGAGCTCTGCTTGGTAGAATACCAA
genomic: CTTATGTCTTCATGAAGAGGTTTCTGAAAGCTGCAGATGCAGATAAACAGgtgaaatatc ... tatctcgcagCTTGAGCTAGCGTCATTTTTCATGCTGGAGCTCTGCTTGGTAGAATACCAA
EST: gi|6601796|gb|AW256237.1|AW256237
EST:     CTTATGTCTTCATGAAGAGGTTTCTGAAAGCTGCAGATGCAGATAAACAG                         CTTGAGCTAGCGTCATTTTTCATGCTGGAGCTCTGCTTGGTAGAATACCAA
genomic: CTTATGTCTTCATGAAGAGGTTTCTGAAAGCTGCAGATGCAGATAAACAGgtgaaatatc ... tatctcgcagCTTGAGCTAGCGTCATTTTTCATGCTGGAGCTCTGCTTGGTAGAATACCAA
EST: gi|30307156|gb|CD001829.1|CD001829
EST:     CTTATGTCTTCATGAAGAGGTTTCTGAAAGCTGCAGATGCAGATAAACAG                         CTTGAGCTAGCGTCATTTTTCATGCTGGAGCTCTGCTTGGTAGAATACCAA
genomic: CTTATGTCTTCATGAAGAGGTTTCTGAAAGCTGCAGATGCAGATAAACAGgtgaaatatc ... tatctcgcagCTTGAGCTAGCGTCATTTTTCATGCTGGAGCTCTGCTTGGTAGAATACCAA

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: 48 (upstream exon), 49 (downstream exon)
Score: 229

GAAAAGTTGATTCTGAACACGCTGCAGTTCAACATGTCTGTTCCAACACCTTATGTCTTCATGAAGAGGTTTCTGAAAGCTGCAGATGCAGATAAACAGgtgaaatatc ... tatctcgcagCTTGAGCTAGCGTCATTTTTCATGCTGGAGCTCTGCTTGGTAGAATACCAAATGCTGAATTATCGGCCTTCGCATCTGGCTGCTGCTGCGGTTTATACTG


Block sizes: 44 (upstream exon), 45 (downstream exon)
Score: 15

GAAAAGTTGATTCTGAACACGCTGCAGTTCAACATGTCTGTTCCAACACCTTATGTCTTCATGAAGAGGTTTCTGAAAGCTGCAGATGCAGATAAACAGgtgaaatatc ... tatctcgcagCTTGAGCTAGCGTCATTTTTCATGCTGGAGCTCTGCTTGGTAGAATACCAAATGCTGAATTATCGGCCTTCGCATCTGGCTGCTGCTGCGGTTTATACTG


Block sizes: 46 (upstream exon), 35 (downstream exon)
Score: 27

GAAAAGTTGATTCTGAACACGCTGCAGTTCAACATGTCTGTTCCAACACCTTATGTCTTCATGAAGAGGTTTCTGAAAGCTGCAGATGCAGATAAACAGgtgaaatatc ... tatctcgcagCTTGAGCTAGCGTCATTTTTCATGCTGGAGCTCTGCTTGGTAGAATACCAAATGCTGAATTATCGGCCTTCGCATCTGGCTGCTGCTGCGGTTTATACTG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 32

GAAAAGTTGATTCTGAACACGCTGCAGTTCAACATGTCTGTTCCAACACCTTATGTCTTCATGAAGAGGTTTCTGAAAGCTGCAGATGCAGATAAACAGgtgaaatatc ... tatctcgcagCTTGAGCTAGCGTCATTTTTCATGCTGGAGCTCTGCTTGGTAGAATACCAAATGCTGAATTATCGGCCTTCGCATCTGGCTGCTGCTGCGGTTTATACTG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAAAAGTTGATTCTGAACACGCTGCAGTTCAACATGTCTGTTCCAACACCTTATGTCTTCATGAAGAGGTTTCTGAAAGCTGCAGATGCAGATAAACAGgtgaaatatcactacactagctcaagctcaagatgcagatgatccgtgttttgtctacttggataaacaaaacacctgtagcagtgatcttttggttttatgattgacactgccccactgttgtatctcgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT