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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatttctcatctctgaatgttcgcaatccttcctgcacactaactggggtgtctttatttccatgttagAAACTGTTCCTTCCTAGGCTCAAGTCTTGGATCCGCAATGTTGTAGCAGAAGGTAATGGCACTGAAGGCAACCAGCTTAAGCCTAGGATTGATGATGAAA

Basic information

species Zea mays
transcript GRMZM2G363460_T05
intron # 4
splice site 3'
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|148971702|gb|EE022431.2|EE022431
EST:     CTGCAGGGCTCTTGCTTGGTTTTGGTGCTAGCGCTGCTGTCTTTATCAAG                         AAACTGTTCCTTCCTAGGCTCAAGTCTTGGATCCGCAATGTTGTAGCAGAA
genomic: CTGCAGGGCTCTTGCTTGGTTTTGGTGCTAGCGCTGCTGTCTTTATCAAGgtatttctca ... tccatgttagAAACTGTTCCTTCCTAGGCTCAAGTCTTGGATCCGCAATGTTGTAGCAGAA
EST: gi|148946560|gb|EC885619.2|EC885619
EST:     CTGCAGGGCTCTTGCTTGGTTTTGGTGCTAGCGCTGCTGTCTTTATCAAG                         AAACTGTTCCTTCCTAGGCTCAAGTCTTGGATCCGCAATGTTGTAGCAGAA
genomic: CTGCAGGGCTCTTGCTTGGTTTTGGTGCTAGCGCTGCTGTCTTTATCAAGgtatttctca ... tccatgttagAAACTGTTCCTTCCTAGGCTCAAGTCTTGGATCCGCAATGTTGTAGCAGAA
EST: gi|148947997|gb|EC893497.2|EC893497
EST:     CTGCAGGGCTCTTGCTTGGTTTTGGTGCTAGCGCTGCTGTCTTTATCAAG                         AAACTGTTCCTTCCTAGGCTCAAGTCTTGGATCCGCAATGTTGTAGCAGAA
genomic: CTGCAGGGCTCTTGCTTGGTTTTGGTGCTAGCGCTGCTGTCTTTATCAAGgtatttctca ... tccatgttagAAACTGTTCCTTCCTAGGCTCAAGTCTTGGATCCGCAATGTTGTAGCAGAA
EST: gi|67019556|gb|CO448305.1|CO448305
EST:     CTGCAGGGCTCTTGCTTGGTTTTGGTGCTAGCGCTGCTGTCTTTATCAAG                         AAACTGTTCCTTCCTNAG-CTCAAGTCTTGGATCCGCAATGTTGTAGCAGA
genomic: CTGCAGGGCTCTTGCTTGGTTTTGGTGCTAGCGCTGCTGTCTTTATCAAGgtatttctca ... tccatgttagAAACTGTTCCTTCCT-AGGCTCAAGTCTTGGATCCGCAATGTTGTAGCAGA
EST: gi|148941345|gb|EC886254.2|EC886254
EST:     CTGCAGGGCTCTTGCTTGGTTTTGGTGCTAGCGCTGCTGTCTTTATCAAG                         AAACTGTTCCTTCCTAGGCTCAAGTCTTGGATCCGCAATGTTGTAGCAGAA
genomic: CTGCAGGGCTCTTGCTTGGTTTTGGTGCTAGCGCTGCTGTCTTTATCAAGgtatttctca ... tccatgttagAAACTGTTCCTTCCTAGGCTCAAGTCTTGGATCCGCAATGTTGTAGCAGAA
EST: gi|149085990|gb|EE175517.2|EE175517
EST:     CTGCAGGGCTCTTGCTTGGTTTTGGTGCTAGCGCTGCTGTCTTTATCAAG                         AAACTGTTCCTTCCTAGGCTCAAGTCTTGGATCCGCAATGTTGTAGCAGAA
genomic: CTGCAGGGCTCTTGCTTGGTTTTGGTGCTAGCGCTGCTGTCTTTATCAAGgtatttctca ... tccatgttagAAACTGTTCCTTCCTAGGCTCAAGTCTTGGATCCGCAATGTTGTAGCAGAA
EST: gi|78109256|gb|DV527672.1|DV527672
EST:     CTGCAGGGCTCTTGCTTGGTTTTGGTGCTAGCGCTGCTGTCTTTATCAAG                         AAACTGTTCCTTCCTAGGCTCAAGTCTTGGATCCGCAATGTTGTAGCAGAA
genomic: CTGCAGGGCTCTTGCTTGGTTTTGGTGCTAGCGCTGCTGTCTTTATCAAGgtatttctca ... tccatgttagAAACTGTTCCTTCCTAGGCTCAAGTCTTGGATCCGCAATGTTGTAGCAGAA
EST: gi|31355282|gb|CD439639.1|CD439639
EST:     CGCTGCTGTCTTTATCAAG                         AAACTGTTCCTTCCTAGGCTCAAGTCTTGGATCCACAATGTTGTAGCAGAA
genomic: CGCTGCTGTCTTTATCAAGgtatttctca ... tccatgttagAAACTGTTCCTTCCTAGGCTCAAGTCTTGGATCCGCAATGTTGTAGCAGAA
EST: gi|76913179|gb|DV165031.1|DV165031
EST:     CTGCAGGGCTCTTGCTTGGTTTTGGTGCTAGCGCTGCTGTCTTTATCAAG                         AAACTGTTCCTTCCTAGGCTCAAGTCTTGGATCCGCAATGTTGTAGCAGAA
genomic: CTGCAGGGCTCTTGCTTGGTTTTGGTGCTAGCGCTGCTGTCTTTATCAAGgtatttctca ... tccatgttagAAACTGTTCCTTCCTAGGCTCAAGTCTTGGATCCGCAATGTTGTAGCAGAA
EST: gi|148980471|gb|EE027160.2|EE027160
EST:     CTGCAGGGCTCTTGCTTGGTTTTGGTGCTAGCGCTGCTGTCTTTATCAAG                         AAACTGTTCCTTCCTAGGCTCAAGTCTTGGATCCGCAATGTTGTAGCAGAA
genomic: CTGCAGGGCTCTTGCTTGGTTTTGGTGCTAGCGCTGCTGTCTTTATCAAGgtatttctca ... tccatgttagAAACTGTTCCTTCCTAGGCTCAAGTCTTGGATCCGCAATGTTGTAGCAGAA

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), 32 (downstream exon)
Score: 63

TGTCGTCCTTCCAACGCAGCCCAGGTTTAGCTGGTACCAAGCATTCCTGGCTGCAGGGCTCTTGCTTGGTTTTGGTGCTAGCGCTGCTGTCTTTATCAAGgtatttctca ... tccatgttagAAACTGTTCCTTCCTAGGCTCAAGTCTTGGATCCGCAATGTTGTAGCAGAAGGTAATGGCACTGAAGGCAACCAGCTTAAGCCTAGGATTGATGATGAAA


Block sizes: 48 (upstream exon), 43 (downstream exon)
Score: 181

TGTCGTCCTTCCAACGCAGCCCAGGTTTAGCTGGTACCAAGCATTCCTGGCTGCAGGGCTCTTGCTTGGTTTTGGTGCTAGCGCTGCTGTCTTTATCAAGgtatttctca ... tccatgttagAAACTGTTCCTTCCTAGGCTCAAGTCTTGGATCCGCAATGTTGTAGCAGAAGGTAATGGCACTGAAGGCAACCAGCTTAAGCCTAGGATTGATGATGAAA


Block sizes: 49 (upstream exon), 43 (downstream exon)
Score: 242

TGTCGTCCTTCCAACGCAGCCCAGGTTTAGCTGGTACCAAGCATTCCTGGCTGCAGGGCTCTTGCTTGGTTTTGGTGCTAGCGCTGCTGTCTTTATCAAGgtatttctca ... tccatgttagAAACTGTTCCTTCCTAGGCTCAAGTCTTGGATCCGCAATGTTGTAGCAGAAGGTAATGGCACTGAAGGCAACCAGCTTAAGCCTAGGATTGATGATGAAA


Block sizes: 43 (upstream exon), 42 (downstream exon)
Score: 105

TGTCGTCCTTCCAACGCAGCCCAGGTTTAGCTGGTACCAAGCATTCCTGGCTGCAGGGCTCTTGCTTGGTTTTGGTGCTAGCGCTGCTGTCTTTATCAAGgtatttctca ... tccatgttagAAACTGTTCCTTCCTAGGCTCAAGTCTTGGATCCGCAATGTTGTAGCAGAAGGTAATGGCACTGAAGGCAACCAGCTTAAGCCTAGGATTGATGATGAAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaatgttcgcaatccttcctgcacactaactggggtgtctttatttccatgttagAAACTGTTCCTTCCTAGGCTCAAGTCTTGGATCCGCAATGTTGTAGCAGAAGGTAATGGCACTGAAGGCAACCAGCTTAAGCCTAGGATTGATGATGAAA
                       cactaac  putative branch site (score: 105)
                                     tctttatttcc  putative PPT
                                     tctttattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatttctcatctctgaatgttcgcaatccttcctgcacactaactggggtgtctttatttccatgttagAAACTGTTCCTTCCTAGGCTCAAGTCTTGGATCCGCAATGTTGTAGCAGAAGGTAATGGCACTGAAGGCAACCAGCTTAAGCCTAGGATTGATGATGAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG