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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGTGGATCCACATGATTCATTATCCCATCCTGCTGGGGTTGCAGATGTTAAAGCTGAATCAGCAACATGTCTGGATCCTGATCTATTCACCAGTTTTTTGgtatgttaaaaacatgctttaggctttagtcctgtaaagcgacacgaacacagatacaatcagtcttctatcgttaaagtttctttttctctgttcttga...

Basic information

species Zea mays
transcript GRMZM2G145376_T01
intron # 6
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|32803235|gb|CD955471.1|CD955471
EST:     GATCCTGATCTATTCACCAGTTTTTTG                         ATTCCTAGTTGGTTTGGGGATGAAGGGCAAGAGCCTATAAACTGCAATCCT
genomic: GATCCTGATCTATTCACCAGTTTTTTGgtatgttaaa ... tcttctgcagATTCCTAGTTGGTTTGGGGATGAAGGGCAAGAGCCTATAAACTGCAATCCT
EST: gi|32788326|gb|CD940562.1|CD940562
EST:     GATCCTGATCTATTCACCAGTTTTTTG                         ATTCCTAGTTGGTTTGGGGATGAAGGGCAAGAGCCTATAAACTGCAATCCT
genomic: GATCCTGATCTATTCACCAGTTTTTTGgtatgttaaa ... tcttctgcagATTCCTAGTTGGTTTGGGGATGAAGGGCAAGAGCCTATAAACTGCAATCCT
EST: gi|110538420|gb|EE042403.1|EE042403
EST:     AGCTGAATCAGCAACATGTCTGGATCCCTGATCTATTCACCAGTTTTTTG                         ATTCCTAGTTGGTTGGGGGATGAAGGGCAAGAGCCTATAAACTGCAATCCT
genomic: AGCTGAATCAGCAACATGTCTGGAT-CCTGATCTATTCACCAGTTTTTTGgtatgttaaa ... tcttctgcagATTCCTAGTTGGTTTGGGGATGAAGGGCAAGAGCCTATAAACTGCAATCCT
EST: gi|4776299|gb|AI665302.1|AI665302
EST:     GAATCAGCAACATGTCTGGATCCTGATCTATTCACCAGTTTTTTG                         ATTCCTAGTTGGTTTGGGGATGAAGGGCAAGAGCCTATAAACTGCAATCCT
genomic: GAATCAGCAACATGTCTGGATCCTGATCTATTCACCAGTTTTTTGgtatgttaaa ... tcttctgcagATTCCTAGTTGGTTTGGGGATGAAGGGCAAGAGCCTATAAACTGCAATCCT
EST: gi|78079826|gb|DV508238.1|DV508238
EST:     AAGCTGAATCAGCAACATGTCTGGATCCTGATCTATTCACCAGTTTTTTG                         ATTCCTAGTTGGTTTGGGGATGAAGGGCAAGAGCCTATAAACTGCAATCCT
genomic: AAGCTGAATCAGCAACATGTCTGGATCCTGATCTATTCACCAGTTTTTTGgtatgttaaa ... tcttctgcagATTCCTAGTTGGTTTGGGGATGAAGGGCAAGAGCCTATAAACTGCAATCCT

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), 46 (downstream exon)
Score: 70

TGTGGATCCACATGATTCATTATCCCATCCTGCTGGGGTTGCAGATGTTAAAGCTGAATCAGCAACATGTCTGGATCCTGATCTATTCACCAGTTTTTTGgtatgttaaa ... tcttctgcagATTCCTAGTTGGTTTGGGGATGAAGGGCAAGAGCCTATAAACTGCAATCCTTTCCCACTGCCTGAAATTTATGAGGCATTCCAAAGCAAAAAG


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 119

TGTGGATCCACATGATTCATTATCCCATCCTGCTGGGGTTGCAGATGTTAAAGCTGAATCAGCAACATGTCTGGATCCTGATCTATTCACCAGTTTTTTGgtatgttaaa ... tcttctgcagATTCCTAGTTGGTTTGGGGATGAAGGGCAAGAGCCTATAAACTGCAATCCTTTCCCACTGCCTGAAATTTATGAGGCATTCCAAAGCAAAAAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 109

TGTGGATCCACATGATTCATTATCCCATCCTGCTGGGGTTGCAGATGTTAAAGCTGAATCAGCAACATGTCTGGATCCTGATCTATTCACCAGTTTTTTGgtatgttaaa ... tcttctgcagATTCCTAGTTGGTTTGGGGATGAAGGGCAAGAGCCTATAAACTGCAATCCTTTCCCACTGCCTGAAATTTATGAGGCATTCCAAAGCAAAAAG


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 120

TGTGGATCCACATGATTCATTATCCCATCCTGCTGGGGTTGCAGATGTTAAAGCTGAATCAGCAACATGTCTGGATCCTGATCTATTCACCAGTTTTTTGgtatgttaaa ... tcttctgcagATTCCTAGTTGGTTTGGGGATGAAGGGCAAGAGCCTATAAACTGCAATCCTTTCCCACTGCCTGAAATTTATGAGGCATTCCAAAGCAAAAAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGTGGATCCACATGATTCATTATCCCATCCTGCTGGGGTTGCAGATGTTAAAGCTGAATCAGCAACATGTCTGGATCCTGATCTATTCACCAGTTTTTTGgtatgttaaaaacatgctttaggctttagtcctgtaaagcgacacgaacacagatacaatcagtcttctatcgttaaagtttctttttctctgttcttga

- - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaaacat