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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGAGCTGCACACACATCTGTGAGTAGAAACCTTGTGCTTGGCGATTTGGCACCCTCAAGTTAATTATCCTTGGTTTGAGGAAGAACAACACTTCAGCCAGgtactaattaagtttcatacttgattagcttgctcggtggtttttgcttgttcatcagtgtgtgcgtgtgttgatctttagtagtagcacgtaaggagca...

Basic information

species Zea mays
transcript GRMZM2G445575_T02
intron # 1
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|148967197|gb|EE018389.2|EE018389
EST:     ACCCTCAAGTTAATTATCCTTGGTTTGAGGAAGAACAACACTTCAGCCAG                         ACATGCTTTAAGCAGGGAGACCATTTTTTATTTCGAGCGCGCTACGATGGA
genomic: ACCCTCAAGTTAATTATCCTTGGTTTGAGGAAGAACAACACTTCAGCCAGgtactaatta ... tgcttggcagACATGCTTTAAGCAGGGAGACCATTTTTTATTTCGAGCGCGCTACGATGGA
EST: gi|94477975|gb|EB706933.1|EB706933
EST:     ACCCTCAAGTTAATTATCCTTGGTTTGAGGAAGAACAACACTTCAGCCAG                         ACATGCTTTAAGCAGGGAGACCATTTTTTATTTCGAGCGCGCTACGATGGA
genomic: ACCCTCAAGTTAATTATCCTTGGTTTGAGGAAGAACAACACTTCAGCCAGgtactaatta ... tgcttggcagACATGCTTTAAGCAGGGAGACCATTTTTTATTTCGAGCGCGCTACGATGGA
EST: gi|148955465|gb|EC901061.2|EC901061
EST:     ACCCTCAAGTTAATTATCCTTGGTTTGAGGAAGAACAACACTTCAGCCAG                         ACATGCTTTAAGCAGGGAGACCATTTTTTATTTCGAGCGCGCTACGATGGA
genomic: ACCCTCAAGTTAATTATCCTTGGTTTGAGGAAGAACAACACTTCAGCCAGgtactaatta ... tgcttggcagACATGCTTTAAGCAGGGAGACCATTTTTTATTTCGAGCGCGCTACGATGGA
EST: gi|148999148|gb|EE036061.2|EE036061
EST:     ACCCTCAAGTTAATTATCCTTGGTTTGAGGAAGAACAACACTTCAGCCAG                         ACATGCTTTAAGCAGGGAGACCATTTTTTATTTCGAGCGCGCTACGATGGA
genomic: ACCCTCAAGTTAATTATCCTTGGTTTGAGGAAGAACAACACTTCAGCCAGgtactaatta ... tgcttggcagACATGCTTTAAGCAGGGAGACCATTTTTTATTTCGAGCGCGCTACGATGGA
EST: gi|37426426|gb|CF650965.1|CF650965
EST:     ACCCTCAAGTTAATTATCCTTGGTTTGAGGAAGAACAACACTTCAGCCAG                         ACATGCTTTAAGCAGGGAGACCATTTTTTATTTCGAGCGCGCTACGATGGA
genomic: ACCCTCAAGTTAATTATCCTTGGTTTGAGGAAGAACAACACTTCAGCCAGgtactaatta ... tgcttggcagACATGCTTTAAGCAGGGAGACCATTTTTTATTTCGAGCGCGCTACGATGGA
EST: gi|149079352|gb|EE168328.2|EE168328
EST:     ACCCTCAAGTTAATTATCCTTGGTTTGAGGAAGAACAACACTTCAGCCAG                         ACATGCTTTAAGCAGGGAGACCATTTTTTATTTCGAGCGCGCTACGATGGA
genomic: ACCCTCAAGTTAATTATCCTTGGTTTGAGGAAGAACAACACTTCAGCCAGgtactaatta ... tgcttggcagACATGCTTTAAGCAGGGAGACCATTTTTTATTTCGAGCGCGCTACGATGGA
EST: gi|148933922|gb|EC877905.2|EC877905
EST:     ACCCTCAAGTTAATTATCCTTGGTTTGAGGAAGAACAACACTTCAGCCAG                         ACATGCTTTAAGCAGGGAGACCATTTTTTATTTCGAGCGCGCTACGATGGA
genomic: ACCCTCAAGTTAATTATCCTTGGTTTGAGGAAGAACAACACTTCAGCCAGgtactaatta ... tgcttggcagACATGCTTTAAGCAGGGAGACCATTTTTTATTTCGAGCGCGCTACGATGGA
EST: gi|148969929|gb|EE020834.2|EE020834
EST:     ACCCTCAAGTTAATTATCCTTGGTTTGAGGAAGAACAACACTTCAGCCAG                         ACATGCTTTAAGCAGGGAGACCATTTTTTATTTCGAGCGCGCTACGATGGA
genomic: ACCCTCAAGTTAATTATCCTTGGTTTGAGGAAGAACAACACTTCAGCCAGgtactaatta ... tgcttggcagACATGCTTTAAGCAGGGAGACCATTTTTTATTTCGAGCGCGCTACGATGGA
EST: gi|74235598|gb|DT643512.1|DT643512
EST:     ACCCTCAAGTTAATTATCCTTGGTTTGAGGAAGAACAACACTTCAGCCAG                         ACATGCTTTAAGCAGGGAGACCATTTTTTATTTCGAGCGCGCTACGATGGA
genomic: ACCCTCAAGTTAATTATCCTTGGTTTGAGGAAGAACAACACTTCAGCCAGgtactaatta ... tgcttggcagACATGCTTTAAGCAGGGAGACCATTTTTTATTTCGAGCGCGCTACGATGGA
EST: gi|149000175|gb|EE037312.2|EE037312
EST:     ACCCTCAAGTTAATTATCCTTGGTTTGAGGAAGAACAACACTTCAGCCAG                         ACATGCTTTAAGCAGGGAGACCATTTTTTATTTCGAGCGCGCTACGATGGA
genomic: ACCCTCAAGTTAATTATCCTTGGTTTGAGGAAGAACAACACTTCAGCCAGgtactaatta ... tgcttggcagACATGCTTTAAGCAGGGAGACCATTTTTTATTTCGAGCGCGCTACGATGGA

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: 34 (upstream exon), 30 (downstream exon)
Score: 4

GGAGCTGCACACACATCTGTGAGTAGAAACCTTGTGCTTGGCGATTTGGCACCCTCAAGTTAATTATCCTTGGTTTGAGGAAGAACAACACTTCAGCCAGgtactaatta ... tgcttggcagACATGCTTTAAGCAGGGAGACCATTTTTTATTTCGAGCGCGCTACGATGGAGCTCTACTCCGGATACCTTGACGACCATTTCAACCCCCACAAGCTAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 175

GGAGCTGCACACACATCTGTGAGTAGAAACCTTGTGCTTGGCGATTTGGCACCCTCAAGTTAATTATCCTTGGTTTGAGGAAGAACAACACTTCAGCCAGgtactaatta ... tgcttggcagACATGCTTTAAGCAGGGAGACCATTTTTTATTTCGAGCGCGCTACGATGGAGCTCTACTCCGGATACCTTGACGACCATTTCAACCCCCACAAGCTAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 250

GGAGCTGCACACACATCTGTGAGTAGAAACCTTGTGCTTGGCGATTTGGCACCCTCAAGTTAATTATCCTTGGTTTGAGGAAGAACAACACTTCAGCCAGgtactaatta ... tgcttggcagACATGCTTTAAGCAGGGAGACCATTTTTTATTTCGAGCGCGCTACGATGGAGCTCTACTCCGGATACCTTGACGACCATTTCAACCCCCACAAGCTAAG


Block sizes: 21 (upstream exon), 42 (downstream exon)
Score: 6

GGAGCTGCACACACATCTGTGAGTAGAAACCTTGTGCTTGGCGATTTGGCACCCTCAAGTTAATTATCCTTGGTTTGAGGAAGAACAACACTTCAGCCAGgtactaatta ... tgcttggcagACATGCTTTAAGCAGGGAGACCATTTTTTATTTCGAGCGCGCTACGATGGAGCTCTACTCCGGATACCTTGACGACCATTTCAACCCCCACAAGCTAAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGAGCTGCACACACATCTGTGAGTAGAAACCTTGTGCTTGGCGATTTGGCACCCTCAAGTTAATTATCCTTGGTTTGAGGAAGAACAACACTTCAGCCAGgtactaattaagtttcatacttgattagcttgctcggtggtttttgcttgttcatcagtgtgtgcgtgtgttgatctttagtagtagcacgtaaggagca

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC