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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cagcattggtgcttcacgatagttacattgtttgcttgttttctaaaaatatcgttccaatttactaaccagtatgatttgcttgtccccttggatgcagTGAGAGAAAGCCTTAAAACTGCAAAGAAGGATTTTACCAAGACTGAGGACGACTTAAAGTCTCTGCAGAGTGTGGGGCAAATAATTGGAGAAGTACTCCG

Basic information

species Zea mays
transcript GRMZM2G165817_T01
intron # 1
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|19770216|gb|BQ034937.1|BQ034937
EST:     CCGCAAGAAGCTGCTCAACTGCAGGGAGCTAGAGTCGCGCGTCGGCACCG                         TGAGAGAAAGCCTTAAAACTGCAAAGAAGGATTTTACCAAGACTGAGGACG
genomic: CCGCAAGAAGCTGCTCAACTGCAGGGAGCTAGAGTCGCGCGTCGGCACCGgtgagtcgtc ... ttggatgcagTGAGAGAAAGCCTTAAAACTGCAAAGAAGGATTTTACCAAGACTGAGGACG
EST: gi|211243468|gb|FL076790.1|FL076790
EST:     CCGCAAGANGCTGCTCAACTGCAGGGAGCTAGAGTCGCGCGTCGGCACCG                         TGAGAGAAAGCCTTAAAACTGCAAAGAAGGATTTTACCAAGACTGAGGACG
genomic: CCGCAAGAAGCTGCTCAACTGCAGGGAGCTAGAGTCGCGCGTCGGCACCGgtgagtcgtc ... ttggatgcagTGAGAGAAAGCCTTAAAACTGCAAAGAAGGATTTTACCAAGACTGAGGACG
EST: gi|211241231|gb|FL076775.1|FL076775
EST:     CCGCAAGANGCTGCTCAACTGCAGGGAGCTAGAGTNGCGCGTCGGCACCG                         TGAGAGAAAGCCTTAAAACTGCAAAGAAGGATTTTACCAAGACTGAGGACG
genomic: CCGCAAGAAGCTGCTCAACTGCAGGGAGCTAGAGTCGCGCGTCGGCACCGgtgagtcgtc ... ttggatgcagTGAGAGAAAGCCTTAAAACTGCAAAGAAGGATTTTACCAAGACTGAGGACG
EST: gi|19822398|gb|BQ048422.1|BQ048422
EST:     CCGCAAGAAGCTGCTCAACTGCAGGGAGCTAGAGTCGCGCGTCGGCACCG                         TGAGAGAAAGCCTTAAAACTGCAAAGAAGGA-TTTACCAAGACTGAGGACG
genomic: CCGCAAGAAGCTGCTCAACTGCAGGGAGCTAGAGTCGCGCGTCGGCACCGgtgagtcgtc ... ttggatgcagTGAGAGAAAGCCTTAAAACTGCAAAGAAGGATTTTACCAAGACTGAGGACG
EST: gi|60400478|gb|DN233285.1|DN233285
EST:     CCGCAAGAAGCTGCTCAACTGCAGGGAGCTAGAGTCGCGCGTCGGCACCG                         TGAGAGAAAGCCTTAAAACTGCAAAGAAGGATTTTACCAAGACTGAGGACG
genomic: CCGCAAGAAGCTGCTCAACTGCAGGGAGCTAGAGTCGCGCGTCGGCACCGgtgagtcgtc ... ttggatgcagTGAGAGAAAGCCTTAAAACTGCAAAGAAGGATTTTACCAAGACTGAGGACG
EST: gi|211238994|gb|FL076765.1|FL076765
EST:     CCGCAAGAVGCTGCTCAACTGCAGGGAGCTAGAGTMGCGCGTCGGCACCG                         TGAGAGAAAGCCTTAAAACTGCAAAGAAGGATTTTACCAAGACTGAGGACG
genomic: CCGCAAGAAGCTGCTCAACTGCAGGGAGCTAGAGTCGCGCGTCGGCACCGgtgagtcgtc ... ttggatgcagTGAGAGAAAGCCTTAAAACTGCAAAGAAGGATTTTACCAAGACTGAGGACG
EST: gi|22472946|gb|BU037426.1|BU037426
EST:     CCGCAAGAAGCTGCTCAACTGCAGGGAGCTAGAGTCGCGCGTCGGCACCG                         TGAGAGAAAGCCTTAAAACTGCAAAGAAGGATTTTACCAAGACTGAGGACG
genomic: CCGCAAGAAGCTGCTCAACTGCAGGGAGCTAGAGTCGCGCGTCGGCACCGgtgagtcgtc ... ttggatgcagTGAGAGAAAGCCTTAAAACTGCAAAGAAGGATTTTACCAAGACTGAGGACG
EST: gi|15499352|gb|BI595865.1|BI595865
EST:     GAGCTAGAGTCGCGCGTCGGCACCG                         TGAGAGAAAGCCTTAAAACTGCAAAGAAGGATTTTACCAAGACTGAGGACG
genomic: GAGCTAGAGTCGCGCGTCGGCACCGgtgagtcgtc ... ttggatgcagTGAGAGAAAGCCTTAAAACTGCAAAGAAGGATTTTACCAAGACTGAGGACG
EST: gi|211239003|gb|FL076774.1|FL076774
EST:     CCGCAAGAHGCTGCTCAACTGCAGGGAGCTAGAGTCGCGCGTCGGCACCG                         TGAGAGAAAGCCTTAAAACTGCAAAGAAGGATTTTACCAAGACTGAGGACG
genomic: CCGCAAGAAGCTGCTCAACTGCAGGGAGCTAGAGTCGCGCGTCGGCACCGgtgagtcgtc ... ttggatgcagTGAGAGAAAGCCTTAAAACTGCAAAGAAGGATTTTACCAAGACTGAGGACG
EST: gi|211243473|gb|FL076795.1|FL076795
EST:     CCGCAAGAMGCTGCTCAACTGCAGGGAGCTAGAGTCGCGCGTCGGCACCG                         TGAGAGAAAGCCTTAAAACTGCAAAGAAGGATTTTACCAAGACTGAGGACG
genomic: CCGCAAGAAGCTGCTCAACTGCAGGGAGCTAGAGTCGCGCGTCGGCACCGgtgagtcgtc ... ttggatgcagTGAGAGAAAGCCTTAAAACTGCAAAGAAGGATTTTACCAAGACTGAGGACG
EST: gi|211243475|gb|FL076797.1|FL076797
EST:     CCGCAAGAMGCTGCTCAACTGCAGGGAGCTAGAGTMGCGCGTCGGCACCG                         TGAGAGAAAGCCTTAAAACTGCAAAGAAGGATTTTACCAAGACTGAGGACG
genomic: CCGCAAGAAGCTGCTCAACTGCAGGGAGCTAGAGTCGCGCGTCGGCACCGgtgagtcgtc ... ttggatgcagTGAGAGAAAGCCTTAAAACTGCAAAGAAGGATTTTACCAAGACTGAGGACG
EST: gi|211243469|gb|FL076791.1|FL076791
EST:     CCGCAAGAAGCTGCTCAACTGCAGGGAGCTAGAGTCGCGCGTCGGCACCG                         TGAGAGAAAGCCTTAAAACTGCAAAGAAGGATTTTACCAAGACTGAGGACG
genomic: CCGCAAGAAGCTGCTCAACTGCAGGGAGCTAGAGTCGCGCGTCGGCACCGgtgagtcgtc ... ttggatgcagTGAGAGAAAGCCTTAAAACTGCAAAGAAGGATTTTACCAAGACTGAGGACG
EST: gi|211241239|gb|FL076783.1|FL076783
EST:     CCGCAAGAHGCTGCTCAACTGCAGGGAGCTAGAGTMGCGCGTCGGCACCG                         TGAGAGAAAGCCTTAAAACTGCAAAGAAGGATTTTACCAAGACTGAGGACG
genomic: CCGCAAGAAGCTGCTCAACTGCAGGGAGCTAGAGTCGCGCGTCGGCACCGgtgagtcgtc ... ttggatgcagTGAGAGAAAGCCTTAAAACTGCAAAGAAGGATTTTACCAAGACTGAGGACG
EST: gi|32830630|gb|CD970308.1|CD970308
EST:     GCTCAACTGCAGGGAGCTAGATTCGCGCGTCGGCACCG                         TGAGAGAAAGCCTTAAAACTGCAAAGAAGGATTTTACCAAGACTGAGGACG
genomic: GCTCAACTGCAGGGAGCTAGAGTCGCGCGTCGGCACCGgtgagtcgtc ... ttggatgcagTGAGAGAAAGCCTTAAAACTGCAAAGAAGGATTTTACCAAGACTGAGGACG
EST: gi|211236768|gb|FL076759.1|FL076759
EST:     CCGCAAGANGCTGCTCAACTGCAGGGAGCTAGAGTNGCGCGTCGGCACCG                         TGAGAGAAAGCCTTAAMACTGCAAAGAAGGATTTTMCCAAGACTGAGGACG
genomic: CCGCAAGAAGCTGCTCAACTGCAGGGAGCTAGAGTCGCGCGTCGGCACCGgtgagtcgtc ... ttggatgcagTGAGAGAAAGCCTTAAAACTGCAAAGAAGGATTTTACCAAGACTGAGGACG
EST: gi|32831771|gb|CD971449.1|CD971449
EST:     CCGCAAGAAGCTGCTCAACTGCAGGGAGCTAGAGTCGCGCGTCGGCACCG                         TGAGAGAAAGCCTTAAAACTGCAAAGAAGGATTTTACCAAGACTGAGGACG
genomic: CCGCAAGAAGCTGCTCAACTGCAGGGAGCTAGAGTCGCGCGTCGGCACCGgtgagtcgtc ... ttggatgcagTGAGAGAAAGCCTTAAAACTGCAAAGAAGGATTTTACCAAGACTGAGGACG
EST: gi|148950536|gb|EC896111.2|EC896111
EST:     CCGCAAGAAGCTGCTCAACTGCAGGGAGCTAGAGTCGCGCGTCGGCACCG                         TGAGAGAAAGCCTTAAAACTGCAAAGAAGGATTTTACCAAGACTGAGGACG
genomic: CCGCAAGAAGCTGCTCAACTGCAGGGAGCTAGAGTCGCGCGTCGGCACCGgtgagtcgtc ... ttggatgcagTGAGAGAAAGCCTTAAAACTGCAAAGAAGGATTTTACCAAGACTGAGGACG
EST: gi|211238993|gb|FL076764.1|FL076764
EST:     CCGCAAGANGCTGCTCAACTGCAGGGAGCTAGAGTNGCGCGTCGGCACCG                         TGAGAGAWAGCCTTAAWACTGCAAAGAAGGATTTTMCCAAGACTGAGGACG
genomic: CCGCAAGAAGCTGCTCAACTGCAGGGAGCTAGAGTCGCGCGTCGGCACCGgtgagtcgtc ... ttggatgcagTGAGAGAAAGCCTTAAAACTGCAAAGAAGGATTTTACCAAGACTGAGGACG

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: 434

GACGGGGAGGACGCCGCCGCCGCGCGCCGCCGGGCCGCCATCACAGACTACCGCAAGAAGCTGCTCAACTGCAGGGAGCTAGAGTCGCGCGTCGGCACCGgtgagtcgtc ... ttggatgcagTGAGAGAAAGCCTTAAAACTGCAAAGAAGGATTTTACCAAGACTGAGGACGACTTAAAGTCTCTGCAGAGTGTGGGGCAAATAATTGGAGAAGTACTCCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 192

GACGGGGAGGACGCCGCCGCCGCGCGCCGCCGGGCCGCCATCACAGACTACCGCAAGAAGCTGCTCAACTGCAGGGAGCTAGAGTCGCGCGTCGGCACCGgtgagtcgtc ... ttggatgcagTGAGAGAAAGCCTTAAAACTGCAAAGAAGGATTTTACCAAGACTGAGGACGACTTAAAGTCTCTGCAGAGTGTGGGGCAAATAATTGGAGAAGTACTCCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 138

GACGGGGAGGACGCCGCCGCCGCGCGCCGCCGGGCCGCCATCACAGACTACCGCAAGAAGCTGCTCAACTGCAGGGAGCTAGAGTCGCGCGTCGGCACCGgtgagtcgtc ... ttggatgcagTGAGAGAAAGCCTTAAAACTGCAAAGAAGGATTTTACCAAGACTGAGGACGACTTAAAGTCTCTGCAGAGTGTGGGGCAAATAATTGGAGAAGTACTCCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 255

GACGGGGAGGACGCCGCCGCCGCGCGCCGCCGGGCCGCCATCACAGACTACCGCAAGAAGCTGCTCAACTGCAGGGAGCTAGAGTCGCGCGTCGGCACCGgtgagtcgtc ... ttggatgcagTGAGAGAAAGCCTTAAAACTGCAAAGAAGGATTTTACCAAGACTGAGGACGACTTAAAGTCTCTGCAGAGTGTGGGGCAAATAATTGGAGAAGTACTCCG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaaatatcgttccaatttactaaccagtatgatttgcttgtccccttggatgcagTGAGAGAAAGCCTTAAAACTGCAAAGAAGGATTTTACCAAGACTGAGGACGACTTAAAGTCTCTGCAGAGTGTGGGGCAAATAATTGGAGAAGTACTCCG
                 tactaac  putative branch site (score: 255)
                                tttgcttgtcccctt  putative PPT
             aatttactaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cagcattggtgcttcacgatagttacattgtttgcttgttttctaaaaatatcgttccaatttactaaccagtatgatttgcttgtccccttggatgcagTGAGAGAAAGCCTTAAAACTGCAAAGAAGGATTTTACCAAGACTGAGGACGACTTAAAGTCTCTGCAGAGTGTGGGGCAAATAATTGGAGAAGTACTCCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - gtgcttc
- - - - - - - - - - - - - - - - tgcttgt
- - - - - - - - - - - - - - - - - - - - - - aaaaata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctaacca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgatttg