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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcttctgtaatttgtaatacgagatagagtgcatcacagcttatctgggatcttgaatactggtgctaatcagtcactggtcgatcctggtttgctacagAGCAGAGGTTGCTTTGGATGCTGTGCTAAGCCAACTCCAATAATAGCAGTAGACGAGCCTTCCAAGCGGTTGAGGATCCAGGGGCGATCAGTAAGGAAGG

Basic information

species Zea mays
transcript GRMZM2G097995_T02
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|211490450|gb|FL154408.1|FL154408
EST:     AGCTGCAGGACCCTCTCCACCTGGGTGCGCCGCCTCGTCGCTTGCATGGG                         AGCAGAGGTTGCTTTGGATGTTGTGCTAAGCCAACTCCAATAATAGCAGTA
genomic: AGCTGCAGGACCCTCTCCACCTGGGTGCGCCGCCTCGTCGCTTGCATGGGgtgcgtcgtg ... tttgctacagAGCAGAGGTTGCTTTGGATGCTGTGCTAAGCCAACTCCAATAATAGCAGTA
EST: gi|211490448|gb|FL154406.1|FL154406
EST:     AGCTGCAGGACCCTCTCCACCTGGGTGCGCCGCCTCGTCGCTTGCATGGG                         AGCAGAGGTTGCTTTGGATGTTGTGCTAAGCCAACTCCAATAATAGCAGTA
genomic: AGCTGCAGGACCCTCTCCACCTGGGTGCGCCGCCTCGTCGCTTGCATGGGgtgcgtcgtg ... tttgctacagAGCAGAGGTTGCTTTGGATGCTGTGCTAAGCCAACTCCAATAATAGCAGTA
EST: gi|211493340|gb|FL154425.1|FL154425
EST:     AGCTGCAGGACCCTCTCCACCTGGGTGCGCCGCCTCGTCGCTTGCATGGG                         AGCAGAGGTTGCTTTGGATGTTGTGCTAAGCCAACTCCAATAATAGCAGTA
genomic: AGCTGCAGGACCCTCTCCACCTGGGTGCGCCGCCTCGTCGCTTGCATGGGgtgcgtcgtg ... tttgctacagAGCAGAGGTTGCTTTGGATGCTGTGCTAAGCCAACTCCAATAATAGCAGTA
EST: gi|4887380|gb|AI677479.1|AI677479
EST:     AGCTGCAGGACCCTCTCCACCTGGGTGCGCCGCCTCGTCGCTTGCAT--G                         -G--GAGGTTGCTTTGGATGCTGTGCTAAGCCAACTCCAATAATAGCAGTA
genomic: AGCTGCAGGACCCTCTCCACCTGGGTGCGCCGCCTCGTCGCTTGCATGGGgtgcgtcgtg ... tttgctacagAGCAGAGGTTGCTTTGGATGCTGTGCTAAGCCAACTCCAATAATAGCAGTA
EST: gi|211490460|gb|FL154418.1|FL154418
EST:     AGCTGCAGGACCCTCTCCACCTGGGTGCGCCGCCTCGTCGCTTGCAT--G                         -G--GAGGTTGCTTTGGATGCTGTGCTAAGCCAACTCCAATAATAGCAGTA
genomic: AGCTGCAGGACCCTCTCCACCTGGGTGCGCCGCCTCGTCGCTTGCATGGGgtgcgtcgtg ... tttgctacagAGCAGAGGTTGCTTTGGATGCTGTGCTAAGCCAACTCCAATAATAGCAGTA
EST: gi|26558641|gb|CA830876.1|CA830876
EST:     TGCGCCGCCTCGTCGCTTGCAT--G                         -G--GAGGTTGCTTTGGATGCTGTGCTAAGCCAACTCCAATAATAGCAGTA
genomic: TGCGCCGCCTCGTCGCTTGCATGGGgtgcgtcgtg ... tttgctacagAGCAGAGGTTGCTTTGGATGCTGTGCTAAGCCAACTCCAATAATAGCAGTA
EST: gi|87156696|gb|DY401485.1|DY401485
EST:     AGCTGCAGGACCCTCTCCACCTGGGTGCGCCGCCTCGTCGCTTGCAT--G                         -G--GAGGTTGCTTTGGATGCTGTGCTAAGCCAACTCCAATAATAGCAGTA
genomic: AGCTGCAGGACCCTCTCCACCTGGGTGCGCCGCCTCGTCGCTTGCATGGGgtgcgtcgtg ... tttgctacagAGCAGAGGTTGCTTTGGATGCTGTGCTAAGCCAACTCCAATAATAGCAGTA
EST: gi|29130220|gb|CB380924.1|CB380924
EST:     AGCTGCAGGACCCTCTCCACCTGGGTGCGCCGCCTCGTCGCTTGCAT--G                         -G--GAGGTTGCTTTGGATGCTGTGCTAAGCCAACTCCAATAATAGCAGTA
genomic: AGCTGCAGGACCCTCTCCACCTGGGTGCGCCGCCTCGTCGCTTGCATGGGgtgcgtcgtg ... tttgctacagAGCAGAGGTTGCTTTGGATGCTGTGCTAAGCCAACTCCAATAATAGCAGTA
EST: gi|28909927|gb|CB331169.1|CB331169
EST:     AGCTGCAGGACCCTCTCCACCTGGGTGCGCCGCCTCGTCGCTTGCAT--G                         -G--GAGGTTGCTTTGGATGCTGTGCTAAGCCAACTCCAATAATAGCAGTA
genomic: AGCTGCAGGACCCTCTCCACCTGGGTGCGCCGCCTCGTCGCTTGCATGGGgtgcgtcgtg ... tttgctacagAGCAGAGGTTGCTTTGGATGCTGTGCTAAGCCAACTCCAATAATAGCAGTA
EST: gi|31664503|gb|CD573436.1|CD573436
EST:     AGCTGCAGGACCCTCTCCACCTGGGTGCGCCGCCTCGTCGCTTGCAT--G                         -G--GAGGTTGCTTTGGATGCTGTGCTAAGCCAACTCCAATAATAGCAGTA
genomic: AGCTGCAGGACCCTCTCCACCTGGGTGCGCCGCCTCGTCGCTTGCATGGGgtgcgtcgtg ... tttgctacagAGCAGAGGTTGCTTTGGATGCTGTGCTAAGCCAACTCCAATAATAGCAGTA
EST: gi|211493339|gb|FL154424.1|FL154424
EST:     AGCTGCAGGACCCTCTCCACCTGGGTGCGCCGCCTCGTCGCTTGCATGGG                         AGCAGAGGTTGCTTTGGATCCTGTGCTAAGCCAACTCCAATAATAGCAGTA
genomic: AGCTGCAGGACCCTCTCCACCTGGGTGCGCCGCCTCGTCGCTTGCATGGGgtgcgtcgtg ... tttgctacagAGCAGAGGTTGCTTTGGATGCTGTGCTAAGCCAACTCCAATAATAGCAGTA
EST: gi|211490454|gb|FL154412.1|FL154412
EST:     AGCTGCAGGACCCTCTCCACCTGGGTGCGCCGCCTCGTCGCTTGCATGGG                         AGCAGAGGTTGCTTTGGATGCTGTGCTAAGCCAACTCCAATAATAGCAGTA
genomic: AGCTGCAGGACCCTCTCCACCTGGGTGCGCCGCCTCGTCGCTTGCATGGGgtgcgtcgtg ... tttgctacagAGCAGAGGTTGCTTTGGATGCTGTGCTAAGCCAACTCCAATAATAGCAGTA
EST: gi|211490455|gb|FL154413.1|FL154413
EST:     AGCTGCAGGACCCTCTCCACCTGGGTGCGCCGCCTCGTCGCTTGCAT--G                         -G--GAGGTTGCTTTGGATGTTGTGCTAAGCCAACTCCAATAATAGCAGTA
genomic: AGCTGCAGGACCCTCTCCACCTGGGTGCGCCGCCTCGTCGCTTGCATGGGgtgcgtcgtg ... tttgctacagAGCAGAGGTTGCTTTGGATGCTGTGCTAAGCCAACTCCAATAATAGCAGTA
EST: gi|29543917|gb|CB604297.1|CB604297
EST:     AGCTGCAGGACCCTCTCCACCTGGGTGCGCCGCCTCGTCGCTTGCAT--G                         -G--GAGGTTGCTTTGGATGCTGTGCTAAGCCAACTCCAATAATAGCAGTA
genomic: AGCTGCAGGACCCTCTCCACCTGGGTGCGCCGCCTCGTCGCTTGCATGGGgtgcgtcgtg ... tttgctacagAGCAGAGGTTGCTTTGGATGCTGTGCTAAGCCAACTCCAATAATAGCAGTA
EST: gi|31909751|gb|CD651076.1|CD651076
EST:     AGCTGCAGGACCCTCTCCACCTGGGTGCGCCGCCTCGTCGCTTGCAT--G                         -G--GAGGTTGCTTTGGATGCTGTGCTAAGCCAACTCCAATAATAGCAGTA
genomic: AGCTGCAGGACCCTCTCCACCTGGGTGCGCCGCCTCGTCGCTTGCATGGGgtgcgtcgtg ... tttgctacagAGCAGAGGTTGCTTTGGATGCTGTGCTAAGCCAACTCCAATAATAGCAGTA
EST: gi|21987228|gb|BQ778756.1|BQ778756
EST:     GCTGCAGGACCCTCTCCACCTGGGTGCGCCGCCTCGCTCGCTTGCAT--G                         -G--GAGGTTGCTTTGGATGCTGTGCTAAGCCAACTCCAATAATAGCAGTA
genomic: GCTGCAGGACCCTCTCCACCTGGGTGCGCCGCCTCG-TCGCTTGCATGGGgtgcgtcgtg ... tttgctacagAGCAGAGGTTGCTTTGGATGCTGTGCTAAGCCAACTCCAATAATAGCAGTA
EST: gi|22472577|gb|BU037057.1|BU037057
EST:     AGCTGCAGGACCCTCTCCACCTGGGTGCGCCGCCTCGTCGCTTGCAT--G                         -G--GAGGTTGCTTTGGATGCTGTGCTAAGCCAACTCCAATAATAGCAGTA
genomic: AGCTGCAGGACCCTCTCCACCTGGGTGCGCCGCCTCGTCGCTTGCATGGGgtgcgtcgtg ... tttgctacagAGCAGAGGTTGCTTTGGATGCTGTGCTAAGCCAACTCCAATAATAGCAGTA

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), 48 (downstream exon)
Score: 34

TCCGACGCGGCACCGGCCCCCGCGCACCGGGCCCGGATGCTATGCTGCTGAGCTGCAGGACCCTCTCCACCTGGGTGCGCCGCCTCGTCGCTTGCATGGGgtgcgtcgtg ... tttgctacagAGCAGAGGTTGCTTTGGATGCTGTGCTAAGCCAACTCCAATAATAGCAGTAGACGAGCCTTCCAAGCGGTTGAGGATCCAGGGGCGATCAGTAAGGAAGG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 17

TCCGACGCGGCACCGGCCCCCGCGCACCGGGCCCGGATGCTATGCTGCTGAGCTGCAGGACCCTCTCCACCTGGGTGCGCCGCCTCGTCGCTTGCATGGGgtgcgtcgtg ... tttgctacagAGCAGAGGTTGCTTTGGATGCTGTGCTAAGCCAACTCCAATAATAGCAGTAGACGAGCCTTCCAAGCGGTTGAGGATCCAGGGGCGATCAGTAAGGAAGG


Block sizes: 48 (upstream exon), 46 (downstream exon)
Score: 22

TCCGACGCGGCACCGGCCCCCGCGCACCGGGCCCGGATGCTATGCTGCTGAGCTGCAGGACCCTCTCCACCTGGGTGCGCCGCCTCGTCGCTTGCATGGGgtgcgtcgtg ... tttgctacagAGCAGAGGTTGCTTTGGATGCTGTGCTAAGCCAACTCCAATAATAGCAGTAGACGAGCCTTCCAAGCGGTTGAGGATCCAGGGGCGATCAGTAAGGAAGG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 41

TCCGACGCGGCACCGGCCCCCGCGCACCGGGCCCGGATGCTATGCTGCTGAGCTGCAGGACCCTCTCCACCTGGGTGCGCCGCCTCGTCGCTTGCATGGGgtgcgtcgtg ... tttgctacagAGCAGAGGTTGCTTTGGATGCTGTGCTAAGCCAACTCCAATAATAGCAGTAGACGAGCCTTCCAAGCGGTTGAGGATCCAGGGGCGATCAGTAAGGAAGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgggatcttgaatactggtgctaatcagtcactggtcgatcctggtttgctacagAGCAGAGGTTGCTTTGGATGCTGTGCTAAGCCAACTCCAATAATAGCAGTAGACGAGCCTTCCAAGCGGTTGAGGATCCAGGGGCGATCAGTAAGGAAGG
                  tgctaat  putative branch site (score: 41)
       ttgaata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcttctgtaatttgtaatacgagatagagtgcatcacagcttatctgggatcttgaatactggtgctaatcagtcactggtcgatcctggtttgctacagAGCAGAGGTTGCTTTGGATGCTGTGCTAAGCCAACTCCAATAATAGCAGTAGACGAGCCTTCCAAGCGGTTGAGGATCCAGGGGCGATCAGTAAGGAAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
tcttctg
- - - - - - - - - - - - - - gtgcatc
- - - - - - - - - - - - - - - - - - - - - - - - - -cttgaat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctggtgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gatcctg