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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaaaacttgctttgctgagcaatacgactcattctattttcttgagtgcatgctacatcaggtattgtttctgacacttgttatgttctctgaattgcagGTTCAGGTTCCAGTTACCTATATGCTCTTCTTGATCATGAATGGAAAGAGGGAATGAGTCAGGAAGAGGCAGAG

Basic information

species Zea mays
transcript GRMZM2G152775_T02
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G152775_T03 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os06g04800.1 (Oryza sativa), 3'ss of exon 5
----aaaaacttgctttgctgagcaatacgactcattctattttcttgagtgcatgctacatcaggtattgtttctgacacttgttatgttctctga--attgcagGTTCAGGTTCCAGTTACCTATATGCTCTTCTTGATCATGAATGGAAAGAGGGAATGAGTCAGGAAGAGGCAGAG
     | ||| |   |     |    | ||| ||   ||| |||    |    ||| || ||||   |  ||||||||| || |   |  | |||||  ||||||||||| |||||||||||||| ||||  || ||||| ||||||||||| ||||| |||   |||||||| || |||
gttgtagaacattgatcataaaattgtccgagtc--cctacttt----accctatgttatatcaatcacagtttctgacgctagccgttatttctgagtattgcagGTTCTGGTTCCAGTTACCTGTATGGACTGCTTGACCATGAATGGAAGGAGGGCATGTCCCAGGAAGAAGCTGAG
















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|21809992|gb|BQ668310.1|BQ668310
EST:     CTCAGTCCCTCTCGGTGGAACGATCTTGAAGCAACCATTTGCAATTGGAG                         GTTCAGGTTCCAGTTACCTATATGCTCTTCTTGATCAAGAATGGAAAGAGG
genomic: CTCAGTCCCTCTTGGTGGAACGATCTTGAAGCAACCATTTGCAATTGGAGgtataattat ... tgaattgcagGTTCAGGTTCCAGTTACCTATATGCTCTTCTTGATCATGAATGGAAAGAGG
EST: gi|22715386|gb|BU197734.1|BU197734
EST:     TCAGTCCCTCTCGAG-GGAACGATCTTGAAGCAACCATTTGCAATTGGAG                         GTTCAGGTTCCAGTTACCTATATGCTCTTCTTGATCATGAATGGAAAGAGG
genomic: TCAGTCCCTCTTG-GTGGAACGATCTTGAAGCAACCATTTGCAATTGGAGgtataattat ... tgaattgcagGTTCAGGTTCCAGTTACCTATATGCTCTTCTTGATCATGAATGGAAAGAGG
EST: gi|78544138|gb|DV621636.1|DV621636
EST:     CTCAGTCCCTCTCGGTGGAACGATCTTGAAGCAACCATTTGCAATTGGAG                         GTTCAGGTTCCAGTTACCTATATGCTCTTCTTGATCATGAATGGAAAGAGG
genomic: CTCAGTCCCTCTTGGTGGAACGATCTTGAAGCAACCATTTGCAATTGGAGgtataattat ... tgaattgcagGTTCAGGTTCCAGTTACCTATATGCTCTTCTTGATCATGAATGGAAAGAGG
EST: gi|22819123|gb|BU499213.1|BU499213
EST:     CTCAGTCCCTCTCGGTGGAACGATCTTGAAGCAACCCTTTGCAATTGGAG                         GTTCAGGTTCCAGTTACCTATATGCTCTTCTTGATCATGAATGGAAAGAGG
genomic: CTCAGTCCCTCTTGGTGGAACGATCTTGAAGCAACCATTTGCAATTGGAGgtataattat ... tgaattgcagGTTCAGGTTCCAGTTACCTATATGCTCTTCTTGATCATGAATGGAAAGAGG
EST: gi|32936732|gb|CF041551.1|CF041551
EST:     CTCAGTCCCTCTCGGTGGAACGATCTTGAAGCAACCATTTGCAATTGGAG                         GTTCAGGTTCCAGTTACCTATATGCTCTTCTTGATCATGAATGGAAAGAGG
genomic: CTCAGTCCCTCTTGGTGGAACGATCTTGAAGCAACCATTTGCAATTGGAGgtataattat ... tgaattgcagGTTCAGGTTCCAGTTACCTATATGCTCTTCTTGATCATGAATGGAAAGAGG
EST: gi|148952878|gb|EC898870.2|EC898870
EST:     CTCAGTCCCTCTTGGTGGAACGATCTTGAAGCAACCATTTGCAATTGGAG                         GTTCAGGTTCCAGTTACCTATATGCTCTTCTTGATCATGAATGGAAAGAGG
genomic: CTCAGTCCCTCTTGGTGGAACGATCTTGAAGCAACCATTTGCAATTGGAGgtataattat ... tgaattgcagGTTCAGGTTCCAGTTACCTATATGCTCTTCTTGATCATGAATGGAAAGAGG
EST: gi|148946911|gb|EC892193.2|EC892193
EST:     CTCAGTCCCTCTTGGTGGAACGATCTTGAAGCAACCATTTGCAATTGGAG                         GTTCAGGTTCCAGTTACCTATATGCTCTTCTTGATCATGAATGGAAAGAGG
genomic: CTCAGTCCCTCTTGGTGGAACGATCTTGAAGCAACCATTTGCAATTGGAGgtataattat ... tgaattgcagGTTCAGGTTCCAGTTACCTATATGCTCTTCTTGATCATGAATGGAAAGAGG
EST: gi|21390127|gb|BQ528176.1|BQ528176
EST:     CTCAGTCCCTCTCGGTGGAACGATCTTGAAGCAACCATTTGCAATTGGAG                         GTTCAGGTTCCAGTTACCTATATGCTCTTCTTGATCATGAATGGAAAGAGG
genomic: CTCAGTCCCTCTTGGTGGAACGATCTTGAAGCAACCATTTGCAATTGGAGgtataattat ... tgaattgcagGTTCAGGTTCCAGTTACCTATATGCTCTTCTTGATCATGAATGGAAAGAGG
EST: gi|148946910|gb|EC892192.2|EC892192
EST:     CTCAGTCCCTCTTGGTGGAACGATCTTGAAGCAACCATTTGCAATTGGAG                         GTTCAGGTTCCAGTTACCTATATGCTCTTCTTGATCATGAATGGAAAGAGG
genomic: CTCAGTCCCTCTTGGTGGAACGATCTTGAAGCAACCATTTGCAATTGGAGgtataattat ... tgaattgcagGTTCAGGTTCCAGTTACCTATATGCTCTTCTTGATCATGAATGGAAAGAGG
EST: gi|26457200|gb|CA828783.1|CA828783
EST:     CTCAGTCCCTCTCGG-GGAACGATCTTGAAGCAACCATTTGCAATTGGAG                         GTTCAGGTTCCAGTTACCTATATGCTCTTCTTGATCATGAATGGAAAGAGG
genomic: CTCAGTCCCTCTTGGTGGAACGATCTTGAAGCAACCATTTGCAATTGGAGgtataattat ... tgaattgcagGTTCAGGTTCCAGTTACCTATATGCTCTTCTTGATCATGAATGGAAAGAGG
EST: gi|9742610|gb|BE518758.1|BE518758
EST:     CTCAGTCCCTCTCGGTGGAACGATCTTGAAGCAACCATTTGCAATTGGAG                         GTTCAGGTTCCAGTTACCTATATGCTCTTCTTGATCATGAATGGAAAGAGG
genomic: CTCAGTCCCTCTTGGTGGAACGATCTTGAAGCAACCATTTGCAATTGGAGgtataattat ... tgaattgcagGTTCAGGTTCCAGTTACCTATATGCTCTTCTTGATCATGAATGGAAAGAGG
EST: gi|21809993|gb|BQ668311.1|BQ668311
EST:     CTCAGTCCCTCTCGG-GGAACGATCTTGAAGCAACCATTTGCAATTGGAG                         GTTCAGGTTCCAGTTACCTATATGCTCTTCTTGATCATGAATGGAAAGAGG
genomic: CTCAGTCCCTCTTGGTGGAACGATCTTGAAGCAACCATTTGCAATTGGAGgtataattat ... tgaattgcagGTTCAGGTTCCAGTTACCTATATGCTCTTCTTGATCATGAATGGAAAGAGG
EST: gi|71303125|gb|DR787668.1|DR787668
EST:     ATCTTGAAGCAACCATTTGCAATTGGAG                         GTTCAGGTTCCAGTTACCTATATGCTCTTCTTGATCATGAATGGAAAGAGG
genomic: ATCTTGAAGCAACCATTTGCAATTGGAGgtataattat ... tgaattgcagGTTCAGGTTCCAGTTACCTATATGCTCTTCTTGATCATGAATGGAAAGAGG
EST: gi|213175464|gb|FM189533.1|FM189533
EST:     CCTCTCGGTGGAACGATCTTGAAGCAACCATTTGCAATTGGAG                         GTTCAGGTTCCAGTTACCTATATGCTCTTCTTGATCATGAATGGAAAGAGG
genomic: CCTCTTGGTGGAACGATCTTGAAGCAACCATTTGCAATTGGAGgtataattat ... tgaattgcagGTTCAGGTTCCAGTTACCTATATGCTCTTCTTGATCATGAATGGAAAGAGG
EST: gi|32848286|gb|CD987967.1|CD987967
EST:     CTCAGTCCCTCTCGGTGGAACGATCTTGAAGCAACCATTTGCAATTGGAG                         GTTCAGGTTCCAGTTACCTATATGCTCTTCTTGATCATGAATGGAAAGAGG
genomic: CTCAGTCCCTCTTGGTGGAACGATCTTGAAGCAACCATTTGCAATTGGAGgtataattat ... tgaattgcagGTTCAGGTTCCAGTTACCTATATGCTCTTCTTGATCATGAATGGAAAGAGG
EST: gi|148937129|gb|EC881304.2|EC881304
EST:     TTCAGTCCCTCTTGGTGGAACGATCTTGAAGCAACCATTTGCAATTGGAG                         GTTCAGGTTCCAGTTACCTATATGCTCTTCTTGATCATGAATGGAAAGAGG
genomic: CTCAGTCCCTCTTGGTGGAACGATCTTGAAGCAACCATTTGCAATTGGAGgtataattat ... tgaattgcagGTTCAGGTTCCAGTTACCTATATGCTCTTCTTGATCATGAATGGAAAGAGG
EST: gi|37379515|gb|CF626500.1|CF626500
EST:     CTCAGTCCCTCTCGGTGGAACGATCTTGAAGCAACCATTTGCAATTGGAG                         GTTCAGGTTCCAGTTACCTATATGCTCTTCTTGATCATGAATGGAAAGAGG
genomic: CTCAGTCCCTCTTGGTGGAACGATCTTGAAGCAACCATTTGCAATTGGAGgtataattat ... tgaattgcagGTTCAGGTTCCAGTTACCTATATGCTCTTCTTGATCATGAATGGAAAGAGG
EST: gi|21391153|gb|BQ529202.1|BQ529202
EST:     CTCAGTCCCTCTCGGTGGAACGATCTTGAAGCAACCATTTGCAATTGGAG                         GTTCAGGTTCCAGTTACCTATATGCTCTTCTTGATCATGAATGGAAAGAGG
genomic: CTCAGTCCCTCTTGGTGGAACGATCTTGAAGCAACCATTTGCAATTGGAGgtataattat ... tgaattgcagGTTCAGGTTCCAGTTACCTATATGCTCTTCTTGATCATGAATGGAAAGAGG
EST: gi|22521594|gb|BU080405.1|BU080405
EST:     CTCAGTCCCTCTCGGTGGAACGATCTTGAAGCAACCCTTTGCAATTGGAG                         GTTCAGGTTCCAGTTACCTATATGCTCTTCTTGATCATGAATGGAAAGAGG
genomic: CTCAGTCCCTCTTGGTGGAACGATCTTGAAGCAACCATTTGCAATTGGAGgtataattat ... tgaattgcagGTTCAGGTTCCAGTTACCTATATGCTCTTCTTGATCATGAATGGAAAGAGG
EST: gi|22521595|gb|BU080406.1|BU080406
EST:     CTCAGTCCCTCTCGGTGGAACGATCTTGAAGCAACCATTTGCAATTGGAG                         GTTCAGGTTCCAGTTACCTATATGCTCTTCTTGATCATGAATGGAAAGAGG
genomic: CTCAGTCCCTCTTGGTGGAACGATCTTGAAGCAACCATTTGCAATTGGAGgtataattat ... tgaattgcagGTTCAGGTTCCAGTTACCTATATGCTCTTCTTGATCATGAATGGAAAGAGG

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: 464

GCTGGCATGATTGTTGGAGGATGGGACAAGTACGAGGGAGGCCAAATTTTCTCAGTCCCTCTTGGTGGAACGATCTTGAAGCAACCATTTGCAATTGGAGgtataattat ... tgaattgcagGTTCAGGTTCCAGTTACCTATATGCTCTTCTTGATCATGAATGGAAAGAGGGAATGAGTCAGGAAGAGGCAGAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 256

GCTGGCATGATTGTTGGAGGATGGGACAAGTACGAGGGAGGCCAAATTTTCTCAGTCCCTCTTGGTGGAACGATCTTGAAGCAACCATTTGCAATTGGAGgtataattat ... tgaattgcagGTTCAGGTTCCAGTTACCTATATGCTCTTCTTGATCATGAATGGAAAGAGGGAATGAGTCAGGAAGAGGCAGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 266

GCTGGCATGATTGTTGGAGGATGGGACAAGTACGAGGGAGGCCAAATTTTCTCAGTCCCTCTTGGTGGAACGATCTTGAAGCAACCATTTGCAATTGGAGgtataattat ... tgaattgcagGTTCAGGTTCCAGTTACCTATATGCTCTTCTTGATCATGAATGGAAAGAGGGAATGAGTCAGGAAGAGGCAGAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 316

GCTGGCATGATTGTTGGAGGATGGGACAAGTACGAGGGAGGCCAAATTTTCTCAGTCCCTCTTGGTGGAACGATCTTGAAGCAACCATTTGCAATTGGAGgtataattat ... tgaattgcagGTTCAGGTTCCAGTTACCTATATGCTCTTCTTGATCATGAATGGAAAGAGGGAATGAGTCAGGAAGAGGCAGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgcatgctacatcaggtattgtttctgacacttgttatgttctctgaattgcagGTTCAGGTTCCAGTTACCTATATGCTCTTCTTGATCATGAATGGAAAGAGGGAATGAGTCAGGAAGAGGCAGAG
                       ttctgac  putative branch site (score: 316)
                                      tgttctct  putative PPT
                 tattgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaaaacttgctttgctgagcaatacgactcattctattttcttgagtgcatgctacatcaggtattgtttctgacacttgttatgttctctgaattgcagGTTCAGGTTCCAGTTACCTATATGCTCTTCTTGATCATGAATGGAAAGAGGGAATGAGTCAGGAAGAGGCAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - tttgctg
- - - - - - - - - - - - - - - - - - -tttcttg
- - - - - - - - - - - - - - - - - - - - - - - tgcatgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttatgtt