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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtatctctctctactgccttaggaataaccaccgcaacatccaaatccttcagagagctcaccaactaattctttgtttcgttttctgtttcagCCCAACAACGGGAGGTGTTACACCTGCCCCAGCAGCAGAGGCTGAATTGAAAGCCAGTGCTTGATTTTTTTTTTCTGTGTTCCCTGAGATCATATTTGGT

Basic information

species Zea mays
transcript GRMZM2G152827_T01
intron # 5
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|113816050|gb|DW935495.1|DW935495
EST:     TGGGGAATTTACGATGCATTCAAAGTGATGGTTGGACT                         CCCAACAACGGGAGGTGTTACACCTGCCCCAGCAGCTAGAGGCTGAATTGA
genomic: TGGGGAATTTACGATGCATTCAAAGTGATGGTTGGACTgtgagtatct ... tctgtttcagCCCAACAACGGGAGGTGTTACACCTGCCCCAGCAGC-AGAGGCTGAATTGA
EST: gi|31612075|gb|CD568697.1|CD568697
EST:     ACTGGTGCTCAGTGGGGAATTTACGATGCATTCAAAGTGATGGTTGGACT                         CCCAACAACGGGAGGTGTTACCCCTGCCCCAGCAGCAGAGGCTGAATTGAA
genomic: ACTGGTGCTCAGTGGGGAATTTACGATGCATTCAAAGTGATGGTTGGACTgtgagtatct ... tctgtttcagCCCAACAACGGGAGGTGTTACACCTGCCCCAGCAGCAGAGGCTGAATTGAA
EST: gi|166544486|gb|EG234876.1|EG234876
EST:     ACTGGTGCTCAGTGGGGAATTTACGATGCATTCAAAGTGATGGTTGGACT                         CCCAACAACGGGAGGTGTTACACCTGCCCCAGCAGCAGAGGCTGAATTG
genomic: ACTGGTGCTCAGTGGGGAATTTACGATGCATTCAAAGTGATGGTTGGACTgtgagtatct ... tctgtttcagCCCAACAACGGGAGGTGTTACACCTGCCCCAGCAGCAGAGGCTGAATTG
EST: gi|5928934|gb|AW056226.1|AW056226
EST:     ACTGGTGCTCAGTGGGGAATTTACGATGCATTCAAAGTGATGGTTGGACT                         CCCAACAACGGGAGGTGTTACACCTGCCCCAGCAGCAGAGGCTGAATTGAA
genomic: ACTGGTGCTCAGTGGGGAATTTACGATGCATTCAAAGTGATGGTTGGACTgtgagtatct ... tctgtttcagCCCAACAACGGGAGGTGTTACACCTGCCCCAGCAGCAGAGGCTGAATTGAA
EST: gi|149100649|gb|EE186737.2|EE186737
EST:     ACTGGTGCTCAGTGGGGAATTTACGATGCATTCAAAGTGATGGTTGGACT                         CCCAACAACGGGAGGTGTTACACCTGCCCCAGCAGCAGAGGCTGAATTGAA
genomic: ACTGGTGCTCAGTGGGGAATTTACGATGCATTCAAAGTGATGGTTGGACTgtgagtatct ... tctgtttcagCCCAACAACGGGAGGTGTTACACCTGCCCCAGCAGCAGAGGCTGAATTGAA
EST: gi|116817564|gb|EC860439.1|EC860439
EST:     ACTGGTGCTCAGTGGGGAATT-ACGATGCATCCAAAGTGATGGTTGGAAT                         CCCGACAACGGGA
genomic: ACTGGTGCTCAGTGGGGAATTTACGATGCATTCAAAGTGATGGTTGGACTgtgagtatct ... tctgtttcagCCCAACAACGGGA
EST: gi|110965377|gb|EE185277.1|EE185277
EST:     ACTGGTGCTCAGTGGGGAATTTACGATGCATTCAAAGTGATGGTTGGACT                         CCCAACAACGGGAGGTGTTACACCTGCCCCAGCAGCAGAGGCTGAATTGAA
genomic: ACTGGTGCTCAGTGGGGAATTTACGATGCATTCAAAGTGATGGTTGGACTgtgagtatct ... tctgtttcagCCCAACAACGGGAGGTGTTACACCTGCCCCAGCAGCAGAGGCTGAATTGAA
EST: gi|113823717|gb|DW941553.1|DW941553
EST:     GGAATTTACGATGCATTCAAAGTGATGGTTGGACT                         CCCAACAACGGGAGGTGTTACACCTGCCCCAGCAGCAGAGGCTGAATTGAA
genomic: GGAATTTACGATGCATTCAAAGTGATGGTTGGACTgtgagtatct ... tctgtttcagCCCAACAACGGGAGGTGTTACACCTGCCCCAGCAGCAGAGGCTGAATTGAA
EST: gi|166547312|gb|EG315874.1|EG315874
EST:     ACTGGTGCTCAGTGGGGAATTTACGATGCATTCAAAGTGATGGTTGGACT                         CCCAACAACGGGAGGTGTTACACCTGCCTCAGCAGCAGAGGC
genomic: ACTGGTGCTCAGTGGGGAATTTACGATGCATTCAAAGTGATGGTTGGACTgtgagtatct ... tctgtttcagCCCAACAACGGGAGGTGTTACACCTGCCCCAGCAGCAGAGGC
EST: gi|15080205|gb|BI388980.1|BI388980
EST:     ACTGGTGCTCAGTGGGGAATTTACGATGCATTCAAAGTGATGGTTGGACT                         CCCAACAACGGGAGGTGTTACACCTGCCCCAGCAGCAGAGGCTGAATTGAA
genomic: ACTGGTGCTCAGTGGGGAATTTACGATGCATTCAAAGTGATGGTTGGACTgtgagtatct ... tctgtttcagCCCAACAACGGGAGGTGTTACACCTGCCCCAGCAGCAGAGGCTGAATTGAA
EST: gi|67021830|gb|CO450579.1|CO450579
EST:     ACTGGTGCTCAGTGGGNAATTTACGATGCATTCAAAGTGATGGTTGGACT                         CCCAACAACGGGAGGTGTTACACCTGCCCCAGCAGCAGAGGCTGAATTGAA
genomic: ACTGGTGCTCAGTGGGGAATTTACGATGCATTCAAAGTGATGGTTGGACTgtgagtatct ... tctgtttcagCCCAACAACGGGAGGTGTTACACCTGCCCCAGCAGCAGAGGCTGAATTGAA

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: 416

GTCTCTTCACTAGAGGACTTCCTCTTCGTATCGTCATGATTGGTACCCTTACTGGTGCTCAGTGGGGAATTTACGATGCATTCAAAGTGATGGTTGGACTgtgagtatct ... tctgtttcagCCCAACAACGGGAGGTGTTACACCTGCCCCAGCAGCAGAGGCTGAATTGAAAGCCAGTGCTTGATTTTTTTTTTCTGTGTTCCCTGAGATCATATTTGGT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 544

GTCTCTTCACTAGAGGACTTCCTCTTCGTATCGTCATGATTGGTACCCTTACTGGTGCTCAGTGGGGAATTTACGATGCATTCAAAGTGATGGTTGGACTgtgagtatct ... tctgtttcagCCCAACAACGGGAGGTGTTACACCTGCCCCAGCAGCAGAGGCTGAATTGAAAGCCAGTGCTTGATTTTTTTTTTCTGTGTTCCCTGAGATCATATTTGGT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 361

GTCTCTTCACTAGAGGACTTCCTCTTCGTATCGTCATGATTGGTACCCTTACTGGTGCTCAGTGGGGAATTTACGATGCATTCAAAGTGATGGTTGGACTgtgagtatct ... tctgtttcagCCCAACAACGGGAGGTGTTACACCTGCCCCAGCAGCAGAGGCTGAATTGAAAGCCAGTGCTTGATTTTTTTTTTCTGTGTTCCCTGAGATCATATTTGGT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 523

GTCTCTTCACTAGAGGACTTCCTCTTCGTATCGTCATGATTGGTACCCTTACTGGTGCTCAGTGGGGAATTTACGATGCATTCAAAGTGATGGTTGGACTgtgagtatct ... tctgtttcagCCCAACAACGGGAGGTGTTACACCTGCCCCAGCAGCAGAGGCTGAATTGAAAGCCAGTGCTTGATTTTTTTTTTCTGTGTTCCCTGAGATCATATTTGGT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tccaaatccttcagagagctcaccaactaattctttgtttcgttttctgtttcagCCCAACAACGGGAGGTGTTACACCTGCCCCAGCAGCAGAGGCTGAATTGAAAGCCAGTGCTTGATTTTTTTTTTCTGTGTTCCCTGAGATCATATTTGGT
                        aactaat  putative branch site (score: 523)
                              ttctttgtttcgtttt  CT-rich tract
                           taattcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtatctctctctactgccttaggaataaccaccgcaacatccaaatccttcagagagctcaccaactaattctttgtttcgttttctgtttcagCCCAACAACGGGAGGTGTTACACCTGCCCCAGCAGCAGAGGCTGAATTGAAAGCCAGTGCTTGATTTTTTTTTTCTGTGTTCCCTGAGATCATATTTGGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA