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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaacgatagtatttcattgatagcaatgtaggcttgtacagccatgaagctctgcagaatgcaagctcctttctattaatgttgtttgcagAATGCAAGCTCAGCCAGCCAATTCAGAGGATCCATATAGGGGGATGACCGATTGTTTCCGGATAACTCTGCGTCGTGAAGGAGTTTCTGGATTTTACAAA

Basic information

species Zea mays
transcript GRMZM2G180971_T01
intron # 3
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|6653802|gb|AW267207.1|AW267207
EST:     GGAGCGCTAGGAGCGACATGCGTTTATCCTTTACAAGTCATCAGAACAAG                         AATGCAAGCTCAGCCAGCCAATTCAGAGGATCCATATAGGGGGATGACCGA
genomic: GGAGCGCTAGGAGCGACATGCGTTTATCCTTTACAAGTCATCAGAACAAGgtaaacgata ... ttgtttgcagAATGCAAGCTCAGCCAGCCAATTCAGAGGATCCATATAGGGGGATGACCGA
EST: gi|71323059|gb|DR798203.1|DR798203
EST:     GGAGCGCTAGGAGCGACATGCGTTTATCCTTTACAAGTCATCAGAACAAG                         AATGCAAGCTCAGCCAGCCAATTCAGAGGATCCATATAGGGGGATGACCGA
genomic: GGAGCGCTAGGAGCGACATGCGTTTATCCTTTACAAGTCATCAGAACAAGgtaaacgata ... ttgtttgcagAATGCAAGCTCAGCCAGCCAATTCAGAGGATCCATATAGGGGGATGACCGA
EST: gi|211507517|gb|FL434573.1|FL434573
EST:     GGAGCGCTAGGAGCGACATGCGTTTATCCTTTACAAGTCATCAGAACAAG                         AATGCAAGCTCAGCCAGCCAATTCAGAGGATCCATATAGGGGGATGACCGA
genomic: GGAGCGCTAGGAGCGACATGCGTTTATCCTTTACAAGTCATCAGAACAAGgtaaacgata ... ttgtttgcagAATGCAAGCTCAGCCAGCCAATTCAGAGGATCCATATAGGGGGATGACCGA
EST: gi|78544099|gb|DV621597.1|DV621597
EST:     GGAGCGCTAGGAGCGACATGCGTTTATCCTTTACAAGTCATCAGAACAAG                         AATGCAAGCTCAGCCAGCCAATTCAGAGGATCCATATAGGGGGATGACCGA
genomic: GGAGCGCTAGGAGCGACATGCGTTTATCCTTTACAAGTCATCAGAACAAGgtaaacgata ... ttgtttgcagAATGCAAGCTCAGCCAGCCAATTCAGAGGATCCATATAGGGGGATGACCGA
EST: gi|149001456|gb|EE038757.2|EE038757
EST:     GGAGCGCTAGGAGCGACATGCGTTTATCCTTTACAAGTCATCAGAACAAG                         AATGCAAGCTCAGCCAGCCAATTCAGAGGATCCATATAGGGGGATGACCGA
genomic: GGAGCGCTAGGAGCGACATGCGTTTATCCTTTACAAGTCATCAGAACAAGgtaaacgata ... ttgtttgcagAATGCAAGCTCAGCCAGCCAATTCAGAGGATCCATATAGGGGGATGACCGA
EST: gi|20336906|gb|BQ172536.1|BQ172536
EST:     GGAGCGCTAGGAGCGACATGCGTTTATCCTTTACAAGTCATCAGAACAAG                         AATGCAAGCTCAGCCAGCCAATTCAGAGGATCCATATAGGGGGATGACCGA
genomic: GGAGCGCTAGGAGCGACATGCGTTTATCCTTTACAAGTCATCAGAACAAGgtaaacgata ... ttgtttgcagAATGCAAGCTCAGCCAGCCAATTCAGAGGATCCATATAGGGGGATGACCGA
EST: gi|88747876|gb|DY532017.1|DY532017
EST:     GGAGCGCTAGGAGCGACATGCGTTTATCCTTTACAAGTCATCAGAACAAG                         AATGCAAGCTCAGCCAGCCAATTCAGAGGATCCATATAGGGGGATGGCCGA
genomic: GGAGCGCTAGGAGCGACATGCGTTTATCCTTTACAAGTCATCAGAACAAGgtaaacgata ... ttgtttgcagAATGCAAGCTCAGCCAGCCAATTCAGAGGATCCATATAGGGGGATGACCGA
EST: gi|211451242|gb|FL460011.1|FL460011
EST:     GGAGCGCTAGGAGCGACATGCGTTTATCCTTTACAAGTCATCAGAACAAG                         AATGCAAGCTCAGCCAGCCAATTCAGAGGATCCATATAGGGGGATGACCGA
genomic: GGAGCGCTAGGAGCGACATGCGTTTATCCTTTACAAGTCATCAGAACAAGgtaaacgata ... ttgtttgcagAATGCAAGCTCAGCCAGCCAATTCAGAGGATCCATATAGGGGGATGACCGA
EST: gi|149107568|gb|EE189450.2|EE189450
EST:     GGAGCGCTAGGAGCGACATGCGTTTATCCTTTACAAGTCATCAGAACAAG                         AATGCAAGTTCAGCCAGCCAATTCAGAGGATCCATATAGGGGGATGACCGA
genomic: GGAGCGCTAGGAGCGACATGCGTTTATCCTTTACAAGTCATCAGAACAAGgtaaacgata ... ttgtttgcagAATGCAAGCTCAGCCAGCCAATTCAGAGGATCCATATAGGGGGATGACCGA
EST: gi|60394866|gb|DN227735.1|DN227735
EST:     GGAGCGCTAGGAGCGACATGCGTTTATCCTTTACAAGTCATCAGAACAAG                         AATGCAAGCTCAGCCAGCCAATTCAGAGGATCCATATAGGGGGATGACCGA
genomic: GGAGCGCTAGGAGCGACATGCGTTTATCCTTTACAAGTCATCAGAACAAGgtaaacgata ... ttgtttgcagAATGCAAGCTCAGCCAGCCAATTCAGAGGATCCATATAGGGGGATGACCGA
EST: gi|88748965|gb|DY533106.1|DY533106
EST:     GGAGCGCTAGGAGCGACATGCGTTTATCCTTTACAAGTCATCAGAACAAG                         AATGCAAGCTCAGCCAGCCAATTCAGAGGATCCATATAGGGGGATGACCGA
genomic: GGAGCGCTAGGAGCGACATGCGTTTATCCTTTACAAGTCATCAGAACAAGgtaaacgata ... ttgtttgcagAATGCAAGCTCAGCCAGCCAATTCAGAGGATCCATATAGGGGGATGACCGA

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: 49 (upstream exon), 49 (downstream exon)
Score: 42

ATCCTGGCCCTTTAGTACAGCTGGGCTGCGGAACAGTCTCTGGAGCGCTAGGAGCGACATGCGTTTATCCTTTACAAGTCATCAGAACAAGgtaaacgata ... ttgtttgcagAATGCAAGCTCAGCCAGCCAATTCAGAGGATCCATATAGGGGGATGACCGATTGTTTCCGGATAACTCTGCGTCGTGAAGGAGTTTCTGGATTTTACAAA


Block sizes: 47 (upstream exon), 38 (downstream exon)
Score: 10

ATCCTGGCCCTTTAGTACAGCTGGGCTGCGGAACAGTCTCTGGAGCGCTAGGAGCGACATGCGTTTATCCTTTACAAGTCATCAGAACAAGgtaaacgata ... ttgtttgcagAATGCAAGCTCAGCCAGCCAATTCAGAGGATCCATATAGGGGGATGACCGATTGTTTCCGGATAACTCTGCGTCGTGAAGGAGTTTCTGGATTTTACAAA


Block sizes: 49 (upstream exon), 33 (downstream exon)
Score: 13

ATCCTGGCCCTTTAGTACAGCTGGGCTGCGGAACAGTCTCTGGAGCGCTAGGAGCGACATGCGTTTATCCTTTACAAGTCATCAGAACAAGgtaaacgata ... ttgtttgcagAATGCAAGCTCAGCCAGCCAATTCAGAGGATCCATATAGGGGGATGACCGATTGTTTCCGGATAACTCTGCGTCGTGAAGGAGTTTCTGGATTTTACAAA


Block sizes: 47 (upstream exon), 42 (downstream exon)
Score: 21

ATCCTGGCCCTTTAGTACAGCTGGGCTGCGGAACAGTCTCTGGAGCGCTAGGAGCGACATGCGTTTATCCTTTACAAGTCATCAGAACAAGgtaaacgata ... ttgtttgcagAATGCAAGCTCAGCCAGCCAATTCAGAGGATCCATATAGGGGGATGACCGATTGTTTCCGGATAACTCTGCGTCGTGAAGGAGTTTCTGGATTTTACAAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tacagccatgaagctctgcagaatgcaagctcctttctattaatgttgtttgcagAATGCAAGCTCAGCCAGCCAATTCAGAGGATCCATATAGGGGGATGACCGATTGTTTCCGGATAACTCTGCGTCGTGAAGGAGTTTCTGGATTTTACAAA
                                     tattaat  putative branch site (score: 21)
 tttctattaatgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaacgatagtatttcattgatagcaatgtaggcttgtacagccatgaagctctgcagaatgcaagctcctttctattaatgttgtttgcagAATGCAAGCTCAGCCAGCCAATTCAGAGGATCCATATAGGGGGATGACCGATTGTTTCCGGATAACTCTGCGTCGTGAAGGAGTTTCTGGATTTTACAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG