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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacaagatatatttccacaagcattagactttaatgaattgctattctagttagtggagtcaaagatgcccttttattttacttcaatgtaaaatggcaaactaaagcatgttgttgttttaaattcagTCCGATCTAGAAATTGAGCCCAGATATCCGTTATTTGGTGGGTGGCACTGCACGTTCACCATTGGCTATGGTCTTCCATTGCAAGATTTTGTCTTTGAGT

Basic information

species Zea mays
transcript GRMZM2G177273_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G177273_T01 (Zea mays), 3'ss of exon 4
lower sequence: 13113.m00157 (Oryza sativa), 3'ss of exon 4
gtacaagatatatttccacaagcattagactttaatgaattgctattctagttagtggagtcaaagatgcccttttattttacttcaatgtaaaatggcaaactaaagc----atgttgttgtttta----aattcagTCCGATCTAGAAATTGAGCCCAGATATCCGTTATTTGGTGGGTGGCACTGCACGTTCACCATTGGCTATGGTCTTCCATTGCAAGATTTTGTCTTTGAGT
||||||||||  | | ||   |        | ||||||||   ||| ||| | |||||| |  |||||  | |||||| ||| |  ||   ||| ||  | |||||       ||||  |||||||     ||| ||||| || || |||||||||||||||||||| ||||||||||| |||||||||||||||||||||||||||||| | ||||||||||||||| ||||||| |
gtacaagatacttcttcatgtgg-------tgtaatgaatca-tatgctaatgagtggaatataagatatcattttatcttaatgtaaaaaaaactg--agactaatattttgatgtgattgtttttctttaatgcagTCAGAACTTGAAATTGAGCCCAGATATCCATTATTTGGTGGTTGGCACTGCACGTTCACCATTGGCTATGGTTTGCCATTGCAAGATTTTCTCTTTGAAT
















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|32930107|gb|CF034919.1|CF034919
EST:     ATGAGATTGGTAACATCTCCTCATCCCATCTGCGCACTGATTCACACAAG                         TCCGATCTAGAAATTGAGCCCAGATATCCGTTATTTGGTGGGTGGCACTGC
genomic: ATGAGATTGGTAACATCTCCTCATCCCATCTGCGCACTGATTCACACAAGgtacaagata ... ttaaattcagTCCGATCTAGAAATTGAGCCCAGATATCCGTTATTTGGTGGGTGGCACTGC
EST: gi|32932468|gb|CF037280.1|CF037280
EST:     ATGAGATTGGTAACATCTCCTCATCCCATCTGCGCACTGATTCACACAAG                         TCCGATCTAGAAATTGAGCCCAGATATCCGTTATTTGGTGGGTGGCACTGC
genomic: ATGAGATTGGTAACATCTCCTCATCCCATCTGCGCACTGATTCACACAAGgtacaagata ... ttaaattcagTCCGATCTAGAAATTGAGCCCAGATATCCGTTATTTGGTGGGTGGCACTGC
EST: gi|78023626|gb|DV492013.1|DV492013
EST:     ATGAGATTGGTAACATCTCCTCATCCCATCTGCGCACTGATTCACACAAG                         TCCGATCTAGAAATTGAGCCCAGATATCCGTTATTTGGTGGGTGGCACTGC
genomic: ATGAGATTGGTAACATCTCCTCATCCCATCTGCGCACTGATTCACACAAGgtacaagata ... ttaaattcagTCCGATCTAGAAATTGAGCCCAGATATCCGTTATTTGGTGGGTGGCACTGC
EST: gi|5468696|gb|AI834487.1|AI834487
EST:     ACATCTCCTCATCCCATCTGCGC-CTGATTCACACAAG                         TCCGATCTAGAAATTGAGCCCAGATATCCGTTATTTGGTGGGTGGCACTGC
genomic: ACATCTCCTCATCCCATCTGCGCACTGATTCACACAAGgtacaagata ... ttaaattcagTCCGATCTAGAAATTGAGCCCAGATATCCGTTATTTGGTGGGTGGCACTGC
EST: gi|17921687|gb|BM259338.1|BM259338
EST:     ATGAGATTGGTAACATCTCCTCATCCCATCTGCGCACTGATTCACACAAG                         TCCGATCTAGAAATTGAGCCCAGATATCCGTTATTTGGTGGGTGGCACTGC
genomic: ATGAGATTGGTAACATCTCCTCATCCCATCTGCGCACTGATTCACACAAGgtacaagata ... ttaaattcagTCCGATCTAGAAATTGAGCCCAGATATCCGTTATTTGGTGGGTGGCACTGC
EST: gi|33093879|gb|CF053873.1|CF053873
EST:     ATGAGATTGGTAACATCTCCTCATCCCATCTGCGCACTGATTCACACAAG                         TCCGATCTAGAAATTGAGCCCAGATATCCGTTATTTGGTGGGTGGCACTGC
genomic: ATGAGATTGGTAACATCTCCTCATCCCATCTGCGCACTGATTCACACAAGgtacaagata ... ttaaattcagTCCGATCTAGAAATTGAGCCCAGATATCCGTTATTTGGTGGGTGGCACTGC
EST: gi|78075801|gb|DV504235.1|DV504235
EST:     ATGAGATTGGTAACATCTCCTCATCCCATCTGCGCACTGATTCACACAAG                         TCCGATCTAGAAATTGAGCCCAGATATCCGTTATTTGGTGGGTGGCACTGC
genomic: ATGAGATTGGTAACATCTCCTCATCCCATCTGCGCACTGATTCACACAAGgtacaagata ... ttaaattcagTCCGATCTAGAAATTGAGCCCAGATATCCGTTATTTGGTGGGTGGCACTGC
EST: gi|33093279|gb|CF053273.1|CF053273
EST:     ATGAGATTGGTAACATCTCCTCATCCCATCTGCGCACTGATTCACACAAG                         TCCGATCTAGAAATTGAGCCCAGATATCCGTTATTTGGTGGGTGGCACTGC
genomic: ATGAGATTGGTAACATCTCCTCATCCCATCTGCGCACTGATTCACACAAGgtacaagata ... ttaaattcagTCCGATCTAGAAATTGAGCCCAGATATCCGTTATTTGGTGGGTGGCACTGC
EST: gi|20803243|gb|BQ294293.1|BQ294293
EST:     ATGAGATTGGTAACATCTCCTCATCCCATCTGCGCACTGATTCACACAAG                         TCCGATCTAGAAATTGAGCCCATATATCCGTTATTTGGTGGGTGGCACTGC
genomic: ATGAGATTGGTAACATCTCCTCATCCCATCTGCGCACTGATTCACACAAGgtacaagata ... ttaaattcagTCCGATCTAGAAATTGAGCCCAGATATCCGTTATTTGGTGGGTGGCACTGC
EST: gi|32932488|gb|CF037300.1|CF037300
EST:     ATGAGATTGGTAACATCTCCTCATCCCATCTGCGCACTGATTCACACAAG                         TCCGATCTAGAAATTGAGCCCAGATATCCGTTATTTGGTGGGTGGCACTGC
genomic: ATGAGATTGGTAACATCTCCTCATCCCATCTGCGCACTGATTCACACAAGgtacaagata ... ttaaattcagTCCGATCTAGAAATTGAGCCCAGATATCCGTTATTTGGTGGGTGGCACTGC
EST: gi|21331859|gb|BQ487240.1|BQ487240
EST:     ATGAGATTGGTAACATCTCCTCATCCCATCTGCGCACTGATTCACACAAG                         TCCGATCTAGAAATTGAGCCCAGATATCCGTTATTTGGTGGGTGGCACTGC
genomic: ATGAGATTGGTAACATCTCCTCATCCCATCTGCGCACTGATTCACACAAGgtacaagata ... ttaaattcagTCCGATCTAGAAATTGAGCCCAGATATCCGTTATTTGGTGGGTGGCACTGC
EST: gi|71763848|gb|DR961785.1|DR961785
EST:     ATGAGATTGGTAACATCTCCTCATCCCATCTGCGCACTGATTCACACAAG                         TCCGATCTAGAAATTGAGCCCAGATATCCGTTATTTGGTGGGTGGCACTGC
genomic: ATGAGATTGGTAACATCTCCTCATCCCATCTGCGCACTGATTCACACAAGgtacaagata ... ttaaattcagTCCGATCTAGAAATTGAGCCCAGATATCCGTTATTTGGTGGGTGGCACTGC
EST: gi|74236700|gb|DT644614.1|DT644614
EST:     ATGAGATTGGTAACATCTCCTCATCCCATCTGCGCACTGATTCACACAAG                         TCCGATCTAGAAATTGAGCCCAGATATCCGTTATTTGGTGGGTGGCACTGC
genomic: ATGAGATTGGTAACATCTCCTCATCCCATCTGCGCACTGATTCACACAAGgtacaagata ... ttaaattcagTCCGATCTAGAAATTGAGCCCAGATATCCGTTATTTGGTGGGTGGCACTGC
EST: gi|60352174|gb|DN219147.1|DN219147
EST:     ATGAGATTGGTAACATCTCCTCATCCCATCTGCGCACTGATTCACACAAG                         TCCGATCTAGAAATTGAGCCCAGATATCCGTTATTTGGTGGGTGGCACTGC
genomic: ATGAGATTGGTAACATCTCCTCATCCCATCTGCGCACTGATTCACACAAGgtacaagata ... ttaaattcagTCCGATCTAGAAATTGAGCCCAGATATCCGTTATTTGGTGGGTGGCACTGC

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: 325

GAATCTTCTTGCAAGGCTGCCACCTCGGGTTCATTCAGTTTACTATCGTGATGAGATTGGTAACATCTCCTCATCCCATCTGCGCACTGATTCACACAAGgtacaagata ... ttaaattcagTCCGATCTAGAAATTGAGCCCAGATATCCGTTATTTGGTGGGTGGCACTGCACGTTCACCATTGGCTATGGTCTTCCATTGCAAGATTTTGTCTTTGAGT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 216

GAATCTTCTTGCAAGGCTGCCACCTCGGGTTCATTCAGTTTACTATCGTGATGAGATTGGTAACATCTCCTCATCCCATCTGCGCACTGATTCACACAAGgtacaagata ... ttaaattcagTCCGATCTAGAAATTGAGCCCAGATATCCGTTATTTGGTGGGTGGCACTGCACGTTCACCATTGGCTATGGTCTTCCATTGCAAGATTTTGTCTTTGAGT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 323

GAATCTTCTTGCAAGGCTGCCACCTCGGGTTCATTCAGTTTACTATCGTGATGAGATTGGTAACATCTCCTCATCCCATCTGCGCACTGATTCACACAAGgtacaagata ... ttaaattcagTCCGATCTAGAAATTGAGCCCAGATATCCGTTATTTGGTGGGTGGCACTGCACGTTCACCATTGGCTATGGTCTTCCATTGCAAGATTTTGTCTTTGAGT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 317

GAATCTTCTTGCAAGGCTGCCACCTCGGGTTCATTCAGTTTACTATCGTGATGAGATTGGTAACATCTCCTCATCCCATCTGCGCACTGATTCACACAAGgtacaagata ... ttaaattcagTCCGATCTAGAAATTGAGCCCAGATATCCGTTATTTGGTGGGTGGCACTGCACGTTCACCATTGGCTATGGTCTTCCATTGCAAGATTTTGTCTTTGAGT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattttacttcaatgtaaaatggcaaactaaagcatgttgttgttttaaattcagTCCGATCTAGAAATTGAGCCCAGATATCCGTTATTTGGTGGGTGGCACTGCACGTTCACCATTGGCTATGGTCTTCCATTGCAAGATTTTGTCTTTGAGT
                         aactaaa  putative branch site (score: 317)
                                        ttgtttt  putative PPT
                                     ttgttgttttaaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacaagatatatttccacaagcattagactttaatgaattgctattctagttagtggagtcaaagatgcccttttattttacttcaatgtaaaatggcaaactaaagcatgttgttgttttaaattcagTCCGATCTAGAAATTGAGCCCAGATATCCGTTATTTGGTGGGTGGCACTGCACGTTCACCATTGGCTATGGTCTTCCATTGCAAGATTTTGTCTTTGAGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA