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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtagttccttttgctaattggtgcctttgtgcactgagcttctatgtaatatctactctaacttgttttgaaattttaaatctctttcagGCTATAATCAATGACCCTTTTATGCTTAACAGTGTGTTATTGGTGTTTGCTAACAAGCAAGACATG

Basic information

species Zea mays
transcript GRMZM2G011518_T04
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G011518_T03 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os10g42940.1 (Oryza sativa), 3'ss of exon 4
--------------gtttgtagttccttttgc--taattggtgcct--ttgtgcactgagcttctatgtaatatctactctaacttgttttgaaattttaaatctctttcagGCTATAATCAATGACCCTTTTATGCTTAACAGTGTGTTATTGGTGTTTGCTAACAAGCAAGACATG
               |   || ||  || ||    |    |||  |  || ||||||||  ||   ||   | | | |||||||||  | ||   |  |   | |||||||||| || || |||||||||||||||||||| |||||  |||||||||||||||||||||||||||||
gtttacatatatgtataaataatttattatgaggcagcaagtgtttgcttctgcactgacatttgttgccttgt-tgctctaacttactgtgtggtaatc--tgtctttcagGCCATTATTAATGACCCTTTTATGCTTAATAGTGTTCTATTGGTGTTTGCTAACAAGCAAGACATG
















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|60357839|gb|DN224812.1|DN224812
EST:     TTGATTCACTGGATAGAGAGAGAATCGGGAGAGCCAGGGCGGAGTTTCAG                         GCTATAATCAATGACCCTTTTATGCTTAACAGTGTGTTATTGGTGTTTGCT
genomic: TTGATTCACTGGATAGAGAGAGAATCGGGAGAGCCAGGGCGGAGTTTCAGgtttgtagtt ... tctctttcagGCTATAATCAATGACCCTTTTATGCTTAACAGTGTGTTATTGGTGTTTGCT
EST: gi|76285293|gb|DV024861.1|DV024861
EST:     TTGATTCACTGGATAGAGAGAGAATCGGGAGAGCCAGGGCGGAGTTTCAG                         GCTATAATCAATGACCCTTTTATGCTTAACAGTGTGTTATTGGTGTTTGCT
genomic: TTGATTCACTGGATAGAGAGAGAATCGGGAGAGCCAGGGCGGAGTTTCAGgtttgtagtt ... tctctttcagGCTATAATCAATGACCCTTTTATGCTTAACAGTGTGTTATTGGTGTTTGCT
EST: gi|60394445|gb|DN227315.1|DN227315
EST:     TTGATTCACTGGATAGAGAGAGAATCGGGAGAGCCAGGGCGGAGTTTCAG                         GCTATAATCAATGACCCTTTTATGCTTAACAGTGTGTTATTGGTGTTTGCT
genomic: TTGATTCACTGGATAGAGAGAGAATCGGGAGAGCCAGGGCGGAGTTTCAGgtttgtagtt ... tctctttcagGCTATAATCAATGACCCTTTTATGCTTAACAGTGTGTTATTGGTGTTTGCT
EST: gi|78021761|gb|DV490148.1|DV490148
EST:     TTGATTCACTGGATAGAGAGAGAATCGGGAGAGCCAGGGCGGAGTTTCAG                         GCTATAATCAATGACCCTTTTATGCTTAACAGTGTGTTATTGGTGTTTGCT
genomic: TTGATTCACTGGATAGAGAGAGAATCGGGAGAGCCAGGGCGGAGTTTCAGgtttgtagtt ... tctctttcagGCTATAATCAATGACCCTTTTATGCTTAACAGTGTGTTATTGGTGTTTGCT
EST: gi|60337699|gb|DN204672.1|DN204672
EST:     TTGATTCACTGGATAGAGAGAGAATCGGGAGAGCCAGGGCGGAGTTTCAG                         GCTATAATCAATGACCCTTTTATGCTTAACAGTGTGTTATTGGTGTTTGCT
genomic: TTGATTCACTGGATAGAGAGAGAATCGGGAGAGCCAGGGCGGAGTTTCAGgtttgtagtt ... tctctttcagGCTATAATCAATGACCCTTTTATGCTTAACAGTGTGTTATTGGTGTTTGCT
EST: gi|166598077|gb|EG306730.1|EG306730
EST:     CCAGGGCGGAGTTTCAG                         GCTATAATCAATGACCCTTTTATGCTTAACAGTGTGTTATTGGTGTTTGCT
genomic: CCAGGGCGGAGTTTCAGgtttgtagtt ... tctctttcagGCTATAATCAATGACCCTTTTATGCTTAACAGTGTGTTATTGGTGTTTGCT
EST: gi|76010832|gb|DT938002.1|DT938002
EST:     TTGATTCACTGGATAGAGAGAGAATCGGGAGAGCCAGGGCGGAGTTTCAG                         GCTATAATCAATGACCCTTTTATGCTTAACAGTGTGTTATTGGTGTTTGCT
genomic: TTGATTCACTGGATAGAGAGAGAATCGGGAGAGCCAGGGCGGAGTTTCAGgtttgtagtt ... tctctttcagGCTATAATCAATGACCCTTTTATGCTTAACAGTGTGTTATTGGTGTTTGCT
EST: gi|60399444|gb|DN232256.1|DN232256
EST:     TTGATTCACTGGATAGAGAGAGAATCGGGAGAGCCAGGGCGGAGTTTCAG                         GCTATAATCAATGACCCTTTTATGCTTAACAGTGTGTTATTGGTGTTTGCT
genomic: TTGATTCACTGGATAGAGAGAGAATCGGGAGAGCCAGGGCGGAGTTTCAGgtttgtagtt ... tctctttcagGCTATAATCAATGACCCTTTTATGCTTAACAGTGTGTTATTGGTGTTTGCT

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: 47 (upstream exon), 45 (downstream exon)
Score: 92

ATTTACGTGGTTGATTCACTGGATAGAGAGAGAATCGGGAGAGCCAGGGCGGAGTTTCAGgtttgtagtt ... tctctttcagGCTATAATCAATGACCCTTTTATGCTTAACAGTGTGTTATTGGTGTTTGCTAACAAGCAAGACATG


Block sizes: 49 (upstream exon), 44 (downstream exon)
Score: 80

ATTTACGTGGTTGATTCACTGGATAGAGAGAGAATCGGGAGAGCCAGGGCGGAGTTTCAGgtttgtagtt ... tctctttcagGCTATAATCAATGACCCTTTTATGCTTAACAGTGTGTTATTGGTGTTTGCTAACAAGCAAGACATG


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 119

ATTTACGTGGTTGATTCACTGGATAGAGAGAGAATCGGGAGAGCCAGGGCGGAGTTTCAGgtttgtagtt ... tctctttcagGCTATAATCAATGACCCTTTTATGCTTAACAGTGTGTTATTGGTGTTTGCTAACAAGCAAGACATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 81

ATTTACGTGGTTGATTCACTGGATAGAGAGAGAATCGGGAGAGCCAGGGCGGAGTTTCAGgtttgtagtt ... tctctttcagGCTATAATCAATGACCCTTTTATGCTTAACAGTGTGTTATTGGTGTTTGCTAACAAGCAAGACATG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gagcttctatgtaatatctactctaacttgttttgaaattttaaatctctttcagGCTATAATCAATGACCCTTTTATGCTTAACAGTGTGTTATTGGTGTTTGCTAACAAGCAAGACATG
                    ctctaac  putative branch site (score: 81)
                                             tctctttc  putative PPT
                       taacttgttttgaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgtagttccttttgctaattggtgcctttgtgcactgagcttctatgtaatatctactctaacttgttttgaaattttaaatctctttcagGCTATAATCAATGACCCTTTTATGCTTAACAGTGTGTTATTGGTGTTTGCTAACAAGCAAGACATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA