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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cgttgagcctttcatgtttacttgaagcatttaatttttgtggttagttttgattagtgaatcggacattatatggttcttcaatttcactgtaatgcagTTTCTGAGTCGCAATGGAATTGAATGCAATGATATTGAAGAATTATTCATCAAAGACCAATCACTGAGTAATGAAA

Basic information

species Zea mays
transcript GRMZM2G052403_T01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G052403_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os11g43970.1 (Oryza sativa), 3'ss of exon 17
-----cgttgagcctttcatgtttacttgaagcatttaatttttgtggttagttttgattagtgaatcggacattatatggttcttcaatttcactgtaatgcagTTTCTGAGTCGCAATGGAATTGAATGCAATGATATTGAAGAATTATTCATCAAAGACCAATCACTGAGTAATGAAA
     |  ||  |   |    | || ||||  |   || |  || | |||    |||| |  |   | |    |||| ||  | |||  || |  |||  ||||||||||||| ||||||||||||||||||| |||  |||||||||||||||||||||| ||||||||||  || ||||
tattccactgcccgaatggcctgtatttgattctccta-tgcttatagttg---ttgaatgcttgctagctatttatgtgaat-ttcgtttgctttgtgttgcagTTTCTGAGCCGCAATGGAATTGAATGCAGTGACCTTGAAGAATTATTCATCAAAGATCAATCACTGACCAACGAAA
















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|211048835|gb|FL187595.1|FL187595
EST:     GTGATGTTGAAACCCTTAAAGCCAAATCAAACATTGGTAGCATTCGCACG                         TTTCTGAGTCGCAATGGAATTGAATGCAATGATATTGAAGAATTATTCATC
genomic: GTGATGTTGAAACCCTTAAAGCCAAATCAAACATTGGTAGCATTCGCACGgtaagctgca ... tgtaatgcagTTTCTGAGTCGCAATGGAATTGAATGCAATGATATTGAAGAATTATTCATC
EST: gi|67034427|gb|CO462977.1|CO462977
EST:     GTGATGTTGAAACCCTTAAAGCCAAATCAAACATTGGTAGCATTCGCACG                         TTTCTGAGTCGCAATGGAATTGAATGCAATGATATTGAAGAATTATTCATC
genomic: GTGATGTTGAAACCCTTAAAGCCAAATCAAACATTGGTAGCATTCGCACGgtaagctgca ... tgtaatgcagTTTCTGAGTCGCAATGGAATTGAATGCAATGATATTGAAGAATTATTCATC
EST: gi|60399121|gb|DN231935.1|DN231935
EST:     GTGATGTTGAAACCCTTAAAGCCAAATCAAACATTGGTAGCATTCGCACG                         TTTCTGAGTCGCAATGGAATTGAATGCAATGATATTGAAGAATTATTCATC
genomic: GTGATGTTGAAACCCTTAAAGCCAAATCAAACATTGGTAGCATTCGCACGgtaagctgca ... tgtaatgcagTTTCTGAGTCGCAATGGAATTGAATGCAATGATATTGAAGAATTATTCATC
EST: gi|211051787|gb|FL187605.1|FL187605
EST:     GTGATGTTGAAACCCTTAAAGCCAAATCAAACATTGGTAGCATTCGCACG                         TTTCTGAGTCGCAATGGAATTGAATGCAATGATATTGAAGAATTATTCATC
genomic: GTGATGTTGAAACCCTTAAAGCCAAATCAAACATTGGTAGCATTCGCACGgtaagctgca ... tgtaatgcagTTTCTGAGTCGCAATGGAATTGAATGCAATGATATTGAAGAATTATTCATC
EST: gi|211051788|gb|FL187606.1|FL187606
EST:     GTGATGTTGAAACCCTTAAAGCCAAATCAAACATTGGTAGCATTCGCACG                         TTTCTGAGTCGCAATGGAATTGAATGCAATGATATTGAAGAATTATTCATC
genomic: GTGATGTTGAAACCCTTAAAGCCAAATCAAACATTGGTAGCATTCGCACGgtaagctgca ... tgtaatgcagTTTCTGAGTCGCAATGGAATTGAATGCAATGATATTGAAGAATTATTCATC
EST: gi|211048839|gb|FL187599.1|FL187599
EST:     GTGATGTTGAAACCCTTAAAGCCAAATCAAACATTGGTAGCATTCGCACG                         TTTCTGAGTCGCAATGGAATTGAATGCAATGATATTGAAGAATTATTCATC
genomic: GTGATGTTGAAACCCTTAAAGCCAAATCAAACATTGGTAGCATTCGCACGgtaagctgca ... tgtaatgcagTTTCTGAGTCGCAATGGAATTGAATGCAATGATATTGAAGAATTATTCATC

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: 139

GATGAAGCTCTACTTACAGATTGGAAGCAGCAGTTGGATCGTGATGTTGAAACCCTTAAAGCCAAATCAAACATTGGTAGCATTCGCACGgtaagctgca ... tgtaatgcagTTTCTGAGTCGCAATGGAATTGAATGCAATGATATTGAAGAATTATTCATCAAAGACCAATCACTGAGTAATGAAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 161

GATGAAGCTCTACTTACAGATTGGAAGCAGCAGTTGGATCGTGATGTTGAAACCCTTAAAGCCAAATCAAACATTGGTAGCATTCGCACGgtaagctgca ... tgtaatgcagTTTCTGAGTCGCAATGGAATTGAATGCAATGATATTGAAGAATTATTCATCAAAGACCAATCACTGAGTAATGAAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 194

GATGAAGCTCTACTTACAGATTGGAAGCAGCAGTTGGATCGTGATGTTGAAACCCTTAAAGCCAAATCAAACATTGGTAGCATTCGCACGgtaagctgca ... tgtaatgcagTTTCTGAGTCGCAATGGAATTGAATGCAATGATATTGAAGAATTATTCATCAAAGACCAATCACTGAGTAATGAAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 189

GATGAAGCTCTACTTACAGATTGGAAGCAGCAGTTGGATCGTGATGTTGAAACCCTTAAAGCCAAATCAAACATTGGTAGCATTCGCACGgtaagctgca ... tgtaatgcagTTTCTGAGTCGCAATGGAATTGAATGCAATGATATTGAAGAATTATTCATCAAAGACCAATCACTGAGTAATGAAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agttttgattagtgaatcggacattatatggttcttcaatttcactgtaatgcagTTTCTGAGTCGCAATGGAATTGAATGCAATGATATTGAAGAATTATTCATCAAAGACCAATCACTGAGTAATGAAA
  ttttgat  putative branch site (score: 189)
                                       tttcact  putative PPT
                    acattatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cgttgagcctttcatgtttacttgaagcatttaatttttgtggttagttttgattagtgaatcggacattatatggttcttcaatttcactgtaatgcagTTTCTGAGTCGCAATGGAATTGAATGCAATGATATTGAAGAATTATTCATCAAAGACCAATCACTGAGTAATGAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - catgttt
- - - - - - - - - - - tgaagca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - gtgaatc