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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtacttcaaaaaagaacaagtgaagggaaatcatatggtgtacaattctaaattccttgtaagtgttggttcgttatatcaaaattcattctgttttcagGTTGCATATAAAGTTTGGTCGGAGTCTTTTGGCATGTACCCTCTACCTATGGTAAAGAGAGTGAGACAATTCTGGACTTCAATGAAAACTTGGTTGTCTG

Basic information

species Zea mays
transcript GRMZM2G173354_T02
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G173354_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os11g16390.1 (Oryza sativa), 3'ss of exon 1
---------gtacttcaaaaaagaacaagtgaagggaaatcatatggtgtacaattctaaattccttgtaagtgttggttcgttatatcaaaattcattctgtttt-cagGTTGCATATAAAGTTTGGTCGGAGTCTTTTGGCATGTACCCTCTACCTATGGTAAAGAGAGTGAGACAATTCTGGACTTCAATGAAAACTTGGTTGTCTG
         ||| ||||||  |     |   ||  ||    ||||| |    ||||   | || ||||   || |  ||||  |||| |||| |||| |   | || |||| ||| ||||||||||||| |||||||||||||||||| ||| ||||| |||||| |||||||| |   ||||||| |||  |||| |  ||| ||||||
attcatgatgtatttcaaattatttttac--aaacgactatatatgtt----aatttacatttacttg---gt-tgagttctgtataacaaacttcagttgatcttacagGATGCCTATAAAGTTTGGTTGGAGTCTTTTGGCATGTATCCTTTACCTCTGGTAAGGAGAGTGAAAATTTTCTGGAGTTCGCTGAAGAGCTGGCTGTCTG
















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|211427670|gb|FK998936.1|FK998936
EST:     GGCTCGACGCTCCCGTCGATCCAGAGGGCCGGCCTCTTCCCTCCTTCCAG                         GTTGCATATAAACTTTGGTTGGAGTCTTTTGGCATGTACCCTCTACCTATG
genomic: GGCTCGACGCTCCCGTCGATCCAGAGGGCCGGCCTCTTCCCTCCTTCCAGgttcgcgatg ... ctgttttcagGTTGCATATAAAGTTTGGTCGGAGTCTTTTGGCATGTACCCTCTACCTATG
EST: gi|211425076|gb|FK998927.1|FK998927
EST:     GGCTCGACGCTCCCGTCGATCCAGAGGGCCGGCCTCTTCCCTCCTTCCAG                         GTTGCATATAAAGTTTGGTCGGAGTCTTTTGGCATGTACCCTCTACCTATG
genomic: GGCTCGACGCTCCCGTCGATCCAGAGGGCCGGCCTCTTCCCTCCTTCCAGgttcgcgatg ... ctgttttcagGTTGCATATAAAGTTTGGTCGGAGTCTTTTGGCATGTACCCTCTACCTATG
EST: gi|211427677|gb|FK998943.1|FK998943
EST:     GGCTCGACGCTCCCGTCGATCCAGAGGGCCGGCCTCTTCCCTCCTTCCAG                         GTTTGCATATAAAGTTTGGTCGGAGTCTTTTGGCATGTACCCTCTACCTAT
genomic: GGCTCGACGCTCCCGTCGATCCAGAGGGCCGGCCTCTTCCCTCCTTCCAGgttcgcgatg ... ctgttttcagGTT-GCATATAAAGTTTGGTCGGAGTCTTTTGGCATGTACCCTCTACCTAT
EST: gi|211427673|gb|FK998939.1|FK998939
EST:     GGCTCGACGCTCCCGTCGATCCAGAGGGCCGGCCTCTTCCCTCCTTCCAG                         GTTGCATATAAAGTTTGGTCGGAGTCTTTTGGCATGTACCCTCTACCTATG
genomic: GGCTCGACGCTCCCGTCGATCCAGAGGGCCGGCCTCTTCCCTCCTTCCAGgttcgcgatg ... ctgttttcagGTTGCATATAAAGTTTGGTCGGAGTCTTTTGGCATGTACCCTCTACCTATG
EST: gi|86467751|gb|DY234121.1|DY234121
EST:     GGCTCGACGCTCCCGTCGATCCAGAGGGCCGGCCTCTTCCCTCCTTCCAG                         GTTGCATATAAAGTTTGGTCGGAGTCTTTTGGCATGTACCCTCTACCTATG
genomic: GGCTCGACGCTCCCGTCGATCCAGAGGGCCGGCCTCTTCCCTCCTTCCAGgttcgcgatg ... ctgttttcagGTTGCATATAAAGTTTGGTCGGAGTCTTTTGGCATGTACCCTCTACCTATG
EST: gi|211432869|gb|FK998973.1|FK998973
EST:     GGCTCGACGCTCCCGTCGATCCAGAGGGCCGGCCTCTTCCCTCCTTCCAG                         GTTGCATATAAAGTTTGGTCGGAGTCTTTTGGCATGTACCCTCTACCTATG
genomic: GGCTCGACGCTCCCGTCGATCCAGAGGGCCGGCCTCTTCCCTCCTTCCAGgttcgcgatg ... ctgttttcagGTTGCATATAAAGTTTGGTCGGAGTCTTTTGGCATGTACCCTCTACCTATG

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), 49 (downstream exon)
Score: 185

CGCCGTTGCCGACGACTCCCTCTGGCGCAGATTCTGCGGTGAGGACCTGGGGCTCGACGCTCCCGTCGATCCAGAGGGCCGGCCTCTTCCCTCCTTCCAGgttcgcgatg ... ctgttttcagGTTGCATATAAAGTTTGGTCGGAGTCTTTTGGCATGTACCCTCTACCTATGGTAAAGAGAGTGAGACAATTCTGGACTTCAATGAAAACTTGGTTGTCTG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 129

CGCCGTTGCCGACGACTCCCTCTGGCGCAGATTCTGCGGTGAGGACCTGGGGCTCGACGCTCCCGTCGATCCAGAGGGCCGGCCTCTTCCCTCCTTCCAGgttcgcgatg ... ctgttttcagGTTGCATATAAAGTTTGGTCGGAGTCTTTTGGCATGTACCCTCTACCTATGGTAAAGAGAGTGAGACAATTCTGGACTTCAATGAAAACTTGGTTGTCTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 139

CGCCGTTGCCGACGACTCCCTCTGGCGCAGATTCTGCGGTGAGGACCTGGGGCTCGACGCTCCCGTCGATCCAGAGGGCCGGCCTCTTCCCTCCTTCCAGgttcgcgatg ... ctgttttcagGTTGCATATAAAGTTTGGTCGGAGTCTTTTGGCATGTACCCTCTACCTATGGTAAAGAGAGTGAGACAATTCTGGACTTCAATGAAAACTTGGTTGTCTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 146

CGCCGTTGCCGACGACTCCCTCTGGCGCAGATTCTGCGGTGAGGACCTGGGGCTCGACGCTCCCGTCGATCCAGAGGGCCGGCCTCTTCCCTCCTTCCAGgttcgcgatg ... ctgttttcagGTTGCATATAAAGTTTGGTCGGAGTCTTTTGGCATGTACCCTCTACCTATGGTAAAGAGAGTGAGACAATTCTGGACTTCAATGAAAACTTGGTTGTCTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctaaattccttgtaagtgttggttcgttatatcaaaattcattctgttttcagGTTGCATATAAAGTTTGGTCGGAGTCTTTTGGCATGTACCCTCTACCTATGGTAAAGAGAGTGAGACAATTCTGGACTTCAATGAAAACTTGGTTGTCTG
 ttctaaa  putative branch site (score: 146)
                                       ttcattctgttttc  putative PPT
                            ttatatcaaaattcat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacttcaaaaaagaacaagtgaagggaaatcatatggtgtacaattctaaattccttgtaagtgttggttcgttatatcaaaattcattctgttttcagGTTGCATATAAAGTTTGGTCGGAGTCTTTTGGCATGTACCCTCTACCTATGGTAAAGAGAGTGAGACAATTCTGGACTTCAATGAAAACTTGGTTGTCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - caaaaaa
- - - - - - -gaacaag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgttggt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -atcaaaa