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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgagcaaggcagtggtgcagtgttgattctgatatgcatatggacttgttggatttgaaaaaggactctgcattaaccatctctcgacacgctcaatcagGTTTACACCAATCTCAAAGGCAACCGAGCTCATGCAGCGAACACTGGTTGGGCCATGCTGGCGCTGATTGATGCAGGACAG

Basic information

species Zea mays
transcript GRMZM2G065494_T01
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G065494_T01 (Zea mays), 3'ss of exon 15
lower sequence: LOC_Os02g04710.1 (Oryza sativa), 3'ss of exon 15
tgagcaaggca-gtggtgcagtgttgattctgatatgcatatggacttgttggatttgaaaaaggactctgcattaaccatctctcgacacgc--tcaatcagGTTTACACCAATCTCAAAGGCAACCGAGCTCATGCAGCGAACACTGGTTGGGCCATGCTGGCGCTGATTGATGCAGGACAG
    ||   |  |   | | || |||||   |   || ||     |||  |  |            || ||| |||||||||||  | |  |   ||||  ||||||| ||||||||| |||| || ||| ||||||| | ||||||||||||||||||||| || || || |||||||| |||
---acagcacttgaaatactgtattgatcaggtattgtattgattcttaatttacacaggtttcatctttgctttaaccatctcgtggcttgttttcaaatagGTTTATACCAATCTCGAAGGGAAGCGACCTCATGCGGTGAACACTGGTTGGGCCATGCTAGCCCTAATCGATGCAGGGCAG
















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|60400796|gb|DN233603.1|DN233603
EST:     AGCTTCCTTCCGGTGGCTGGGGAGAAAGCTATTTATCGTCTCAAGACCAG                         GTTTACACCAATCTCAAAGGCAACCGAGCTCATGCAGCGAACACTGGTTGG
genomic: AGCTTCCTTCCGGTGGCTGGGGAGAAAGCTATTTATCGTCTCAAGACCAGgtaaatccac ... gctcaatcagGTTTACACCAATCTCAAAGGCAACCGAGCTCATGCAGCGAACACTGGTTGG
EST: gi|32838148|gb|CD977826.1|CD977826
EST:     AGCTTCCTTCCGGTGGCTGGGGAGAAAGCTATTTATCGTCTCAAGACCAG                         GTTTACACCAATCTCAAAGGCAACCGAGCTCATGCAGCGAACACTGGTTGG
genomic: AGCTTCCTTCCGGTGGCTGGGGAGAAAGCTATTTATCGTCTCAAGACCAGgtaaatccac ... gctcaatcagGTTTACACCAATCTCAAAGGCAACCGAGCTCATGCAGCGAACACTGGTTGG
EST: gi|17352566|gb|BM173680.1|BM173680
EST:     AGCTTCCTTCCGGTGGCTGGGGAGAAAGCTATTTATCGTCTCAAGACCAG                         GTTTACACCAATCTCAAAGGCAACCGAGCTCATGCAGCGAACACTGGTTGG
genomic: AGCTTCCTTCCGGTGGCTGGGGAGAAAGCTATTTATCGTCTCAAGACCAGgtaaatccac ... gctcaatcagGTTTACACCAATCTCAAAGGCAACCGAGCTCATGCAGCGAACACTGGTTGG
EST: gi|32839382|gb|CD979063.1|CD979063
EST:     AGCTTCCTTCCGGTGGCTGGGGAGAAAGCTATTTATCGTCTCAAGACCAG                         GTTTACACCAATCTCAAAGGCAACCGAGCTCATGCAGCGAACACTGGTTGG
genomic: AGCTTCCTTCCGGTGGCTGGGGAGAAAGCTATTTATCGTCTCAAGACCAGgtaaatccac ... gctcaatcagGTTTACACCAATCTCAAAGGCAACCGAGCTCATGCAGCGAACACTGGTTGG
EST: gi|31357306|gb|CD441663.1|CD441663
EST:     AGCTTCCTTCCGGTGGCTGGGGAGAAAGCTATTTATCGTCTCAAGACCAG                         GTTTACACCAATCTCAAAGGCAACCGAGCTCATGCAGCGAACACTGGTTGG
genomic: AGCTTCCTTCCGGTGGCTGGGGAGAAAGCTATTTATCGTCTCAAGACCAGgtaaatccac ... gctcaatcagGTTTACACCAATCTCAAAGGCAACCGAGCTCATGCAGCGAACACTGGTTGG
EST: gi|18179995|gb|BM381205.1|BM381205
EST:     AGCTTCCTTCCGGTGGCTGGGGAGAAAGCTATTTATCGTCTCAAGACCAG                         GTTTACACCAATCTCAAAGGCAACCGAGCTCATGCAGCGAACACTGGTTGG
genomic: AGCTTCCTTCCGGTGGCTGGGGAGAAAGCTATTTATCGTCTCAAGACCAGgtaaatccac ... gctcaatcagGTTTACACCAATCTCAAAGGCAACCGAGCTCATGCAGCGAACACTGGTTGG
EST: gi|31357419|gb|CD441776.1|CD441776
EST:     AGCTTCCTTCCGGTGGCTGGGGAGAAAGCTATTTATCGTCTCAAGACCAG                         GTTTACACCAATCTCAAAGGCAACCGAGCTCATGCAGCGAACACTGGTTGG
genomic: AGCTTCCTTCCGGTGGCTGGGGAGAAAGCTATTTATCGTCTCAAGACCAGgtaaatccac ... gctcaatcagGTTTACACCAATCTCAAAGGCAACCGAGCTCATGCAGCGAACACTGGTTGG
EST: gi|33094833|gb|CF054827.1|CF054827
EST:     AGCTTCCTTCCGGTGGCTGGGGAGAAAGCTATTTATCGTCTCAAGGCCAG                         GTTTACACCAATCTCAAAGGCAACCGAGCTCATGCAGCGAACACTGGTTGG
genomic: AGCTTCCTTCCGGTGGCTGGGGAGAAAGCTATTTATCGTCTCAAGACCAGgtaaatccac ... gctcaatcagGTTTACACCAATCTCAAAGGCAACCGAGCTCATGCAGCGAACACTGGTTGG
EST: gi|149084840|gb|EE174345.2|EE174345
EST:     AGCTTCCTTCCGGTGGCTGGGGAGAAAGCTATTTATCGTCTCAAGACCAG                         GTTTACACCAATCTCAAAGGCAACCGAGCTCATGCAGCGAACACTGGTTGG
genomic: AGCTTCCTTCCGGTGGCTGGGGAGAAAGCTATTTATCGTCTCAAGACCAGgtaaatccac ... gctcaatcagGTTTACACCAATCTCAAAGGCAACCGAGCTCATGCAGCGAACACTGGTTGG
EST: gi|211125929|gb|FL443336.1|FL443336
EST:     TCCTTCCGGTGGCTGGGGAGAAAGCTATTTATCGTCTCAAGACCAG                         GTTTACACCAATCTCAAAGGCAACCGAGCTCATGCAGCGAACACTGGTTGG
genomic: TCCTTCCGGTGGCTGGGGAGAAAGCTATTTATCGTCTCAAGACCAGgtaaatccac ... gctcaatcagGTTTACACCAATCTCAAAGGCAACCGAGCTCATGCAGCGAACACTGGTTGG
EST: gi|12967988|gb|BG264935.1|BG264935
EST:     AGCTTCCTTCCGGTGGCTGGGGAGAAAGCTATTTATCGTCTCAAGACCAG                         GTTTACACCAATCTCAAAGGCAACCGAGCTCATGCAGCGAACACTGGTTGG
genomic: AGCTTCCTTCCGGTGGCTGGGGAGAAAGCTATTTATCGTCTCAAGACCAGgtaaatccac ... gctcaatcagGTTTACACCAATCTCAAAGGCAACCGAGCTCATGCAGCGAACACTGGTTGG

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), 48 (downstream exon)
Score: 199

TGAGAGCAGTCCTGCAATCAGAAAGGCATGCGGCTTTCTGTTATCAAAAGAGCTTCCTTCCGGTGGCTGGGGAGAAAGCTATTTATCGTCTCAAGACCAGgtaaatccac ... gctcaatcagGTTTACACCAATCTCAAAGGCAACCGAGCTCATGCAGCGAACACTGGTTGGGCCATGCTGGCGCTGATTGATGCAGGACAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 147

TGAGAGCAGTCCTGCAATCAGAAAGGCATGCGGCTTTCTGTTATCAAAAGAGCTTCCTTCCGGTGGCTGGGGAGAAAGCTATTTATCGTCTCAAGACCAGgtaaatccac ... gctcaatcagGTTTACACCAATCTCAAAGGCAACCGAGCTCATGCAGCGAACACTGGTTGGGCCATGCTGGCGCTGATTGATGCAGGACAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 105

TGAGAGCAGTCCTGCAATCAGAAAGGCATGCGGCTTTCTGTTATCAAAAGAGCTTCCTTCCGGTGGCTGGGGAGAAAGCTATTTATCGTCTCAAGACCAGgtaaatccac ... gctcaatcagGTTTACACCAATCTCAAAGGCAACCGAGCTCATGCAGCGAACACTGGTTGGGCCATGCTGGCGCTGATTGATGCAGGACAG


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

TGAGAGCAGTCCTGCAATCAGAAAGGCATGCGGCTTTCTGTTATCAAAAGAGCTTCCTTCCGGTGGCTGGGGAGAAAGCTATTTATCGTCTCAAGACCAGgtaaatccac ... gctcaatcagGTTTACACCAATCTCAAAGGCAACCGAGCTCATGCAGCGAACACTGGTTGGGCCATGCTGGCGCTGATTGATGCAGGACAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgttggatttgaaaaaggactctgcattaaccatctctcgacacgctcaatcagGTTTACACCAATCTCAAAGGCAACCGAGCTCATGCAGCGAACACTGGTTGGGCCATGCTGGCGCTGATTGATGCAGGACAG
                         cattaac  putative branch site (score: 161)
       atttgaaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgagcaaggcagtggtgcagtgttgattctgatatgcatatggacttgttggatttgaaaaaggactctgcattaaccatctctcgacacgctcaatcagGTTTACACCAATCTCAAAGGCAACCGAGCTCATGCAGCGAACACTGGTTGGGCCATGCTGGCGCTGATTGATGCAGGACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - -ggtgcag
- - - - - - - - - - tgttgat
- - - - - - - - - - - - - - - - -atgcata
- - - - - - - - - - - - - - - - - - - - - - cttgttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - gaaaaagg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgcatt