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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttaatgcataagcctaccttacagagctctgttaaacataaactatattaatgtctgttgataatacacaagcataacctcatattttctgtatttttagATGACACCAAATGGGATGCAAGATTCTTCTTCCAAAGGAAGAAATGGAACAGGATTCCTTCATGGAGCTCGTGTTGGCATTGTGGCTAAACCCTCTCCTG

Basic information

species Zea mays
transcript GRMZM2G460078_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G460078_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os01g55590.1 (Oryza sativa), 3'ss of exon 2
-------------------------------------------------------ttaatgcataagcctaccttacagagctctgttaaacataaactatattaatgtctgttgataatacacaagcataacctcatattttctgtatttttagATGACACCAAATGGGATGCAAGATTCTTCTTCCAAAGGAAGAAATGGAACAGGATTCCTTCATGGAGCTCGTGTTGGCATTGTGGCTAAACCCTCTCCTG
                                                        |  |   | |   ||   |    | | |  |   |  | |||   || |||| |||||||| || |   | ||   | || |  | | | |  || ||||||||||  ||||| |    || ||| |||  |||||||| ||||||||| |||||||||  |||||||||| ||||||| ||||||||||| |||||||
gtaccaccgctctccttctctgtatgttgttttatcttcgttcacttgagatttcctgttatgtgattataatatgtttatcacgatcttatcttaacctgatcaatggctgttgatgatgcctgatcacctcttc-tgctgttttt-cttgtagATGACACAGAATGGAAGTACAGGTTCATCTGTCAAAGGAATAAATGGAACTGGATTCCTTGGTGGAGCTCGTATTGGCATAGTGGCTAAACCTTCTCCTG
















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|78111750|gb|DV530147.1|DV530147
EST:     AGCTCATTGCAGCCTCTTTTGATGTCTACAACATTTTGTGCAGCAAAAAT                         ATGACACCAAATGGGATGCAAGATTCTTCTTCCAAAGGAAGAAATGGAACA
genomic: AGCTCATTGCAGCCTCTTTTGATGTCTACAACATTTTGTGCAGCAAAAATgtacggcagc ... gtatttttagATGACACCAAATGGGATGCAAGATTCTTCTTCCAAAGGAAGAAATGGAACA
EST: gi|91049611|gb|EB160029.1|EB160029
EST:     AGCTCATTGCAGCCTCTTTTGATGTCTACAACATTTTGTGCAGCAAAAAT                         ATGACACCAAATGGGATGCAAGATTCTTCTTCCAAAGGAAGAAATGGAACA
genomic: AGCTCATTGCAGCCTCTTTTGATGTCTACAACATTTTGTGCAGCAAAAATgtacggcagc ... gtatttttagATGACACCAAATGGGATGCAAGATTCTTCTTCCAAAGGAAGAAATGGAACA
EST: gi|211025828|gb|FK982703.1|FK982703
EST:     AGCTCATTGCAGCCTCTTTTGATGTCTACAACATTTTGTGCAGCAAAAAT                         ATGACACCAAATGGGATGCAAGATTCTTCTTCCAAAGGAAGAAATGGAACA
genomic: AGCTCATTGCAGCCTCTTTTGATGTCTACAACATTTTGTGCAGCAAAAATgtacggcagc ... gtatttttagATGACACCAAATGGGATGCAAGATTCTTCTTCCAAAGGAAGAAATGGAACA
EST: gi|211025826|gb|FK982701.1|FK982701
EST:     AGCTCATTGCAGCCTCTTTTGATGTCTACAACATTTTGTGCAGCAAAAAT                         ATGACACCAAATGGGATGCAAGATTCTTCTTCCAAAGGAAGAAATGGAACA
genomic: AGCTCATTGCAGCCTCTTTTGATGTCTACAACATTTTGTGCAGCAAAAATgtacggcagc ... gtatttttagATGACACCAAATGGGATGCAAGATTCTTCTTCCAAAGGAAGAAATGGAACA
EST: gi|211025831|gb|FK982706.1|FK982706
EST:     AGCTCATTGCAGCCTCTTTTGATGTCTACAACATTTTGTGCAGCAAAAAT                         ATGACACCAAATGGGATGCAAGATTCTTCTTCCAAAGGAAGAAATGGAACA
genomic: AGCTCATTGCAGCCTCTTTTGATGTCTACAACATTTTGTGCAGCAAAAATgtacggcagc ... gtatttttagATGACACCAAATGGGATGCAAGATTCTTCTTCCAAAGGAAGAAATGGAACA
EST: gi|71434528|gb|DR815578.1|DR815578
EST:     AGCTCATTGCAGCCTCTTTTGATGTCTACAACATTTTGTGCAGCAAAAAT                         ATGACACCAAATGGGATGCAAGATTCTTCTTCCAAAGGAAGAAATGGAACA
genomic: AGCTCATTGCAGCCTCTTTTGATGTCTACAACATTTTGTGCAGCAAAAATgtacggcagc ... gtatttttagATGACACCAAATGGGATGCAAGATTCTTCTTCCAAAGGAAGAAATGGAACA
EST: gi|71332183|gb|DR803010.1|DR803010
EST:     AGCTCATTGCAGCCTCTTTTGATGTCTACAACATTTTGTGCAGCAAAAAT                         ATGACACCAAATGGGATGCAAGATTCTTCTTCCAAAGGAAGAAATGGAACA
genomic: AGCTCATTGCAGCCTCTTTTGATGTCTACAACATTTTGTGCAGCAAAAATgtacggcagc ... gtatttttagATGACACCAAATGGGATGCAAGATTCTTCTTCCAAAGGAAGAAATGGAACA
EST: gi|211025829|gb|FK982704.1|FK982704
EST:     AGCTCATTGCAGCCTCTTTTGATGTCTACAACATTTTGTGCAGCAAAAAT                         ATGACACCAAATGGGATGCAAGATTCTTCTTCCAAAGGAAG
genomic: AGCTCATTGCAGCCTCTTTTGATGTCTACAACATTTTGTGCAGCAAAAATgtacggcagc ... gtatttttagATGACACCAAATGGGATGCAAGATTCTTCTTCCAAAGGAAG
EST: gi|93012882|gb|EB638402.1|EB638402
EST:     AGCTCATTGCAGCCTCTTTTGATGTCTACAACATTTTGTGCAGCAAAAAT                         ATGACACCAAATGGGATGCAAGATTCTTCTTCCAAAGGAAGAAATGGAACA
genomic: AGCTCATTGCAGCCTCTTTTGATGTCTACAACATTTTGTGCAGCAAAAATgtacggcagc ... gtatttttagATGACACCAAATGGGATGCAAGATTCTTCTTCCAAAGGAAGAAATGGAACA
EST: gi|148961982|gb|EE012780.2|EE012780
EST:     AGCTCATTGCAGCCTCTTTTGATGTCTACAACATTTTGTGCAGCAAAAAT                         ATGACACCAAATGGGATGCAAGATTCTTCTTCCAAAGGAAGAAATGGAACA
genomic: AGCTCATTGCAGCCTCTTTTGATGTCTACAACATTTTGTGCAGCAAAAATgtacggcagc ... gtatttttagATGACACCAAATGGGATGCAAGATTCTTCTTCCAAAGGAAGAAATGGAACA
EST: gi|211025830|gb|FK982705.1|FK982705
EST:     AGCTCATTGCAGCCTCTTTTGATGTCTACAACATTTTRTGCAGCAAAAAT                         ATGACACCAAATGGGATGCAAGATTCTTCTTCCAAAGGAAGAAATGGAACA
genomic: AGCTCATTGCAGCCTCTTTTGATGTCTACAACATTTTGTGCAGCAAAAATgtacggcagc ... gtatttttagATGACACCAAATGGGATGCAAGATTCTTCTTCCAAAGGAAGAAATGGAACA
EST: gi|76925597|gb|DV170498.1|DV170498
EST:     AGCTCATTGCAGCCTCTTTTGATGTCTACAACATTTTGTGCAGCAAAAAT                         ATGACACCAAATGGGATGCAAGATTCTTCTTCCAAAGGAAGAAATGGAACA
genomic: AGCTCATTGCAGCCTCTTTTGATGTCTACAACATTTTGTGCAGCAAAAATgtacggcagc ... gtatttttagATGACACCAAATGGGATGCAAGATTCTTCTTCCAAAGGAAGAAATGGAACA

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: 46 (upstream exon), 49 (downstream exon)
Score: 104

TAGTGTCCGTGCTGTCATAAGAGCTAACAAAAAGAGCTACAGCCTTGTCCAGCTCATTGCAGCCTCTTTTGATGTCTACAACATTTTGTGCAGCAAAAATgtacggcagc ... gtatttttagATGACACCAAATGGGATGCAAGATTCTTCTTCCAAAGGAAGAAATGGAACAGGATTCCTTCATGGAGCTCGTGTTGGCATTGTGGCTAAACCCTCTCCTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 117

TAGTGTCCGTGCTGTCATAAGAGCTAACAAAAAGAGCTACAGCCTTGTCCAGCTCATTGCAGCCTCTTTTGATGTCTACAACATTTTGTGCAGCAAAAATgtacggcagc ... gtatttttagATGACACCAAATGGGATGCAAGATTCTTCTTCCAAAGGAAGAAATGGAACAGGATTCCTTCATGGAGCTCGTGTTGGCATTGTGGCTAAACCCTCTCCTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 89

TAGTGTCCGTGCTGTCATAAGAGCTAACAAAAAGAGCTACAGCCTTGTCCAGCTCATTGCAGCCTCTTTTGATGTCTACAACATTTTGTGCAGCAAAAATgtacggcagc ... gtatttttagATGACACCAAATGGGATGCAAGATTCTTCTTCCAAAGGAAGAAATGGAACAGGATTCCTTCATGGAGCTCGTGTTGGCATTGTGGCTAAACCCTCTCCTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 428

TAGTGTCCGTGCTGTCATAAGAGCTAACAAAAAGAGCTACAGCCTTGTCCAGCTCATTGCAGCCTCTTTTGATGTCTACAACATTTTGTGCAGCAAAAATgtacggcagc ... gtatttttagATGACACCAAATGGGATGCAAGATTCTTCTTCCAAAGGAAGAAATGGAACAGGATTCCTTCATGGAGCTCGTGTTGGCATTGTGGCTAAACCCTCTCCTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattaatgtctgttgataatacacaagcataacctcatattttctgtatttttagATGACACCAAATGGGATGCAAGATTCTTCTTCCAAAGGAAGAAATGGAACAGGATTCCTTCATGGAGCTCGTGTTGGCATTGTGGCTAAACCCTCTCCTG
                                       ttttctgtattttt  CT-rich tract
                                    atattttctgtatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttaatgcataagcctaccttacagagctctgttaaacataaactatattaatgtctgttgataatacacaagcataacctcatattttctgtatttttagATGACACCAAATGGGATGCAAGATTCTTCTTCCAAAGGAAGAAATGGAACAGGATTCCTTCATGGAGCTCGTGTTGGCATTGTGGCTAAACCCTCTCCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT