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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgctgcaccatgcctgcccttcacattccttgataaataaagtaataaaatgtttaatttctctgaatttgttcccatgtatgtgtttttctttttgcagCAATTTGAGTGGTTAGTTGGGATGCAATACAAGCCAATGGAGCTGTCAAAGTCAGATTGGGCTTCAATTAGAAAATCACCTCCGTGGGCCATTGATTCTT

Basic information

species Zea mays
transcript GRMZM2G098078_T04
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G098078_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os01g60440.1 (Oryza sativa), 3'ss of exon 5
---tgctgcaccatgcctgcccttcacattccttgataaataaagtaataaaatgtttaatttctctgaatttgttcccatgtatgtgtttttctttttgcagCAATTTGAGTGGTTAGTTGGGATGCAATACAAGCCAATGGAGCTGTCAAAGTCAGATTGGGCTTCAATTAGAAAATCACCTCCGTGGGCCATTGATTCTT
         |  ||   | | ||| |   ||   || |   ||  | ||| |  |    || |  |   | || ||   |  ||  | | || ||||  |||||||||||| ||||||||||| |  ||||| ||||||||||||||  |||||||||||||||  |||||||| ||||||||||| ||||| |||||||| |
tagaaagtaagaattggtactctttaatatcagggaaattcaacatgatagagggagatatatacc-atacttctttttacatacttatgttccttt--gcagCAATTTGAATGGTTAGTTGGAACACAATATAAGCCAATGGAGCTAACAAAGTCAGATTGGGTGTCAATTAGGAAATCACCTCCATGGGCAATTGATTCCT

upper sequence: GRMZM2G098078_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA20G36180.1 (Glycine max), 3'ss of exon 5
tgctgcaccatg-cctgcccttcacattccttgataaataaagtaataaaatgtttaatttctctgaatttgttcccatgtatgtgtttttctttttgcagCAATTTGAGTGGTTAGTTGGGATGCAATACAAGCCAATGGAGCTGTCAAAGTCAGATTGGGCTTCAATTAGAAAATCACCTCCGTGGGCCATTGATTCTT
  |    | | |   ||     ||  ||  ||| |  | ||| ||| || |  || || |  |   |  |  |    ||   |    | || | | | ||||||| ||  ||| | |||||    |||||||| |||||||| ||| |||| || || |||||| ||||||  || || ||||| ||||||||||||||||
gaccttgcaaggatttgtgaggcatttttattgttttaaaaaataaaaaga-attcaagtagtgaaacctaatatatattcctcacatgttttctattcagCAATATGCTTGGCTTGTTGGATCACAATACAAACCAATGGAACTGGCAAAATCTGACTGGGCTGCAATTAAGAAGTCTCCTCCATGGGCCATTGATTCTT

upper sequence: GRMZM2G098078_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA09G38740.1 (Glycine max), 3'ss of exon 5
tgctgcaccatgcctgcccttcacattccttgataaataaagtaataaaatgtttaatttctctgaatttgttcccat--gtatgtgtttttctttttgcagCAATTTGAGTGGTTAGTTGGGATGCAATACAAGCCAATGGAGCTGTCAAAGTCAGATTGGGCTTCAATTAGAAAATCACCTCCGTGGGCCATTGATTCTT
  |      |||  |     |    ||| ||  |  | ||   |  | |  |  ||      |  || |||| | ||   || |   |  ||| | || ||||||| ||  ||| | |||||    |||||||| ||||||||| || |||| ||||| |||| | ||||||  || || ||||| ||||||||||||||||
-cccttgtaatgatttgatctgggcttctttattttaaaataaaggatatggaatagggaaaccaaaattgtcctcacaagttttcatgcttcctgtt-cagCAATATGCATGGCTTGTTGGATCACAATACAAACCAATGGAGTTGGCAAAATCAGACTGGGATGCAATTAAGAAGTCTCCTCCATGGGCCATTGATTCTT

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|211086448|gb|FL450103.1|FL450103
EST:     TTCTGTCAGAATTTGATGCTAACAATGAAGCCTCTGGTAGCCCCATGCTG                         CAATTTGAGTGGTTAGTTGGGATGCAA
genomic: TTCTGTCAGAATTTGATGCTAACAATGAAGCCTCTGGTAGCCCCATGCTGgtaaggactt ... ctttttgcagCAATTTGAGTGGTTAGTTGGGATGCAA
EST: gi|76289771|gb|DV029339.1|DV029339
EST:     TTCTGTCAGAATTTGATGCTAACAATGAAGCCTCTGGTAGCCCCATGCTG                         CAATTTGAGTGGTTAGTTGGGATGCAATACAAGCCAATGGAGCTGTCAAAG
genomic: TTCTGTCAGAATTTGATGCTAACAATGAAGCCTCTGGTAGCCCCATGCTGgtaaggactt ... ctttttgcagCAATTTGAGTGGTTAGTTGGGATGCAATACAAGCCAATGGAGCTGTCAAAG
EST: gi|211352110|gb|FL449964.1|FL449964
EST:     TTCTGTCAGAATTTGATGCTAACAATGAAGCCTCTGGTAGCCCCATGCTG                         CAATTTGAGTGGTTAGTCGGGAT
genomic: TTCTGTCAGAATTTGATGCTAACAATGAAGCCTCTGGTAGCCCCATGCTGgtaaggactt ... ctttttgcagCAATTTGAGTGGTTAGTTGGGAT

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: 101

CAGTGTTGTTGTTACACAAACCCTGGATTGGAAGCTTCATGCCTTCGATGTTCTGTCAGAATTTGATGCTAACAATGAAGCCTCTGGTAGCCCCATGCTGgtaaggactt ... ctttttgcagCAATTTGAGTGGTTAGTTGGGATGCAATACAAGCCAATGGAGCTGTCAAAGTCAGATTGGGCTTCAATTAGAAAATCACCTCCGTGGGCCATTGATTCTT


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 87

CAGTGTTGTTGTTACACAAACCCTGGATTGGAAGCTTCATGCCTTCGATGTTCTGTCAGAATTTGATGCTAACAATGAAGCCTCTGGTAGCCCCATGCTGgtaaggactt ... ctttttgcagCAATTTGAGTGGTTAGTTGGGATGCAATACAAGCCAATGGAGCTGTCAAAGTCAGATTGGGCTTCAATTAGAAAATCACCTCCGTGGGCCATTGATTCTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 82

CAGTGTTGTTGTTACACAAACCCTGGATTGGAAGCTTCATGCCTTCGATGTTCTGTCAGAATTTGATGCTAACAATGAAGCCTCTGGTAGCCCCATGCTGgtaaggactt ... ctttttgcagCAATTTGAGTGGTTAGTTGGGATGCAATACAAGCCAATGGAGCTGTCAAAGTCAGATTGGGCTTCAATTAGAAAATCACCTCCGTGGGCCATTGATTCTT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 126

CAGTGTTGTTGTTACACAAACCCTGGATTGGAAGCTTCATGCCTTCGATGTTCTGTCAGAATTTGATGCTAACAATGAAGCCTCTGGTAGCCCCATGCTGgtaaggactt ... ctttttgcagCAATTTGAGTGGTTAGTTGGGATGCAATACAAGCCAATGGAGCTGTCAAAGTCAGATTGGGCTTCAATTAGAAAATCACCTCCGTGGGCCATTGATTCTT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taaaatgtttaatttctctgaatttgttcccatgtatgtgtttttctttttgcagCAATTTGAGTGGTTAGTTGGGATGCAATACAAGCCAATGGAGCTGTCAAAGTCAGATTGGGCTTCAATTAGAAAATCACCTCCGTGGGCCATTGATTCTT
      gtttaat  putative branch site (score: 126)
                                    tgtgtttttcttttt  putative PPT
                                        tttttcttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgctgcaccatgcctgcccttcacattccttgataaataaagtaataaaatgtttaatttctctgaatttgttcccatgtatgtgtttttctttttgcagCAATTTGAGTGGTTAGTTGGGATGCAATACAAGCCAATGGAGCTGTCAAAGTCAGATTGGGCTTCAATTAGAAAATCACCTCCGTGGGCCATTGATTCTT

tgctgca
- - - - - tgcctgc
- - - - - - - - - - -cacattc
- - - - - - - - - - - - - - - - - aaataaa
- - - - - - - - - - - - - - - - - - - - - -aataaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - atgtatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgttttt