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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgggtgtttgcttaccatagatttccaatattccaagcattctataatgttatattcaaattacttttaatgctccagTCAATCAATAAAAGCTTGTCGGCTTTGAGCGATGTAATCTTCGCGATCGCAAAAGGAGATGACCACGTTCCGTTCAGAAATTCAAAACTTACATACCTAT

Basic information

species Zea mays
transcript GRMZM2G114861_T01
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G114861_T01 (Zea mays), 3'ss of exon 14
lower sequence: LOC_Os04g53760.1 (Oryza sativa), 3'ss of exon 14
gtgggtgtttgcttaccatagatttccaatattccaagcattctataatgttatat--tcaaattactt--ttaatgctccagTCAATCAATAAAAGCTTGTCGGCTTTGAGCGATGTAATCTTCGCGATCGCAAAAGGAGATGACCACGTTCCGTTCAGAAATTCAAAACTTACATACCTAT
||| ||||  | | | || | |||| ||||||||  |       || |  || | |  ||   ||  ||  || ||| | ||| ||||||||||||||||||| ||| | |||||||| ||||| || || || |||||||| || || || || ||||| || ||||||||||||||||| |
gtgagtgt--gttcatcacaaatttacaatattcttatttgataatcacattgtcttatctgtttgttttctttatgtttcagGCAATCAATAAAAGCTTGTCAGCTCTTAGCGATGTTATCTTTGCAATTGCGAAAGGAGACGATCATGTGCCCTTCAGGAACTCAAAACTTACATACCTTT
















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|211045020|gb|FL382451.1|FL382451
EST:     AGCGTCTTGCTAAAAGTGGCTCCACAGGTGATCGCTTGAAGGAAACTCAG                         TCAATCAATAAAAGCTTGTCGGCTTTGAGCGATGTAATCTTCGCGATCGCA
genomic: AGCGTCTTGCTAAAAGTGGCTCCACAGGTGATCGCTTGAAGGAAACTCAGgtgggtgttt ... aatgctccagTCAATCAATAAAAGCTTGTCGGCTTTGAGCGATGTAATCTTCGCGATCGCA
EST: gi|71757388|gb|DR955325.1|DR955325
EST:     AGCGTCTTGCTAAAAGTGGCTCCACAGGTGATCGCTTGAAGGAAACTCAG                         TCAATCAATAAAAGCTTGTCGGCTTTGAGCGATGTAATCTTCGCGATCGCA
genomic: AGCGTCTTGCTAAAAGTGGCTCCACAGGTGATCGCTTGAAGGAAACTCAGgtgggtgttt ... aatgctccagTCAATCAATAAAAGCTTGTCGGCTTTGAGCGATGTAATCTTCGCGATCGCA
EST: gi|14244176|gb|BG841853.2|BG841853
EST:     AGCGTCTTGCTAAAAGTGGCTCCACAGGTGATCGCTTGAAGGAAACTCAG                         TCAATCAATAAAAGCTTGTCGGCTTTGAGCGATGTAATCTTCGCGATCGCA
genomic: AGCGTCTTGCTAAAAGTGGCTCCACAGGTGATCGCTTGAAGGAAACTCAGgtgggtgttt ... aatgctccagTCAATCAATAAAAGCTTGTCGGCTTTGAGCGATGTAATCTTCGCGATCGCA
EST: gi|32945905|gb|CF050724.1|CF050724
EST:     AGCGTCTTGCTAAAAGTGGCTCCACAGGTGATCGCTTGAAGGAAACTCAG                         TCAATCAATAAAAGCTTGTCGGCTTTGAGCGATGTAATCTTCGCGATCGCA
genomic: AGCGTCTTGCTAAAAGTGGCTCCACAGGTGATCGCTTGAAGGAAACTCAGgtgggtgttt ... aatgctccagTCAATCAATAAAAGCTTGTCGGCTTTGAGCGATGTAATCTTCGCGATCGCA
EST: gi|4646866|gb|AI621941.1|AI621941
EST:     AGGTGATCGCTTGAAGGAAACTCAG                         TCAATCAATAAAAGCTTGTCGGCTTTGAGCGATGTAATCTTGGCGATCGCA
genomic: AGGTGATCGCTTGAAGGAAACTCAGgtgggtgttt ... aatgctccagTCAATCAATAAAAGCTTGTCGGCTTTGAGCGATGTAATCTTCGCGATCGCA
EST: gi|18167051|gb|BM336890.1|BM336890
EST:     AGCGTCTTGCTAAAAGTGGCTCCACAGGTGATCGCTTGAAGGAAACTCAG                         TCATTTTTTAAAAGCTTGTCGGCTTTGAGCGATGTAATCTTCGCGATCGCA
genomic: AGCGTCTTGCTAAAAGTGGCTCCACAGGTGATCGCTTGAAGGAAACTCAGgtgggtgttt ... aatgctccagTCAATCAATAAAAGCTTGTCGGCTTTGAGCGATGTAATCTTCGCGATCGCA
EST: gi|18167204|gb|BM337043.1|BM337043
EST:     AGCGTCTTGCTAAAAGTGGCTCCACAGGTGATCGCTTGAAGGAAACTCAT                         TCAATCAATAAAAGCTTGTCGGCTTTGAGCGATGTAATCTTCGCGATCGCA
genomic: AGCGTCTTGCTAAAAGTGGCTCCACAGGTGATCGCTTGAAGGAAACTCAGgtgggtgttt ... aatgctccagTCAATCAATAAAAGCTTGTCGGCTTTGAGCGATGTAATCTTCGCGATCGCA
EST: gi|5607865|gb|AI901532.1|AI901532
EST:     AGCGTCTTGCTAAAAGTGGTTCCNCAGGTGATCGCTTGAAGGAAACTCAG                         TCAATCAATAAAAGCTTGTCGGCTTTGAGCGATGTAATCTTCGCGATCGCA
genomic: AGCGTCTTGCTAAAAGTGGCTCCACAGGTGATCGCTTGAAGGAAACTCAGgtgggtgttt ... aatgctccagTCAATCAATAAAAGCTTGTCGGCTTTGAGCGATGTAATCTTCGCGATCGCA
EST: gi|211207046|gb|FL397891.1|FL397891
EST:     AGCGTCTTGCTAAAAGTGGCTCCACAGGTGATCGCTTGAAGGAAACTCAG                         TCAATCAATAAAAGCTTGTCGGCTTTGAGCGATGTAATCTTCGCGATCGCA
genomic: AGCGTCTTGCTAAAAGTGGCTCCACAGGTGATCGCTTGAAGGAAACTCAGgtgggtgttt ... aatgctccagTCAATCAATAAAAGCTTGTCGGCTTTGAGCGATGTAATCTTCGCGATCGCA
EST: gi|78085386|gb|DV513779.1|DV513779
EST:     AGCGTCTTGCTAAAAGTGGCTCCACAGGTGATCGCTTGAAGGAAACTCAG                         TCAATCAATAAAAGCTTGTCGGCTTTGAGCGATGTAATCTTCGCGATCGCA
genomic: AGCGTCTTGCTAAAAGTGGCTCCACAGGTGATCGCTTGAAGGAAACTCAGgtgggtgttt ... aatgctccagTCAATCAATAAAAGCTTGTCGGCTTTGAGCGATGTAATCTTCGCGATCGCA

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: 42 (upstream exon), 49 (downstream exon)
Score: 88

AGGCCAAAATGTCCAAGGAGTCCTTAACTTGATTGATTTAGCTGGGAGTGAGCGTCTTGCTAAAAGTGGCTCCACAGGTGATCGCTTGAAGGAAACTCAGgtgggtgttt ... aatgctccagTCAATCAATAAAAGCTTGTCGGCTTTGAGCGATGTAATCTTCGCGATCGCAAAAGGAGATGACCACGTTCCGTTCAGAAATTCAAAACTTACATACCTAT


Block sizes: 45 (upstream exon), 46 (downstream exon)
Score: 19

AGGCCAAAATGTCCAAGGAGTCCTTAACTTGATTGATTTAGCTGGGAGTGAGCGTCTTGCTAAAAGTGGCTCCACAGGTGATCGCTTGAAGGAAACTCAGgtgggtgttt ... aatgctccagTCAATCAATAAAAGCTTGTCGGCTTTGAGCGATGTAATCTTCGCGATCGCAAAAGGAGATGACCACGTTCCGTTCAGAAATTCAAAACTTACATACCTAT


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 28

AGGCCAAAATGTCCAAGGAGTCCTTAACTTGATTGATTTAGCTGGGAGTGAGCGTCTTGCTAAAAGTGGCTCCACAGGTGATCGCTTGAAGGAAACTCAGgtgggtgttt ... aatgctccagTCAATCAATAAAAGCTTGTCGGCTTTGAGCGATGTAATCTTCGCGATCGCAAAAGGAGATGACCACGTTCCGTTCAGAAATTCAAAACTTACATACCTAT


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 169

AGGCCAAAATGTCCAAGGAGTCCTTAACTTGATTGATTTAGCTGGGAGTGAGCGTCTTGCTAAAAGTGGCTCCACAGGTGATCGCTTGAAGGAAACTCAGgtgggtgttt ... aatgctccagTCAATCAATAAAAGCTTGTCGGCTTTGAGCGATGTAATCTTCGCGATCGCAAAAGGAGATGACCACGTTCCGTTCAGAAATTCAAAACTTACATACCTAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tccaatattccaagcattctataatgttatattcaaattacttttaatgctccagTCAATCAATAAAAGCTTGTCGGCTTTGAGCGATGTAATCTTCGCGATCGCAAAAGGAGATGACCACGTTCCGTTCAGAAATTCAAAACTTACATACCTAT
                                         ttttaat  putative branch site (score: 169)
               attctataatgttata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgggtgtttgcttaccatagatttccaatattccaagcattctataatgttatattcaaattacttttaatgctccagTCAATCAATAAAAGCTTGTCGGCTTTGAGCGATGTAATCTTCGCGATCGCAAAAGGAGATGACCACGTTCCGTTCAGAAATTCAAAACTTACATACCTAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG