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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttggcctgtgacccccctgttgtattctgtaattattactttgtttaatgagggacaatgacatatgtattcagagatctgatgttgactggtttttcggcagGTCGAGCATTTTTTGGGCATCAAACGAAGTGCCAAGCCTGGAAGCTTACCTCCTCCAGTCCCAAAGAAACCGAAGAACTGAACCTGGTGGTAGCACTCAG

Basic information

species Zea mays
transcript GRMZM2G109284_T01
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G109284_T01 (Zea mays), 3'ss of exon 12
lower sequence: LOC_Os02g30730.1 (Oryza sativa), 3'ss of exon 11
-------------------------------gttggcctgtgacccccctgttg--tattctgtaattattactttgttta-atgagggacaatgacatatgtattcagagatctgatgttgactggtttttcggcagGTCGAGCATTTTTTGGGCATCAAACGAAGTGCCAAGCCTGGAAGCTTACCTCCTCCAGTCCCAAAGAAACCGAAGAACTGAACCTGGTGGTAGCACTCAG--
                                ||      | |      |||||  | ||  |||||   ||   |||  | |||     |||      ||  |||||||   |||   ||| ||  | ||| ||||||||||||| ||| |||||||||||||||| ||| ||  |||| | || ||||| |||   |||||||| || ||||||||||||||   || | |||  |  
gtatggcattccctgttccattaagtaattactttatgaataaattatttgttgggtgttaggtaatgtataagctgtacatatgtaatccaacttaccat--attcagaatcctgtctttgcctt-tcttttggcagGTCGAGCACTTTCTGGGCATCAAACGAAGCGCCCAGGGTGGAGGATTGCCTCCACCACCTCCAAAGAAGCCAAAGAACTGAACCTG-CAGTGG-ACTTGGCT
















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|24768397|gb|CA403526.1|CA403526
EST:     TGGAGACAGAGCAACCTGGGAGCCTAACGCCCATGCTTGGGGACAAAAAG                         GTCGAGCATTTTTTGGGCATCAAACGAAGTGCCAAGCCTGGAAGCTTACCT
genomic: TGGAGACAGAGCAACCTGGGAGCCTAACGCCCATGCTTGGGGACAAAAAGgttggcctgt ... ttttcggcagGTCGAGCATTTTTTGGGCATCAAACGAAGTGCCAAGCCTGGAAGCTTACCT
EST: gi|32866127|gb|CF005809.1|CF005809
EST:     TGGAGACAGAGCAACCTGGGAGCCTAACGCCCATGCTTGGGGACAAAAAG                         GTCGAGCATTTTTTGGGCATCAAACGAAGTGCCAAGCCTGGAAGCTTACCT
genomic: TGGAGACAGAGCAACCTGGGAGCCTAACGCCCATGCTTGGGGACAAAAAGgttggcctgt ... ttttcggcagGTCGAGCATTTTTTGGGCATCAAACGAAGTGCCAAGCCTGGAAGCTTACCT
EST: gi|32858341|gb|CD998022.1|CD998022
EST:     TGGAGACAGAGCAACCTGGGAGCCTAACGCCCATGCTTGGGGACAAAAAG                         GTCGAGCATTTTTTGGGCATCAAACGAAGTGCCAAGCCTGGAAGCTTACCT
genomic: TGGAGACAGAGCAACCTGGGAGCCTAACGCCCATGCTTGGGGACAAAAAGgttggcctgt ... ttttcggcagGTCGAGCATTTTTTGGGCATCAAACGAAGTGCCAAGCCTGGAAGCTTACCT
EST: gi|32915382|gb|CF020194.1|CF020194
EST:     TGGAGACAGAGCAACCTGGGAGCCTAACGCCCATGCTTGGGGACAAAAAG                         GTCGAGCATTTTTTGGGCATCAAACGAAGTGCCAAGCCTGGAAGCTTACCT
genomic: TGGAGACAGAGCAACCTGGGAGCCTAACGCCCATGCTTGGGGACAAAAAGgttggcctgt ... ttttcggcagGTCGAGCATTTTTTGGGCATCAAACGAAGTGCCAAGCCTGGAAGCTTACCT
EST: gi|67015766|gb|CO444515.1|CO444515
EST:     TGGAGACAGAGCAACCTGGGAGCCTAACGCCCATGCTTGGGGACAAAAAG                         GTCGAGCATTTTTTGGGCATCAAACGAAGTGCCAAGCCTGGAAGCTTACCT
genomic: TGGAGACAGAGCAACCTGGGAGCCTAACGCCCATGCTTGGGGACAAAAAGgttggcctgt ... ttttcggcagGTCGAGCATTTTTTGGGCATCAAACGAAGTGCCAAGCCTGGAAGCTTACCT
EST: gi|40303475|gb|CK347862.1|CK347862
EST:     TGGAGACAGAGCAACCTGGGAGCCTAACGCCCATGCTTGGGGACAAAAAG                         GTCGAGCATTTTTTGGGCATCAAACGAAGTGCCAAGCCTGGAAGCTTACCT
genomic: TGGAGACAGAGCAACCTGGGAGCCTAACGCCCATGCTTGGGGACAAAAAGgttggcctgt ... ttttcggcagGTCGAGCATTTTTTGGGCATCAAACGAAGTGCCAAGCCTGGAAGCTTACCT
EST: gi|32907200|gb|CF012013.1|CF012013
EST:     TGGAGACAGAGCAACCTGGGAGCCTAACGCCCATGCTTGGGGACAAAAAG                         GTCGAGCATTTTTTGGGCATCAAACGAAGTGCCAAGCCTGGAAGCTTACCT
genomic: TGGAGACAGAGCAACCTGGGAGCCTAACGCCCATGCTTGGGGACAAAAAGgttggcctgt ... ttttcggcagGTCGAGCATTTTTTGGGCATCAAACGAAGTGCCAAGCCTGGAAGCTTACCT
EST: gi|32907199|gb|CF012012.1|CF012012
EST:     TGGAGACAGAGCAACCTGGGAGCCTAACGCCCATGCTTGGGGACAAAAAG                         GTCGAGCATTTTTTGGGCATCAAACGAAGTGCCAAGCCTGGAAGCTTACCT
genomic: TGGAGACAGAGCAACCTGGGAGCCTAACGCCCATGCTTGGGGACAAAAAGgttggcctgt ... ttttcggcagGTCGAGCATTTTTTGGGCATCAAACGAAGTGCCAAGCCTGGAAGCTTACCT
EST: gi|14245628|gb|BG874210.1|BG874210
EST:     TGGAGACAGAGCAACCTGGGAGCCTAACGCCCATGCTTGGGGACAAAAAG                         GTCGAGCATTTTTTGGGCATCAAACGAAGTGCCAAGCCTGGAAGCTTACCT
genomic: TGGAGACAGAGCAACCTGGGAGCCTAACGCCCATGCTTGGGGACAAAAAGgttggcctgt ... ttttcggcagGTCGAGCATTTTTTGGGCATCAAACGAAGTGCCAAGCCTGGAAGCTTACCT
EST: gi|5816421|gb|AI987337.1|AI987337
EST:     TGGAGACAGAGCAACCTGGGAGCCTAACGCCCATGCTTGGGGACAAAAAG                         GTCGAGCATTTTTTGGGCATCAAACGAAGTGCCAAGCCTGGAAGCTTACCT
genomic: TGGAGACAGAGCAACCTGGGAGCCTAACGCCCATGCTTGGGGACAAAAAGgttggcctgt ... ttttcggcagGTCGAGCATTTTTTGGGCATCAAACGAAGTGCCAAGCCTGGAAGCTTACCT
EST: gi|60337809|gb|DN204782.1|DN204782
EST:     TGGAGACAGAGCAACCTGGGAGCCTAACGCCCATGCTTGGGGACAAAAAG                         GTCGAGCATTTTTTGGGCATCAAACGAAGTGCCAAGCCTGGAAGCTTACCT
genomic: TGGAGACAGAGCAACCTGGGAGCCTAACGCCCATGCTTGGGGACAAAAAGgttggcctgt ... ttttcggcagGTCGAGCATTTTTTGGGCATCAAACGAAGTGCCAAGCCTGGAAGCTTACCT

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: 171

TCAAACAAGTGATAGCGGCGGCTATGCTACCTTGGAGACAGAGCAACCTGGGAGCCTAACGCCCATGCTTGGGGACAAAAAGgttggcctgt ... ttttcggcagGTCGAGCATTTTTTGGGCATCAAACGAAGTGCCAAGCCTGGAAGCTTACCTCCTCCAGTCCCAAAGAAACCGAAGAACTGAACCTGGTGGTAGCACTCAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 92

TCAAACAAGTGATAGCGGCGGCTATGCTACCTTGGAGACAGAGCAACCTGGGAGCCTAACGCCCATGCTTGGGGACAAAAAGgttggcctgt ... ttttcggcagGTCGAGCATTTTTTGGGCATCAAACGAAGTGCCAAGCCTGGAAGCTTACCTCCTCCAGTCCCAAAGAAACCGAAGAACTGAACCTGGTGGTAGCACTCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 159

TCAAACAAGTGATAGCGGCGGCTATGCTACCTTGGAGACAGAGCAACCTGGGAGCCTAACGCCCATGCTTGGGGACAAAAAGgttggcctgt ... ttttcggcagGTCGAGCATTTTTTGGGCATCAAACGAAGTGCCAAGCCTGGAAGCTTACCTCCTCCAGTCCCAAAGAAACCGAAGAACTGAACCTGGTGGTAGCACTCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 88

TCAAACAAGTGATAGCGGCGGCTATGCTACCTTGGAGACAGAGCAACCTGGGAGCCTAACGCCCATGCTTGGGGACAAAAAGgttggcctgt ... ttttcggcagGTCGAGCATTTTTTGGGCATCAAACGAAGTGCCAAGCCTGGAAGCTTACCTCCTCCAGTCCCAAAGAAACCGAAGAACTGAACCTGGTGGTAGCACTCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgagggacaatgacatatgtattcagagatctgatgttgactggtttttcggcagGTCGAGCATTTTTTGGGCATCAAACGAAGTGCCAAGCCTGGAAGCTTACCTCCTCCAGTCCCAAAGAAACCGAAGAACTGAACCTGGTGGTAGCACTCAG
                                  tgttgac  putative branch site (score: 88)
                                            tttttc  putative PPT
              atatgtatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttggcctgtgacccccctgttgtattctgtaattattactttgtttaatgagggacaatgacatatgtattcagagatctgatgttgactggtttttcggcagGTCGAGCATTTTTTGGGCATCAAACGAAGTGCCAAGCCTGGAAGCTTACCTCCTCCAGTCCCAAAGAAACCGAAGAACTGAACCTGGTGGTAGCACTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG