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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aatagttttgaccagtagttaaatatttgcatcttatttttgcaatgggaatatttaaattgaaatgtcttgatgctgatgtgttgcctgtctatttcagGCATTTGCTGCGGCTGGGACACTCAAACAAAACTATGCCAACATCCTTTTAATGTTGCTGCGACTTCGGCAAGCCTGTGATCATCCTATTCTTGTAAAGG

Basic information

species Zea mays
transcript GRMZM2G449355_T02
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G449355_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os08g08220.2 (Oryza sativa), 3'ss of exon 6
--aatagttttgaccagtagttaaatatttgcatcttatttttgc-aatgggaatatttaaattgaaatgtcttgatgctgatgtgttgcctgtctatttcagGCATTTGCTGCGGCTGGGACACTCAAACAAAACTATGCCAACATCCTTTTAATGTTGCTGCGACTTCGGCAAGCCTGTGATCATCCTATTCTTGTAAAGG
  ||  ||| | |  ||| | |    |||||  |    || |    | |||  || |   || || | | |||  |||||||| | |||    || |||||||||||  ||||| ||||| ||||||||||| |||||||||||||| ||| ||||| || |||| ||| |||| ||||| ||||||||| ||||||| ||||
tcaaatgttataa--agtggatgttaatttgtgttcccttctgattactggagatttcacaagtgtagtttctgaatgctgatatattgtg-atccatttcagGCATACGCTGCTGCTGGTACACTCAAACAGAACTATGCCAACATTCTTCTAATGCTGTTGCGCCTTAGGCAGGCCTGCGATCATCCTCTTCTTGTGAAGG
















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|211322657|gb|FL233007.1|FL233007
EST:     AGCGGTCGTTTTATTTGATGCTGGAAGAACGCTCTCGGCAACAATTCAAG                         GCATTTGCTGCGGCTGGGACACTCAAACAAAACTATGCCAACATCCTTTTA
genomic: AGCGGTCGTTTTATTTGATGCTGGAAGAACGCTCTCGGCAACAATTCAAGgttggttatg ... tctatttcagGCATTTGCTGCGGCTGGGACACTCAAACAAAACTATGCCAACATCCTTTTA
EST: gi|211322659|gb|FL233009.1|FL233009
EST:     AGCGGTCGTTTTATTTGATGCTGGAAGAACGCTCTCGGCAACAATTCAAG                         GCATTTGCTGCGGCTGGGACACTCAAACAAAACTATGC
genomic: AGCGGTCGTTTTATTTGATGCTGGAAGAACGCTCTCGGCAACAATTCAAGgttggttatg ... tctatttcagGCATTTGCTGCGGCTGGGACACTCAAACAAAACTATGC
EST: gi|32931031|gb|CF035843.1|CF035843
EST:     TGCGGTCGTTTTATTTGATGCTGGAAGAACGCTCTCGGCAACAATTCAAG                         GCATTTGCTGCGGCTGGGACACTCAAACAAAACTATGCCAACATCCTTTTA
genomic: AGCGGTCGTTTTATTTGATGCTGGAAGAACGCTCTCGGCAACAATTCAAGgttggttatg ... tctatttcagGCATTTGCTGCGGCTGGGACACTCAAACAAAACTATGCCAACATCCTTTTA
EST: gi|76911600|gb|DV164339.1|DV164339
EST:     TTGATGCTGGAAGAACGCTCTCGGCAACAATTCAAG                         GCATTTGCTGCGGCTGGGACACTCAAACAAAACTATGCCAACATCCTTTTA
genomic: TTGATGCTGGAAGAACGCTCTCGGCAACAATTCAAGgttggttatg ... tctatttcagGCATTTGCTGCGGCTGGGACACTCAAACAAAACTATGCCAACATCCTTTTA
EST: gi|211322654|gb|FL233004.1|FL233004
EST:     AGCGGTCGTTTTATTTGATGCYGGAAGAACGCTCTCGGCAACAATTCAAG                         GCATTTGCTGCGGCTGGGACACTCAAAACAAAAACTATGCCAACATC
genomic: AGCGGTCGTTTTATTTGATGCTGGAAGAACGCTCTCGGCAACAATTCAAGgttggttatg ... tctatttcagGCATTTGCTGCGGCTGGGACACTCAAA-CAAAA-CTATGCCAACATC

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: 129

TTTACCTCCTAAGACAATTAATCTGAATAAAGTAGATTTCACACAAGAGGAGCGGTCGTTTTATTTGATGCTGGAAGAACGCTCTCGGCAACAATTCAAGgttggttatg ... tctatttcagGCATTTGCTGCGGCTGGGACACTCAAACAAAACTATGCCAACATCCTTTTAATGTTGCTGCGACTTCGGCAAGCCTGTGATCATCCTATTCTTGTAAAGG


Block sizes: 36 (upstream exon), 49 (downstream exon)
Score: 28

TTTACCTCCTAAGACAATTAATCTGAATAAAGTAGATTTCACACAAGAGGAGCGGTCGTTTTATTTGATGCTGGAAGAACGCTCTCGGCAACAATTCAAGgttggttatg ... tctatttcagGCATTTGCTGCGGCTGGGACACTCAAACAAAACTATGCCAACATCCTTTTAATGTTGCTGCGACTTCGGCAAGCCTGTGATCATCCTATTCTTGTAAAGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 31

TTTACCTCCTAAGACAATTAATCTGAATAAAGTAGATTTCACACAAGAGGAGCGGTCGTTTTATTTGATGCTGGAAGAACGCTCTCGGCAACAATTCAAGgttggttatg ... tctatttcagGCATTTGCTGCGGCTGGGACACTCAAACAAAACTATGCCAACATCCTTTTAATGTTGCTGCGACTTCGGCAAGCCTGTGATCATCCTATTCTTGTAAAGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 55

TTTACCTCCTAAGACAATTAATCTGAATAAAGTAGATTTCACACAAGAGGAGCGGTCGTTTTATTTGATGCTGGAAGAACGCTCTCGGCAACAATTCAAGgttggttatg ... tctatttcagGCATTTGCTGCGGCTGGGACACTCAAACAAAACTATGCCAACATCCTTTTAATGTTGCTGCGACTTCGGCAAGCCTGTGATCATCCTATTCTTGTAAAGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgggaatatttaaattgaaatgtcttgatgctgatgtgttgcctgtctatttcagGCATTTGCTGCGGCTGGGACACTCAAACAAAACTATGCCAACATCCTTTTAATGTTGCTGCGACTTCGGCAAGCCTGTGATCATCCTATTCTTGTAAAGG
                            tgctgat  putative branch site (score: 55)
                                             tctatttc  putative PPT
     atatttaaattgaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aatagttttgaccagtagttaaatatttgcatcttatttttgcaatgggaatatttaaattgaaatgtcttgatgctgatgtgttgcctgtctatttcagGCATTTGCTGCGGCTGGGACACTCAAACAAAACTATGCCAACATCCTTTTAATGTTGCTGCGACTTCGGCAAGCCTGTGATCATCCTATTCTTGTAAAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC