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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggcagtttatttgccagactactcttgcagctaagttcaatacccagcataaatctgtacttgtctactaagttgcaccatgattgattgattactttattaatgaatcgtgtaatgattttgtacagAGGAACTGATATGACAAGTCCACATGGTATACCGGTGGATCTTCTAGATAGGCTGGTGATTATTCGGACAGAGACATATGGCCCTACTGAGATGATACAG

Basic information

species Zea mays
transcript GRMZM2G018697_T02
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G018697_T04 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os07g08170.1 (Oryza sativa), 3'ss of exon 8
gtaggcagttt-atttgccagacta--ctcttgcagctaagttcaatacccagcataaatctgtacttgtctactaagttgcaccatgattgattgattactttattaatgaatcgtgtaatgattttgtacagAGGAACTGATATGACAAGTCCACATGGTATACCGGTGGATCTTCTAGATAGGCTGGTGATTATTCGGACAGAGACATATGGCCCTACTGAGATGATACAG
|||  |||||| |||| |||| | |  | ||    ||||  ||  |   ||||  |||   |||  |||||   |   ||  |  |  ||    |  |||   | |||   | || ||| ||| || ||| |||||||||||||||||||||||||||||||||||| || ||||||||||| ||  ||||||||||||| ||||| |||||||| || ||||||||||| |||
gtaaacagtttgatttaccagtcgaagcactctgcgctacattataataccagactaatcatgtgtttgtcagtttgttt--attaccatatgctccttaaagt-ttacaaagtcttgttatgcttgtgtccagAGGAACTGATATGACAAGTCCACATGGTATACCAGTTGATCTTCTAGACAGATTGGTGATTATTCGAACAGAAACATATGGTCCCACTGAGATGATCCAG

upper sequence: GRMZM2G018697_T04 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os01g62040.1 (Oryza sativa), 3'ss of exon 8
gtaggcagttt-atttgccagactactcttgcagctaagttcaatacccagcataaatctgtacttgtctactaagttgc-accatgatt-----gattgattactttattaatgaatcgtgtaatgattttgtacagAGGAACTGATATGACAAGTCCACATGGTATACCGGTGGATCTTCTAGATAGGCTGGTGATTATTCGGACAGAGACATATGGCCCTACTGAGATGATACAG
|||  | |||| |||| ||   | |  |   | |  |  ||  |   ||||  |||  |||    | ||   |    |   || ||| |        || |  | | | |||   | | ||||   || | ||| |||||||||||||||||||||||| ||||||||||| || |||||||||||| |  ||||||||||||| ||||| ||||| || || ||||||||||| |||
gtaaacggtttgatttaccgctcgaagcactctgtcacattgcagtaccagagtaatactgcgtctatcagtttgtctattactatgctccttaaagttaacaagtcttttatatacttgtgt---gaatgtgtccagAGGAACTGATATGACAAGTCCGCATGGTATACCAGTTGATCTTCTAGATCGATTGGTGATTATTCGAACAGAAACATACGGTCCCACTGAGATGATCCAG

upper sequence: GRMZM2G018697_T04 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA08G21830.1 (Glycine max), 3'ss of exon 8
gtaggcagtttatttgccagactactcttgcagctaagttcaatacccagcataaatctgtacttgtctacta-agttgcaccatgattgattgattacttt---attaatgaatcgtgtaatgatttt-gtacagAGGAACTGATATGACAAGTCCACATGGTATACCGGTGGATCTTCTAGATAGGCTGGTGATTATTCGGACAGAGACATATGGCCCTACTGAGATGATACAG
                                    |  |||||   ||   | | |   |  | |  |  ||  ||       | |||  || |  |   |   ||| | | ||| |    || ||||  |||||||||||||||||||||||||| ||||| ||||| || || ||  | ||| || ||||||| ||||| ||  | |||||||| ||| |||| |||||||||
------------------------------------aagtcaatggtcatattgattagttgttggattgatatggtcctgttttcattattttacaatgcttaaatttaagcatcattgcctgctttttatacagAGGAACTGATATGACAAGTCCTCATGGCATACCTGTTGACCTGTTGGATCGGTTGGTGATCATTCGAACGCAAACATATGGTCCTGCTGAAATGATACAG

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|60340836|gb|DN207809.1|DN207809
EST:     TTATCACCAATCGTGATACTTGCTACAAATAGGGGAATATGTAATGTAAG                         AGGAACTGATATGACAAGTCCACATGGTATACCGGTGGATCTTCTAGATAG
genomic: TTATCACCAATCGTGATACTTGCTACAAATAGGGGAATATGTAATGTAAGgtaggcagtt ... ttttgtacagAGGAACTGATATGACAAGTCCACATGGTATACCGGTGGATCTTCTAGATAG
EST: gi|22490622|gb|BU050545.1|BU050545
EST:     TTATCACCAATCGTGATACTTGCTACAAATAGGGGAATATGTAATGTAAG                         AGGAACTGATATGACAAGTCCACATGGTATACCGGTGGATCTTCTAGATAG
genomic: TTATCACCAATCGTGATACTTGCTACAAATAGGGGAATATGTAATGTAAGgtaggcagtt ... ttttgtacagAGGAACTGATATGACAAGTCCACATGGTATACCGGTGGATCTTCTAGATAG
EST: gi|61118430|gb|DN559391.1|DN559391
EST:     TTATCACCAATTGTGATACTTGCTACGAATAGGGGAATATGTAATGTAAG                         AGGAACTGATATGACAAGTCCACATGGTATACCAGTGGATCTTCTAAATAG
genomic: TTATCACCAATCGTGATACTTGCTACAAATAGGGGAATATGTAATGTAAGgtaggcagtt ... ttttgtacagAGGAACTGATATGACAAGTCCACATGGTATACCGGTGGATCTTCTAGATAG
EST: gi|87152471|gb|DY397260.1|DY397260
EST:     TTATCACCAATCGTGATACTTGCTACAAATAGGGGAATATGTAATGTAAG                         AGGAACTGATATGACAAGTCCACATGGTATACCGGTGGATCTTCTAGATAG
genomic: TTATCACCAATCGTGATACTTGCTACAAATAGGGGAATATGTAATGTAAGgtaggcagtt ... ttttgtacagAGGAACTGATATGACAAGTCCACATGGTATACCGGTGGATCTTCTAGATAG
EST: gi|61118429|gb|DN559390.1|DN559390
EST:     TTATCACCAATTGTGATACTTGCTACGAATAGGGGAATATGTAATGTAAG                         AGGAACTGATATGACAAGTCCACATGGTATACCAGTGGATCTTCTAGATAG
genomic: TTATCACCAATCGTGATACTTGCTACAAATAGGGGAATATGTAATGTAAGgtaggcagtt ... ttttgtacagAGGAACTGATATGACAAGTCCACATGGTATACCGGTGGATCTTCTAGATAG
EST: gi|31612365|gb|CD568987.1|CD568987
EST:     ATAGGGGAATATGTAATGTAAG                         AGGATCTGATATGACAAGTCCACATGGTATACCGGTGGATCTTCTAGATAG
genomic: ATAGGGGAATATGTAATGTAAGgtaggcagtt ... ttttgtacagAGGAACTGATATGACAAGTCCACATGGTATACCGGTGGATCTTCTAGATAG
EST: gi|31612366|gb|CD568988.1|CD568988
EST:     TTATCACCAATCGTGATACTTGCTACAAATAGGGGAATATGTAATGTAAG                         AGGAACTGATATGACAAGTCCACATGGTATACCGGNGGATCTTCTAGATAG
genomic: TTATCACCAATCGTGATACTTGCTACAAATAGGGGAATATGTAATGTAAGgtaggcagtt ... ttttgtacagAGGAACTGATATGACAAGTCCACATGGTATACCGGTGGATCTTCTAGATAG
EST: gi|213174323|gb|FM191608.1|FM191608
EST:     TTATCACCAATTGTGATACTTGCTACGAATAGGGGAATATGTAATGTAAG                         AGGAACTGATATGACAAGTCCACATGGTATACCAGTGGATCTTCTAGATAG
genomic: TTATCACCAATCGTGATACTTGCTACAAATAGGGGAATATGTAATGTAAGgtaggcagtt ... ttttgtacagAGGAACTGATATGACAAGTCCACATGGTATACCGGTGGATCTTCTAGATAG
EST: gi|149051700|gb|EE155813.2|EE155813
EST:     AAATAGGGGAATATGTAATGTAAG                         AGGAACTGATATGACAAGTCCACATGGTATACCGGTGGATCTTCTAGATAG
genomic: AAATAGGGGAATATGTAATGTAAGgtaggcagtt ... ttttgtacagAGGAACTGATATGACAAGTCCACATGGTATACCGGTGGATCTTCTAGATAG

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: 48 (upstream exon), 49 (downstream exon)
Score: 174

TGTTGGATATCGAATGTTTTTCTTATCTTAACCGTGCATTGGAGAGCCCATTATCACCAATCGTGATACTTGCTACAAATAGGGGAATATGTAATGTAAGgtaggcagtt ... ttttgtacagAGGAACTGATATGACAAGTCCACATGGTATACCGGTGGATCTTCTAGATAGGCTGGTGATTATTCGGACAGAGACATATGGCCCTACTGAGATGATACAG


Block sizes: 44 (upstream exon), 49 (downstream exon)
Score: 69

TGTTGGATATCGAATGTTTTTCTTATCTTAACCGTGCATTGGAGAGCCCATTATCACCAATCGTGATACTTGCTACAAATAGGGGAATATGTAATGTAAGgtaggcagtt ... ttttgtacagAGGAACTGATATGACAAGTCCACATGGTATACCGGTGGATCTTCTAGATAGGCTGGTGATTATTCGGACAGAGACATATGGCCCTACTGAGATGATACAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 104

TGTTGGATATCGAATGTTTTTCTTATCTTAACCGTGCATTGGAGAGCCCATTATCACCAATCGTGATACTTGCTACAAATAGGGGAATATGTAATGTAAGgtaggcagtt ... ttttgtacagAGGAACTGATATGACAAGTCCACATGGTATACCGGTGGATCTTCTAGATAGGCTGGTGATTATTCGGACAGAGACATATGGCCCTACTGAGATGATACAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 165

TGTTGGATATCGAATGTTTTTCTTATCTTAACCGTGCATTGGAGAGCCCATTATCACCAATCGTGATACTTGCTACAAATAGGGGAATATGTAATGTAAGgtaggcagtt ... ttttgtacagAGGAACTGATATGACAAGTCCACATGGTATACCGGTGGATCTTCTAGATAGGCTGGTGATTATTCGGACAGAGACATATGGCCCTACTGAGATGATACAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcaccatgattgattgattactttattaatgaatcgtgtaatgattttgtacagAGGAACTGATATGACAAGTCCACATGGTATACCGGTGGATCTTCTAGATAGGCTGGTGATTATTCGGACAGAGACATATGGCCCTACTGAGATGATACAG
                        tattaat  putative branch site (score: 165)
         attgattgattacttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaggcagtttatttgccagactactcttgcagctaagttcaatacccagcataaatctgtacttgtctactaagttgcaccatgattgattgattactttattaatgaatcgtgtaatgattttgtacagAGGAACTGATATGACAAGTCCACATGGTATACCGGTGGATCTTCTAGATAGGCTGGTGATTATTCGGACAGAGACATATGGCCCTACTGAGATGATACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG