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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaacttgcttctggtatctcagtaatctacctctccctctctctgcttatccaatttttttcttggtggaacactgcagaactattgatatcagtttggtggcataaacatgaaccgcctgattgatttctaaatgtatacacagGCTTATATTGAGAAAGAGGATAGCAAGAAGTTGAAACAGAAACAGCGTGAGCGTATGCAGCCCAAGATGGGCAAAATGGATATAGATTATCAG

Basic information

species Zea mays
transcript GRMZM2G132060_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G132060_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA13G31550.2 (Glycine max), 3'ss of exon 6
gtaacttgcttctggtatctcagtaatctacctctccctctctctgcttatccaatttttttcttggtggaacactgcagaactattgatatcagtttggtggcataaacatgaaccgcctgattgatttctaaatgtatacacagGCTTATATTGAGAAAGAGGATAGCAAGAAGTTGAAACAGAAACAGCGTGAGCGTATGCAGCCCAAGATGGGCAAAATGGATATAGATTATCAG
                                               || ||     | |||    |||     ||    |   ||| |  | | |    ||   ||  |          | ||||   | |        |  |||||||||||||||||||||||||| |||||| ||||||| || ||  | ||||| ||||| || || ||||| |||||||||||||||||||||
--------------------------------------------aagttttctgtgctctttacatgtgtgtgtcttttaattaatttacctaaatc-attgctgtagtcgctg-ttttttaattgtcatatgttgtctcatgcagGCTTATATTGAGAAAGAGGATAGTAAGAAGCTGAAACAAAAGCAAAGGGAGCGCATGCAACCAAAAATGGGGAAAATGGATATAGATTATCAG

upper sequence: GRMZM2G132060_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA15G07760.1 (Glycine max), 3'ss of exon 6
gtaacttgcttctggtatctcagtaatctacctctccctctctctgcttatccaatttttttcttggtggaacactgcagaactattgatatcagtttggtggcataaacatgaaccgcctgattgatttctaaatgtatacacagGCTTATATTGAGAAAGAGGATAGCAAGAAGTTGAAACAGAAACAGCGTGAGCGTATGCAGCCCAAGATGGGCAAAATGGATATAGATTATCAG
                             |  | | | |  ||||  |||  ||  | | || |   |     ||  |  ||  |||  | | ||||  |  |  |     | ||  | |  || | | |||        |  |||||||||||||||||||||||||| |||||| ||||||| || ||  | ||||| ||||| || || ||||| |||||||||||||||||||||
--------------------------agaagtttttcgttgctct--ttacacatgtgtcttttaattaatttac--ctaaataatttctgt-agtt--gctgttt-----ttaattgtcatat-gttatct-------catgcagGCTTATATTGAGAAAGAGGATAGTAAGAAGCTGAAACAAAAGCAAAGGGAGCGCATGCAACCAAAAATGGGGAAAATGGATATAGATTATCAG
















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|211159306|gb|FL243892.1|FL243892
EST:     AGCTTCCTGACTTNCAT-GCTGNCA-CTGGAATAGAAAAGGATA-GACAG                         -CTTATATTGAGGAAGAGGAT
genomic: AGCTTCCTGACTT-CATTGCTG-CAACTGGAATAGAAAAG-ATAAGACAGgtaacttgct ... gtatacacagGCTTATATTGAGAAAGAGGAT
EST: gi|31359279|gb|CD443636.1|CD443636
EST:     TCCAGCTTCCTGACTTCATTGCTGCAACTGGAATAGAAAAGATAAGACAG                         GCTTATATTGAGAAAGAGGATAGCAAGAAGTTGAAACAGAAACAGCGTGAG
genomic: TCCAGCTTCCTGACTTCATTGCTGCAACTGGAATAGAAAAGATAAGACAGgtaacttgct ... gtatacacagGCTTATATTGAGAAAGAGGATAGCAAGAAGTTGAAACAGAAACAGCGTGAG
EST: gi|148944299|gb|EC889396.2|EC889396
EST:     TCCAGCTTCCTGACTTCATTGCTGCAACTGGAATAGAAAAGATAAGACAG                         GCTTATATTGAGAAAGAGGATAGCAAGAAGTTGAAACAGAAACAGCGTGAG
genomic: TCCAGCTTCCTGACTTCATTGCTGCAACTGGAATAGAAAAGATAAGACAGgtaacttgct ... gtatacacagGCTTATATTGAGAAAGAGGATAGCAAGAAGTTGAAACAGAAACAGCGTGAG
EST: gi|148931686|gb|EC874876.2|EC874876
EST:     TCCAGCTTCCTGACTTCATTGCTGCAACTGGAATAGAAAAGATAAGACAG                         GCTTATATTGAGAAAGAGGATAGCAAGAAGTTGAAACAGAAACAGCGTGAG
genomic: TCCAGCTTCCTGACTTCATTGCTGCAACTGGAATAGAAAAGATAAGACAGgtaacttgct ... gtatacacagGCTTATATTGAGAAAGAGGATAGCAAGAAGTTGAAACAGAAACAGCGTGAG
EST: gi|22521467|gb|BU080278.1|BU080278
EST:     TCCAGCTTCCTGACTTCATTGCTGCAACTGGAATAGAAAAGATAAGACAG                         GCTTATATTGAGAAAGAGGATAGCAAGAAGTTGAAACAGAAACAGCGTGAG
genomic: TCCAGCTTCCTGACTTCATTGCTGCAACTGGAATAGAAAAGATAAGACAGgtaacttgct ... gtatacacagGCTTATATTGAGAAAGAGGATAGCAAGAAGTTGAAACAGAAACAGCGTGAG
EST: gi|21843267|gb|BQ703848.1|BQ703848
EST:     TCCAGCTTCCTGACTTCATTGCTGCAACTGGAATAGAAAAGATAAGACAG                         GCTTATATTGAGAAAGAGGATAGCAAGAAGTTGAAACAGAAACAGCGTGAG
genomic: TCCAGCTTCCTGACTTCATTGCTGCAACTGGAATAGAAAAGATAAGACAGgtaacttgct ... gtatacacagGCTTATATTGAGAAAGAGGATAGCAAGAAGTTGAAACAGAAACAGCGTGAG
EST: gi|148931684|gb|EC874873.2|EC874873
EST:     CCAGCTTCCTGACTTCATTGCTGNCA-CTGGAATAGAAAAGATAAGACAG                         GCTTATATTGAGAAAGAGGATAGCAAGAAGTTGAAACAGAAACAGCGTGAG
genomic: CCAGCTTCCTGACTTCATTGCTG-CAACTGGAATAGAAAAGATAAGACAGgtaacttgct ... gtatacacagGCTTATATTGAGAAAGAGGATAGCAAGAAGTTGAAACAGAAACAGCGTGAG
EST: gi|26557871|gb|CA830106.1|CA830106
EST:     CCAGCTTCCTGACTTCATTGCTGCAACTGGAATAGGAAAAGATAAGACAG                         GCTTATATTGAGAAAGAGGATAGCAAGAAGTTGAAACAGAAACAGCGTGAG
genomic: CCAGCTTCCTGACTTCATTGCTGCAACTGGAATAG-AAAAGATAAGACAGgtaacttgct ... gtatacacagGCTTATATTGAGAAAGAGGATAGCAAGAAGTTGAAACAGAAACAGCGTGAG
EST: gi|148966452|gb|EE017460.2|EE017460
EST:     TCCAGCTTCCTGACTTCATTGCTGCAACTGGAATAGAAAAGATAAGACAG                         GCTTATATTGAGAAAGAGGATAGCAAGAAGTTGAAACAGAAACAGCGTGAG
genomic: TCCAGCTTCCTGACTTCATTGCTGCAACTGGAATAGAAAAGATAAGACAGgtaacttgct ... gtatacacagGCTTATATTGAGAAAGAGGATAGCAAGAAGTTGAAACAGAAACAGCGTGAG
EST: gi|21843287|gb|BQ703868.1|BQ703868
EST:     TCCAGCTTCCTGACTTCATTGCTGCAACTGGAATAGAAAAGATAAGACAG                         GGTTATATTGAGAAAGAGGATAGCAAGAAGTTGAAACAGAAACAGCGTGAG
genomic: TCCAGCTTCCTGACTTCATTGCTGCAACTGGAATAGAAAAGATAAGACAGgtaacttgct ... gtatacacagGCTTATATTGAGAAAGAGGATAGCAAGAAGTTGAAACAGAAACAGCGTGAG

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: 863

GGGAAGAGAGGTATTGAGAAACAGCCTTTCCAGCTTCCTGACTTCATTGCTGCAACTGGAATAGAAAAGATAAGACAGgtaacttgct ... gtatacacagGCTTATATTGAGAAAGAGGATAGCAAGAAGTTGAAACAGAAACAGCGTGAGCGTATGCAGCCCAAGATGGGCAAAATGGATATAGATTATCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 413

GGGAAGAGAGGTATTGAGAAACAGCCTTTCCAGCTTCCTGACTTCATTGCTGCAACTGGAATAGAAAAGATAAGACAGgtaacttgct ... gtatacacagGCTTATATTGAGAAAGAGGATAGCAAGAAGTTGAAACAGAAACAGCGTGAGCGTATGCAGCCCAAGATGGGCAAAATGGATATAGATTATCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 570

GGGAAGAGAGGTATTGAGAAACAGCCTTTCCAGCTTCCTGACTTCATTGCTGCAACTGGAATAGAAAAGATAAGACAGgtaacttgct ... gtatacacagGCTTATATTGAGAAAGAGGATAGCAAGAAGTTGAAACAGAAACAGCGTGAGCGTATGCAGCCCAAGATGGGCAAAATGGATATAGATTATCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 465

GGGAAGAGAGGTATTGAGAAACAGCCTTTCCAGCTTCCTGACTTCATTGCTGCAACTGGAATAGAAAAGATAAGACAGgtaacttgct ... gtatacacagGCTTATATTGAGAAAGAGGATAGCAAGAAGTTGAAACAGAAACAGCGTGAGCGTATGCAGCCCAAGATGGGCAAAATGGATATAGATTATCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcagtttggtggcataaacatgaaccgcctgattgatttctaaatgtatacacagGCTTATATTGAGAAAGAGGATAGCAAGAAGTTGAAACAGAAACAGCGTGAGCGTATGCAGCCCAAGATGGGCAAAATGGATATAGATTATCAG
                                     ttctaaa  putative branch site (score: 465)
                                   atttctaaatgtata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaacttgcttctggtatctcagtaatctacctctccctctctctgcttatccaatttttttcttggtggaacactgcagaactattgatatcagtttggtggcataaacatgaaccgcctgattgatttctaaatgtatacacagGCTTATATTGAGAAAGAGGATAGCAAGAAGTTGAAACAGAAACAGCGTGAGCGTATGCAGCCCAAGATGGGCAAAATGGATATAGATTATCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG