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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TACACATGGAGAAAATACTGGCTACGAAGTTCCTTGCTTGATAGTTGCTGCAAAAGATGATCTTGACCAATCTTCACAAGCTCTACAAGAATCGACTAGAgtaagttttttaactgttaattatgtagacatagtggaaccaagataagatatcaggacgagtttgcaatcagattgctacatacgtgactttaagttgt...

Basic information

species Zea mays
transcript GRMZM2G004459_T02
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G004459_T02 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os03g59590.1 (Oryza sativa), 5'ss of exon 12
TACACATGGAGAAAATACTGGCTACGAAGTTCCTTGCTTGATAGTTGCTGCAAAAGATGATCTTGACCAATCTTCACAAGCTCTACAAGAATCGACTAGAgtaagttttttaactgttaattatgtagacat-agtggaaccaagataagatatcaggacgagtttgcaatcagattgctacatacgtgactttaagttgt-
|||||||||||||||||||||||| |||||||||||  |||| |||||||| || |||||||||||||||||| ||   ||||| || ||||| || |||||||| ||  ||  ||||  ||||  |    | | |   ||   || ||    |    ||   | ||        |||  ||  |  |   ||| | || | 
TACACATGGAGAAAATACTGGCTATGAAGTTCCTTGTCTGATTGTTGCTGCTAAGGATGATCTTGACCAATCTCCATTGGCTCTGCAGGAATCAACGAGAgtaagcttactacatgttcgttattgatttgtcatttttactctgaaaatcatttgccactgttctgtgtcatagttggcactaaaata--tttgatttttc

upper sequence: GRMZM2G004459_T02 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os01g62570.1 (Oryza sativa), 5'ss of exon 13
TACACATGGAGAAAATACTGGCTACGAAGTTCCTTGCTTGATAGTTGCTGCAAAAGATGATCTTGACCAATCTTCACAAGCTCTACAAGAATCGACTAGAgtaagtttt--ttaactgttaatt-atgtagacatagtggaaccaagataagatatcaggacgagtttgcaatcagattgctacatacgtgactttaagttgt
 ||||  ||| |||| |||||||| |||||||||||  ||||||||||||| || ||||| || ||||||||| |    ||||| || || || ||||||||||| ||   |  | | || ||| || |  | |  ||   |      | |  | | || |  | ||  |  |    |||  |||   |     || |  || 
CACACGGGGAAAAAACACTGGCTATGAAGTTCCTTGTCTGATAGTTGCTGCTAAGGATGACCTCGACCAATCTCCGTTGGCTCTGCAGGACTCAACTAGAgtaagcttcaatacaatattgattcatttttaaactgttatattttatttacctctgagaatcatttgtccttt---ttggcacagttggttggttgaactgg
















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|60397275|gb|DN230091.1|DN230091
EST:     CAAAAGATGATCTTGACCAATCTTCACAAGCTCTACAAGAATCGACTAGA                         GTGAGCCAAGACATGGGAATTGAAACACCAATTCCGATCAGCGTGAAGCTG
genomic: CAAAAGATGATCTTGACCAATCTTCACAAGCTCTACAAGAATCGACTAGAgtaagttttt ... tactttccagGTGAGCCAAGACATGGGAATTGAAACACCAATTCCGATCAGCGTGAAGCTG
EST: gi|60343446|gb|DN210419.1|DN210419
EST:     CAAAAGATGATCTTGACCAATCTTCACAAGCTCTACAAGAATCGACTAGA                         GTGAGCCAAGACATGGGAATTGAAACACCAATTCCGATCAGCGTGAAGCTG
genomic: CAAAAGATGATCTTGACCAATCTTCACAAGCTCTACAAGAATCGACTAGAgtaagttttt ... tactttccagGTGAGCCAAGACATGGGAATTGAAACACCAATTCCGATCAGCGTGAAGCTG
EST: gi|60347607|gb|DN214580.1|DN214580
EST:     CAAAAGATGATCTTGACCAATCTTCACAAGCTCTACAAGAATCGACTAGA                         GTGAGCCAAGACATGGGAATTGAAACACCAATTCCGATCAGCGTGAAGCTG
genomic: CAAAAGATGATCTTGACCAATCTTCACAAGCTCTACAAGAATCGACTAGAgtaagttttt ... tactttccagGTGAGCCAAGACATGGGAATTGAAACACCAATTCCGATCAGCGTGAAGCTG
EST: gi|211170842|gb|FL475250.1|FL475250
EST:     CAAAAGATGATCTTGACCAATCTTCACAAGCTCTACAAGAATCGACTAGA                         GTGAGCCAAGACATGGGAATTGAAACACCAATTCCGATCAGCGTGAAGCTG
genomic: CAAAAGATGATCTTGACCAATCTTCACAAGCTCTACAAGAATCGACTAGAgtaagttttt ... tactttccagGTGAGCCAAGACATGGGAATTGAAACACCAATTCCGATCAGCGTGAAGCTG
EST: gi|60399644|gb|DN232454.1|DN232454
EST:     CAAAAGATGATCTTGACCAATCTTCACAAGCTCTACAAGAATCGACTAGA                         GTGAGCCAAGACATGGGAATTGAAACACCAATTCCGATCAGCGTGAAGCTG
genomic: CAAAAGATGATCTTGACCAATCTTCACAAGCTCTACAAGAATCGACTAGAgtaagttttt ... tactttccagGTGAGCCAAGACATGGGAATTGAAACACCAATTCCGATCAGCGTGAAGCTG
EST: gi|31362359|gb|CD446716.1|CD446716
EST:     CAAAAGATGATCTTGACCAATCTTCACAAGCTCTACAAGAATCGACTAGA                         GTGAGCCAAGACATGGGAATTGAAACACCAATTCCGATCAGCGTGAAGCTG
genomic: CAAAAGATGATCTTGACCAATCTTCACAAGCTCTACAAGAATCGACTAGAgtaagttttt ... tactttccagGTGAGCCAAGACATGGGAATTGAAACACCAATTCCGATCAGCGTGAAGCTG
EST: gi|60356872|gb|DN223845.1|DN223845
EST:     CAAAAGATGATCTTGACCAATCTTCACAAGCTCTACAAGAATCGACTAGA                         GTGAGCCAAGACATGGGAATTGAAACACCAATTCCGATCAGCGTGAAGCTG
genomic: CAAAAGATGATCTTGACCAATCTTCACAAGCTCTACAAGAATCGACTAGAgtaagttttt ... tactttccagGTGAGCCAAGACATGGGAATTGAAACACCAATTCCGATCAGCGTGAAGCTG
EST: gi|31351610|gb|CD435967.1|CD435967
EST:     CAAAAGATGATCTTGACCAATCTTCACAAGCTCTACAAGAATCGACTAGA                         GTGAGCCAAGACATGGGAATTGAAACACCAATTCCGATCAGCGTGAAGCTG
genomic: CAAAAGATGATCTTGACCAATCTTCACAAGCTCTACAAGAATCGACTAGAgtaagttttt ... tactttccagGTGAGCCAAGACATGGGAATTGAAACACCAATTCCGATCAGCGTGAAGCTG
EST: gi|60337295|gb|DN204268.1|DN204268
EST:     TCACAAGCTCTACAAGAATCGACTAGA                         GTGAGCCAAGACATGGGAATTGAAACACCAATTCCGATCAGCGTGAAGCTG
genomic: TCACAAGCTCTACAAGAATCGACTAGAgtaagttttt ... tactttccagGTGAGCCAAGACATGGGAATTGAAACACCAATTCCGATCAGCGTGAAGCTG
EST: gi|24765757|gb|CA400916.1|CA400916
EST:     AAGAATCGACTAGA                         GTGAGCCAAGACATGGGAATTGAAACACCAATTCCGATCAGCGTGAAGCTG
genomic: AAGAATCGACTAGAgtaagttttt ... tactttccagGTGAGCCAAGACATGGGAATTGAAACACCAATTCCGATCAGCGTGAAGCTG
EST: gi|83279244|gb|DV943252.1|DV943252
EST:     CAAAAGATGATCTTGACCAATCTTCACAAGCTCTACAAGAATCGACTAGA                         GTGAGCCAAGACATGGGAATTGAAACACCAATTCCGATCAGCGTGAAGCTG
genomic: CAAAAGATGATCTTGACCAATCTTCACAAGCTCTACAAGAATCGACTAGAgtaagttttt ... tactttccagGTGAGCCAAGACATGGGAATTGAAACACCAATTCCGATCAGCGTGAAGCTG
EST: gi|78084948|gb|DV513341.1|DV513341
EST:     CAAAAGATGATCTTGACCAATCTTCACAAGCTCTACAAGAATCGAGTAGA                         GTGAGCCAAGACATGGGAATTGAAACACCAATTCCGATCAGCGTGAAGCTG
genomic: CAAAAGATGATCTTGACCAATCTTCACAAGCTCTACAAGAATCGACTAGAgtaagttttt ... tactttccagGTGAGCCAAGACATGGGAATTGAAACACCAATTCCGATCAGCGTGAAGCTG
EST: gi|31352762|gb|CD437119.1|CD437119
EST:     CAAAAGATGATCTTGACCAATCTTCACAAGCTCTACAAGAATCGACTAGA                         GTGAGCCAAGACATGGGAATTGAAACACCAATTCCGATCAGCGTGAAGCTG
genomic: CAAAAGATGATCTTGACCAATCTTCACAAGCTCTACAAGAATCGACTAGAgtaagttttt ... tactttccagGTGAGCCAAGACATGGGAATTGAAACACCAATTCCGATCAGCGTGAAGCTG

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: 174

TACACATGGAGAAAATACTGGCTACGAAGTTCCTTGCTTGATAGTTGCTGCAAAAGATGATCTTGACCAATCTTCACAAGCTCTACAAGAATCGACTAGAgtaagttttt ... tactttccagGTGAGCCAAGACATGGGAATTGAAACACCAATTCCGATCAGCGTGAAGCTGAGAGATTTGAACAACATTTTCTGCAGAATCGTGCATGCTGCGCAGCAGC


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 71

TACACATGGAGAAAATACTGGCTACGAAGTTCCTTGCTTGATAGTTGCTGCAAAAGATGATCTTGACCAATCTTCACAAGCTCTACAAGAATCGACTAGAgtaagttttt ... tactttccagGTGAGCCAAGACATGGGAATTGAAACACCAATTCCGATCAGCGTGAAGCTGAGAGATTTGAACAACATTTTCTGCAGAATCGTGCATGCTGCGCAGCAGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 59

TACACATGGAGAAAATACTGGCTACGAAGTTCCTTGCTTGATAGTTGCTGCAAAAGATGATCTTGACCAATCTTCACAAGCTCTACAAGAATCGACTAGAgtaagttttt ... tactttccagGTGAGCCAAGACATGGGAATTGAAACACCAATTCCGATCAGCGTGAAGCTGAGAGATTTGAACAACATTTTCTGCAGAATCGTGCATGCTGCGCAGCAGC


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 133

TACACATGGAGAAAATACTGGCTACGAAGTTCCTTGCTTGATAGTTGCTGCAAAAGATGATCTTGACCAATCTTCACAAGCTCTACAAGAATCGACTAGAgtaagttttt ... tactttccagGTGAGCCAAGACATGGGAATTGAAACACCAATTCCGATCAGCGTGAAGCTGAGAGATTTGAACAACATTTTCTGCAGAATCGTGCATGCTGCGCAGCAGC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TACACATGGAGAAAATACTGGCTACGAAGTTCCTTGCTTGATAGTTGCTGCAAAAGATGATCTTGACCAATCTTCACAAGCTCTACAAGAATCGACTAGAgtaagttttttaactgttaattatgtagacatagtggaaccaagataagatatcaggacgagtttgcaatcagattgctacatacgtgactttaagttgt

- - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caagataa