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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTGGTTCTGGTGGGGAGAGCTGCATTTGTTTTCCCATTGTCGTTTTTGTCCAACCTGACAAAGAAGTCTCCATTGGAGAAAATAACATTTAGACAGCAAgtgagtgattgctgcataatcacagcatctttcatatgtttatttttttgtttacaaaaggaccatctaatttggttaactgaattctctgatag

Basic information

species Zea mays
transcript GRMZM2G027851_T03
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G027851_T02 (Zea mays), 5'ss of exon 10
lower sequence: GLYMA17G02560.1 (Glycine max), 5'ss of exon 10
GTTGGTTCTGGTGGGGAGAGCTGCATTTGTTTTCCCATTGTCGTTTTTGTCCAACCTGACAAAGAAGTCTCCATTGGAGAAAATAACATTTAGACAGCAAgtgagtgattgctgcataatcacagcatctttcatatgtttatttttttgtttacaaaaggaccatctaatttggttaactgaattctctgatag
  |  |  | ||||| |||||||||||||||||||| ||||| || || |||||| ||   |||||||||| ||  ||||||||    || | ||| |||||  ||| || |  |    |  |      | |||     ||    | ||| | ||  | |    |  |   |  | | |     || | | | ||
ACTTATCTTAGTGGGAAGAGCTGCATTTGTTTTCCCTTTGTCCTTCTTATCCAACTTGCTTAAGAAGTCTCAATCTGAGAAAATTGAGTTAAAACAACAAgtatgtgctttcctcccgtttcc-----ttgtcagggtcttgagctcttgataactgaggtgttacattcctgcgatgatc---ttgtttcacag

upper sequence: GRMZM2G027851_T02 (Zea mays), 5'ss of exon 10
lower sequence: GLYMA07G38160.1 (Glycine max), 5'ss of exon 11
GTTGGTTCTGGTGGGGAGAGCTGCATTTGTTTTCCCATTGTCGTTTTTGTCCAACCTGACAAAGAAGTCTCCATTGGAGAAAATAACATTTAGACAGCAAgtgagtgattgctgcataatcacagcatctttcatatgtttatttttttgtttacaaaaggaccatctaatttggttaactgaattctctgatag
  |  |  ||||||| |||||||||||||||||||| ||||| || || |||||| ||   ||||| |||| ||  ||||||||    || | ||| |||||  ||| || |  |    |  |         ||     ||    | ||| | |   | |    |  | | |  | | | |     || | | ||
ACTTATCTTGGTGGGAAGAGCTGCATTTGTTTTCCCTTTGTCCTTCTTATCCAACTTGCTTAAGAACTCTCAATCTGAGAAAATTGAGTTAAAACAACAAgtatgtgttttcctccagtttgc--ttgtcagcagggtcttgaactcttgataattgaggtgttacattactgcgatgatttttggct-tcacag
















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|93281413|gb|EB673677.1|EB673677
EST:     CCAACCTGACAAAGAAGTCTCCATTGGAGAAAATAACATTTAGACAGCAA                         ATTGTAATATGGTGGGCCGGACTGATGAGAGGTGCCGTGTCCATTGCTCTC
genomic: CCAACCTGACAAAGAAGTCTCCATTGGAGAAAATAACATTTAGACAGCAAgtgagtgatt ... tctctgatagATTGTAATATGGTGGGCCGGACTGATGAGAGGTGCCGTGTCCATTGCTCTC
EST: gi|50333104|gb|CO528230.1|CO528230
EST:     CCAACCTGACAAAGAAGTCTCCATTGGAGAAAATAACATTTAGACAGCAA                         ATTGTAATATGGTGGGCCGGACTGATGAGAGGTGCCGTGTCCATTGCTCTC
genomic: CCAACCTGACAAAGAAGTCTCCATTGGAGAAAATAACATTTAGACAGCAAgtgagtgatt ... tctctgatagATTGTAATATGGTGGGCCGGACTGATGAGAGGTGCCGTGTCCATTGCTCTC
EST: gi|89755588|gb|DY685957.1|DY685957
EST:     CCAACCTGACAAAGAAGTCTCCATTGGAGAAAATAACATTTAGACAGCAA                         ATTGTAATATGGTGGGCCGGACTGATGAGAGGTGCCGTGTCCATTGCTCTC
genomic: CCAACCTGACAAAGAAGTCTCCATTGGAGAAAATAACATTTAGACAGCAAgtgagtgatt ... tctctgatagATTGTAATATGGTGGGCCGGACTGATGAGAGGTGCCGTGTCCATTGCTCTC
EST: gi|93282180|gb|EB674444.1|EB674444
EST:     CCATTGGAGAAAATAACATTTTAGACAGCAA                         ATTGTAATATGGTGGGCCGGACTGATGAGAGGTGCCGTGTCCATTGCTCTC
genomic: CCATTGGAGAAAATAACA-TTTAGACAGCAAgtgagtgatt ... tctctgatagATTGTAATATGGTGGGCCGGACTGATGAGAGGTGCCGTGTCCATTGCTCTC
EST: gi|71437105|gb|DR818155.1|DR818155
EST:     CCAACCTGACAAAGAAGTCTCCATTGGAGAAAATAACATTTAGACAGCAA                         ATTGTAATATGGTGGGCCGGACTGATGAGAGGTGCCGTGTCCATTGCTCTC
genomic: CCAACCTGACAAAGAAGTCTCCATTGGAGAAAATAACATTTAGACAGCAAgtgagtgatt ... tctctgatagATTGTAATATGGTGGGCCGGACTGATGAGAGGTGCCGTGTCCATTGCTCTC
EST: gi|74238598|gb|DT646512.1|DT646512
EST:     CCAACCTGACAAAGAAGTCTCCATTGGAGAAAATAACATTTAGACAGCAA                         ATTGTAATATGGTGGGCCGGACTGATGAGAGGTGCCGTGTCCATTGCTCTC
genomic: CCAACCTGACAAAGAAGTCTCCATTGGAGAAAATAACATTTAGACAGCAAgtgagtgatt ... tctctgatagATTGTAATATGGTGGGCCGGACTGATGAGAGGTGCCGTGTCCATTGCTCTC
EST: gi|78093452|gb|DV521826.1|DV521826
EST:     CCAACCTGACAAAGAAGTCTCCATTGGAGAAAATAACATTTAGACAGCAA                         ATTGTAATATGGTGGGCCGGACTGATGAGAGGTGCCGTGTCCATTGCTCTC
genomic: CCAACCTGACAAAGAAGTCTCCATTGGAGAAAATAACATTTAGACAGCAAgtgagtgatt ... tctctgatagATTGTAATATGGTGGGCCGGACTGATGAGAGGTGCCGTGTCCATTGCTCTC
EST: gi|71760181|gb|DR958118.1|DR958118
EST:     CCAACCTGACAAAGAAGTCTCCATTGGAGAAAATAACATTTAGACAGCAA                         ATTGTAATATGGTGGGCCGGACTGATGAGAGGTGCCGTGTCCATTGCTCTC
genomic: CCAACCTGACAAAGAAGTCTCCATTGGAGAAAATAACATTTAGACAGCAAgtgagtgatt ... tctctgatagATTGTAATATGGTGGGCCGGACTGATGAGAGGTGCCGTGTCCATTGCTCTC
EST: gi|71761590|gb|DR959527.1|DR959527
EST:     CCAACCTGACAAAGAAGTCTCCATTGGAGAAAATAACATTTAGACAGCAA                         ATTGTAATATGGTGGGCCGGACTGATGAGAGGTGCCGTGTCCATTGCTCTC
genomic: CCAACCTGACAAAGAAGTCTCCATTGGAGAAAATAACATTTAGACAGCAAgtgagtgatt ... tctctgatagATTGTAATATGGTGGGCCGGACTGATGAGAGGTGCCGTGTCCATTGCTCTC
EST: gi|88750196|gb|DY534337.1|DY534337
EST:     CCAACCTGACAAAGAAGTCTCCATTGGAGAAAATAACATTTAGACAGCAA                         ATTGTAATATGGTGGGCCGGACTGATGAGAGGTGCCGTGTCCATTGCTCTC
genomic: CCAACCTGACAAAGAAGTCTCCATTGGAGAAAATAACATTTAGACAGCAAgtgagtgatt ... tctctgatagATTGTAATATGGTGGGCCGGACTGATGAGAGGTGCCGTGTCCATTGCTCTC
EST: gi|71446906|gb|DR827956.1|DR827956
EST:     CCAACCTGACAAAGAAGTCTCCATTGGAGAAAATAACATTTAGACAGCAA                         ATTGTAATATGGTGGGCCGGACTGATGAGAGGTGCCGTGTCCATTGCTCTC
genomic: CCAACCTGACAAAGAAGTCTCCATTGGAGAAAATAACATTTAGACAGCAAgtgagtgatt ... tctctgatagATTGTAATATGGTGGGCCGGACTGATGAGAGGTGCCGTGTCCATTGCTCTC
EST: gi|71758416|gb|DR956353.1|DR956353
EST:     CCAACCTGACAAAGAAGTCTCCATTGGAGAAAATAACATTTAGACAGCAA                         ATTGTAATATGGTGGGCCGGACTGATGAGAGGTGCCGTGTCCATTGCTCTC
genomic: CCAACCTGACAAAGAAGTCTCCATTGGAGAAAATAACATTTAGACAGCAAgtgagtgatt ... tctctgatagATTGTAATATGGTGGGCCGGACTGATGAGAGGTGCCGTGTCCATTGCTCTC
EST: gi|78074782|gb|DV503216.1|DV503216
EST:     CCAACCTGACAAAGAAGTCTCCATTGGAGAAAATAACATTTAGACAGCAA                         ATTGTAATATGGTGGGCCGGACTGATGAGAGGTGCCGTGTCCATTGCTCTC
genomic: CCAACCTGACAAAGAAGTCTCCATTGGAGAAAATAACATTTAGACAGCAAgtgagtgatt ... tctctgatagATTGTAATATGGTGGGCCGGACTGATGAGAGGTGCCGTGTCCATTGCTCTC
EST: gi|93281414|gb|EB673678.1|EB673678
EST:     CCAACCTGACAAAGAAGTCTCCATTGGAGAAAATAACATTTAGACAGCAA                         ATTGTAATATGGTGGGCCGGACTGATGAGAGGTGCCGTGTCCATTGCTCTC
genomic: CCAACCTGACAAAGAAGTCTCCATTGGAGAAAATAACATTTAGACAGCAAgtgagtgatt ... tctctgatagATTGTAATATGGTGGGCCGGACTGATGAGAGGTGCCGTGTCCATTGCTCTC
EST: gi|37382323|gb|CF628103.1|CF628103
EST:     CCAACCTGACAAAGAAGTCTCCATTGGAGAAAATAACATTTAGACAGCAA                         ATTGTAATATGGTGGGCCGGACTGATGAGAGGTGCCGTGTCCATTGCTCTC
genomic: CCAACCTGACAAAGAAGTCTCCATTGGAGAAAATAACATTTAGACAGCAAgtgagtgatt ... tctctgatagATTGTAATATGGTGGGCCGGACTGATGAGAGGTGCCGTGTCCATTGCTCTC
EST: gi|76013009|gb|DT940179.1|DT940179
EST:     CCAACCTGACAAAGAAGTCTCCATTGGAGAAAATAACATTTAGACAGCAA                         ATTGTAATATGGTGGGCCGGACTGATGAGAGGTGCCGTGTCCATTGCTCTC
genomic: CCAACCTGACAAAGAAGTCTCCATTGGAGAAAATAACATTTAGACAGCAAgtgagtgatt ... tctctgatagATTGTAATATGGTGGGCCGGACTGATGAGAGGTGCCGTGTCCATTGCTCTC
EST: gi|76293702|gb|DV033270.1|DV033270
EST:     CCAACCTGACAAAGAAGTCTCCATTGGAGAAAATAACATTTAGACAGCAA                         ATTGTAATATGGTGGGCCGGACTGATGAGAGGTGCCGTGTCCATTGCTCTC
genomic: CCAACCTGACAAAGAAGTCTCCATTGGAGAAAATAACATTTAGACAGCAAgtgagtgatt ... tctctgatagATTGTAATATGGTGGGCCGGACTGATGAGAGGTGCCGTGTCCATTGCTCTC
EST: gi|74239374|gb|DT647288.1|DT647288
EST:     CCAACCTGACAAAGAAGTCTCCATTGGAGAAAATAACATTTAGACAGCAA                         ATTGTAATATGGTGGGCCGGACTGATGAGAGGTGCCGTGTCCATTGCTCTC
genomic: CCAACCTGACAAAGAAGTCTCCATTGGAGAAAATAACATTTAGACAGCAAgtgagtgatt ... tctctgatagATTGTAATATGGTGGGCCGGACTGATGAGAGGTGCCGTGTCCATTGCTCTC
EST: gi|71427238|gb|DR808288.1|DR808288
EST:     CCAACCTGACAAAGAAGTCTCCATTGGAGAAAATAACATTTAGACAGCAA                         ATTGTAATATGGTGGGCCGGACTGATGAGAGGTGCCGTGTCCATTGCTCTC
genomic: CCAACCTGACAAAGAAGTCTCCATTGGAGAAAATAACATTTAGACAGCAAgtgagtgatt ... tctctgatagATTGTAATATGGTGGGCCGGACTGATGAGAGGTGCCGTGTCCATTGCTCTC
EST: gi|78115472|gb|DV533860.1|DV533860
EST:     CCAACCTGACAAAGAAGTCTCCATTGGAGAAAATAACATTTAGACAGCAA                         ATTGTAATATGGTGGGCCGGACTGATGAGAGGTGCCGTGTCCATTGCTCTC
genomic: CCAACCTGACAAAGAAGTCTCCATTGGAGAAAATAACATTTAGACAGCAAgtgagtgatt ... tctctgatagATTGTAATATGGTGGGCCGGACTGATGAGAGGTGCCGTGTCCATTGCTCTC
EST: gi|37399694|gb|CF637180.1|CF637180
EST:     GGAGAAAATAACATTTAGACAGCAA                         ATTGTAATATGGTGGGCCGGAATGATGAGAGGTGCCGTGTCCATTGCTCTC
genomic: GGAGAAAATAACATTTAGACAGCAAgtgagtgatt ... tctctgatagATTGTAATATGGTGGGCCGGACTGATGAGAGGTGCCGTGTCCATTGCTCTC
EST: gi|71760562|gb|DR958499.1|DR958499
EST:     CCAACCTGACAAAGAAGTCTCCATTGGAGAAAATAACATTTAGACAGCAA                         ATTGTAATATGGTGGGCCGGACTGATGAGAGGTGCCGTGTCCATTGCTCTC
genomic: CCAACCTGACAAAGAAGTCTCCATTGGAGAAAATAACATTTAGACAGCAAgtgagtgatt ... tctctgatagATTGTAATATGGTGGGCCGGACTGATGAGAGGTGCCGTGTCCATTGCTCTC
EST: gi|76936699|gb|DV174843.1|DV174843
EST:     CCAACCTGACAAAGAAGTCTCCATTGGAGAAAATAACATTTAGACAGCAA                         ATTGTAATATGGTGG
genomic: CCAACCTGACAAAGAAGTCTCCATTGGAGAAAATAACATTTAGACAGCAAgtgagtgatt ... tctctgatagATTGTAATATGGTGG
EST: gi|71440636|gb|DR821686.1|DR821686
EST:     CCAACCTGACAAAGAAGTCTCCATTGGAGAAAATAACATTTAGACAGCAA                         ATTGTAATATGGTGGGCCGGACTGATGAGAGGTGCCGTGTCCATTGCTCTC
genomic: CCAACCTGACAAAGAAGTCTCCATTGGAGAAAATAACATTTAGACAGCAAgtgagtgatt ... tctctgatagATTGTAATATGGTGGGCCGGACTGATGAGAGGTGCCGTGTCCATTGCTCTC
EST: gi|78080129|gb|DV508541.1|DV508541
EST:     CCAACCTGACAAAGAAGTCTCCATTGGAGAAAATAACATTTAGACAGCAA                         ATTGTAATATGGTGGGCCGGACTGATGAGAGGTGCCGTGTCCATTGCTCTC
genomic: CCAACCTGACAAAGAAGTCTCCATTGGAGAAAATAACATTTAGACAGCAAgtgagtgatt ... tctctgatagATTGTAATATGGTGGGCCGGACTGATGAGAGGTGCCGTGTCCATTGCTCTC

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 5 RNA-Seq libraries.


Block sizes: 47 (upstream exon), 42 (downstream exon)
Score: 75

GTTGGTTCTGGTGGGGAGAGCTGCATTTGTTTTCCCATTGTCGTTTTTGTCCAACCTGACAAAGAAGTCTCCATTGGAGAAAATAACATTTAGACAGCAAgtgagtgatt ... tctctgatagATTGTAATATGGTGGGCCGGACTGATGAGAGGTGCCGTGTCCATTGCTCTCGCTTACAACAAG


Block sizes: 43 (upstream exon), 43 (downstream exon)
Score: 17

GTTGGTTCTGGTGGGGAGAGCTGCATTTGTTTTCCCATTGTCGTTTTTGTCCAACCTGACAAAGAAGTCTCCATTGGAGAAAATAACATTTAGACAGCAAgtgagtgatt ... tctctgatagATTGTAATATGGTGGGCCGGACTGATGAGAGGTGCCGTGTCCATTGCTCTCGCTTACAACAAG


Block sizes: 49 (upstream exon), 44 (downstream exon)
Score: 8

GTTGGTTCTGGTGGGGAGAGCTGCATTTGTTTTCCCATTGTCGTTTTTGTCCAACCTGACAAAGAAGTCTCCATTGGAGAAAATAACATTTAGACAGCAAgtgagtgatt ... tctctgatagATTGTAATATGGTGGGCCGGACTGATGAGAGGTGCCGTGTCCATTGCTCTCGCTTACAACAAG


Block sizes: 28 (upstream exon), 48 (downstream exon)
Score: 3

GTTGGTTCTGGTGGGGAGAGCTGCATTTGTTTTCCCATTGTCGTTTTTGTCCAACCTGACAAAGAAGTCTCCATTGGAGAAAATAACATTTAGACAGCAAgtgagtgatt ... tctctgatagATTGTAATATGGTGGGCCGGACTGATGAGAGGTGCCGTGTCCATTGCTCTCGCTTACAACAAG


Block sizes: 48 (upstream exon), 38 (downstream exon)
Score: 30

GTTGGTTCTGGTGGGGAGAGCTGCATTTGTTTTCCCATTGTCGTTTTTGTCCAACCTGACAAAGAAGTCTCCATTGGAGAAAATAACATTTAGACAGCAAgtgagtgatt ... tctctgatagATTGTAATATGGTGGGCCGGACTGATGAGAGGTGCCGTGTCCATTGCTCTCGCTTACAACAAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTGGTTCTGGTGGGGAGAGCTGCATTTGTTTTCCCATTGTCGTTTTTGTCCAACCTGACAAAGAAGTCTCCATTGGAGAAAATAACATTTAGACAGCAAgtgagtgattgctgcataatcacagcatctttcatatgtttatttttttgtttacaaaaggaccatctaatttggttaactgaattctctgatag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA