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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcagtcaatcagtattacagcttagttacggtaatcaactgtttcactttattattagtcactgaaatttcatatcgaccaccagGAAAATGGATCGAGTTTGATGATGACAACCCAAACATCCGCAAGGAGGAAGACATTTTGAAACTATCTGGTGGAG

Basic information

species Zea mays
transcript GRMZM2G017086_T04
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G017086_T03 (Zea mays), 3'ss of exon 16
lower sequence: LOC_Os01g36930.1 (Oryza sativa), 3'ss of exon 16
gtcag-tcaatcagtattacagcttagttacggtaatcaactgtttcactttattattagtcactgaaatttcatatcgaccaccagGAAAATGGATCGAGTTTGATGATGACAACCCAAACATCCGCAAGGAGGAAGACATTTTGAAACTATCTGGTGGAG
||  |  ||   | |  | ||| ||| |||  | | ||||||||||   ||||  ||   |||||||   ||   | |       ||| |||||||| || ||||||||||||||||| | ||| |||||||||||||| ||||| ||  ||||||||||||
gtagggccagctactcatgcag-ttaattattggagtcaactgttta--tttacgatc--tcactgatgattatgagc--tttttagGGAAATGGATTGAATTTGATGATGACAACCCTAGCATACGCAAGGAGGAAGAGATTTTAAAGTTATCTGGTGGAG
















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|211283634|gb|FL461525.1|FL461525
EST:     AAGAAGTGCAGACTCTGGCCACTATGTTGGCTGGGTAAAGCAAGATGACG                         GAAAATGGATCGAGTTTGATGATGACAATCCAAACATCCGCAAGGAGGAAG
genomic: AAGAAGTGCAGACTCTGGCCACTATGTTGGCTGGGTAAAGCAAGATGACGgtcagtcaat ... cgaccaccagGAAAATGGATCGAGTTTGATGATGACAACCCAAACATCCGCAAGGAGGAAG
EST: gi|5871756|gb|AW018227.1|AW018227
EST:     AAGAAGTGCAGACTCTGGCCACTATGTTGGCTGGGTAAAGCAAGATGACG                         GAAAATGGATCGAGTTTGATGATGACAACCCAAACATCCGCAAGGAGGAAG
genomic: AAGAAGTGCAGACTCTGGCCACTATGTTGGCTGGGTAAAGCAAGATGACGgtcagtcaat ... cgaccaccagGAAAATGGATCGAGTTTGATGATGACAACCCAAACATCCGCAAGGAGGAAG
EST: gi|13316051|gb|BG410498.1|BG410498
EST:     AAGAAGTGCAGACTCTGGCCACTATGTTGGCTGGGTAAAGCAAGATGACG                         GAAAATGGTTTGTGTTTGATGATGACAACCCAAACATCCGCAAGGAGGAAG
genomic: AAGAAGTGCAGACTCTGGCCACTATGTTGGCTGGGTAAAGCAAGATGACGgtcagtcaat ... cgaccaccagGAAAATGGATCGAGTTTGATGATGACAACCCAAACATCCGCAAGGAGGAAG
EST: gi|13316052|gb|BG410499.1|BG410499
EST:     AAGAAGTGCAGACTCTGGCCACTATGTTGGCTGGGTAAAGCAAGATGACG                         GATTATGGATCGAGTTTGATGATGACAACCCAAACATCCGCAAGGAGGAAG
genomic: AAGAAGTGCAGACTCTGGCCACTATGTTGGCTGGGTAAAGCAAGATGACGgtcagtcaat ... cgaccaccagGAAAATGGATCGAGTTTGATGATGACAACCCAAACATCCGCAAGGAGGAAG
EST: gi|12968041|gb|BG264988.1|BG264988
EST:     AAGAAGTGCAGACTCTGGCCACTATGTTGGCTGGGTAAAGCAAGATGACG                         GAAAATGGATCGAGTTTGATGATGACAACCCAAACATCCGCAAGGAGGAAG
genomic: AAGAAGTGCAGACTCTGGCCACTATGTTGGCTGGGTAAAGCAAGATGACGgtcagtcaat ... cgaccaccagGAAAATGGATCGAGTTTGATGATGACAACCCAAACATCCGCAAGGAGGAAG
EST: gi|31363376|gb|CD447733.1|CD447733
EST:     GCAAGATGACG                         GAAAATGGATCGAGTTTGATGATGACAATCCAAACATCCGCAAGGAGGAAG
genomic: GCAAGATGACGgtcagtcaat ... cgaccaccagGAAAATGGATCGAGTTTGATGATGACAACCCAAACATCCGCAAGGAGGAAG
EST: gi|113672679|gb|DW824943.1|DW824943
EST:     AGAAGTGCAGACTCTGGACCACTATGTTGGCTGGGTAAAGCAAGATGACGG                         GAAAATGGATCGAGTTTGATGATGACAACCCAAACATCCGCAAGGAGGAA
genomic: AGAAGTGCAGACTCTGG-CCACTATGTTGGCTGGGTAAAGCAAGATGAC-Ggtcagtcaat ... cgaccaccagGAAAATGGATCGAGTTTGATGATGACAACCCAAACATCCGCAAGGAGGAA
EST: gi|33093667|gb|CF053661.1|CF053661
EST:     ATGTTGGCTGGGTAAAGCAAGATGACG                         GAAAATGGATCGAGTTTGATGATGACAACCCAAACATCCGCAAGGAGGAAG
genomic: ATGTTGGCTGGGTAAAGCAAGATGACGgtcagtcaat ... cgaccaccagGAAAATGGATCGAGTTTGATGATGACAACCCAAACATCCGCAAGGAGGAAG
EST: gi|32944644|gb|CF049463.1|CF049463
EST:     AAGAAGTGCAGACTCTGGCCACTATGTTGGCTGGGTAAAGCAAGATGACG                         GAAAATGGATCGAGTTTGATGATGACAACCCAAACATCCGCAAGGAGGAAG
genomic: AAGAAGTGCAGACTCTGGCCACTATGTTGGCTGGGTAAAGCAAGATGACGgtcagtcaat ... cgaccaccagGAAAATGGATCGAGTTTGATGATGACAACCCAAACATCCGCAAGGAGGAAG
EST: gi|32930721|gb|CF035533.1|CF035533
EST:     AAGAAGTGCAGACTCTGGCCACTATGTTGGCTGGGTAAAGCAAGATGACG                         GAAAATGGATCGAGTTTGATGATGACAACCCAAACATCCGCAAGGAGGAAG
genomic: AAGAAGTGCAGACTCTGGCCACTATGTTGGCTGGGTAAAGCAAGATGACGgtcagtcaat ... cgaccaccagGAAAATGGATCGAGTTTGATGATGACAACCCAAACATCCGCAAGGAGGAAG
EST: gi|32866634|gb|CF006316.1|CF006316
EST:     AAGAAGTGCAGACTCTGGCCACTATGTTGGCTGGGTAAAGCAAGATGACG                         GAAAATGGATCGAGTTTGATGATGACAACCCAAACATCCGCAAGGAGGAAG
genomic: AAGAAGTGCAGACTCTGGCCACTATGTTGGCTGGGTAAAGCAAGATGACGgtcagtcaat ... cgaccaccagGAAAATGGATCGAGTTTGATGATGACAACCCAAACATCCGCAAGGAGGAAG
EST: gi|31910881|gb|CD651645.1|CD651645
EST:     AAGAAGTGCAGACTCTGGCCGCTATGTTGGCTGGGTAAAGCAAGATGACG                         GAAAATGGATCGAGTTTGATGATGACAACCCAAACATCCGCAAGGAGGAAG
genomic: AAGAAGTGCAGACTCTGGCCACTATGTTGGCTGGGTAAAGCAAGATGACGgtcagtcaat ... cgaccaccagGAAAATGGATCGAGTTTGATGATGACAACCCAAACATCCGCAAGGAGGAAG
EST: gi|67013124|gb|CO441873.1|CO441873
EST:     AAGAAGTGCAGACTCTGGCCACTATGTTGGCTGGGTAAAGCAAGATGACG                         GAAAATGGATCGAGTTTGATGATGACAACCCAAACATCCGCAAGGAGGAAG
genomic: AAGAAGTGCAGACTCTGGCCACTATGTTGGCTGGGTAAAGCAAGATGACGgtcagtcaat ... cgaccaccagGAAAATGGATCGAGTTTGATGATGACAACCCAAACATCCGCAAGGAGGAAG
EST: gi|32932882|gb|CF037694.1|CF037694
EST:     AAGAAGTGCAGACTCTGGCCACTATGTTGGCTGGGTAAAGCAAGATGACG                         GAAAATGGATCGAGTTTGATGATGACAACCCAAACATCCGCAAGGAGGAAG
genomic: AAGAAGTGCAGACTCTGGCCACTATGTTGGCTGGGTAAAGCAAGATGACGgtcagtcaat ... cgaccaccagGAAAATGGATCGAGTTTGATGATGACAACCCAAACATCCGCAAGGAGGAAG
EST: gi|13177837|gb|BG349020.1|BG349020
EST:     AAGAAGTGCAGACTCTGGCCACTATGTTGGCTGGGTAAAGCAAGATGACG                         GAAAATGGATCGAGTTTGATGATGACAACCCAAACATCCGCAAGGAGGAAG
genomic: AAGAAGTGCAGACTCTGGCCACTATGTTGGCTGGGTAAAGCAAGATGACGgtcagtcaat ... cgaccaccagGAAAATGGATCGAGTTTGATGATGACAACCCAAACATCCGCAAGGAGGAAG
EST: gi|16378498|gb|BI992465.1|BI992465
EST:     AAGAAGTGCAGACTCTGGCCACTATGTTGGCTGGGTAAAGCAAGATGACG                         GAAAATGGATCGAGTTTGATGATGACAACCCAAACATCCGCAAGGAGGAAG
genomic: AAGAAGTGCAGACTCTGGCCACTATGTTGGCTGGGTAAAGCAAGATGACGgtcagtcaat ... cgaccaccagGAAAATGGATCGAGTTTGATGATGACAACCCAAACATCCGCAAGGAGGAAG
EST: gi|12968042|gb|BG264989.1|BG264989
EST:     AAGAAGTGCAGACTCTGGCCACTATGTTGGCTGGGTAAAGCAAGATGACG                         GAAAATGGATCGAGTTTGATGATGACAACCCAAACATCCGCAAGGAGGAAG
genomic: AAGAAGTGCAGACTCTGGCCACTATGTTGGCTGGGTAAAGCAAGATGACGgtcagtcaat ... cgaccaccagGAAAATGGATCGAGTTTGATGATGACAACCCAAACATCCGCAAGGAGGAAG
EST: gi|50332355|gb|CO527481.1|CO527481
EST:     AAGAAGTGCAGACTTTGGCCACTATGTTGGCTGGGTAAAGCAAGATGACG                         GAAAATGGATCGAGTTTGATGATGACAACCCAAACATCCGCAAGGAGGAAG
genomic: AAGAAGTGCAGACTCTGGCCACTATGTTGGCTGGGTAAAGCAAGATGACGgtcagtcaat ... cgaccaccagGAAAATGGATCGAGTTTGATGATGACAACCCAAACATCCGCAAGGAGGAAG
EST: gi|32944893|gb|CF049712.1|CF049712
EST:     AAGAAGTGCAGACTCTGGCCACTATGTTGGCTGGGTAAAGCAAGATGACG                         GAAAATGGATCGAGTTTGATGATGACAACCCAAACATCCGCAAGGAGGAAG
genomic: AAGAAGTGCAGACTCTGGCCACTATGTTGGCTGGGTAAAGCAAGATGACGgtcagtcaat ... cgaccaccagGAAAATGGATCGAGTTTGATGATGACAACCCAAACATCCGCAAGGAGGAAG
EST: gi|60352250|gb|DN219223.1|DN219223
EST:     AAGAAGTGCAGACTCTGGCCACTATGTTGGCTGGGTAAAGCAAGATGACG                         GAAAATGGATCGAGTTTGATGATGACAACCCAAACATCCGCAAGGAGGAAG
genomic: AAGAAGTGCAGACTCTGGCCACTATGTTGGCTGGGTAAAGCAAGATGACGgtcagtcaat ... cgaccaccagGAAAATGGATCGAGTTTGATGATGACAACCCAAACATCCGCAAGGAGGAAG
EST: gi|13177836|gb|BG349019.1|BG349019
EST:     AAGAAGTGCAGACTCTGGCCACTATGTTGGCTGGGTAAAGCAAGATGACG                         GAAAATGGATCGAGTTTGATGATGACAACCCAAACATCCGCAAGGAGGAAG
genomic: AAGAAGTGCAGACTCTGGCCACTATGTTGGCTGGGTAAAGCAAGATGACGgtcagtcaat ... cgaccaccagGAAAATGGATCGAGTTTGATGATGACAACCCAAACATCCGCAAGGAGGAAG
EST: gi|211211022|gb|FL456134.1|FL456134
EST:     AAGAAGTGCAGACTCTGGCCACTATGTTGGCTGGGTAAAGCAAGATGACG                         GAAAATGGATCGAGTTTGATGATGACAATCCAAACATCCGCAAGGAGGAAG
genomic: AAGAAGTGCAGACTCTGGCCACTATGTTGGCTGGGTAAAGCAAGATGACGgtcagtcaat ... cgaccaccagGAAAATGGATCGAGTTTGATGATGACAACCCAAACATCCGCAAGGAGGAAG
EST: gi|5919412|gb|AW054509.1|AW054509
EST:     AAGAAGTGCAGACTCTGGCCACTATGTTGGCTGGGTAAAGCAAGATGACG                         GAAAATGGATCGAGTTTGATGATGCCAACCCAAACATCCGCAAGGAGGAAG
genomic: AAGAAGTGCAGACTCTGGCCACTATGTTGGCTGGGTAAAGCAAGATGACGgtcagtcaat ... cgaccaccagGAAAATGGATCGAGTTTGATGATGACAACCCAAACATCCGCAAGGAGGAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtaatcaactgtttcactttattattagtcactgaaatttcatatcgaccaccagGAAAATGGATCGAGTTTGATGATGACAACCCAAACATCCGCAAGGAGGAAGACATTTTGAAACTATCTGGTGGAG
           tttcactttattatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcagtcaatcagtattacagcttagttacggtaatcaactgtttcactttattattagtcactgaaatttcatatcgaccaccagGAAAATGGATCGAGTTTGATGATGACAACCCAAACATCCGCAAGGAGGAAGACATTTTGAAACTATCTGGTGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG