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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagcctgttgttgtctatatcatgggctgcattattttgtatgttggactctttaagtggtaactgtgctcttatatgtagTTTGGCTATATCGTGCTTACAACCTCTGCGGGAATTATGGATCACGAGGAGGCCCGACGCAAGAACGTCGGAGGCAAAGTCCTTGGTTTCTTTTATTAAT

Basic information

species Zea mays
transcript GRMZM2G083497_T04
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G083497_T04 (Zea mays), 3'ss of exon 2
lower sequence: PP1S115_101V6.1 (Physcomitrella patens), 3'ss of exon 2
------------gttagcctgttgttgtctatatcatgggctgcatta----ttttgtatgttggactc--tttaagtggtaactgtgctcttatatgtagTTTGGCTATATCGTGCTTACAACCTCTGCGGGAATTATGGATCACGAGGAGGCCCGACGCAAGAACGTCGGAGGCAAAGTCCTTGGTTTCTTTTATTAAT
              |||  ||  |   |   ||    |   ||| ||      || |  | || |  ||  ||    || |    ||  |||| | |||||||||| || || ||  | ||||| ||||| ||||||||||| ||||| |||||| |  | |||||||| ||||| || || |||||||||||||| | ||
acttaagttgacagtagtgtggggaatttcgtagtgagtattgcctttgactcttagggtatttggttccattctgctgatgctcgt-ttcttgtttgtagTTTGGATACATTGTTTTGACAACATCTGCTGGAATTATGGACCACGACGAGGCCAGGAGAAAGAACGTAGGAGGAAAGGTTCTTGGTTTCTTTTACTGAT

upper sequence: GRMZM2G083497_T04 (Zea mays), 3'ss of exon 2
lower sequence: PP1S426_18V6.1 (Physcomitrella patens), 3'ss of exon 2
------------------gttagcctgttgttgtctatatcatgggctgcattattttgtatgttggactctttaagtggtaactgtgctcttatatgtagTTTGGCTATATCGTGCTTACAACCTCTGCGGGAATTATGGATCACGAGGAGGCCCGACGCAAGAACGTCGGAGGCAAAGTCCTTGGTTTCTTTTATTAAT
                   |||   | |||    | |    |||  |  ||  | || | |      |   | | |  |     ||   | ||    | |||| || || || ||  | || ||||| || || |||||||||||||| |||||| | || |||||||| |||||||||||||| |||||||| |||| | 
tctgtatttggcattcacattattgtcttggcaacaagtcaatgaacc-cacgaattggaagagcatatcttctcatggacttgtgatttttttggggcagTTCGGTTACATTGTATTGACGACCTCAGCTGGTATTATGGATCACGATGAGGCCAGGCGTAAGAACGTAGGAGGCAAAGTCCTGGGTTTCTTCTATTGAG

upper sequence: GRMZM2G083497_T04 (Zea mays), 3'ss of exon 2
lower sequence: PP1S45_88V6.1 (Physcomitrella patens), 3'ss of exon 2
----------gttagcctgttgttgtctatatcatgggctgcatt-------attttgtatgttggactctttaagtggtaactgtgctcttata-tgtagTTTGGCTATATCGTGCTTACAACCTCTGCGGGAATTATGGATCACGAGGAGGCCCGACGCAAGAACGTCGGAGGCAAAGTCCTTGGTTTCTTTTATTAAT
            |  |   | | | || | || || |  |  |||       | |      ||  | |   |  | | ||   | || | || |  || ||||||| || || ||| | ||||| || || || |||||||||||||| |||||| | || |||||||| |||||||| |||||||| |||||||| | | 
gtttctctactcttccgcatcgctttcaaaat-atagcttctatttcaagaaaataaacccgtaagccgtatcgacttgttgttttggttttgtggtgcagTTTGGTTACATTGTGATGACAACGTCAGCTGGCATTATGGATCACGATGAGGCCAGGCGAAAGAACGTAGGAGGCAAGGTCCTTGGCTTCTTTTACTGAG

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|211287849|gb|FL261562.1|FL261562
EST:     GGGTAAAGGAAATCGAAGGCTGGACTGCGAGGCTGCTTCCGTCTCGCCAG                         TTTGGCTATATCGTGCTTACAACCTCTGCGGGAATTATGGATCACGAGGAG
genomic: GGGTAAAGGAAATCGAAGGCTGGACTGCGAGGCTGCTTCCGTCTCGCCAGgttagcctgt ... ttatatgtagTTTGGCTATATCGTGCTTACAACCTCTGCGGGAATTATGGATCACGAGGAG
EST: gi|211289986|gb|FL261571.1|FL261571
EST:     GGGTAAAGGAAATCGAAGGCTGGACTGCGAGGCTGCTTCCGTCTCGCCAG                         TTTTGGCTATATCGTGCTTACAACCTCTGCGGGAATTATGGATCACGAGGA
genomic: GGGTAAAGGAAATCGAAGGCTGGACTGCGAGGCTGCTTCCGTCTCGCCAGgttagcctgt ... ttatatgtagTTT-GGCTATATCGTGCTTACAACCTCTGCGGGAATTATGGATCACGAGGA
EST: gi|211294273|gb|FL261606.1|FL261606
EST:     GGGTAAAGGAAATCGAAGGCTGGACTGCGAGGCTGCTTCCGTCTCGCCAG                         TTTGGCTATATCGTGCTTACAACCTCTGCGGGAATTATGGATCACGAGGAG
genomic: GGGTAAAGGAAATCGAAGGCTGGACTGCGAGGCTGCTTCCGTCTCGCCAGgttagcctgt ... ttatatgtagTTTGGCTATATCGTGCTTACAACCTCTGCGGGAATTATGGATCACGAGGAG
EST: gi|45847067|gb|CN071010.1|CN071010
EST:     GGGTAAAGGAAATCGAAGGCTGGACTGCGAGGCTGCTTCCGTCTCGCCAG                         TTTGGCTATATCGTGCTTACAACCTCTGCGGGAATTATGGATCACGAGGAG
genomic: GGGTAAAGGAAATCGAAGGCTGGACTGCGAGGCTGCTTCCGTCTCGCCAGgttagcctgt ... ttatatgtagTTTGGCTATATCGTGCTTACAACCTCTGCGGGAATTATGGATCACGAGGAG
EST: gi|166471928|gb|EG129190.1|EG129190
EST:     GGGTAAAGGAAATCGAAGGCTGGACTGCCAGGCTGCTTCCGTCTCGCCAG                         TTTGGCTATATCGTGC
genomic: GGGTAAAGGAAATCGAAGGCTGGACTGCGAGGCTGCTTCCGTCTCGCCAGgttagcctgt ... ttatatgtagTTTGGCTATATCGTGC
EST: gi|211294277|gb|FL261610.1|FL261610
EST:     GGGTAAAGGAAATCGAAGGCTGGACTGCGAGGCTGCTTCCGTCTCGCCAG                         TTTGGCTATATCGTGCTTACAACCTCTGCGGGAATTATGGATCACGAGGAG
genomic: GGGTAAAGGAAATCGAAGGCTGGACTGCGAGGCTGCTTCCGTCTCGCCAGgttagcctgt ... ttatatgtagTTTGGCTATATCGTGCTTACAACCTCTGCGGGAATTATGGATCACGAGGAG
EST: gi|211296414|gb|FL261620.1|FL261620
EST:     GGGTAAAGGAAATCGAAGGCTGGACTGCGAGGCTGCTTCCGTCTCGCCAG                         TTTGGCTATATCGTGCTTACAACCTCTGCGGGAATTATGGATCACGAGGAG
genomic: GGGTAAAGGAAATCGAAGGCTGGACTGCGAGGCTGCTTCCGTCTCGCCAGgttagcctgt ... ttatatgtagTTTGGCTATATCGTGCTTACAACCTCTGCGGGAATTATGGATCACGAGGAG
EST: gi|211164278|gb|FL261545.1|FL261545
EST:     GGGTAAAGGAAATCGAAGGCTGGACTGCGAGGCTGCTTCCGTCTCGCCAG                         TTTNGCTATATCGTGCTTACAACCTCTGCGGGAATTATGGATCACGAGGAG
genomic: GGGTAAAGGAAATCGAAGGCTGGACTGCGAGGCTGCTTCCGTCTCGCCAGgttagcctgt ... ttatatgtagTTTGGCTATATCGTGCTTACAACCTCTGCGGGAATTATGGATCACGAGGAG
EST: gi|211292125|gb|FL261586.1|FL261586
EST:     GGGTAAAGTAAATCGAAGGCTGGACTGCGAGGCTGCTTCCGTMTCGCCAG                         TTTGGCTATATCGTGC
genomic: GGGTAAAGGAAATCGAAGGCTGGACTGCGAGGCTGCTTCCGTCTCGCCAGgttagcctgt ... ttatatgtagTTTGGCTATATCGTGC
EST: gi|211294276|gb|FL261609.1|FL261609
EST:     GGGTAAAGGAAATCGAAGGCTGGACTGCGAGGCTGCTTCCGTCTCGCCAG                         TTTGGCTATAT
genomic: GGGTAAAGGAAATCGAAGGCTGGACTGCGAGGCTGCTTCCGTCTCGCCAGgttagcctgt ... ttatatgtagTTTGGCTATAT
EST: gi|211164281|gb|FL261548.1|FL261548
EST:     GGGTAAAGGAAATCGAAGGCTGGACTGCGAGGCTGCTTCCGTCTCGCCAG                         TTTGGCTATATCGTGCTTACAACCTCTGCGGGAATTATGGATCACGAGGAG
genomic: GGGTAAAGGAAATCGAAGGCTGGACTGCGAGGCTGCTTCCGTCTCGCCAGgttagcctgt ... ttatatgtagTTTGGCTATATCGTGCTTACAACCTCTGCGGGAATTATGGATCACGAGGAG
EST: gi|166696475|gb|EG168737.1|EG168737
EST:     AGGCTGCTTCCGTCTCGCCAG                         TTTGGCTATATCGTGCTTACAACTTCTGCGGGAATTATGGATCACGAGGAG
genomic: AGGCTGCTTCCGTCTCGCCAGgttagcctgt ... ttatatgtagTTTGGCTATATCGTGCTTACAACCTCTGCGGGAATTATGGATCACGAGGAG
EST: gi|161583119|gb|EY957270.1|EY957270
EST:     GGGTAAAGGAAATCGAAGGCTGGACTGCGAGGCTGCTTCCGTCTCGCCAG                         TTTGGCTATATCGTGCTTACAACCTCTGGCGGGAATTATGGA
genomic: GGGTAAAGGAAATCGAAGGCTGGACTGCGAGGCTGCTTCCGTCTCGCCAGgttagcctgt ... ttatatgtagTTTGGCTATATCGTGCTTACAACCTCTG-CGGGAATTATGGA
EST: gi|211164272|gb|FL261539.1|FL261539
EST:     GGGTAAAGGAAATCGAAGGCTGGACTGCGAGGCTGCTTCCGTCTCGCCAG                         TTTGGCTATATCGTGCTTACAACCTCTGCGGGAATTATGGATCACGAGGAG
genomic: GGGTAAAGGAAATCGAAGGCTGGACTGCGAGGCTGCTTCCGTCTCGCCAGgttagcctgt ... ttatatgtagTTTGGCTATATCGTGCTTACAACCTCTGCGGGAATTATGGATCACGAGGAG
EST: gi|211289991|gb|FL261576.1|FL261576
EST:     GGGTAAAGGAAATCGAAGGCTGGACTGCGAGGCTGCTTCCGTCTCGCCAG                         TTTGGCTATATCGTGCTTACAACCTCTGCGGGAATTATGGATCACGAGGAG
genomic: GGGTAAAGGAAATCGAAGGCTGGACTGCGAGGCTGCTTCCGTCTCGCCAGgttagcctgt ... ttatatgtagTTTGGCTATATCGTGCTTACAACCTCTGCGGGAATTATGGATCACGAGGAG
EST: gi|14569318|gb|BI097641.1|BI097641
EST:     GGGTAAAGGAAATCGAAGGCTGGACTGCGAGGCTGCTTCCGTCTCGCCAG                         TTTGGCTATATCGTGCTTACAACCTCTGCGGGAATTATGGATCACGAGGAG
genomic: GGGTAAAGGAAATCGAAGGCTGGACTGCGAGGCTGCTTCCGTCTCGCCAGgttagcctgt ... ttatatgtagTTTGGCTATATCGTGCTTACAACCTCTGCGGGAATTATGGATCACGAGGAG
EST: gi|211164280|gb|FL261547.1|FL261547
EST:     GGGTAAAGGAAATCGAAGGCTGGACTGCGAGGCTGCTTCCGTCTCGCCAG                         TTTGGCTATATCGTGCTTACAACCTCTGCGGGAATTATGGATCACGAGGAG
genomic: GGGTAAAGGAAATCGAAGGCTGGACTGCGAGGCTGCTTCCGTCTCGCCAGgttagcctgt ... ttatatgtagTTTGGCTATATCGTGCTTACAACCTCTGCGGGAATTATGGATCACGAGGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgcattattttgtatgttggactctttaagtggtaactgtgctcttatatgtagTTTGGCTATATCGTGCTTACAACCTCTGCGGGAATTATGGATCACGAGGAGGCCCGACGCAAGAACGTCGGAGGCAAAGTCCTTGGTTTCTTTTATTAAT
                               tggtaac  putative branch site (score: 2)
                                        tgctctt  putative PPT
     ttattttgtatgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagcctgttgttgtctatatcatgggctgcattattttgtatgttggactctttaagtggtaactgtgctcttatatgtagTTTGGCTATATCGTGCTTACAACCTCTGCGGGAATTATGGATCACGAGGAGGCCCGACGCAAGAACGTCGGAGGCAAAGTCCTTGGTTTCTTTTATTAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG