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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatagttaaggcaatcgatcttgtagtggatatacttttttagtcatgttgcacttgttattcataagatggatttgatttgttaggtgcctttggttttcagcgaaggaccttcttgtaacatattaactgcttttgcagGAAGTATCTTGTAGAGGCCACAAAAGAAGCATCCAATTCTTATAATGAAGCG

Basic information

species Zea mays
transcript GRMZM2G068277_T02
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G068277_T02 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os02g02690.1 (Oryza sativa), 3'ss of exon 10
gtatagttaaggcaatcgatcttgtag---tggatat-acttttttagtcatgttgcacttgttattcataagatggatttgatttgttaggtgcctttggttttcagcgaaggaccttcttgtaacatattaactgctt-ttgcagGAAGTATCTTGTAGAGGCCACAAAAGAAGCATCCAATTCTTATAATGAAGCG
||| ||  |    ||| ||| |   |      || || |  | || ||| | || | || | || |    || |  |||   || ||||  |||| |||  |||||||  ||   | || ||   || |||| || | || ||||||||| ||||| ||||||||||| |||||||||||||||||||||| |||||||
gtaaagccagtttaattgatttaaaaaaaactgacatgatatcttgagttaagtggtacatcttctc---aaaacagatccaatatgttgagtgcttttc-ttttcaggaaaatgcatttttt--acttatttaccgtttcttgcagGAAATATCTAGTAGAGGCCACGAAAGAAGCATCCAATTCTTATACTGAAGCG
















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|211432853|gb|FL453388.1|FL453388
EST:     TTGCGTGACACTTACACCAAGGACACAGTACCAGCACTGCACAGGATCAG                         GAAGTATCTTGTAGAGGCCACAAAAGAAGCATCCAADTCTTATAATGAAGC
genomic: TTGCGTGACACTTACACCAAGGACACAGTACCAGCACTGCACAGGATCAGgtatagttaa ... gcttttgcagGAAGTATCTTGTAGAGGCCACAAAAGAAGCATCCAATTCTTATAATGAAGC
EST: gi|60400409|gb|DN233216.1|DN233216
EST:     TTGCGTGACACTTACACCAAGGACACAGTACCAGCACTGCACAGGATCAG                         GAAGTATCTTGTAGAGGCCACAAAAGAAGCATCCAATTCTTATAATGAAGC
genomic: TTGCGTGACACTTACACCAAGGACACAGTACCAGCACTGCACAGGATCAGgtatagttaa ... gcttttgcagGAAGTATCTTGTAGAGGCCACAAAAGAAGCATCCAATTCTTATAATGAAGC
EST: gi|211359393|gb|FL440514.1|FL440514
EST:     TTGCGTGACACTTACACCAAGGACACAGTACCAGCACTGCACAGGATCAG                         GAAGTATCTTGTAGAGGCCACAAAAGAAGCATCCAANTCTTATAATGAAGC
genomic: TTGCGTGACACTTACACCAAGGACACAGTACCAGCACTGCACAGGATCAGgtatagttaa ... gcttttgcagGAAGTATCTTGTAGAGGCCACAAAAGAAGCATCCAATTCTTATAATGAAGC
EST: gi|71428336|gb|DR809386.1|DR809386
EST:     TTGCGTGACACTTACACCAAGGACACAGTACCAGCACTGCACAGGATCAG                         GAAGTATCTTGTAGAGGCCACAAAAGAAGCATCCAATTCTTATAATGAAGC
genomic: TTGCGTGACACTTACACCAAGGACACAGTACCAGCACTGCACAGGATCAGgtatagttaa ... gcttttgcagGAAGTATCTTGTAGAGGCCACAAAAGAAGCATCCAATTCTTATAATGAAGC
EST: gi|60401584|gb|DN234391.1|DN234391
EST:     TTGCGTGACACTTACACCAAGGACACAGTACCAGCACTGCACAGGATCAG                         GAAGTATCTTGTAGAGGCCACAAAAGAAGCATCCAATTCTTATAATGAAGC
genomic: TTGCGTGACACTTACACCAAGGACACAGTACCAGCACTGCACAGGATCAGgtatagttaa ... gcttttgcagGAAGTATCTTGTAGAGGCCACAAAAGAAGCATCCAATTCTTATAATGAAGC
EST: gi|71443220|gb|DR824270.1|DR824270
EST:     TTGCGTGACACTTACACCAAGGACACAGTACCAGCACTGCACAGGATCAG                         GAAGTATCTTGTAGAGGCCACAAAAGAAGCATCCAATTCTTATAATGAAGC
genomic: TTGCGTGACACTTACACCAAGGACACAGTACCAGCACTGCACAGGATCAGgtatagttaa ... gcttttgcagGAAGTATCTTGTAGAGGCCACAAAAGAAGCATCCAATTCTTATAATGAAGC
EST: gi|76281959|gb|DV021527.1|DV021527
EST:     TTGCGTGACACTTACACCAAGGACACAGTACCAGCACTGCACAGGATCAG                         GAAGTATCTTGTAGAGGCCACAAAAGAAGCATCCAATTCTTATAATGAAGC
genomic: TTGCGTGACACTTACACCAAGGACACAGTACCAGCACTGCACAGGATCAGgtatagttaa ... gcttttgcagGAAGTATCTTGTAGAGGCCACAAAAGAAGCATCCAATTCTTATAATGAAGC
EST: gi|71443221|gb|DR824271.1|DR824271
EST:     TTGCGTGACACTTACACCAAGGACACAGTACCAGCACTGCACAGGATCAG                         GAAGTATCTTGTAGAGGCCACAAAAGAAGCATCCAATTCTTATAATGAAG
genomic: TTGCGTGACACTTACACCAAGGACACAGTACCAGCACTGCACAGGATCAGgtatagttaa ... gcttttgcagGAAGTATCTTGTAGAGGCCACAAAAGAAGCATCCAATTCTTATAATGAAG
EST: gi|78122195|gb|DV540579.1|DV540579
EST:     TTGCGTGACACTTACACCAAGGACACAGTACCAGCACTGCACAGGATCAG                         GAAGTATCTTGTAGAGGCCACAAAAGAAGCATCCAATTCTTATAATGAAGC
genomic: TTGCGTGACACTTACACCAAGGACACAGTACCAGCACTGCACAGGATCAGgtatagttaa ... gcttttgcagGAAGTATCTTGTAGAGGCCACAAAAGAAGCATCCAATTCTTATAATGAAGC
EST: gi|211426623|gb|FL412861.1|FL412861
EST:     TTGCGTGACACTTACACCAAGGACACAGTACCAGCACTGCACAGGATCAG                         GAAGTATCTTGTAGAGGCCACAAAAGAAGCATCCA
genomic: TTGCGTGACACTTACACCAAGGACACAGTACCAGCACTGCACAGGATCAGgtatagttaa ... gcttttgcagGAAGTATCTTGTAGAGGCCACAAAAGAAGCATCCA
EST: gi|5895704|gb|AW036950.1|AW036950
EST:     TTACGTGACACTTACACCAAGGACACAGTACCAGCACTGCACAGGATCAG                         GAAGTATCTTGTAGAGGCCACAAAAGAAGCATCCAATTCTTATAATGAAGC
genomic: TTGCGTGACACTTACACCAAGGACACAGTACCAGCACTGCACAGGATCAGgtatagttaa ... gcttttgcagGAAGTATCTTGTAGAGGCCACAAAAGAAGCATCCAATTCTTATAATGAAGC
EST: gi|50331676|gb|CO526802.1|CO526802
EST:     TTGCGTGACACTTACACCAAGGACACAGTACCAGCACTGCACAGGATCAG                         GAAGTATCTTGTAGAGGCCACAAAAGAAGCATCCAATTCTTATAATGAAGC
genomic: TTGCGTGACACTTACACCAAGGACACAGTACCAGCACTGCACAGGATCAGgtatagttaa ... gcttttgcagGAAGTATCTTGTAGAGGCCACAAAAGAAGCATCCAATTCTTATAATGAAGC
EST: gi|110488821|gb|EE012728.1|EE012728
EST:     TTGCGTGACACTTACACCAAGGACACAGTACCAGCACTGCACAGGATCAG                         GAAGTATCTTGTAGAGGCCACAAAAGAAGCATCCAATTCTTATAATGAAGC
genomic: TTGCGTGACACTTACACCAAGGACACAGTACCAGCACTGCACAGGATCAGgtatagttaa ... gcttttgcagGAAGTATCTTGTAGAGGCCACAAAAGAAGCATCCAATTCTTATAATGAAGC
EST: gi|45568053|gb|CK985878.1|CK985878
EST:     TTGCGTGACACTTACACCAAGGACACAGTACCAGCACTGCACAGGATCAG                         GAAGTATCTTGTAGAGGCCACAAAAGAAGCATCCAATTCTTATAATGAAGC
genomic: TTGCGTGACACTTACACCAAGGACACAGTACCAGCACTGCACAGGATCAGgtatagttaa ... gcttttgcagGAAGTATCTTGTAGAGGCCACAAAAGAAGCATCCAATTCTTATAATGAAGC
EST: gi|148948940|gb|EC894359.2|EC894359
EST:     TTGCGTGACACTTACACCAAGGACACAGTACCAGCACTGCACAGGATCAG                         GAAGTATCTTGTAGAGGCCACAAAAGAAGCATCCAATTCTTATAATGAAGC
genomic: TTGCGTGACACTTACACCAAGGACACAGTACCAGCACTGCACAGGATCAGgtatagttaa ... gcttttgcagGAAGTATCTTGTAGAGGCCACAAAAGAAGCATCCAATTCTTATAATGAAGC
EST: gi|110504829|gb|EE017437.1|EE017437
EST:     TTGCGTGACACTTACACCAAGGACACAGTACCAGCACTGCACAGGATCAG                         GAAGTATTTTGTAGAGGCCACAAAAGAAGCATCCAATTCTTATAATGAAGC
genomic: TTGCGTGACACTTACACCAAGGACACAGTACCAGCACTGCACAGGATCAGgtatagttaa ... gcttttgcagGAAGTATCTTGTAGAGGCCACAAAAGAAGCATCCAATTCTTATAATGAAGC
EST: gi|60347346|gb|DN214319.1|DN214319
EST:     TTGCGTGACACTTACACCAAGGACACAGTACCAGCACTGCACAGGATCAG                         GAAGTATCTTGTAGAGGCCACAAAAGAAGCATCCAATTCTTATAATGAAGC
genomic: TTGCGTGACACTTACACCAAGGACACAGTACCAGCACTGCACAGGATCAGgtatagttaa ... gcttttgcagGAAGTATCTTGTAGAGGCCACAAAAGAAGCATCCAATTCTTATAATGAAGC
EST: gi|50324448|gb|CO519574.1|CO519574
EST:     TTGCGTGACACTTACACCAAGGACACAGTACCAGCACTGCACAGGATCAG                         GAAGTATCTTGTAGAGGCCACAAAAGAAGCATCCAATTCTTATAATGAAGC
genomic: TTGCGTGACACTTACACCAAGGACACAGTACCAGCACTGCACAGGATCAGgtatagttaa ... gcttttgcagGAAGTATCTTGTAGAGGCCACAAAAGAAGCATCCAATTCTTATAATGAAGC
EST: gi|211359065|gb|FL430712.1|FL430712
EST:     TTGCGTGACACTTACACCAAGGACACAGTACCAGCACTGCACAGGATCAG                         GAAGTATCTTGTAGAGGCCACAAAAGAAGCATCCAADTCTTATAATGAAGC
genomic: TTGCGTGACACTTACACCAAGGACACAGTACCAGCACTGCACAGGATCAGgtatagttaa ... gcttttgcagGAAGTATCTTGTAGAGGCCACAAAAGAAGCATCCAATTCTTATAATGAAGC
EST: gi|44900277|gb|CK826822.1|CK826822
EST:     TTGCGTGACACTTACACCAAGGACACAGTACCAGCACTGCACAGGATCAG                         GAAGTATCTTGTAGAGGCCACAAAAGAAGCATCCAATTCTTATAATGAAGC
genomic: TTGCGTGACACTTACACCAAGGACACAGTACCAGCACTGCACAGGATCAGgtatagttaa ... gcttttgcagGAAGTATCTTGTAGAGGCCACAAAAGAAGCATCCAATTCTTATAATGAAGC
EST: gi|211478808|gb|FL379717.1|FL379717
EST:     TTGCGTGACACTTACACCAAGGACACAGTACCAGCACTGCACAGGATCAG                         GAAGTATCTTGTAGAGGCCACAAAAGAAGCATCCAATTCTTATAATGAAGC
genomic: TTGCGTGACACTTACACCAAGGACACAGTACCAGCACTGCACAGGATCAGgtatagttaa ... gcttttgcagGAAGTATCTTGTAGAGGCCACAAAAGAAGCATCCAATTCTTATAATGAAGC
EST: gi|74237081|gb|DT644995.1|DT644995
EST:     TTGCGTGACACTTACACCAAGGACACAGTACCAGCACTGCACAGGATCAG                         GAAGTATCTTGTAGAGGCCACAAAAGAAGCATCCAATTCTTATAATGAAGC
genomic: TTGCGTGACACTTACACCAAGGACACAGTACCAGCACTGCACAGGATCAGgtatagttaa ... gcttttgcagGAAGTATCTTGTAGAGGCCACAAAAGAAGCATCCAATTCTTATAATGAAGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgcctttggttttcagcgaaggaccttcttgtaacatattaactgcttttgcagGAAGTATCTTGTAGAGGCCACAAAAGAAGCATCCAATTCTTATAATGAAGCG
                                     tattaac  putative branch site (score: 1)
                                           ctgctttt  CT-rich tract
                             ttgtaacatattaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatagttaaggcaatcgatcttgtagtggatatacttttttagtcatgttgcacttgttattcataagatggatttgatttgttaggtgcctttggttttcagcgaaggaccttcttgtaacatattaactgcttttgcagGAAGTATCTTGTAGAGGCCACAAAAGAAGCATCCAATTCTTATAATGAAGCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC