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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...actcatgtgggagcctttggcaatgggtctgcccatcactgtttttttttcttcaagcttcatggtaatctagttttcctccttcatatgtgttttccagAGTGCTTATTTGCGAAGAAGGTTTGGAATGCACAAAATGCTGGTGCCTCTGCAGTACTTGTAGTTGATGACAAGGATGAACCATTGATAACAATGGATTT

Basic information

species Zea mays
transcript GRMZM2G303631_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G303631_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os10g20630.1 (Oryza sativa), 3'ss of exon 1
--actcatgtgggagcctttggcaatgggtctgcccatcactgtttttttttcttcaagcttcatggtaatctagttttcctccttcatatgtgttttccagAGTGCTTATTTGCGAAGAAGGTTTGGAATGCACAAAATGCTGGTGCCTCTGCAGTACTTGTAGTTGATGACAAGGATGAACCATTGATAACAATGGATTT
  || |   |  |||  |||   ||||  | |     |    | |   |  ||    |||||     ||| |     |   | |  | ||| | ||||||||| ||| ||||||| ||||||||||||||||| ||||||||||||||||| || || ||||| ||||||||||||||||| ||| |||| || ||||| ||
ggacac-catcagagtgttttataatgt-tatctatgttctagctagctgctcagttagcttggacataaacactaatgttttccccttatatcttttccagATTGCCTATTTGCTAAGAAGGTTTGGAATGCGCAAAATGCTGGTGCCTCAGCGGTCCTTGTGGTTGATGACAAGGATGAGCCACTGATTACTATGGACTT
















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|211020412|gb|FL417361.1|FL417361
EST:     CCGTG-CAAGCCTGGCGCGATGCCCACGTTCCTCCTCATCGACCGCGGTG                         AGTGCTTATTTGCGAAGAAGGTTTGGAATGCACAAAATGCTGGTGCCTCTG
genomic: CCGTGCCAAGCCTGGCGCGATGCCCACGTTCCTCCTCATCGACCGCGGTGgtaagtgctc ... tgttttccagAGTGCTTATTTGCGAAGAAGGTTTGGAATGCACAAAATGCTGGTGCCTCTG
EST: gi|71446773|gb|DR827823.1|DR827823
EST:     CCGTGCCAAGCCTGGCGCGATGCCCACGTTCCTCCTCATCGACCGCGGTG                         AGTGCTTATTTGCGAAGAAGGTTTGGAATGCACAAAATGCTGGTGCCTCTG
genomic: CCGTGCCAAGCCTGGCGCGATGCCCACGTTCCTCCTCATCGACCGCGGTGgtaagtgctc ... tgttttccagAGTGCTTATTTGCGAAGAAGGTTTGGAATGCACAAAATGCTGGTGCCTCTG
EST: gi|211182204|gb|FL384683.1|FL384683
EST:     CCGTGCCAAGCCTGGCGCGATGCCCACGTTCCTCCTCATCGACCGCGGTG                         AGTGCTTATTTGCGAAGAAGGTTTGGAATGCACAAAATGCTGGTGCCTCTG
genomic: CCGTGCCAAGCCTGGCGCGATGCCCACGTTCCTCCTCATCGACCGCGGTGgtaagtgctc ... tgttttccagAGTGCTTATTTGCGAAGAAGGTTTGGAATGCACAAAATGCTGGTGCCTCTG
EST: gi|149015111|gb|EE044871.2|EE044871
EST:     CCGTGCCAAGCCTGGCGCGATGCCCACGTTCCTCCTCATCGACCGCGGTG                         AGTGCTTATTTGCGAAGAAGGTTTGGAATGCACAAAATGCTGGTGCCTCTG
genomic: CCGTGCCAAGCCTGGCGCGATGCCCACGTTCCTCCTCATCGACCGCGGTGgtaagtgctc ... tgttttccagAGTGCTTATTTGCGAAGAAGGTTTGGAATGCACAAAATGCTGGTGCCTCTG
EST: gi|211343291|gb|FL376431.1|FL376431
EST:     CCGTGCCAAGCCTGGCGCGATGCCCACGTTCCTCCTCATCGACCGCGGTG                         AGTGCTTATTTGCGAAGAAGGTTTGGAATGCACAAAATGCTGGTGCCTCTG
genomic: CCGTGCCAAGCCTGGCGCGATGCCCACGTTCCTCCTCATCGACCGCGGTGgtaagtgctc ... tgttttccagAGTGCTTATTTGCGAAGAAGGTTTGGAATGCACAAAATGCTGGTGCCTCTG
EST: gi|211016651|gb|FL375786.1|FL375786
EST:     CCGTGCCAAGCCTGGCGCGATGCCCACGTTCCTCCTCATCGACCGCGGTG                         AGTGCTTATTTGCGAAGAAGGTTTGGAATGCACAAAATGCTGGTGCCTCTG
genomic: CCGTGCCAAGCCTGGCGCGATGCCCACGTTCCTCCTCATCGACCGCGGTGgtaagtgctc ... tgttttccagAGTGCTTATTTGCGAAGAAGGTTTGGAATGCACAAAATGCTGGTGCCTCTG
EST: gi|149071471|gb|EE159864.2|EE159864
EST:     CCGTGCCAAGCCTGGCGCGATGCCCACGTTCCTCCTCATCGACCGCGGTG                         AGTGCTTATTTGCGAAGAAGGTTTGGAATGCACAAAATGCTGGTGCCTCTG
genomic: CCGTGCCAAGCCTGGCGCGATGCCCACGTTCCTCCTCATCGACCGCGGTGgtaagtgctc ... tgttttccagAGTGCTTATTTGCGAAGAAGGTTTGGAATGCACAAAATGCTGGTGCCTCTG
EST: gi|211507024|gb|FL412043.1|FL412043
EST:     CCGTGCCAAGCCTGGCGCGATGCCCACGTTCCTCCTCATCGACCGCGGTG                         AGTGCTTATTTGCGAAGAAGGTTTGGAATGCACAAAATGCTGGTGCCTCTG
genomic: CCGTGCCAAGCCTGGCGCGATGCCCACGTTCCTCCTCATCGACCGCGGTGgtaagtgctc ... tgttttccagAGTGCTTATTTGCGAAGAAGGTTTGGAATGCACAAAATGCTGGTGCCTCTG
EST: gi|211464207|gb|FL411574.1|FL411574
EST:     CCGTGCCAAGCCTGGCGCGATGCCCACGTTCCTCCTCATCGACCGCGGNG                         AGTGCTTATTTGCGAAGAAGGTTTGGAATGCACAAAATGCTGGTGCCTCTG
genomic: CCGTGCCAAGCCTGGCGCGATGCCCACGTTCCTCCTCATCGACCGCGGTGgtaagtgctc ... tgttttccagAGTGCTTATTTGCGAAGAAGGTTTGGAATGCACAAAATGCTGGTGCCTCTG
EST: gi|211079484|gb|FL399069.1|FL399069
EST:     CCGTGCCAAGCCTGGCGCGATGCCCACGTTCCTCCTCATCGACCGCGGTG                         AGTGCTTATTTGCGAAGAAGGTTTGGAATGCACAAAATGCTGGTGCCTCTG
genomic: CCGTGCCAAGCCTGGCGCGATGCCCACGTTCCTCCTCATCGACCGCGGTGgtaagtgctc ... tgttttccagAGTGCTTATTTGCGAAGAAGGTTTGGAATGCACAAAATGCTGGTGCCTCTG
EST: gi|211382334|gb|FL400547.1|FL400547
EST:     CCGTGCCAAGCCTGGCGCGATGCCCACGTTCCTCCTCATCGACCGCGGTG                         AGTGCTTATTTGCGAAGAAGGTTTGGAATGCACAAAATGCTGGTGCCTCTG
genomic: CCGTGCCAAGCCTGGCGCGATGCCCACGTTCCTCCTCATCGACCGCGGTGgtaagtgctc ... tgttttccagAGTGCTTATTTGCGAAGAAGGTTTGGAATGCACAAAATGCTGGTGCCTCTG
EST: gi|211479856|gb|FL422857.1|FL422857
EST:     CCGTGCCAAGCCTGGCGCGATGCCCACGTTCCTCCTCATCGACCGCGGTG                         AGTGCTTATTTGCGAAGAAGGTTTGGAATGCACAAAATGCTGGTGCCTCTG
genomic: CCGTGCCAAGCCTGGCGCGATGCCCACGTTCCTCCTCATCGACCGCGGTGgtaagtgctc ... tgttttccagAGTGCTTATTTGCGAAGAAGGTTTGGAATGCACAAAATGCTGGTGCCTCTG
EST: gi|211332401|gb|FL404939.1|FL404939
EST:     CCGTGCCAAGCCTGGCGCGATGCCCACGTTCCTCCTCATCGACCGCGGTG                         AGTGCTTATTTGCGAAGAAGGTTTGGAATGCACAAAATGCTGGTGCCTCTG
genomic: CCGTGCCAAGCCTGGCGCGATGCCCACGTTCCTCCTCATCGACCGCGGTGgtaagtgctc ... tgttttccagAGTGCTTATTTGCGAAGAAGGTTTGGAATGCACAAAATGCTGGTGCCTCTG
EST: gi|211153696|gb|FL418633.1|FL418633
EST:     CCGTGCCAAGCCTGGCGCGATGCCCACGTTCCTCCTCATCGACCGCGGTG                         AGTGCTTATTTGCGAAGAAGGTTTGGAATGCACAAAATGCTGGTGCCTCTG
genomic: CCGTGCCAAGCCTGGCGCGATGCCCACGTTCCTCCTCATCGACCGCGGTGgtaagtgctc ... tgttttccagAGTGCTTATTTGCGAAGAAGGTTTGGAATGCACAAAATGCTGGTGCCTCTG
EST: gi|211273942|gb|FL428380.1|FL428380
EST:     CCGTGCCAAGCCTGGCGCGATGCCCACGTTNCTCCTCATCGACCGCGGTG                         AGTGCTTATTTGCGAAGAAGGTTTGGAATGCACAAAATGCTGGTGCCTCTG
genomic: CCGTGCCAAGCCTGGCGCGATGCCCACGTTCCTCCTCATCGACCGCGGTGgtaagtgctc ... tgttttccagAGTGCTTATTTGCGAAGAAGGTTTGGAATGCACAAAATGCTGGTGCCTCTG
EST: gi|211432184|gb|FL426792.1|FL426792
EST:     CCGTGCCAAGCCTGGCGCGATGCCCACGTTCCTCCTCATCGACCGCGGTG                         AGTGCTTATTTGCGAAGAAGGTTTGGAATGCACAAAATGCTGGTGCCTCTG
genomic: CCGTGCCAAGCCTGGCGCGATGCCCACGTTCCTCCTCATCGACCGCGGTGgtaagtgctc ... tgttttccagAGTGCTTATTTGCGAAGAAGGTTTGGAATGCACAAAATGCTGGTGCCTCTG
EST: gi|211464202|gb|FL411569.1|FL411569
EST:     CCGTGCCAAGCCTGGCGCGATGCCCACGTTCCTCCTCATCGACCGCGGTG                         AGTGCTTATTTGCGAAGAAGGTTTGGAATGCACAAAATGCTGGTGCCTCTG
genomic: CCGTGCCAAGCCTGGCGCGATGCCCACGTTCCTCCTCATCGACCGCGGTGgtaagtgctc ... tgttttccagAGTGCTTATTTGCGAAGAAGGTTTGGAATGCACAAAATGCTGGTGCCTCTG
EST: gi|211085794|gb|FL424016.1|FL424016
EST:     CCGTGCCAAGCCTGGCGCGATGCCCACGTTCCTCCTCATCGACCGCGGTG                         AGTGCTTATTTGCGAAGAAGGTTTGGAATGCACAAAATGCTGGTGCCTCTG
genomic: CCGTGCCAAGCCTGGCGCGATGCCCACGTTCCTCCTCATCGACCGCGGTGgtaagtgctc ... tgttttccagAGTGCTTATTTGCGAAGAAGGTTTGGAATGCACAAAATGCTGGTGCCTCTG
EST: gi|211271880|gb|FL420615.1|FL420615
EST:     CCGTGCCAAGCCTGGCGCGATGCCCACGTTCCTCCTCATCGACCGCGGTG                         AGTGCTTATTTGCGAAGAAGGTTTGGAATGCACAAAATGCTGGTGCCTCTG
genomic: CCGTGCCAAGCCTGGCGCGATGCCCACGTTCCTCCTCATCGACCGCGGTGgtaagtgctc ... tgttttccagAGTGCTTATTTGCGAAGAAGGTTTGGAATGCACAAAATGCTGGTGCCTCTG
EST: gi|211089832|gb|FL381142.1|FL381142
EST:     CCGTGCCAAGCCTGGCGCGATGCCCACGTTCCTCCTCATCGACCGCGGTG                         AGTGCTTATTTGCGAAGAAGGTTTGGAATGCACAAAATGCTGGTGCCTCTG
genomic: CCGTGCCAAGCCTGGCGCGATGCCCACGTTCCTCCTCATCGACCGCGGTGgtaagtgctc ... tgttttccagAGTGCTTATTTGCGAAGAAGGTTTGGAATGCACAAAATGCTGGTGCCTCTG
EST: gi|211517986|gb|FL372291.1|FL372291
EST:     CCGTGCCAAGCCTGGCGCGATGCCCACGTTCCTCCTCATCGACCGCGGTG                         AGTGCTTATTTGCGAAGAAGGTTTGGAATGCACAAAATGCTGGTGCCTCTG
genomic: CCGTGCCAAGCCTGGCGCGATGCCCACGTTCCTCCTCATCGACCGCGGTGgtaagtgctc ... tgttttccagAGTGCTTATTTGCGAAGAAGGTTTGGAATGCACAAAATGCTGGTGCCTCTG
EST: gi|33095145|gb|CF055139.1|CF055139
EST:     CCGTGCCAAGCCTGGTGCGATGCCCACGTTCCTCCTCATCGACCGCGGTG                         AGTGCTTATTTGCGAAGAAGGTTTGGAATGCACAAAATGCTGGTGCCTCTG
genomic: CCGTGCCAAGCCTGGCGCGATGCCCACGTTCCTCCTCATCGACCGCGGTGgtaagtgctc ... tgttttccagAGTGCTTATTTGCGAAGAAGGTTTGGAATGCACAAAATGCTGGTGCCTCTG
EST: gi|211298416|gb|FL370615.1|FL370615
EST:     CCGTGCCAAGCCTGGCGCGATGCCCACGTTCCTCCTCATCGACCGCGGTG                         AGTGCTTATTTGCGAAGAAGGTTTGGAATGCACAAAATGCTGGTGCCTCTG
genomic: CCGTGCCAAGCCTGGCGCGATGCCCACGTTCCTCCTCATCGACCGCGGTGgtaagtgctc ... tgttttccagAGTGCTTATTTGCGAAGAAGGTTTGGAATGCACAAAATGCTGGTGCCTCTG
EST: gi|211106506|gb|FL388546.1|FL388546
EST:     CCGTGCCAAGCCTGGCGCGATGCCCACGTTCCTCCTCATCGACCGCGGTG                         AGTGCTTATTTGCGAAGAAGGTTTGGAATGCACAAAATGCTGGTGCCTCTG
genomic: CCGTGCCAAGCCTGGCGCGATGCCCACGTTCCTCCTCATCGACCGCGGTGgtaagtgctc ... tgttttccagAGTGCTTATTTGCGAAGAAGGTTTGGAATGCACAAAATGCTGGTGCCTCTG
EST: gi|211207319|gb|FL408311.1|FL408311
EST:     CCGTGCCAAGCCTGGCGCGATGCCCACGTTCCTCCTCATCGACCGCGGTG                         AGTGCTTATTTGCGAAGAAGGTTTGGAATGCACAAAATGCTGGTGCCTCTG
genomic: CCGTGCCAAGCCTGGCGCGATGCCCACGTTCCTCCTCATCGACCGCGGTGgtaagtgctc ... tgttttccagAGTGCTTATTTGCGAAGAAGGTTTGGAATGCACAAAATGCTGGTGCCTCTG
EST: gi|211164583|gb|FL395494.1|FL395494
EST:     CCGTGCCAAGCCTGGCGCGATGCCCACGTTCTTCCTCNTCGACCGCGGTG                         AGTGCTTATTTGCGAAGAAGGTTTGGAATGCACAAAATGCTGGTGCCTCTG
genomic: CCGTGCCAAGCCTGGCGCGATGCCCACGTTCCTCCTCATCGACCGCGGTGgtaagtgctc ... tgttttccagAGTGCTTATTTGCGAAGAAGGTTTGGAATGCACAAAATGCTGGTGCCTCTG
EST: gi|211153129|gb|FL380299.1|FL380299
EST:     CCGTGCCAAGCCTGGCGCGATGCCCACGTTCCTCCTCATCGACCGCGGTG                         AGTGCTTATTTGCGAAGAAGGTTTGGAATGCACAAAATGCTGGTGCCTCTG
genomic: CCGTGCCAAGCCTGGCGCGATGCCCACGTTCCTCCTCATCGACCGCGGTGgtaagtgctc ... tgttttccagAGTGCTTATTTGCGAAGAAGGTTTGGAATGCACAAAATGCTGGTGCCTCTG
EST: gi|211332396|gb|FL404934.1|FL404934
EST:     CCGTGCCAAGCCTGGCGCGATGCCCACGTTCCTCCTCATCGACCGCGGTG                         AGTGCTTATTTGCGAAGAAGGTTTGGAATGCACAAAATGCTGGTGCCTCTG
genomic: CCGTGCCAAGCCTGGCGCGATGCCCACGTTCCTCCTCATCGACCGCGGTGgtaagtgctc ... tgttttccagAGTGCTTATTTGCGAAGAAGGTTTGGAATGCACAAAATGCTGGTGCCTCTG
EST: gi|211054452|gb|FL405166.1|FL405166
EST:     CCGTGCCAAGCCTGGCGCGATGCCCACGTTCCTCCTCATCGACCGCGGTG                         AGTGCTTATTTGCGAAGAAGGTTTGGAATGCACAAAATGCTGGTGCCTCTG
genomic: CCGTGCCAAGCCTGGCGCGATGCCCACGTTCCTCCTCATCGACCGCGGTGgtaagtgctc ... tgttttccagAGTGCTTATTTGCGAAGAAGGTTTGGAATGCACAAAATGCTGGTGCCTCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttttcttcaagcttcatggtaatctagttttcctccttcatatgtgttttccagAGTGCTTATTTGCGAAGAAGGTTTGGAATGCACAAAATGCTGGTGCCTCTGCAGTACTTGTAGTTGATGACAAGGATGAACCATTGATAACAATGGATTT
                                             tgttttcc  CT-rich tract
                    taatcta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
actcatgtgggagcctttggcaatgggtctgcccatcactgtttttttttcttcaagcttcatggtaatctagttttcctccttcatatgtgttttccagAGTGCTTATTTGCGAAGAAGGTTTGGAATGCACAAAATGCTGGTGCCTCTGCAGTACTTGTAGTTGATGACAAGGATGAACCATTGATAACAATGGATTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG