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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatcacttcgattctttatcgccattatttgagcagtattgtaaggattgtcttatttcttatttcagCTACACCGGCGAAGATGGTTTTGAGATCTCTGTTCCGTCAGAGAATGCAGTGGATCTTGCAGAGGCCATCCTAGAGAGATCGGAAGGCAAGGTGCGGCTG

Basic information

species Zea mays
transcript GRMZM5G876898_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G876898_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os04g53230.1 (Oryza sativa), 3'ss of exon 2
----------------------------------------gtatcacttcgattctttatcgccattatttgagcagtattgtaaggattgtcttatttcttatttcagCTACACCGGCGAAGATGGTTTTGAGATCTCTGTTCCGTCAGAGAATGCAGTGGATCTTGCAGAGGCCATCCTAGAGAGATCGGAAGGCAAGGTGCGGCTG
                                         |   ||| |  || |||   |  |||||||    |  | | |    ||  ||| |    || || ||| || ||||| |||||||| ||||| ||||||||||| |||||||||||||| ||||||||| ||||| |||| |||| ||| |||||||||||| | |||
gtatgcttcatttgatcctttagccaagttgttaacaaccatgctactacctttgttttgtggaattattttg--aacactatgtcaatattctgagaatttcttacagTTATACCGGTGAAGATGGGTTTGAAATCTCTGTTCCATCAGAGAATGCAGTTGATCTTGCAAAGGCCCTCCTGGAGAAATCTGAAGGCAAGGTGAGACTG

upper sequence: GRMZM5G876898_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA17G01550.1 (Glycine max), 3'ss of exon 3
------------------------------gtatcacttcgattctttatcgccattatttgagc--agtattgtaaggattgtcttatttcttatttcagCTACACCGGCGAAGATGGTTTTGAGATCTCTGTTCCGTCAGAGAATGCAGTGGATCTTGCAGAGGCCATCCTAGAGAGATCGGAAGGCAAGGTGCGGCTG
                                |      | || | | |||  ||||  |||  |  || ||  |||   ||   | |||     |||||| || || || |||||||| ||||||||||| ||||| |||||| ||| ||| ||||||||  | || || || || | ||| ||||| |||||  |  ||
tgcatgtttgtgttattagctcagagtttctcagggacaccatgcctaatc-tcattgattgtaccaagcataataaccttttcttgattgggactttcagGTATACTGGGGAAGATGGATTTGAGATCTCAGTTCCTTCAGAGCATGGAGTAGATCTTGCCAAAGCAATACTGGAAAAATCTGAAGGGAAGGTAAGATTG

upper sequence: GRMZM5G876898_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA09G00710.1 (Glycine max), 3'ss of exon 3
------------------------gtatcacttcgattctttatcgccatta-tttgagcagtattgtaaggattgtcttatttctta-------tttcagCTACACCGGCGAAGATGGTTTTGAGATCTCTGTTCCGTCAGAGAATGCAGTGGATCTTGCAGAGGCCATCCTAGAGAGATCGGAAGGCAAGGTGCGGCTG
                           ||| || |  | ||| | |  ||||  ||  | |||| |||      |     | |  | |       |||||| || || || |||||||| |||||||| ||  |||| ||||||| |||||||||||||||  |||| || || || | ||| ||||| ||| |  |  ||
tgatataatgagtgcaatttcataaattcagttagcctttttgt-gtaattagcttagggagtactgtgcatgataagacactcttcactgagactttcagGTATACTGGGGAAGATGGATTTGAGATATCAATTCCCTCAGAGAGTGCAGTGGATCTTGCCAAGGCAATTCTTGAAAAATCTGAAGGGAAGATAAGATTG

upper sequence: GRMZM5G876898_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA15G11590.1 (Glycine max), 3'ss of exon 3
------------------------gtatcacttcgattctttatcgccatta-tttgagcagtattgtaaggattgtcttatttctta-------tttcagCTACACCGGCGAAGATGGTTTTGAGATCTCTGTTCCGTCAGAGAATGCAGTGGATCTTGCAGAGGCCATCCTAGAGAGATCGGAAGGCAAGGTGCGGCTG
                         | ||| || |  | ||| | |  ||||  ||  | |||| |||    | |  |  | |  | |       |||||| || || || |||||||| |||||||| ||  |||| ||||||| |||||||||||||||  |||| || || || | ||| ||||| ||| |  | |||
tgatataacgagtgcaatttcataatttcagttagtctttttgt-gttattagcttagggagtactgtgcataataacacactcttcactgagactttcagGTATACTGGGGAAGATGGATTTGAGATATCAATTCCCTCAGAGAGTGCAGTGGATCTTGCCAAGGCAATTCTGGAAAAATCTGAAGGGAAGATAAGACTG

upper sequence: GRMZM5G876898_T01 (Zea mays), 3'ss of exon 2
lower sequence: Vv10s0116g01540.t01 (Vitis vinifera), 3'ss of exon 2
-------------------------gtatcacttcgattcttt--atcgccattatttg-agcagtattgtaaggattgtcttatttctta---tttcagCTACACCGGCGAAGATGGTTTTGAGATCTCTGTTCCGTCAGAGAATGCAGTGGATCTTGCAGAGGCCATCCTAGAGAGATCGGAAGGCAAGGTGCGGCTG
                         | |  |    || | | |  |||  ||        | ||  |   |    ||| ||||    |  |   |||||| ||||| || |||||||| ||||| || || ||||| || ||||||||||| ||||||||  | || ||| | |||| ||| ||||| |||||  || | 
taatgatttagtcacaatccaaattgcaatatgatgactgtctgaatcaacaaaccccacaacaagacacttgatattttctttacacgaaaattttcagGTACACAGGTGAAGATGGATTTGAAATTTCAGTTCCTTCCGAGAATGCAGTAGATCTTGCCAAAGCAATCTTGGAGAAATCTGAAGGGAAGGTAAGGTTA

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|101384898|gb|EB814495.1|EB814495
EST:     TTCAAGATGATTGACATCAATGGATATGCATGCTTTCTGACGAGAACTGG                         CTACACCGGCGAAGATGGTTTTGAGATCTCTGTTCCGTCAGAGAATGCAGT
genomic: TTCAAGATGATTGACATCAATGGATATGCATGCTTTCTGACGAGAACTGGgtatcacttc ... cttatttcagCTACACCGGCGAAGATGGTTTTGAGATCTCTGTTCCGTCAGAGAATGCAGT
EST: gi|149081734|gb|EE170887.2|EE170887
EST:     GATGATTGACATCAATGGATATGCATGCTTTCTGACGAGAACTGG                         CTACACCGGCGAAGATGGTTTTGAGATCTCTGTTCCGTCAGAGAATGCAGT
genomic: GATGATTGACATCAATGGATATGCATGCTTTCTGACGAGAACTGGgtatcacttc ... cttatttcagCTACACCGGCGAAGATGGTTTTGAGATCTCTGTTCCGTCAGAGAATGCAGT
EST: gi|71298695|gb|DR785329.1|DR785329
EST:     GATATGCATGCTTTTTGACGAGAACTGG                         CTACACCGGCGAAGATGGTTTTGAGATCTCTGTTCCGTCAGAGAATGCAGT
genomic: GATATGCATGCTTTCTGACGAGAACTGGgtatcacttc ... cttatttcagCTACACCGGCGAAGATGGTTTTGAGATCTCTGTTCCGTCAGAGAATGCAGT
EST: gi|149070658|gb|EE159071.2|EE159071
EST:     TTCAAGATGATTGACATCAATGGATATGCATGCTTTCTGACGAGAACTGG                         CTACACCGGCGAAGATGGTTTTGAGATCTCTGTTCCGTCAGAGAATGCAGT
genomic: TTCAAGATGATTGACATCAATGGATATGCATGCTTTCTGACGAGAACTGGgtatcacttc ... cttatttcagCTACACCGGCGAAGATGGTTTTGAGATCTCTGTTCCGTCAGAGAATGCAGT
EST: gi|78077069|gb|DV505503.1|DV505503
EST:     TTCAAGATGATTGACATCAATGGATATGCATGCTTTCTGACGAGAACTGG                         CTACACCGGCGAAGATGGTTTTGAGATCTCTGTTCCGTCAGAGAATGCAGT
genomic: TTCAAGATGATTGACATCAATGGATATGCATGCTTTCTGACGAGAACTGGgtatcacttc ... cttatttcagCTACACCGGCGAAGATGGTTTTGAGATCTCTGTTCCGTCAGAGAATGCAGT
EST: gi|6057020|gb|AW091425.1|AW091425
EST:     TTCAAGATGATTGACATCAATGGATATGCATGCTTTCTGACGAGAACTGG                         CTACACCGGCGAAGATG
genomic: TTCAAGATGATTGACATCAATGGATATGCATGCTTTCTGACGAGAACTGGgtatcacttc ... cttatttcagCTACACCGGCGAAGATG
EST: gi|78105884|gb|DV524302.1|DV524302
EST:     ATGCTTTCTGACGAGAACTGG                         CTACACCGGCGAAGATGGTTTTGAGATCTCTGTTCCGTCAGAGAATGCAGT
genomic: ATGCTTTCTGACGAGAACTGGgtatcacttc ... cttatttcagCTACACCGGCGAAGATGGTTTTGAGATCTCTGTTCCGTCAGAGAATGCAGT
EST: gi|78108488|gb|DV526906.1|DV526906
EST:     TCAATGGATATGCATGCTTTCTGACGAGAACTGG                         CTACACCGGCGAAGATGGTTTTGAGATCTCTGTTCCGTCAGAGAATGCAGT
genomic: TCAATGGATATGCATGCTTTCTGACGAGAACTGGgtatcacttc ... cttatttcagCTACACCGGCGAAGATGGTTTTGAGATCTCTGTTCCGTCAGAGAATGCAGT
EST: gi|211083360|gb|FK979333.1|FK979333
EST:     TTCAAGATGATTGACATCAATGGATATGCATGCTTTCTGACGAGAACTGG                         CTACACCGGCGAAGATGGTTTTGAGATCTCTGTTCNGTCAGAGAATGCAGT
genomic: TTCAAGATGATTGACATCAATGGATATGCATGCTTTCTGACGAGAACTGGgtatcacttc ... cttatttcagCTACACCGGCGAAGATGGTTTTGAGATCTCTGTTCCGTCAGAGAATGCAGT
EST: gi|149105650|gb|EE291204.2|EE291204
EST:     TTCAAGATGATTGACATCAATGGATATGCATGCTTTCTGACGAGAACTGG                         CTACACCGGCGAAGATGGTTTTGAGATCTCTGTTCCGTCAGAGAATGCAGT
genomic: TTCAAGATGATTGACATCAATGGATATGCATGCTTTCTGACGAGAACTGGgtatcacttc ... cttatttcagCTACACCGGCGAAGATGGTTTTGAGATCTCTGTTCCGTCAGAGAATGCAGT
EST: gi|89763865|gb|DY690880.1|DY690880
EST:     TCAAAGATGATTGACATCAATGGATATGCATGCTTTCTGACGAGAACTGG                         CTACACCGGCGAAGATGGTTTTGAGATCTCTGTTCCGTCAGAGAATGCAGT
genomic: TC-AAGATGATTGACATCAATGGATATGCATGCTTTCTGACGAGAACTGGgtatcacttc ... cttatttcagCTACACCGGCGAAGATGGTTTTGAGATCTCTGTTCCGTCAGAGAATGCAGT
EST: gi|148946694|gb|EC891957.2|EC891957
EST:     TTCAAGATGATTGACATCAATGGATATGCATGCTTTCTGACGAGAACTGG                         CTACACCGGCGAAGATGGTTTTGAGATCTCTGTTCCGTCAGAGAATGCAGT
genomic: TTCAAGATGATTGACATCAATGGATATGCATGCTTTCTGACGAGAACTGGgtatcacttc ... cttatttcagCTACACCGGCGAAGATGGTTTTGAGATCTCTGTTCCGTCAGAGAATGCAGT
EST: gi|149086495|gb|EE176039.2|EE176039
EST:     TTCAAGATGATTGACATCAATGGATATGCATGCTTTCTGACGAGAACTGG                         CTACACCGGCGAAGATGGTTTTGAGATCTCTGTTCCGTCAGAGAATGCAGT
genomic: TTCAAGATGATTGACATCAATGGATATGCATGCTTTCTGACGAGAACTGGgtatcacttc ... cttatttcagCTACACCGGCGAAGATGGTTTTGAGATCTCTGTTCCGTCAGAGAATGCAGT
EST: gi|110525157|gb|EE029341.1|EE029341
EST:     TGCTTTTTGACGGGAACTGG                         CTACACCGGCGAAGATGGTTTTGAGATCTCTGTTCCGTCAGAGAATGCAGT
genomic: TGCTTTCTGACGAGAACTGGgtatcacttc ... cttatttcagCTACACCGGCGAAGATGGTTTTGAGATCTCTGTTCCGTCAGAGAATGCAGT
EST: gi|211083361|gb|FK979334.1|FK979334
EST:     TTCAAGATGATTGACATCAATGGATATGCATGCTTTCTGACGAGAACTGG                         CTACACCGGCGAAGATGGTTTTGAGATCTCTGTTCCGTCAGAGAATGCAGT
genomic: TTCAAGATGATTGACATCAATGGATATGCATGCTTTCTGACGAGAACTGGgtatcacttc ... cttatttcagCTACACCGGCGAAGATGGTTTTGAGATCTCTGTTCCGTCAGAGAATGCAGT
EST: gi|211013840|gb|FL029530.1|FL029530
EST:     TTCAAGATGATTGACATCAATGGATATGCATGCTTTCTGACGAGAACTGG                         CTACACCGGCGAAGATGGTTTTGAGATCTCTGTTCCGTCAGAGAATGCAGT
genomic: TTCAAGATGATTGACATCAATGGATATGCATGCTTTCTGACGAGAACTGGgtatcacttc ... cttatttcagCTACACCGGCGAAGATGGTTTTGAGATCTCTGTTCCGTCAGAGAATGCAGT
EST: gi|71764601|gb|DR962538.1|DR962538
EST:     TTCAAGATGATTGACATCAATGGATATGCATGCTTTCTGACGAGAACTGG                         CTACACCGGCGAAGATGGTTGTGAGATCTCTGTTCCGTCAGAGAATGCAGT
genomic: TTCAAGATGATTGACATCAATGGATATGCATGCTTTCTGACGAGAACTGGgtatcacttc ... cttatttcagCTACACCGGCGAAGATGGTTTTGAGATCTCTGTTCCGTCAGAGAATGCAGT
EST: gi|78107530|gb|DV525948.1|DV525948
EST:     ATATGCATGCTTTCTGACGAGAACTGG                         CTACACCGGCGAAGATGGTTTTGAGATCTCTGTTCCGTCAGAGAATGCAGT
genomic: ATATGCATGCTTTCTGACGAGAACTGGgtatcacttc ... cttatttcagCTACACCGGCGAAGATGGTTTTGAGATCTCTGTTCCGTCAGAGAATGCAGT
EST: gi|211083363|gb|FK979336.1|FK979336
EST:     TTCAAGATGATTGACATCAATGGATATGCATGCTTTCTGACGAGAACTGG                         CTACACCGGCGAAGATGGTTTTGAGATCTCTGTTCCGTCAGAGAATGCAGT
genomic: TTCAAGATGATTGACATCAATGGATATGCATGCTTTCTGACGAGAACTGGgtatcacttc ... cttatttcagCTACACCGGCGAAGATGGTTTTGAGATCTCTGTTCCGTCAGAGAATGCAGT
EST: gi|211083362|gb|FK979335.1|FK979335
EST:     TTCAAGATGATTGACATCAATGGATATGCATGCTTTCTGACGAGAACTGG                         CTACACCGGCGAAGATGGTTTTGAGATCTCTGTTCCGTCAGAGAATGCAGT
genomic: TTCAAGATGATTGACATCAATGGATATGCATGCTTTCTGACGAGAACTGGgtatcacttc ... cttatttcagCTACACCGGCGAAGATGGTTTTGAGATCTCTGTTCCGTCAGAGAATGCAGT
EST: gi|211013839|gb|FL029529.1|FL029529
EST:     TTCAAGATGATTGACATCAATGGATATGCATGCTTTCTGACGAGAACTGG                         CTACACCGGCGAAGATGGTTTTGAGATCTCTGTTCCGTCAGAGAATGCAGT
genomic: TTCAAGATGATTGACATCAATGGATATGCATGCTTTCTGACGAGAACTGGgtatcacttc ... cttatttcagCTACACCGGCGAAGATGGTTTTGAGATCTCTGTTCCGTCAGAGAATGCAGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctttatcgccattatttgagcagtattgtaaggattgtcttatttcttatttcagCTACACCGGCGAAGATGGTTTTGAGATCTCTGTTCCGTCAGAGAATGCAGTGGATCTTGCAGAGGCCATCCTAGAGAGATCGGAAGGCAAGGTGCGGCTG
                                     tcttatttcttatttc  CT-rich tract
                                     tcttatttcttattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatcacttcgattctttatcgccattatttgagcagtattgtaaggattgtcttatttcttatttcagCTACACCGGCGAAGATGGTTTTGAGATCTCTGTTCCGTCAGAGAATGCAGTGGATCTTGCAGAGGCCATCCTAGAGAGATCGGAAGGCAAGGTGCGGCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC