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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgggttttaatactattctatgaatattttcatcataggcaattaaacttttgagtttagctaacgacagctttattactgtctgcagCTATCTGGCTCCTGAATATGCACAGAGTGGGCAAATAACAGAGAAGGCTGATGTATACTCTTTCGGGGTTGTGTTAGTGGAACTTGTCACTGGGCGGAAG

Basic information

species Zea mays
transcript GRMZM2G480607_T04
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G480607_T04 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os01g41870.1 (Oryza sativa), 3'ss of exon 7
gtgggttttaatactattctatgaatattttcatcataggcaattaaacttttgagtttagctaacgacagctttatt--actgtctgcagCTATCTGGCTCCTGAATATGCACAGAGTGGGCAAATAACAGAGAAGGCTGATGTATACTCTTTCGGGGTTGTGTTAGTGGAACTTGTCACTGGGCGGAAG
||   | || | | |      ||  | || | | |||  ||| ||     || |    |   ||||||  ||| |  |   |||||||||| |||||||| || ||||| ||||||||||| |||||||||||||| ||||||||||||||||| |||||||||||||| ||||||||||||||||| |||
gtaaatattgagatttgcaactgtgtgttgtaaccatgtgcagtt-----ttgggcacttattaacga-ggctctgcttggctgtctgcagTTATCTGGCACCAGAATACGCACAGAGTGGACAAATAACAGAGAAAGCTGATGTATACTCTTTTGGGGTTGTGTTAGTTGAACTTGTCACTGGGCGCAAG

upper sequence: GRMZM2G480607_T04 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA15G02680.1 (Glycine max), 3'ss of exon 6
----gtgg-gttttaatactattctatgaatattttcatcataggcaattaaacttttg-agtttagctaacgacagctttattactgtct--gcagCTATCTGGCTCCTGAATATGCACAGAGTGGGCAAATAACAGAGAAGGCTGATGTATACTCTTTCGGGGTTGTGTTAGTGGAACTTGTCACTGGGCGGAAG
    |||| |  ||||| |||||   |    ||| ||    ||| || |  ||  |    | || | ||||     ||||| ||  || |   | || ||  ||||||| |||||||| || || || |||||||| || ||||| ||||| || |||||||| || || || ||||||||||| || || || |||
gtatgtggtgcattaatcctatttagttt-cattgtctagttagtcagtacaatatcaacaattcaactaa-----gctttgttggtgccatggtagGTACTTGGCTCCAGAATATGCTCAAAGCGGCCAAATAACTGAAAAGGCAGATGTTTATTCTTTCGGTGTGGTATTGGTGGAACTTGTTACAGGACGAAAG

upper sequence: GRMZM2G480607_T04 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA08G20750.1 (Glycine max), 3'ss of exon 6
gtgggttttaatactattctatgaatattttcatcataggcaattaaacttttgagt-ttagctaacgac--agctttattactgtc-tgcagCTATCTGGCTCCTGAATATGCACAGAGTGGGCAAATAACAGAGAAGGCTGATGTATACTCTTTCGGGGTTGTGTTAGTGGAACTTGTCACTGGGCGGAAG
||  || ||  || | | ||   || | ||||||| |    | ||  |  |   | | | || |  | ||  |||| |   | |    || || ||| |||||||||||||||| || ||||| ||||| || || || |||||||| || || || ||||| || |||||||| ||||| |||||| | || 
gtaagtattg-tattgtgcttgaaacaatttcatccttaa-acttgtatatgaaaatatcagattgcaactaagctatgccatttctgtgtagGTATTTGGCTCCTGAATATGCTCAAAGTGGCCAAATCACTGAAAAAGCTGATGTTTATTCCTTTGGGGTGGTATTAGTGGAGCTTGTTACTGGGAGAAAA

upper sequence: GRMZM2G480607_T04 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA13G42760.2 (Glycine max), 3'ss of exon 9
----gtgg-gttttaatactattctatgaatattttcatcataggcaattaaacttttg-agtttagctaacgacagctttattactgtc-tgcagCTATCTGGCTCCTGAATATGCACAGAGTGGGCAAATAACAGAGAAGGCTGATGTATACTCTTTCGGGGTTGTGTTAGTGGAACTTGTCACTGGGCGGAAG
    || | |  ||||| || ||   |    ||| ||    ||| |  |  ||  |    | || | ||||     ||||| ||  |||| || || ||  ||||||| |||||||| || || || |||||||| || ||||||||||| || |||||||| || || || ||||||||||| || || || |||
gtatgtagtgcattaatcctgtttagttt-cattgtctagttagtcggtacaatatcaacaattcaactaa-----gctttgttggtgtcatgtagGTACTTGGCTCCAGAATATGCTCAAAGCGGCCAAATAACTGAAAAGGCTGATGTTTATTCTTTCGGTGTGGTATTGGTGGAACTTGTTACAGGACGAAAG

upper sequence: GRMZM2G480607_T04 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA07G01350.1 (Glycine max), 3'ss of exon 6
gtgggttttaatactattctatgaatattttcatcataggcaattaaacttttgagtttagctaacgac--agctttattactgtc-tgcagCTATCTGGCTCCTGAATATGCACAGAGTGGGCAAATAACAGAGAAGGCTGATGTATACTCTTTCGGGGTTGTGTTAGTGGAACTTGTCACTGGGCGGAAG
||  || ||  || |  |||   || | ||||||| |    | ||  |      |    || |||| ||  |||| |   | |    || || ||| |||||||||||||||| || ||||| ||||| || || || |||||||| || || || ||||| || |||||||| ||||| || ||| | || 
gtaagtgttg-tattgatcttgaaacagtttcatccttaa-atttgtataagcaatgcgagataacaactaagctatgccatttctgtgtagGTATTTGGCTCCTGAATATGCTCAAAGTGGCCAAATCACTGAAAAAGCTGATGTTTATTCCTTTGGGGTGGTATTAGTGGAGCTTGTTACAGGGAGAAAA

upper sequence: GRMZM2G480607_T04 (Zea mays), 3'ss of exon 6
lower sequence: AT3G13690.1 (Arabidopsis thaliana), 3'ss of exon 7
gtgggttttaatactattctatgaatattttcatcataggcaattaaacttttgagtttagctaacgacagctttattactg-tctgcagCTATCTGGCTCCTGAATATGCACAGAGTGGGCAAATAACAGAGAAGGCTGATGTATACTCTTTCGGGGTTGTGTTAGTGGAACTTGTCACTGGGCGGAAG
    ||   |   ||| |  |   ||  |||       |  | ||||   ||||  | | |||||    |  |   |   || | ||||||||||| ||||| |||||||| || || |||||||| ||||| || |||||||| ||||| |||||||||||  |||| || || |||||||| || || 
----gtgagacacctactaaagctatcattttgctcctgaaacttaacaatttgtctgttgctaaaagaaattgcttggttggtgtgcagCTATCTAGCTCCCGAATATGCTCAAAGCGGGCAAATCACAGAAAAAGCTGATGTCTACTCGTTCGGGGTTGTTCTAGTTGAGCTAGTCACTGGCCGCAAA

upper sequence: GRMZM2G480607_T04 (Zea mays), 3'ss of exon 6
lower sequence: AT1G55200.1 (Arabidopsis thaliana), 3'ss of exon 6
gtgggttttaatactattctatgaatattttcatcataggcaattaaacttttgagtttagctaacgacagctttattactgtctgcagCTATCTGGCTCCTGAATATGCACAGAGTGGGCAAATAACAGAGAAGGCTGATGTATACTCTTTCGGGGTTGTGTTAGTGGAACTTGTCACTGGGCGGAAG
        ||| |  ||| ||| | ||  | ||||||   || |  |   |   | |||  | |       || | || ||   |  |||||| | ||||| || ||||| || ||||| ||||| |||||||| || ||||| ||||| ||||||||||| ||  | |||||  |||| || || || 
-------gtaacaaaatt-tataactaaat-catcattctcactctagagt---aatttctcaactactttctgtgtttcttgttttagCTATTTAGCTCCAGAGTATGCTCAAAGTGGACAAATCACAGAGAAAGCCGATGTTTACTCGTTCGGGGTTGTATTGATCGAACTAATCACGGGTCGTAAA

upper sequence: GRMZM2G480607_T04 (Zea mays), 3'ss of exon 6
lower sequence: Vv09s0002g02420.t01 (Vitis vinifera), 3'ss of exon 6
gtgggtttt-aatactattctatgaatattttcatcatag-gcaattaaacttttgagtttagctaacga-cagctttattactg--tctgcagCTATCTGGCTCCTGAATATGCACAGAGTGGGCAAATAACAGAGAAGGCTGATGTATACTCTTTCGGGGTTGTGTTAGTGGAACTTGTCACTGGGCGGAAG
||   |  | |||   |   | ||     ||| |   ||  ||  | | ||| ||    | | | || || |   | |  | ||   | || || ||| ||||||| |||||||| || || || ||||| ||||| |||||||||||||| ||||| |||||||| || ||||| |||||||| || || || 
gtaactactgaatgacagcttttg----ctttaactttaatgctttcacactgttatagt-atcaaatgagctattctgctccttgttatgtagGTATTTGGCTCCAGAATATGCTCAAAGCGGCCAAATCACAGAAAAGGCTGATGTATATTCTTTTGGGGTTGTCTTGGTGGAGCTTGTCACAGGACGAAAA

upper sequence: GRMZM2G480607_T04 (Zea mays), 3'ss of exon 6
lower sequence: Vv11s0016g02430.t01 (Vitis vinifera), 3'ss of exon 6
gtgggttttaatactattctatgaatattttcatcataggcaattaaacttttgagtttagctaacgac-agctttattactgtctgcagCTATCTGGCTCCTGAATATGCACAGAGTGGGCAAATAACAGAGAAGGCTGATGTATACTCTTTCGGGGTTGTGTTAGTGGAACTTGTCACTGGGCGGAAG
||       ||    |  || |      || |||||     |  ||||  |    |     | ||| |  |   ||| |  |||   ||| || ||| |||| |||||||| || ||||| ||||| ||||| || |||||||||||||| || || || ||||| ||||| ||  | || || ||||| 
gtaaacaagaaggacaagcttttggc--ttccatcaatactagctaaaaataatggcaagtcaaaccattaatcttacttttgt--acagGTACCTGTCTCCAGAATATGCTCAAAGTGGCCAAATCACAGAAAAAGCTGATGTATACTCCTTTGGAGTAGTGTTGGTGGAGCTCATTACAGGACGGAAA

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|211499478|gb|FL286053.1|FL286053
EST:     CAACCCGATGGAGACATGGGCGTTGAAACAAGAGTTATCGGCACATTCGG                         CTATCTGGCTCCTGAATATGCACAGAGTGGGCAAATAACAGAGAAGGCTGA
genomic: CAACCCGATGGAGACATGGGCGTTGAAACAAGAGTTATCGGCACATTCGGgtgggtttta ... ctgtctgcagCTATCTGGCTCCTGAATATGCACAGAGTGGGCAAATAACAGAGAAGGCTGA
EST: gi|32809375|gb|CD961609.1|CD961609
EST:     CAACCTGATGGAGACATGGGCGTTGAAACAAGAGTTATCGGCACATTCGG                         CTATCTGGCTCCTGAATATGCACAGAGTGGGCAAATAACAGAGAAGGCTGA
genomic: CAACCCGATGGAGACATGGGCGTTGAAACAAGAGTTATCGGCACATTCGGgtgggtttta ... ctgtctgcagCTATCTGGCTCCTGAATATGCACAGAGTGGGCAAATAACAGAGAAGGCTGA
EST: gi|29129926|gb|CB380630.1|CB380630
EST:     CAACCCGATGGAGACATGGGCGTTGAAACAAGAGTTATCGGCACATTCGG                         CTATCTGGCTCCTGAATATGCACAGAGTGGGCAAATAACAGAGAAGGCTGA
genomic: CAACCCGATGGAGACATGGGCGTTGAAACAAGAGTTATCGGCACATTCGGgtgggtttta ... ctgtctgcagCTATCTGGCTCCTGAATATGCACAGAGTGGGCAAATAACAGAGAAGGCTGA
EST: gi|32827128|gb|CD966806.1|CD966806
EST:     CAACCTGATGGAGACATGGGCGTTGAAACAAGAGTTATCGGCACATTCGG                         CTATCTGGCTCCTGAATATGCACAGAGTGGGCAAATAACAGAGAAGGCTGA
genomic: CAACCCGATGGAGACATGGGCGTTGAAACAAGAGTTATCGGCACATTCGGgtgggtttta ... ctgtctgcagCTATCTGGCTCCTGAATATGCACAGAGTGGGCAAATAACAGAGAAGGCTGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cataggcaattaaacttttgagtttagctaacgacagctttattactgtctgcagCTATCTGGCTCCTGAATATGCACAGAGTGGGCAAATAACAGAGAAGGCTGATGTATACTCTTTCGGGGTTGTGTTAGTGGAACTTGTCACTGGGCGGAAG
                         agctaac  putative branch site (score: 2)
       aattaaacttttga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgggttttaatactattctatgaatattttcatcataggcaattaaacttttgagtttagctaacgacagctttattactgtctgcagCTATCTGGCTCCTGAATATGCACAGAGTGGGCAAATAACAGAGAAGGCTGATGTATACTCTTTCGGGGTTGTGTTAGTGGAACTTGTCACTGGGCGGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA