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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atatgcaaactactcttgtctgtactgaacatttgtggacttcgttggcaattgtgtaatgcatcattaatgaatcatgcgacaaattttgtggttttagGGATCATGCTGGTGGCAATGAGAAGATGAGGCTGCAGGTGCCAGGGATAAAGGTATTTGGAGGATCCCTGGACAATGTGAAAGGCTGCACTGATCAGGTG

Basic information

species Zea mays
transcript GRMZM2G031825_T03
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G031825_T05 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os03g21460.1 (Oryza sativa), 3'ss of exon 2
atatgcaaactactcttgtctgtactgaacatttgtggacttcgttggcaattgtgtaatgcatcattaat-gaatcatgcgacaaatt-----ttgtggttttagGGATCATGCTGGTGGCAATGAGAAGATGAGGCTGCAGGTGCCAGGGATAAAGGTATTTGGAGGATCCCTGGACAATGTGAAAGGCTGCACTGATCAGGTG
||    | | || | ||     | |   |  ||||  || ||| || ||||   ||||  | |    |||| |||     | || |||      |||||||| |||||||||||||||||||||||| ||||||  || |   ||||||||||| ||||| | ||||||||||||||||||||||||||| |||||||||||||||
atgcatagaatattatt-----tgccagat-tttgctgaattcattagcaacgatgtagagaagtggtaattgaaaagcccaactaatccgtggttgtggttgtagGGATCATGCTGGTGGCAATGAAAAGATGGCGCAGTCAGTGCCAGGGATTAAGGTCTATGGAGGATCCCTGGACAATGTGAAAGGATGCACTGATCAGGTG
















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|211455844|gb|FL371246.1|FL371246
EST:     GGCGAGGTCGGCGCCTACGTCGACTGCGTTCTCACCACCCATCACCACTG                         GGATCATGCTGGTGGCAATGAGAAGATGAGGCTGCAGGTGCCAGGGATAAA
genomic: GGCGAGGTCGGCGCCTACGTCGACTGCGTTCTCACCACCCATCACCACTGgtataccata ... gtggttttagGGATCATGCTGGTGGCAATGAGAAGATGAGGCTGCAGGTGCCAGGGATAAA
EST: gi|211282892|gb|FL423639.1|FL423639
EST:     GGCGAGGTCGGCGCCTACGTCGACTGCGTTCTCACCACCCATCACCACTG                         GGATCATGCTGGTGGCAATGAGAAGATGAGGCTGCAGGTGCCAGGGATAAA
genomic: GGCGAGGTCGGCGCCTACGTCGACTGCGTTCTCACCACCCATCACCACTGgtataccata ... gtggttttagGGATCATGCTGGTGGCAATGAGAAGATGAGGCTGCAGGTGCCAGGGATAAA
EST: gi|211276907|gb|FL386582.1|FL386582
EST:     GGCGAGGTCGGCGCCTACGTCGACTGCGTTCTCACCACCCATCACCACTG                         GGGATCATGCTGGTGGCAATGAGAAGATGAGGCTGCAGGTGCCAGGGATAA
genomic: GGCGAGGTCGGCGCCTACGTCGACTGCGTTCTCACCACCCATCACCACTGgtataccata ... gtggttttagGG-ATCATGCTGGTGGCAATGAGAAGATGAGGCTGCAGGTGCCAGGGATAA
EST: gi|211487768|gb|FL393005.1|FL393005
EST:     GGCGAGGTCGGCGCCTACGTCGACTGCGTTCTCACCACCCATCACCACTG                         GGATCATGCTGGTGGCAATGAGAAGATGAGGCTGCAGGTGCCAGGGATAAA
genomic: GGCGAGGTCGGCGCCTACGTCGACTGCGTTCTCACCACCCATCACCACTGgtataccata ... gtggttttagGGATCATGCTGGTGGCAATGAGAAGATGAGGCTGCAGGTGCCAGGGATAAA
EST: gi|211436196|gb|FL370281.1|FL370281
EST:     GGCGAGGTCGGCGCCTACGTCGACTGCGTTCTCACCACCCATCACCACTG                         GGATCATGCTGGTGGCAATGAGAAGATGAGGCTGCAGGTGCCAGGGATAAA
genomic: GGCGAGGTCGGCGCCTACGTCGACTGCGTTCTCACCACCCATCACCACTGgtataccata ... gtggttttagGGATCATGCTGGTGGCAATGAGAAGATGAGGCTGCAGGTGCCAGGGATAAA
EST: gi|211112220|gb|FL429165.1|FL429165
EST:     GGCGAGGTCGGCGCCTACGTCGACTGCGTTCTCACCACCCATCACCACTG                         GGATCATGCTGGTGGCAATGAGAAGATGAGGCTGCAGGTGCCAGGGATAAA
genomic: GGCGAGGTCGGCGCCTACGTCGACTGCGTTCTCACCACCCATCACCACTGgtataccata ... gtggttttagGGATCATGCTGGTGGCAATGAGAAGATGAGGCTGCAGGTGCCAGGGATAAA
EST: gi|211201689|gb|FL384215.1|FL384215
EST:     GGCGAGGTCGGCGCCTACGTCGACTGCGTTCTCACCACCCATCACCACTG                         GGATCATGCTGGTGGCAATGAGAAGATGAGGCYGCAGGTGCCAGGGATAAA
genomic: GGCGAGGTCGGCGCCTACGTCGACTGCGTTCTCACCACCCATCACCACTGgtataccata ... gtggttttagGGATCATGCTGGTGGCAATGAGAAGATGAGGCTGCAGGTGCCAGGGATAAA
EST: gi|211251969|gb|FL399229.1|FL399229
EST:     GGCGAGGTCGGCGCCTACGTCGACTGCGTTCTCACCACCCATCACCACTG                         GGATCATGCTGGTGGCAATGAGAAGATGAGGCTGCAGGTGCCAGGGATAAA
genomic: GGCGAGGTCGGCGCCTACGTCGACTGCGTTCTCACCACCCATCACCACTGgtataccata ... gtggttttagGGATCATGCTGGTGGCAATGAGAAGATGAGGCTGCAGGTGCCAGGGATAAA
EST: gi|211539553|gb|FL409993.1|FL409993
EST:     GGCGAGGTCGGCGCCTACGTCGACTGCGTTCTCACCACCCATCACCACTG                         GGATCATGCTGGTGGCAATGAGAAGATGAGGCTGCAGGTGCCAGGGATAAA
genomic: GGCGAGGTCGGCGCCTACGTCGACTGCGTTCTCACCACCCATCACCACTGgtataccata ... gtggttttagGGATCATGCTGGTGGCAATGAGAAGATGAGGCTGCAGGTGCCAGGGATAAA
EST: gi|32910784|gb|CF015596.1|CF015596
EST:     GGCGAGGTCGGCGCCTACGTCGACTGCGTTCTCACCACCCATCACCACTG                         GGATCATGCTGGTGGCAATGAGAAGATGAGGCTGCAGGTGCCAGGGATAAA
genomic: GGCGAGGTCGGCGCCTACGTCGACTGCGTTCTCACCACCCATCACCACTGgtataccata ... gtggttttagGGATCATGCTGGTGGCAATGAGAAGATGAGGCTGCAGGTGCCAGGGATAAA
EST: gi|211133046|gb|FL407432.1|FL407432
EST:     GGCGAGGTCGGCGCCTACGTCGACTGCGTTCTCACCACCCATCACCACTG                         GGATCATGCTGGTGGCAATGAGAAGATGAGGCTGCAGGTGCCAGGGATAAA
genomic: GGCGAGGTCGGCGCCTACGTCGACTGCGTTCTCACCACCCATCACCACTGgtataccata ... gtggttttagGGATCATGCTGGTGGCAATGAGAAGATGAGGCTGCAGGTGCCAGGGATAAA
EST: gi|211445202|gb|FL371167.1|FL371167
EST:     GGCGAGGTCGGCGCCTACGTCGACTGCGTTCTCACCACCCATCACCACTG                         GGATCATGCTGGTGGCAATGAGAAGATGAGGCTGCAGGTGCCAGGGATAAA
genomic: GGCGAGGTCGGCGCCTACGTCGACTGCGTTCTCACCACCCATCACCACTGgtataccata ... gtggttttagGGATCATGCTGGTGGCAATGAGAAGATGAGGCTGCAGGTGCCAGGGATAAA
EST: gi|211451679|gb|FL376124.1|FL376124
EST:     GGCGAGGTCGGCGCCTACGTCGACTGCGTTCTCACCACCCATCACCACTG                         GGATCATGCTGGTGGCAATGAGAAGATGAGGCTGCAGGTGCCAGGGATAAA
genomic: GGCGAGGTCGGCGCCTACGTCGACTGCGTTCTCACCACCCATCACCACTGgtataccata ... gtggttttagGGATCATGCTGGTGGCAATGAGAAGATGAGGCTGCAGGTGCCAGGGATAAA
EST: gi|211520775|gb|FL373480.1|FL373480
EST:     GGCGANGTCNGCGCCTACGTCGACTGCGTTCTCACCACCCATCACCACTG                         GGATCATGCTGGTGGCAATGA
genomic: GGCGAGGTCGGCGCCTACGTCGACTGCGTTCTCACCACCCATCACCACTGgtataccata ... gtggttttagGGATCATGCTGGTGGCAATGA
EST: gi|211143159|gb|FL403015.1|FL403015
EST:     GGCGAGGTCGGCGCCTACGTCGACTGCGTTCTCACCACCCATCACCACTG                         GGATCATGCTGGTGGCMATGAGAAGATGAGGCTGCAGGTGCCAGGGATAAA
genomic: GGCGAGGTCGGCGCCTACGTCGACTGCGTTCTCACCACCCATCACCACTGgtataccata ... gtggttttagGGATCATGCTGGTGGCAATGAGAAGATGAGGCTGCAGGTGCCAGGGATAAA
EST: gi|211265984|gb|FL369214.1|FL369214
EST:     GGCGAGGTCGGCGCCTACGTCGACTGCGTTCTCACCACCCATCACCACTG                         GGATCATGCTGGTGGCAATGAGAAGATGAGGCTGCAGGTGCCAGGGATAAA
genomic: GGCGAGGTCGGCGCCTACGTCGACTGCGTTCTCACCACCCATCACCACTGgtataccata ... gtggttttagGGATCATGCTGGTGGCAATGAGAAGATGAGGCTGCAGGTGCCAGGGATAAA
EST: gi|32910981|gb|CF015793.1|CF015793
EST:     GGCGAGGTCGGCGCCTACGTCGACTGCGTTCTCACCACCCATCACCACTG                         GGATCATGCTGGTGGCAATGAGAAGATGAGGCTGCAGGTGCCAGGGATAAA
genomic: GGCGAGGTCGGCGCCTACGTCGACTGCGTTCTCACCACCCATCACCACTGgtataccata ... gtggttttagGGATCATGCTGGTGGCAATGAGAAGATGAGGCTGCAGGTGCCAGGGATAAA
EST: gi|211497290|gb|FL426479.1|FL426479
EST:     GGCGAGGTCGGCGCCTACGTCGACTGCGTTCTCACCACCCATCACCACTG                         GGATCATGCTGGTGGCAATGAGAAGATGAGGCTGCAG
genomic: GGCGAGGTCGGCGCCTACGTCGACTGCGTTCTCACCACCCATCACCACTGgtataccata ... gtggttttagGGATCATGCTGGTGGCAATGAGAAGATGAGGCTGCAG
EST: gi|211231771|gb|FL389681.1|FL389681
EST:     GGCGAGGTCGGCGCCTACGTCGACTGCGTTCTCACCACCCATCACCACTG                         GGATCATGCTGGTGGCAATGAGAAGATGAGGCTGCAGGTGCCAGGGATAAA
genomic: GGCGAGGTCGGCGCCTACGTCGACTGCGTTCTCACCACCCATCACCACTGgtataccata ... gtggttttagGGATCATGCTGGTGGCAATGAGAAGATGAGGCTGCAGGTGCCAGGGATAAA
EST: gi|32803246|gb|CD955482.1|CD955482
EST:     GGCGAGGTCGGCGCCTACGTCGACTGCGTTCTCACCACCCATCACCACTG                         GGATCATGCTGGTGGCAATGAGAAGATGAGGCTGCAGGTGCCAGGGATAAA
genomic: GGCGAGGTCGGCGCCTACGTCGACTGCGTTCTCACCACCCATCACCACTGgtataccata ... gtggttttagGGATCATGCTGGTGGCAATGAGAAGATGAGGCTGCAGGTGCCAGGGATAAA
EST: gi|211090884|gb|FL430012.1|FL430012
EST:     GGCGAGGTCGGCGCCTACGTCGACTGCGTTCTCACCACCCATCACCACTG                         GGATCATGCTGGTGGCAATGAGAAGATGAGGCTGCAGGTGCCAGGGATAAA
genomic: GGCGAGGTCGGCGCCTACGTCGACTGCGTTCTCACCACCCATCACCACTGgtataccata ... gtggttttagGGATCATGCTGGTGGCAATGAGAAGATGAGGCTGCAGGTGCCAGGGATAAA
EST: gi|211108385|gb|FL394493.1|FL394493
EST:     GGCGAGGTCGGCGCCTACGTCGACTGCGTTCTCACCACCCATCACCACTG                         GGATCATGCTGGTGGCAATGAGAAGATGAGGCTGCAGGTGCCAGGGATAAA
genomic: GGCGAGGTCGGCGCCTACGTCGACTGCGTTCTCACCACCCATCACCACTGgtataccata ... gtggttttagGGATCATGCTGGTGGCAATGAGAAGATGAGGCTGCAGGTGCCAGGGATAAA
EST: gi|211529760|gb|FL372707.1|FL372707
EST:     GGCGAGGTCGGCGCCTACGTCGACTGCGTTCTCACCACCCATCACCACTG                         GGATCATGCTGGTGGCAATGAGAAGATGAGGCTGCAGGTGCCAGGGATAAA
genomic: GGCGAGGTCGGCGCCTACGTCGACTGCGTTCTCACCACCCATCACCACTGgtataccata ... gtggttttagGGATCATGCTGGTGGCAATGAGAAGATGAGGCTGCAGGTGCCAGGGATAAA
EST: gi|211464411|gb|FL419842.1|FL419842
EST:     GGCGAGGTCGGCGCCTACGTCGACTGCGTTCTCACCACCCATCACCACTG                         GGATCATGCTGGTGGCAATGAGAAGATGAGGCTGCAGGTGCCAGGGATAAA
genomic: GGCGAGGTCGGCGCCTACGTCGACTGCGTTCTCACCACCCATCACCACTGgtataccata ... gtggttttagGGATCATGCTGGTGGCAATGAGAAGATGAGGCTGCAGGTGCCAGGGATAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggcaattgtgtaatgcatcattaatgaatcatgcgacaaattttgtggttttagGGATCATGCTGGTGGCAATGAGAAGATGAGGCTGCAGGTGCCAGGGATAAAGGTATTTGGAGGATCCCTGGACAATGTGAAAGGCTGCACTGATCAGGTG
                   cattaat  putative branch site (score: 3)
                    attaatgaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atatgcaaactactcttgtctgtactgaacatttgtggacttcgttggcaattgtgtaatgcatcattaatgaatcatgcgacaaattttgtggttttagGGATCATGCTGGTGGCAATGAGAAGATGAGGCTGCAGGTGCCAGGGATAAAGGTATTTGGAGGATCCCTGGACAATGTGAAAGGCTGCACTGATCAGGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
-tatgcaa
- - - - - - - - - - tgtactg
- - - - - - - - - - - - - - acatttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - atgcatc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cgacaaa