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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCATCCCACGGAGAAAAGGGACCTCTATGATGCTGACCACGGGAAGAAGGTTTTGAGCATGGCTCCTGGCCTCGAGAGGCTCAACATCCTTCCTTTCAAGgtatgccatccttcctgaccagatctcttccttccatgcacatccagtgagtaaaagaacgtattgcaatcagcatttttcttcacatctatacacatgtcaatctttgatgttttttagttatcaagaaaatagaaagatttattgtttgtctgttttcttgacatttttcttgtctgttattccggatcag

Basic information

species Zea mays
transcript GRMZM2G051270_T02
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G051270_T02 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os03g53230.1 (Oryza sativa), 5'ss of exon 3
CCATCCCACGGAGAAAAGGGACCTCTATGATGCTGACCACGGGAAGAAGGTTTTGAGCATGGCTCCTGGCCTCGAGAGGCTCAACATCCTTCCTTTCAAGgtatgccatccttcctgaccagatctc---ttccttccatgcacatccagtgagtaaaagaacgtattgcaatcagcatttttcttcacatctatacacatgtcaatctttgatgttttttagttatcaagaaaatagaaagatttattgtttgtctgttttcttgacatttttcttg-tctgttattccggatcag
||| || || || || |||||||| ||||||||||| || ||||| ||||| ||||||||||||||||| || |||| |||||| |||||||||||||||||||| |||||| || |||||||| || || || |||||| | | || ||| || | || | || | || | || ||||||| | | | |||||||| ||| ||| || |||| | |||||||| ||| || || | |||| | | |
CCACCCAACTGAAAAGAGGGACCTGTATGATGCTGATCATGGGAAAAAGGTGTTGAGCATGGCTCCTGGGCTTGAGAAGCTCAATATCCTTCCTTTCAAGgtatgtcatcctaccagaccagatatcacattttttggatgcac-tagattgtgtagttcgctagcttactgtcca---tcttgtacatttgaatttggatgtcaagc---aacatattttagttttcagataaac-------cttgttgt--attctttttcttggcatgactcctgatttgttttatcag-----

upper sequence: GRMZM2G051270_T02 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA10G38760.1 (Glycine max), 5'ss of exon 3
CCATCCCACGGAGAAAAGGGACCTCTATGATGCTGACCACGGGAAGAAGGTTTTGAGCATGGCTCCTGGCCTCGAGAGGCTCAACATCCTTCCTTTCAAGgtatgccatccttcctgaccagatctcttccttccatgcacatccagtgagtaaaagaacgtattgcaatcagcatttttcttcacatctatacacatgtcaatctttgatgttttttagttatcaagaaaatagaaagatttattgtttgtctgttttcttgacatttttcttgtctgttattccggatcag
|||||| |||||||| || || |||||||||||||| || ||||| || ||||||||||| || || || ||| | || ||||| |||||||||| |||| ||| | | | ||| | | || ||||| || | || | || || | || | | ||| || || | ||| ||
CCATCCAGTTGAGAAAAGAGATCTGTATGATGCTGACCATGGAAAGAAAGTATTGAGCATGGCACCGGGACTAGAGCGTCTAAACATTCTTCCTTTCAGGgta-------------attgagaatttgccttctcattaata--cactgagtgaag--------ttcacttag--gccactttgatatatgtgttgatgatcattttcattcatttacag-------------------------------------------------------------------------

upper sequence: GRMZM2G051270_T02 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA20G28980.2 (Glycine max), 5'ss of exon 3
CCATCCCACGGAGAAAAGGGACCTCTATGATGCTGACCACGGGAAGAAGGTTTTGAGCATGGCTCCTGGCCTCGAGAGGCTCAACATCCTTCCTTTCAAGgtatgccatccttcctgaccagatctcttccttccatgcacatccagtgagtaaaagaacgtattgcaatcagcatttttcttcacatctatacacatgtcaatctttgatgttttttagttatcaagaaaatagaaagatttattgtttgtctgttttcttgacatttttcttgtctgttattccggatcag
|||||| |||||||| || || |||||||||||||| |||||||| || ||||||||||| || || || ||| | || ||||| |||||||||| |||| ||| | | | ||| || | ||||| || | || | || ||| | | | | ||| ||| || || || |
CCATCCAGTTGAGAAAAGAGATCTGTATGATGCTGACCATGGGAAGAAAGTATTGAGCATGGCACCGGGACTAGAGCGTCTAAACATTCTTCCTTTCAGGgta-------------attgagaatttgccttctcattagtataaactgagtgaag--------ttcacttagg--------ccactttgaaatatgtgttgatcattttcattcatttgcag----------------------------------------------------------------------

upper sequence: GRMZM2G051270_T02 (Zea mays), 5'ss of exon 4
lower sequence: AT4G14680.1 (Arabidopsis thaliana), 5'ss of exon 3
CCATCCCACGGAGAAAAGGGACCTCTATGATGCTGACCACGGGAAGAAGGTTTTGAGCATGGCTCCTGGCCTCGAGAGGCTCAACATCCTTCCTTTCAAGgtatgc-catccttcctgaccagatctcttccttc-catgcacatccagtgagtaaaagaacgtattgcaatcagcatttttcttcacatctatacacatgtcaatctttgatgttttttagttatcaagaaaatagaaagatttattgtttgtctgttttcttgacatttttcttgtctgttattccggatcag
|||||| ||||||| | || || || |||||||| ||||||||||| ||| | |||||||||||||| ||||| | |||||||| |||||||||| ||||| ||| | | | ||| ||| || | | || || | | | | ||| || | || | || || | |
TCATCCCGTGGAGAAACGTGATCTGTACGATGCTGATCACGGGAAGAAAGTTCTAAGCATGGCTCCTGGACTCGAACGACTCAACATTCTTCCTTTCAGGgtatattcatagaaaccgcataatactcaaacttggtatcttccttcaaagatttagg---ctttttgagttctgatttctggtttcaattggtgtag-------------------------------------------------------------------------------------------------

upper sequence: GRMZM2G051270_T02 (Zea mays), 5'ss of exon 4
lower sequence: Vv05s0020g04210.t01 (Vitis vinifera), 5'ss of exon 3
CCATCCCACGGAGAAAAGGGACCTCTATGATGCTGACCACGGGAAGAAGGTTTTGAGCATGGCTCCTGGCCTCGAGAGGCTCAACATCCTTCCTTTCAAGgtatgccatccttcctgac-cagatctcttccttccatgcacatccagtgagtaaaagaacgtattgcaatcagcatttttcttcacatctatacacatgtcaatctttgatgttttttagttatcaagaaaatagaaagatttattgtttgtctgttttcttgacatttttcttgtctgttattccggatcag
||| || ||||| || ||| | |||||||||||||| ||||||||||| ||||||||||||||||| || || |||| |||||||||||||||||||||| | | | | | | || | ||| | | | | | ||| | || || || | | | |
CCACCCAGTTGAGAAGAGAGACTTATATGATGCTGACCATGGGAAGAAGGTATTGAGCATGGCTCCTGGACTGGAACGGCTAAACATCCTTCCTTTCAAGgtatataaactattgtagctcttatgaaactcaaaattgctttcctgtttaatttatgaaatctgtaggattcacaagttgaggtataattgcag---------------------------------------------------------------------------------------------------

upper sequence: GRMZM2G051270_T02 (Zea mays), 5'ss of exon 4
lower sequence: PP1S331_37V6.1 (Physcomitrella patens), 5'ss of exon 5
CCATCCCACGGAGAAAAGGGACCTCTATGATGCTGACCACGGGAAGAAGGTTTTGAGCATGGCTCCTGGCCTCGAGAGGCTCAACATCCTTCCTTTCAAGgtatgccatccttcctgaccagatctcttccttccatgcacatccagtgagtaaaagaacgtattgcaatcagcatttttcttcacatct-atacacatgtcaatctttgatgttttttagttatcaagaaaatagaaagatttattgtttgtctgttttcttgacatttttcttgtctgttattccggatcag
||| ||||| | | || ||||| || || |||||||| |||| ||| | ||||||||||||||||| |||| ||||||||| || || |||| |||| ||| |||| || | | ||| || | || || ||| | || | | || | ||||| | ||| |||| | ||
CCACCCCACTGCCGGGCGCGATCTCTACGACGCAGACCACGGAAAGATGGTGCTCAGCATGGCTCCTGGCCTTGAGAAGCTCAACATTCTGCCCTTCAGGgtaat---tccagaatgacagcccctatctgataaatgtttctctgtcgttta------tgttgtgctgtgag-actactcagctcatctgaaacaaatgtgtagaaatg------------------------------------------------------------------------------------

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|32842084|gb|CD981765.1|CD981765
EST:     TTATGAGCATGGCTCCTGGCCTCGAGAGGCTCATCATCCTTACTTTCAAG                         GTGGCTGCATATGACACAAAGCAAAAGAAAATGGATTTCTTCGATCCATCA
genomic: TTTTGAGCATGGCTCCTGGCCTCGAGAGGCTCAACATCCTTCCTTTCAAGgtatgccatc ... tccggatcagGTGGCTGCATATGACACAAAGCAAAAGAAAATGGATTTCTTCGATCCATCA
EST: gi|32840548|gb|CD980229.1|CD980229
EST:     TTTTGAGCATGGCTCCTGGCCTCGAGAGGCTCAACATCCTTCCTTTCAAG                         GTGGCTGCATATGACACAAAGCAAAAGAAAATGGATTTCTTCGATCCATCA
genomic: TTTTGAGCATGGCTCCTGGCCTCGAGAGGCTCAACATCCTTCCTTTCAAGgtatgccatc ... tccggatcagGTGGCTGCATATGACACAAAGCAAAAGAAAATGGATTTCTTCGATCCATCA
EST: gi|32840519|gb|CD980200.1|CD980200
EST:     TTTTGAGCATGGCTCCTGGCCTCGAGAGGCTCAACATCCTTCCTTTCAAG                         GTGGCTGCATATGACACAAAGCAAAAGAAAATGGATTTCTTCGATCCATCA
genomic: TTTTGAGCATGGCTCCTGGCCTCGAGAGGCTCAACATCCTTCCTTTCAAGgtatgccatc ... tccggatcagGTGGCTGCATATGACACAAAGCAAAAGAAAATGGATTTCTTCGATCCATCA
EST: gi|32830689|gb|CD970367.1|CD970367
EST:     TTTTGAGCATGGCTCCTGGCCTCGAGAGGCTCAACATCCTTCCTTTCAAG                         GTGGCTGCATATGACACAAAGC
genomic: TTTTGAGCATGGCTCCTGGCCTCGAGAGGCTCAACATCCTTCCTTTCAAGgtatgccatc ... tccggatcagGTGGCTGCATATGACACAAAGC
EST: gi|32836595|gb|CD976273.1|CD976273
EST:     TTTTGAGCATGGCTCCTGGCCTCGAGAGGCTCAACATCCTTCCTTTCAAG                         GTGGCTGCATATGACACAAAGCAAAAGAAAATGGATTTCTTCGATCCATCA
genomic: TTTTGAGCATGGCTCCTGGCCTCGAGAGGCTCAACATCCTTCCTTTCAAGgtatgccatc ... tccggatcagGTGGCTGCATATGACACAAAGCAAAAGAAAATGGATTTCTTCGATCCATCA
EST: gi|111191745|gb|EE289881.1|EE289881
EST:     TTTTGAGCATGGCTCCTGGCCTCGAGAGGCTCAACATCCTTCCTTTCAAG                         GTGGTTGCATATGACACAAAGCAAAAGAAAATGGATTTTTTCGATCCATCA
genomic: TTTTGAGCATGGCTCCTGGCCTCGAGAGGCTCAACATCCTTCCTTTCAAGgtatgccatc ... tccggatcagGTGGCTGCATATGACACAAAGCAAAAGAAAATGGATTTCTTCGATCCATCA
EST: gi|110219906|gb|EC901804.1|EC901804
EST:     TTTTGAGCATGGCTCCTGGCCTCGAGAGGCTCAACATCCTTCCTTTCAAG                         GTGGCTGCATATGACACAAAGCAAAAGAAAATGGATTTCTTCGATCCATCA
genomic: TTTTGAGCATGGCTCCTGGCCTCGAGAGGCTCAACATCCTTCCTTTCAAGgtatgccatc ... tccggatcagGTGGCTGCATATGACACAAAGCAAAAGAAAATGGATTTCTTCGATCCATCA
EST: gi|12046747|gb|BF728886.1|BF728886
EST:     TTTTGAGCATGGCTCCTGGCCTCGAGAGGCTCAACATCCTTCCTTTCAAG                         GTGGCTGCATATGACACAAAGCAAAAGAAAATGGATTTCTTCGATCCATCA
genomic: TTTTGAGCATGGCTCCTGGCCTCGAGAGGCTCAACATCCTTCCTTTCAAGgtatgccatc ... tccggatcagGTGGCTGCATATGACACAAAGCAAAAGAAAATGGATTTCTTCGATCCATCA
EST: gi|110961857|gb|EE181909.1|EE181909
EST:     TTTTGAGCATGGCTCCTGGCCTCGAGAGGCTCAACATCCTTCCTTTCAAG                         GTGGCGGCATATGACACAAAGCAAAAGAAAATGGATTTCTTCGATCCATCA
genomic: TTTTGAGCATGGCTCCTGGCCTCGAGAGGCTCAACATCCTTCCTTTCAAGgtatgccatc ... tccggatcagGTGGCTGCATATGACACAAAGCAAAAGAAAATGGATTTCTTCGATCCATCA
EST: gi|148943164|gb|EC888223.2|EC888223
EST:     TTTTGAGCATGGCTCCTGGCCTCGAGAGGCTCAACATCCTTCCTTTCAAG                         GTGGCTGCATATGACACAAAGCAAAAGAAAATGGATTTTTTCGATCCATCA
genomic: TTTTGAGCATGGCTCCTGGCCTCGAGAGGCTCAACATCCTTCCTTTCAAGgtatgccatc ... tccggatcagGTGGCTGCATATGACACAAAGCAAAAGAAAATGGATTTCTTCGATCCATCA
EST: gi|149102605|gb|EE287963.2|EE287963
EST:     AGGCTCAACATCCTTCCTTTCAAG                         GTGGCTGCATATGACACAAAGCAAAAGAAAATGGATTTCTTCGATCCATCA
genomic: AGGCTCAACATCCTTCCTTTCAAGgtatgccatc ... tccggatcagGTGGCTGCATATGACACAAAGCAAAAGAAAATGGATTTCTTCGATCCATCA
EST: gi|149076868|gb|EE165524.2|EE165524
EST:     TTTTGAGCATGGCTCCTGGCCTCGAGAGGCTCAACATCCTTCCTTTCAAG                         GTGGCGGCATATGACACAAAGCAAAAGAAAATGGATTTTTTCGATCCATCA
genomic: TTTTGAGCATGGCTCCTGGCCTCGAGAGGCTCAACATCCTTCCTTTCAAGgtatgccatc ... tccggatcagGTGGCTGCATATGACACAAAGCAAAAGAAAATGGATTTCTTCGATCCATCA
EST: gi|76921061|gb|DV168441.1|DV168441
EST:     TTTTGAGCATGGCTCCTGGCCTCGAGAGGCTCAACATCCTTCCTTTCAAG                         GTGGCTGCATATGACACAAAGCAAAAGAAAATGGATTTCTTCGATCCATCA
genomic: TTTTGAGCATGGCTCCTGGCCTCGAGAGGCTCAACATCCTTCCTTTCAAGgtatgccatc ... tccggatcagGTGGCTGCATATGACACAAAGCAAAAGAAAATGGATTTCTTCGATCCATCA
EST: gi|32926464|gb|CF031276.1|CF031276
EST:     TTTTGAGCATGGCTCCTGGCCTCGAGAGGCTCAACATCCTTCCTTTCAAG                         GTGGCTGCATATGACACAAAGCAAAAGAAAATGGATTTCTTCGATCCATCA
genomic: TTTTGAGCATGGCTCCTGGCCTCGAGAGGCTCAACATCCTTCCTTTCAAGgtatgccatc ... tccggatcagGTGGCTGCATATGACACAAAGCAAAAGAAAATGGATTTCTTCGATCCATCA
EST: gi|32924998|gb|CF029810.1|CF029810
EST:     TTTTGAGCATGGCTCCTGGCCTCGAGAGGCTCAACATCCTTCCTTTCAAG                         GTGGCTGCATATGACACAAAGCAAAAGAAAATGGATTTCTTCGATCCATCA
genomic: TTTTGAGCATGGCTCCTGGCCTCGAGAGGCTCAACATCCTTCCTTTCAAGgtatgccatc ... tccggatcagGTGGCTGCATATGACACAAAGCAAAAGAAAATGGATTTCTTCGATCCATCA
EST: gi|32842063|gb|CD981744.1|CD981744
EST:     TTTTGAGCATGGCTCCTGGCCTCGAGAGGCTCAACATCCTTCCTTTCAAG                         GTGGCTGCATATGACACAAAGCAAAAGAAAATGGATTTCTTCGATCCATCA
genomic: TTTTGAGCATGGCTCCTGGCCTCGAGAGGCTCAACATCCTTCCTTTCAAGgtatgccatc ... tccggatcagGTGGCTGCATATGACACAAAGCAAAAGAAAATGGATTTCTTCGATCCATCA
EST: gi|110533959|gb|EE038139.1|EE038139
EST:     TTTTGAGCATGGCTCCTGGCCTCGAGAGGCTCAACATCCTTCCTTTCAAG                         GTGGCTGCATATGACACAAAGCAAAAGAAAATGGATTTTTTCGATCCATCA
genomic: TTTTGAGCATGGCTCCTGGCCTCGAGAGGCTCAACATCCTTCCTTTCAAGgtatgccatc ... tccggatcagGTGGCTGCATATGACACAAAGCAAAAGAAAATGGATTTCTTCGATCCATCA
EST: gi|111190608|gb|EE288744.1|EE288744
EST:     TTTTGAGCATGGCTCCTGGCCTCGAGAGGCTCAACATCCTTCCTTTCAAG                         GTGGCTGCATATGACACAAAGCAAAAGAAAATGGATTTTTTCGATCCATCA
genomic: TTTTGAGCATGGCTCCTGGCCTCGAGAGGCTCAACATCCTTCCTTTCAAGgtatgccatc ... tccggatcagGTGGCTGCATATGACACAAAGCAAAAGAAAATGGATTTCTTCGATCCATCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCATCCCACGGAGAAAAGGGACCTCTATGATGCTGACCACGGGAAGAAGGTTTTGAGCATGGCTCCTGGCCTCGAGAGGCTCAACATCCTTCCTTTCAAGgtatgccatccttcctgaccagatctcttccttccatgcacatccagtgagtaaaagaacgtattgcaatcagcatttttcttcacatctatacacatgtcaatctttgatgttttttagttatcaagaaaatagaaagatttattgtttgtctgttttcttgacatttttcttgtctgttattccggatcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG