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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aactagtggcataacttgtacacaaacccacgcctagagtaaagcctcaggttgctagcagcacatccttatatcttcacaatgcacattttactgacagATCTTCGAGATGACAAGCAGTTCTTTGTGGACCATCCTGGTGCTGTTCCTATCACTACTGCTCAG

Basic information

species Zea mays
transcript GRMZM5G803949_T02
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G803949_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os02g02840.1 (Oryza sativa), 3'ss of exon 4
-aactag-tggcataacttgtacaca-aacccacgcctaga---gtaaagcctcaggttgctagcagcacatccttatatcttcacaatgcacattttactgacagATCTTCGAGATGACAAGCAGTTCTTTGTGGACCATCCTGGTGCTGTTCCTATCACTACTGCTCAG
 || ||  |  ||    || |||| | ||    | | | ||   ||||||   ||  |     | ||| ||     || | |||||| ||   |||  |||| ||||||||||||||||||||||||| |||||||||||||||||||||||||||||||| |||||||||
aaattaaattccaatcattctacagataatatccccttcgacctgtaaagatccaact-----gtagcccacttacat-ttttcacattgtttattgcactggcagATCTTCGAGATGACAAGCAGTTTTTTGTGGACCATCCTGGTGCTGTTCCTATCACCACTGCTCAG

upper sequence: GRMZM5G803949_T02 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA16G23340.1 (Glycine max), 3'ss of exon 4
-------aactagtggcataacttgtacacaaacccacgcctagagtaaagcctcaggttgctagcagcacatccttatatcttcacaatgcacattttactgacagATCTTCGAGATGACAAGCAGTTCTTTGTGGACCATCCTGGTGCTGTTCCTATCACTACTGCTCAG
       ||  |    | |  | | |||||| ||   | || |  ||    | |    ||   ||      ||  |   || ||   |||    | |     |||||| ||||||||||| |||||||||||  | ||||||||||||||||| || || || || | ||||
ttttgttaaaaatattcttggcctctacacatactatcaccaattgtt---ctttcaattaagagttagttatt-taccattttttgaatttgaaatga---gacagACCTTCGAGATGATAAGCAGTTCTTCATAGACCATCCTGGTGCTGTACCCATTACCACCGTTCAG

upper sequence: GRMZM5G803949_T02 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA11G11510.1 (Glycine max), 3'ss of exon 4
--aactagtggcataacttgtacacaaacccacgcctagagtaaagcctcaggttgctagcagcacatccttatatcttcacaa-tgcacattttactgacagATCTTCGAGATGACAAGCAGTTCTTTGTGGACCATCCTGGTGCTGTTCCTATCACTACTGCTCAG
     || | | ||  ||| |       ||   | | |   ||||||  |   |   |||     | |    || || | |||| |  |  |||  ||   ||||||||| ||||| ||||||||||||   |||||||||||||| || |||||||| || || |||
tagtttaattgtatg-cttttgatggttccattgaccatgataaagctgcca-tgattagtt-tgcttgggcatttcatgacaactaaatctttgtcttgtagATCTTCGGGATGATAAGCAGTTCTTTCAAGACCATCCTGGTGCAGTGCCTATCACCACAGCACAG

upper sequence: GRMZM5G803949_T02 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA04G02530.3 (Glycine max), 3'ss of exon 4
aactagtg-gcataacttgtacacaaacccacgcctagagtaaagcctcaggttgctagcagcacatccttatatcttcacaatgcacattttactgacagATCTTCGAGATGACAAGCAGTTCTTTGTGGACCATCCTGGTGCTGTTCCTATCACTACTGCTCAG
|| |  ||  | |      | |   |    ||   |   |   |                 | |     | | | ||  | ||||||   |||   | |||||||||| ||||| ||||| || ||| |||||||||||||||| || || || ||||| || |||
aattcctgtacgtggtcaatgctgcatgtaacagtttctggccaattcatatccaaagttggaatggtttgacaactcta-aatgcatgatttgtcggcagATCTTCGGGATGATAAGCAATTTTTTATGGACCATCCTGGTGCAGTGCCAATTACTACAGCACAG

upper sequence: GRMZM5G803949_T02 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA02G05160.1 (Glycine max), 3'ss of exon 4
aactagtggcataacttgtacacaaacccacgcctag--agtaaagcctcaggttgctagcagcacatccttatatcttcacaatgcacattttactgacagATCTTCGAGATGACAAGCAGTTCTTTGTGGACCATCCTGGTGCTGTTCCTATCACTACTGCTCAG
|  | ||   | || || |  ||     ||    |    |  ||    ||     | ||  ||   |||||| || | |     |        |   |||||| ||||||||||| ||||||||||| || || ||||||||||| || || || || |||| ||| 
attttgttaaaaaatttctcaacctctacatattttatcaccaattgttctttcagttaagagttaatcctt-taccgtttttttatttgaaatga-gacagACCTTCGAGATGATAAGCAGTTCTTCGTAGATCATCCTGGTGCCGTACCCATTACCACTGTTCAA

upper sequence: GRMZM5G803949_T02 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA12G03660.1 (Glycine max), 3'ss of exon 4
aactagtggcataacttgtacacaaacccac---gcctagagtaaagcctcaggttgctagcagcacatccttatatcttcacaatgcacatttta-ctgacagATCTTCGAGATGACAAGCAGTTCTTTGTGGACCATCCTGGTGCTGTTCCTATCACTACTGCTCAG
     ||    |      |  | |    |||   | | |   ||||||  |   |   |||     | |    || || | ||||   |   | |  ||   ||||||||| ||||| ||||||||||||   |||||||||||||| || |||||||| || || |||
--tctgtaaatttttccattaatagtttcactttgaccacgataaagctgcca-tgattagtt-tgcttgggcatttcatgacaaccaaatctctgtcttgtagATCTTCGGGATGATAAGCAGTTCTTTCAAGACCATCCTGGTGCAGTGCCTATCACCACAGCACAG

upper sequence: GRMZM5G803949_T02 (Zea mays), 3'ss of exon 4
lower sequence: AT2G17800.2 (Arabidopsis thaliana), 3'ss of exon 5
-----aactagtggcataacttgtacacaaacccacgcctagagtaaagcctcaggttgctagcagcacatccttatatcttcacaatgcacattttactgacagATCTTCGAGATGACAAGCAGTTCTTTGTGGACCATCCTGGTGCTGTTCCTATCACTACTGCTCAG
     ||||   ||| |    | |  |     | |  ||||   | ||   | | |    |  |  |   | ||||| | ||     | ||   | || || |||||||||| |||||||| ||||||||  | ||||| ||||| ||||| || || ||||||||||||
tgcttaactttcggcctgctgtctg-atccgtctagacctacttttaatagttatgagttt--cgtctggtgcttatgt-tttgtgtttcatcatata-tgccagATCTTCGGGATGACAAACAGTTCTTCATTGACCACCCTGGCGCTGTACCAATTACTACTGCTCAG

upper sequence: GRMZM5G803949_T02 (Zea mays), 3'ss of exon 4
lower sequence: AT4G35950.1 (Arabidopsis thaliana), 3'ss of exon 4
-------aactagtggcataacttgtacacaaacccacgcctagagtaaagcctcaggttgctagcagcacatccttatatcttcacaatgcacattttactgacagATCTTCGAGATGACAAGCAGTTCTTTGTGGACCATCCTGGTGCTGTTCCTATCACTACTGCTCAG
       | | ||||  ||| ||| || | ||    || | |  |  | | | ||||    ||       |   | | | |  |       |     ||  || ||||||||||||||||||| ||||| ||  | ||||||||||||||||| ||||| || |||| ||||
actgtatagcaagtg-tatacctt-tataaaag---acacttgca--agatcttcagtcaactcatgatcctggcctttttgattgtctaaccttggttgttgtcagATCTTCGAGATGACAAACAGTTTTTCATCGACCATCCTGGTGCTGTCCCTATTACCACTGTTCAG

upper sequence: GRMZM5G803949_T02 (Zea mays), 3'ss of exon 4
lower sequence: Vv04s0023g03860.t01 (Vitis vinifera), 3'ss of exon 5
---aactagtggcataacttgtacacaaacccacgcctagagtaaagcctcaggttgctagcagcacatccttatatc-ttcacaatgcacattttactgacagATCTTCGAGATGACAAGCAGTTCTTTGTGGACCATCCTGGTGCTGTTCCTATCACTACTGCTCAG
   || |||| | |  | || | ||  |      |  ||          |  | |   || ||     |  || | |  ||  |||||   |||   ||   ||||||||| || ||||||||||||||  | ||||||||||||||||| || ||| || | ||||||
ctaaattagtagaaggaatt-tgcagtaggagtaggttatttatggttttgtgataattaacaaattttttttgtctgattttcaatgttaattgagct---agATCTTCGGGAAGACAAGCAGTTCTTCATAGACCATCCTGGTGCTGTGCCCATCTCTGCAGCTCAG

upper sequence: GRMZM5G803949_T02 (Zea mays), 3'ss of exon 4
lower sequence: PP1S126_126V6.2 (Physcomitrella patens), 3'ss of exon 5
---------------------------------------------------------------------aactagtggcataacttgtacacaa-acccacgcctaga---gtaaagcctcaggttgctagcagcacatccttatatcttc---------acaatgcacatttta-ctgacagATCTTCGAGATGACAAGCAGTTCTTTGTGGACCATCCTGGTGCTGTTCCTATCACTACTGCTCAG
                                                                         | ||    || | | ||| || |  |  ||   ||   |    ||    | |||  |     |    |   ||| ||          |||     |   | |  || |||||||||||||||| || ||||||||||  ||||||||||| || | ||| || || ||  |||| 
gtataaaactccggcttcacttgtggtttgggaatgtgctactgacaagtttattcaatcggatgtaatccacaatgctgaaaatcgaacaaaacattctagcacggatgcgctgtgctcttgcttgtcatttttattctcaagtatttttcactctcttacagctggcgcgtcaattggcagATCTTCGAGATGATAAACAGTTCTTTGCTGACCATCCTGGAGCGGCTCCAATTACAACCTCTCAA

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|88752310|gb|DY536451.1|DY536451
EST:     GAAGCATTATGCACCTGGTGTGCCAATAATTCTCGTAGGGACAAAGCTTG                         ATCTTCGAGATGACAAGCAGTTCTTTGTGGACCATCCTGGTGCTGTTCCTA
genomic: GAAGCATTATGCACCTGGTGTGCCAATAATTCTCGTAGGGACAAAGCTTGgtaagtatga ... ttactgacagATCTTCGAGATGACAAGCAGTTCTTTGTGGACCATCCTGGTGCTGTTCCTA
EST: gi|211356952|gb|FL222516.1|FL222516
EST:     GAAGCATTATGCACCTGGTGTGCCAATAATTCTCGTARGGACAAAGCTTG                         ATCTTCGAGATGACAAGCAGTTCTTTGTGGACCATCCTGGTGCTGTTCCCN
genomic: GAAGCATTATGCACCTGGTGTGCCAATAATTCTCGTAGGGACAAAGCTTGgtaagtatga ... ttactgacagATCTTCGAGATGACAAGCAGTTCTTTGTGGACCATCCTGGTGCTGTTCC--
EST: gi|37392412|gb|CF633455.1|CF633455
EST:     GAAGCATTATGCACCTGGTGTGCCAATAATTCTCGTAGGGACAAAGCTTG                         ATCTTCGAGATGACAAGCAGTTCTTTGTGGACCATCCTGGTGCTGTTCCTA
genomic: GAAGCATTATGCACCTGGTGTGCCAATAATTCTCGTAGGGACAAAGCTTGgtaagtatga ... ttactgacagATCTTCGAGATGACAAGCAGTTCTTTGTGGACCATCCTGGTGCTGTTCCTA
EST: gi|74240918|gb|DT648832.1|DT648832
EST:     GAAGCATTATGCACCTGGTGTGCCAATAATTCTCGTAGGGACAAAGCTTG                         ATCTTCGAGATGACAAGCAGTTCTTTGTGGACCATCCTGGTGCTGTTCCTA
genomic: GAAGCATTATGCACCTGGTGTGCCAATAATTCTCGTAGGGACAAAGCTTGgtaagtatga ... ttactgacagATCTTCGAGATGACAAGCAGTTCTTTGTGGACCATCCTGGTGCTGTTCCTA
EST: gi|211082361|gb|FK946337.1|FK946337
EST:     GAAGCATTATGCACCTGGTGTGCCAATAATTCTCGTAGGGACAAAGCTTG                         ATCTTCGAGATGACAAGCAGTTCTTTGTGGATCATCCTGGTGCTGTTCCTA
genomic: GAAGCATTATGCACCTGGTGTGCCAATAATTCTCGTAGGGACAAAGCTTGgtaagtatga ... ttactgacagATCTTCGAGATGACAAGCAGTTCTTTGTGGACCATCCTGGTGCTGTTCCTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctcaggttgctagcagcacatccttatatcttcacaatgcacattttactgacagATCTTCGAGATGACAAGCAGTTCTTTGTGGACCATCCTGGTGCTGTTCCTATCACTACTGCTCAG
                                           ttttact  CT-rich tract
                       ttatatctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aactagtggcataacttgtacacaaacccacgcctagagtaaagcctcaggttgctagcagcacatccttatatcttcacaatgcacattttactgacagATCTTCGAGATGACAAGCAGTTCTTTGTGGACCATCCTGGTGCTGTTCCTATCACTACTGCTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT