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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttctccgtttgtttagaggacttgttttcttaatctcagcattctatgccttctttgatgttaaactgacatgatcatattttctgtacttgattcccagGGTGTTGGTCACAATGATGATAAAGTTCTTGTTCTTGCTGCCACGAATACGCCATATGCTCTGGACCAG

Basic information

species Zea mays
transcript GRMZM2G088834_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G088834_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os01g04814.3 (Oryza sativa), 3'ss of exon 3
ttctccgtttgtttagaggact---tgttttcttaatctcagcattctatgccttctttgatgt-taaactgacatgat-----catattttctgtacttgattcccagGGTGTTGGTCACAATGATGATAAAGTTCTTGTTCTTGCTGCCACGAATACGCCATATGCTCTGGACCAG
        || | |  || | |   || ||| |||| ||     ||  ||||| | |||| |     |||| || |        | |  ||||  |  |  ||  |||||||||||| || |||||||| ||||| || ||||||||||| || || |||||||||||||| ||||||
------tgttatctgaagcattccatggtttgttaaactat---ttagatgccctttttgttacaccaacttacttaccttttgctttgtttcgctggtgaatgtccagGGTGTTGGCCATAATGATGACAAAGTACTGGTTCTTGCTGCTACAAACACGCCATATGCTCTAGACCAG

upper sequence: GRMZM2G088834_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA13G39410.1 (Glycine max), 3'ss of exon 4
-ttctccgtttgtttagaggacttgttttcttaatctcagcattctatgccttctttgatgttaaactgacatgatcatattttctgtacttgattcccagGGTGTTGGTCACAATGATGATAAAGTTCTTGTTCTTGCTGCCACGAATACGCCATATGCTCTGGACCAG
 || | |  ||      ||| |   ||     | | |  |||||   |  || ||||    ||    | |  | ||  || ||| |  || |  ||   ||||||| || ||||||||| | ||||||||||||||||| || || |||||||| |||||  | ||||||
tttttgctattaacatcagggcagtttccaacatttttggcatttcttctctcctttttgattctctttatttaat-gtactttatccacatactttgtagGGTGTAGGACACAATGATCAGAAAGTTCTTGTTCTTGCAGCAACAAATACGCCCTATGCCTTAGACCAG

upper sequence: GRMZM2G088834_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA11G19120.1 (Glycine max), 3'ss of exon 3
ttctccgtttgtttagaggactt---gttttcttaatctcagcattctatgccttctttgatgttaaactgacatgatcatat--tttctgtacttgat-tcccagGGTGTTGGTCACAATGATGATAAAGTTCTTGTTCTTGCTGCCACGAATACGCCATATGCTCTGGACCAG
       ||| ||  || ||      |||| |   | ||  |   || ||      |||   |||        || || || |  ||| |  |||| |  |   ||||||| || ||||||||| | ||||||||||||||||| || || ||||| || |||||||| ||||||
------attttttcggaagatccaaggtttccaacagctttggcgtcaattttcattttcgcgtttgttcctaatcataatgtagtttatccacttcacattgtagGGTGTGGGACACAATGATCAGAAAGTTCTTGTTCTTGCAGCTACAAATACACCTTATGCTCTAGACCAG

upper sequence: GRMZM2G088834_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA12G30910.1 (Glycine max), 3'ss of exon 3
ttctccgtttgtttagaggacttgttttcttaatctcagcat-tctatgccttctttgatgttaaactgacatgatcatattttc-tgtacttgattcccagGGTGTTGGTCACAATGATGATAAAGTTCTTGTTCTTGCTGCCACGAATACGCCATATGCTCTGGACCAG
 |  |  ||    | |||| |   ||     | | | || || | |   |  | |||  | || || |  | | ||  || | |  | ||  |  ||   ||||||| || ||||||||| | ||||||||||||||||| || || |||||||| |||||| | ||||||
-ttgctattaacat-gagggcagtttccaacatttttagtatatattctctcttttttttttttaattctctttattttaatgtagtttatctactttgtagGGTGTAGGACACAATGATCAGAAAGTTCTTGTTCTTGCAGCAACAAATACGCCCTATGCTTTAGACCAG

upper sequence: GRMZM2G088834_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA12G09300.1 (Glycine max), 3'ss of exon 3
ttctccgtttgtttagaggactt---gttttcttaatctcagcattctatgccttctttgatgttaaactgacatgatcatattttctgtac---ttgattcccagGGTGTTGGTCACAATGATGATAAAGTTCTTGTTCTTGCTGCCACGAATACGCCATATGCTCTGGACCAG
        |  || ||| ||      |||| |   | ||  |   || ||    | |||  ||||        || || || |  | ||| |   ||   |   |||||||||| ||||||||| | |||||||||||||| || || || ||||| || |||||||| ||||||
------cctaattcagaagatccaaggtttccaacagctttggtgtcaattttctttttcgtgtttgttcctaatcataatgtagtttgtccgctttacattgtagGGTGTTGGACACAATGATCAGAAAGTTCTTGTTCTAGCAGCTACAAATACACCTTATGCTCTAGACCAG

upper sequence: GRMZM2G088834_T01 (Zea mays), 3'ss of exon 3
lower sequence: AT2G27600.1 (Arabidopsis thaliana), 3'ss of exon 3
ttctccgtttgtttagaggacttgttttcttaatctcagcattctatgccttctttgatgttaaactgacatgatcatattttctgtacttgattcccagGGTGTTGGTCACAATGATGATAAAGTTCTTGTTCTTGCTGCCACGAATACGCCATATGCTCTGGACCAG
                  |  | | ||     | || | |    | |   ||  |||  | | || |  |  |    |   || | |  ||   |   |||||||||| ||||||||||| ||||| ||||| ||||| || || ||||| || |||||||| || |||
----------------gtgcatagcttatccgaactaaactccatgtcttttagttgtagctgaaatttc-cgtctctgacttatctctttttcttttagGGTGTTGGACACAATGATGAGAAAGTACTTGTACTTGCAGCAACCAATACACCCTATGCTCTTGATCAG

upper sequence: GRMZM2G088834_T01 (Zea mays), 3'ss of exon 3
lower sequence: Vv13s0106g00490.t01 (Vitis vinifera), 3'ss of exon 3
--ttctccgtttgtttagaggacttgttttcttaatctcagcattctatgccttctttgatgttaaactgacatgatcatattttctgtacttgattcccagGGTGTTGGTCACAATGATGATAAAGTTCTTGTTCTTGCTGCCACGAATACGCCATATGCTCTGGACCAG
   |   | |||    | |   ||     |  | || |    ||| |  |   |||| | |  | |  |   |  ||    |||| | || ||   |   ||||||| || ||||||||| | ||||||||||||||||| ||||| || || || ||| | ||||| |||
tgcttctcatttacacacacacctatgcatactcatgtagagatttttcgggctcttcgcttctcattttcaa--atggggttttatctatttacattttagGGTGTAGGGCACAATGATCAGAAAGTTCTTGTTCTTGCAGCCACAAACACTCCCTATTCCCTGGATCAG

upper sequence: GRMZM2G088834_T01 (Zea mays), 3'ss of exon 3
lower sequence: Vv06s0080g00160.t01 (Vitis vinifera), 3'ss of exon 3
------------ttctccgtttgtttagaggacttgttttcttaatctcagcattctatgccttctttgatgttaaactgacatgatcatattttctgtacttgattcccagGGTGTTGGTCACAATGATGATAAAGTTCTTGTTCTTGCTGCCACGAATACGCCATATGCTCTGGACCAG
               |  |    ||| ||    | | ||  | | |         || | ||    || ||||| | |||    || | |||  | |         | ||||||||| || ||||||||| | ||||| ||||||||||| ||||| ||||| || ||||| ||||| |||
ttgagaagggaaaattttgaaacttttgatagttagattcttcagttct--ttccctgtcccagtcttaatgttgagctggtg-gaccttatccttt---------ttccagGGTGTAGGACACAATGATCAGAAAGTCCTTGTTCTTGCCGCCACAAATACTCCTTATGCCCTGGATCAG

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|26559939|gb|CA832174.1|CA832174
EST:     AAAGTGAAGCATCTAGGAGAATTAAGACTGAACTTCTTGTGCAAATGCAG                         GGTGTTGGTCACAATGATGATAAAGTTCTTGTTCTTGCTGCCACGAATACG
genomic: AAAGTGAAGCATCTAGGAGAATTAAGACTGAACTTCTTGTGCAAATGCAGgtgaagtatt ... tgattcccagGGTGTTGGTCACAATGATGATAAAGTTCTTGTTCTTGCTGCCACGAATACG
EST: gi|87157780|gb|DY402569.1|DY402569
EST:     AAAGTGAAGCATCTAGGAGAATTAAGACTGAACTTCTTGTGCAAATGCAG                         GGTGTTGGTCACAATGATGATAAAGTTCTTGTTCTTGCTGCCACGAATACG
genomic: AAAGTGAAGCATCTAGGAGAATTAAGACTGAACTTCTTGTGCAAATGCAGgtgaagtatt ... tgattcccagGGTGTTGGTCACAATGATGATAAAGTTCTTGTTCTTGCTGCCACGAATACG
EST: gi|22935971|gb|BU572246.1|BU572246
EST:     AAAGTGAAGCATCTAGGAGAATTAAGACTGAACTTCTTGTGCAAATGCAG                         GGTGTTGGTCACAATGATGATAAAGGTCTTGTTCTTGCTGCCACGAATACG
genomic: AAAGTGAAGCATCTAGGAGAATTAAGACTGAACTTCTTGTGCAAATGCAGgtgaagtatt ... tgattcccagGGTGTTGGTCACAATGATGATAAAGTTCTTGTTCTTGCTGCCACGAATACG
EST: gi|60341830|gb|DN208803.1|DN208803
EST:     AAAGTGAAGCATCTAGGAGAATTAAGACTGAACTTCTTGTGCAAATGCAG                         GGTGTTGGTCACAATGATGATAAAGTTCTTGTTCTTGCTGCCACGAATACG
genomic: AAAGTGAAGCATCTAGGAGAATTAAGACTGAACTTCTTGTGCAAATGCAGgtgaagtatt ... tgattcccagGGTGTTGGTCACAATGATGATAAAGTTCTTGTTCTTGCTGCCACGAATACG
EST: gi|91874145|gb|EB404102.1|EB404102
EST:     AAAGTGAAGCATCTAGGAGAATTAAGACTGAACTTCTTGTGCAAATGCAG                         GGTGTTGGTCACAATGATGATAAAGTTCTTGTTCTTGCTGCCACGAATACG
genomic: AAAGTGAAGCATCTAGGAGAATTAAGACTGAACTTCTTGTGCAAATGCAGgtgaagtatt ... tgattcccagGGTGTTGGTCACAATGATGATAAAGTTCTTGTTCTTGCTGCCACGAATACG
EST: gi|60346571|gb|DN213544.1|DN213544
EST:     AAAGTGAAGCATCTAGGAGAATTAAGACTGAACTTCTTGTGCAAATGCAG                         GGTGTTGGTCACAATGATGATAAAGTTCTTGTTCTTGCTGCCACGAATACG
genomic: AAAGTGAAGCATCTAGGAGAATTAAGACTGAACTTCTTGTGCAAATGCAGgtgaagtatt ... tgattcccagGGTGTTGGTCACAATGATGATAAAGTTCTTGTTCTTGCTGCCACGAATACG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgccttctttgatgttaaactgacatgatcatattttctgtacttgattcccagGGTGTTGGTCACAATGATGATAAAGTTCTTGTTCTTGCTGCCACGAATACGCCATATGCTCTGGACCAG
                                                ttccc  CT-rich tract
                            atcatatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttctccgtttgtttagaggacttgttttcttaatctcagcattctatgccttctttgatgttaaactgacatgatcatattttctgtacttgattcccagGGTGTTGGTCACAATGATGATAAAGTTCTTGTTCTTGCTGCCACGAATACGCCATATGCTCTGGACCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - cttgttt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -catgatc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttttctg