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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtgaaatatatcttttcttctagttttaagctgctaccgagttgctcgtggtagatttgtacaagttcttcagcggtgaattttattgatttgttgaatattgtctttttttgcagGGAGAAATGCAGCAACTCCGGGACAAACTTGCTATTGCAGAAAGGGCTGCAAGATCAGAAGCTCAACTGAAA

Basic information

species Zea mays
transcript GRMZM2G017525_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G017525_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os12g44340.1 (Oryza sativa), 3'ss of exon 7
----------------------------------------------------gta-agtgaaatatatcttttcttctagt-tttaagctgctaccgagt--tgctcgtggtagatttgtacaagttcttcagcggtgaattttattg--atttgttgaatattgtctttttttgcagGGAGAAATGCAGCAACTCCGGGACAAACTTGCTATTGCAGAAAGGGCTGCAAGATCAGAAGCTCAACTGAAA
                                                     || ||||||   | |   | |  | | | |||   ||  | || | |  |   ||  ||| | |        |  ||  | |||  | ||| |||  | || |    | ||   || ||||||||||||||||||||||||||||||| ||||| ||||| ||||||||||| ||| |||||||||||||| |||||
gtaagtaatgctatcatttaattatgtgctattgctgacttgttctggatggatacagtgaagccttttaatgcaacaattgttttcacttttccccactcctaaacggagtatactatggttcatctttttggggtctaatttgttgggaattttcttttctttctttcttttgcagGGAGAAATGCAGCAACTCCGGGATAAACTGGCTATAGCAGAAAGGGCCGCACGATCAGAAGCTCAATTGAAA

upper sequence: GRMZM2G017525_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA07G26540.1 (Glycine max), 3'ss of exon 7
------------------------gtaagtgaaatatatcttttcttctagttttaagctgctac----cgagttgctcgtggtagat---ttgtacaagttcttcagcggtgaattttattgatttgttgaatattgtctt---tttttgcagGGAGAAATGCAGCAACTCCGGGACAAACTTGCTATTGCAGAAAGGGCTGCAAGATCAGAAGCTCAACTGAAA
                          || | |  |  || |  |  |  |||| |   || | |     |   |||||  |  |   |   || ||  | ||   ||    ||  ||   ||  |  | | | ||||   ||   || ||  ||||||||||||||||||| || ||||| |||||||| |  ||  | |||||||  || ||||| ||| |||||
gtaatatttttttgctttactctgccaattcatctgaatttagtggttgagttcttgacttccatgactctttttgcttatatttcttcttttatattaatttcccacatttggcttcgctt--tccgcttattattaaattgcattcttatagGGAGAAATGCAGCAACTTCGTGACAAGCTTGCTATAGTTGAGCGCGCTGCAAAGTCTGAAGCACAATTGAAA

upper sequence: GRMZM2G017525_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA02G09390.1 (Glycine max), 3'ss of exon 7
------------------------gtaagtgaaatatatcttttcttctagttttaagctgctaccgagtt----gctcgtggtagatttgtacaa-gttcttcagcggtgaattttattgatttgttgaatattgtctt---tttttgcagGGAGAAATGCAGCAACTCCGGGACAAACTTGCTATTGCAGAAAGGGCTGCAAGATCAGAAGCTCAACTGAAA
                          || | |  |  || |  |  |  ||||||    | | |      |    |||  |  |   ||| || |    | | | ||       ||   |  |    | | ||||   ||   || ||  ||||||||||||||||||| || ||||| |||||||| |  ||  | ||||||| ||  ||||| ||  |||||
gtaatatttttttgttttactctgccaattcatctgaatttagtggttgagtttttgaattccattactctttctgcttatatttcttttttatagtaatttcccgcatctggcttcgctt-tccacttattattaaattgaattcttatagGGAGAAATGCAGCAACTTCGTGACAAGCTTGCTATAGTTGAGCGCGCTGCAAAATATGAAGCACAGTTGAAA

upper sequence: GRMZM2G017525_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA08G05100.1 (Glycine max), 3'ss of exon 7
gtaagtgaaatatatcttttcttctagttttaagctgctaccgagttgctcgtg-gtagatttgtacaagttcttcagcggtgaattttatt--gatttgttgaatattgtctt------------tttttgcagGGAGAAATGCAGCAACTCCGGGACAAACTTGCTATTGCAGAAAGGGCTGCAAGATCAGAAGCTCAACTGAAA
||   |   || | |  || ||| | | ||||| ||  |      ||  |  |    | |   ||| |  |  |   ||  |   |||   |   ||  | |    ||| | ||            ||||   ||||||| ||||||||||| |||||||| ||||||||  | ||  |  ||||||  || ||||| ||  | |||
gtggatatcatttctgattcctt-tggatttaatcttttgtgcctttttttttataaaaaaaagtatatatcttcttgcatttggtttcccttcaatacggtttccatttttttaccaaactacacttttattagGGAGAGATGCAGCAACTTCGGGACAAGCTTGCTATAACTGAGCGAACTGCAAAGTCTGAAGCACAGTTAAAA

upper sequence: GRMZM2G017525_T01 (Zea mays), 3'ss of exon 3
lower sequence: AT1G14840.1 (Arabidopsis thaliana), 3'ss of exon 7
---gtaagtgaaatatatcttttcttctagttttaagctgctaccgagttgctcgtggtagatttgtacaagttcttcagcggtgaattttattgatttgttgaatattgtctttttttg-cagGGAGAAATGCAGCAACTCCGGGACAAACTTGCTATTGCAGAAAGGGCTGCAAGATCAGAAGCTCAACTGAAA
    |   ||| | ||||   |  ||  | | |   ||||||  | | |||         ||||  ||     |   | | | | || || ||    |||   |  |  ||  | ||| | |||||||||||||| ||||| || ||||||||||| || || ||  | ||||||| ||| |||||||| ||||| 
gtcattgctgatacatattaatatttaaattctcttgctgct-tcaaattgt--------gattcata-----ttcacggagattaactt-atactattgcc-accaccgttatgtttggacagGGAGAAATGCAACAACTACGCGACAAACTTGCCATAGCTGACCGAGCTGCAAAATCTGAAGCTCAGCTGAAG

upper sequence: GRMZM2G017525_T01 (Zea mays), 3'ss of exon 3
lower sequence: AT1G24764.1 (Arabidopsis thaliana), 3'ss of exon 7
------gtaagtgaaatatatcttttcttctagttttaagctgctaccgagttgctcgtggtagatttgtacaagttcttcagcggtgaattttattgatttgttgaatattgtctttttttgcagGGAGAAATGCAGCAACTCCGGGACAAACTTGCTATTGCAGAAAGGGCTGCAAGATCAGAAGCTCAACTGAAA
       |   |   ||    | | || |  | | ||| |  ||     | ||  | |  ||          | |  | ||       |  ||   | | || ||||   |   ||||||| ||||||||||||||||||||| || || || || || ||  ||||  ||||||||| ||| || || ||  | |||
gtttactttgatatgatggcccctctcctagattcttaggacgc----aaattatttgcagtgagca-----aggcccatccatatctacattc--tcacttcttgatcctcaactttttt-gcagGGAGAAATGCAGCAACTTCGTGATAAGCTCGCCATAACAGACCGGGCTGCAAAATCCGAGGCACAGTTAAAA

upper sequence: GRMZM2G017525_T01 (Zea mays), 3'ss of exon 3
lower sequence: AT1G68060.1 (Arabidopsis thaliana), 3'ss of exon 7
gtaagtgaaatatatcttttcttctagttttaagctgctaccgagttgctcgtggt-agatttgtacaagttcttcagcggtg-aattttattgatttgttgaatattgtctttttttgcagGGAGAAATGCAGCAACTCCGGGACAAACTTGCTATTGCAGAAAGGGCTGCAAGATCAGAAGCTCAACTGAAA
              | |  | |  ||   ||   ||  | |  | ||  | |     |||||  |  ||||     ||      ||  |||     |   |   ||   ||| || |||||||||||||||||||||||||| || || ||||| ||  ||||  | ||||| | ||| ||||| || || |||
-------------gtttactttgatatgattgcccttttcctaaatttgtggaatccagattctttgaagtgacaaaggcacacaaccttacattctcactctttaac-tctcttcttgcagGGAGAAATGCAGCAACTCCGCGATAAGCTTGCCATATCAGATCGAGCTGCGAAATCTGAAGCACAGCTAAAA

upper sequence: GRMZM2G017525_T01 (Zea mays), 3'ss of exon 3
lower sequence: AT1G14840.2 (Arabidopsis thaliana), 3'ss of exon 7
----------------------gtaagtgaaatatatcttttc------ttctagttttaagctgctaccgagttgctcgtggtagatttgtacaagttcttcagcggtgaatttta--ttgatttgttg--aatattgtctttttttg-cagGGAGAAATGCAGCAACTCCGGGACAAACTTGCTATTGCAGAAAGGGCTGCAAGATCAGAAGCTCAACTGAAA
                       | |   |  || || ||| |      ||   | |  |   |  ||   |  | ||| || |   |        | |    |     | |  |||  ||    | |||  |  |  ||  | ||| | |||||||||||||| ||||| || ||||||||||| || || ||  | ||||||| ||| |||||||| ||||| 
gtgatgcctgtaaggcagtggcttgaagaacgtagatttttgcaggtcattgctgatacatattaatatttaaattctcttgctgcttcaaattgtgattcatattcacggagattaacttatactattgccaccaccgttatgtttggacagGGAGAAATGCAACAACTACGCGACAAACTTGCCATAGCTGACCGAGCTGCAAAATCTGAAGCTCAGCTGAAG

upper sequence: GRMZM2G017525_T01 (Zea mays), 3'ss of exon 3
lower sequence: Vv01s0011g05790.t01 (Vitis vinifera), 3'ss of exon 7
gtaagtg----aaatatatcttttcttctagttttaagctgctaccga--gttgctcgtggtagatttgtacaagttcttcagcggtgaattttattgatttgttgaatattgtc------tttttttgcagGGAGAAATGCAGCAACTCCGGGACAAACTTGCTATTGCAGAAAGGGCTGCAAGATCAGAAGCTCAACTGAAA
|||| |      ||  | |  ||  ||| |   || ||||  ||   |  ||| ||  |  |    |  |    ||  ||      || | |||    | ||  | | | ||  |      | || || ||||| ||||||||||||||| ||||||| ||||||||  | |||||  |||||| ||| ||||| ||| |||||
gtaaatactctgaagttcttattgtttcaaaacttgagctattatttactgtttctttttctttgatcatgactgtgtttggcttttgtagtttccacagtttgtaattgttaccaaaacctcttgttacagGGGGAAATGCAGCAACTCAGGGACAAGCTTGCTATAACGGAAAGAACTGCAAAATCTGAAGCACAATTGAAA

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|20803194|gb|BQ294244.1|BQ294244
EST:     ATAAAGTAATGCCTGTTAAACGATGGCTCGAGGAGCGAAGGATTCTGCAA                         GGAGAAATGCAGCAACTCCGGGACAAACTTGCTATTGTTTAAAGGGCTGTA
genomic: ATAAAGTAATGCCTGTTAAACGATGGCTCGAGGAGCGAAGGATTCTGCAAgtaagtgaaa ... ttttttgcagGGAGAAATGCAGCAACTCCGGGACAAACTTGCTATTGCAGAAAGGGCTGCA
EST: gi|18660383|gb|BM500833.1|BM500833
EST:     ATAAAGTAATGCCTGTTAAACGATGGCTCGAGGAGCGAAGGATTCTGCAA                         GGAGAAATGCAGCAACTCCGGGACAAACTTGCTATTGCAGAAAGGGCTGCA
genomic: ATAAAGTAATGCCTGTTAAACGATGGCTCGAGGAGCGAAGGATTCTGCAAgtaagtgaaa ... ttttttgcagGGAGAAATGCAGCAACTCCGGGACAAACTTGCTATTGCAGAAAGGGCTGCA
EST: gi|23199547|gb|BU582112.1|BU582112
EST:     ATAAAGTAATGCCTGTTAAACGATGGCTCGAGGAGCGAAGGATTCTGCAA                         GGAGAAATGCAGCAACTCCGGGACAAACTTGCTATTGCAGAAAGGGCTGCA
genomic: ATAAAGTAATGCCTGTTAAACGATGGCTCGAGGAGCGAAGGATTCTGCAAgtaagtgaaa ... ttttttgcagGGAGAAATGCAGCAACTCCGGGACAAACTTGCTATTGCAGAAAGGGCTGCA
EST: gi|67023844|gb|CO452593.1|CO452593
EST:     ATAAAGTAATGCCTGTTAAACGATGGCTCGAGGAGCGAAGGATTCTGCAA                         GGAGAAATGCAGCAACTCCGGGACAAACTTGCTATTGCAGAAAGGGCTGCA
genomic: ATAAAGTAATGCCTGTTAAACGATGGCTCGAGGAGCGAAGGATTCTGCAAgtaagtgaaa ... ttttttgcagGGAGAAATGCAGCAACTCCGGGACAAACTTGCTATTGCAGAAAGGGCTGCA
EST: gi|22521576|gb|BU080387.1|BU080387
EST:     ATAAAGTAATGCCTGTTAAACGATGGCTCGAGGAGCGAAGGATTCTGCAA                         GGAGAAATGCAGCAACTCCGGGACAAACTTGCTATTGCAGAAAGGGCTGCA
genomic: ATAAAGTAATGCCTGTTAAACGATGGCTCGAGGAGCGAAGGATTCTGCAAgtaagtgaaa ... ttttttgcagGGAGAAATGCAGCAACTCCGGGACAAACTTGCTATTGCAGAAAGGGCTGCA
EST: gi|24765000|gb|CA400161.1|CA400161
EST:     ATAAAGTAATGCCTGTTAAACGATGGCTCGAGGAGCGAAGGATTCTGCAA                         GGAGAAATGCAGCAACTCCGGGACAAACTTGCTA
genomic: ATAAAGTAATGCCTGTTAAACGATGGCTCGAGGAGCGAAGGATTCTGCAAgtaagtgaaa ... ttttttgcagGGAGAAATGCAGCAACTCCGGGACAAACTTGCTA
EST: gi|6859889|gb|AW355883.1|AW355883
EST:     ATAAAGTAATGCCTGTTAAACGATGGCTCGAGGAGCGAAGGATTCTGCAA                         GGAGAAATGCAGCAACTCCGGGACAAACTTGCTATTGCAGAAAGGGCTGCA
genomic: ATAAAGTAATGCCTGTTAAACGATGGCTCGAGGAGCGAAGGATTCTGCAAgtaagtgaaa ... ttttttgcagGGAGAAATGCAGCAACTCCGGGACAAACTTGCTATTGCAGAAAGGGCTGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caagttcttcagcggtgaattttattgatttgttgaatattgtctttttttgcagGGAGAAATGCAGCAACTCCGGGACAAACTTGCTATTGCAGAAAGGGCTGCAAGATCAGAAGCTCAACTGAAA
                      tattgat  putative branch site (score: 3)
                                     tattgtcttttttt  putative PPT
                 aattttattgatttgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtgaaatatatcttttcttctagttttaagctgctaccgagttgctcgtggtagatttgtacaagttcttcagcggtgaattttattgatttgttgaatattgtctttttttgcagGGAGAAATGCAGCAACTCCGGGACAAACTTGCTATTGCAGAAAGGGCTGCAAGATCAGAAGCTCAACTGAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA