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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtgttactcttacattgcatcctatagtaatttagcaatcgtctcagcgtggatgtcaacatctaacctggtgcatctttgatgcagTCGTACCACAGCAACAACCAAATGCCTTAACTTGGGTTCCTATAACTACCTTGGTTTTGCTGCGGCTGATGAGTACTGCACCCCTCGTGTTATTGAGTCA

Basic information

species Zea mays
transcript GRMZM2G010202_T02
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G010202_T02 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os01g70380.1 (Oryza sativa), 3'ss of exon 3
gtgtgttactcttacattgcatcctatagtaatttagca----------------atcgtctcagcgtggatgtcaacatctaacctggtgcatctttgatgcagTCGTACCACAGCAACAACCAAATGCCTTAACTTGGGTTCCTATAACTACCTTGGTTTTGCTGCGGCTGATGAGTACTGCACCCCTCGTGTTATTGAGTCA
|| |||   ||| ||||   || |   |   | ||||||                ||  ||| ||  || |||  |   ||| | |   ||| ||||  ||||||||||||||||  |||| | || ||||||||||| |||||||| ||||||||||| ||||| ||||| ||||| |||||||||||||||||||||||||||
gtatgtatttctcacatctgattcagcacctagttagcataagaaaatgctgaatattatcttaggatgcatgctattctctgatccaatgcttcttcaatgcagTCGTACCACAAAAACATCTAAGTGCCTTAACTTAGGTTCCTACAACTACCTTGGCTTTGCCGCGGCAGATGAATACTGCACCCCTCGTGTTATTGAGTCA

upper sequence: GRMZM2G010202_T02 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os01g70370.1 (Oryza sativa), 3'ss of exon 3
gtgtgttactcttacattgcatcctatagtaatttagc--aatcgtctcagcg--tggatgtcaa-----catctaacctggtgcatctttgat----gcagTCGTACCACAGCAACAACCAAATGCCTTAACTTGGGTTCCTATAACTACCTTGGTTTTGCTGCGGCTGATGAGTACTGCACCCCTCGTGTTATTGAGTCA
   |  ||  | || |    || ||   |  || || |  |||  | | || |  || |||  |       |||| |||   ||| ||| ||||    |||| |||||||||  |||| |||  ||||||||||| |||||||| || |||||||| ||||||||||| ||||| |||||||| ||||||||||||||||||
-cctaataagcata-agcaaatgctgcggatatatatcttaattatattagaggatgcatgctagaaattaatctgacccaatgcttctctgatatatgcagCCGTACCACAAAAACATCCAGGTGCCTTAACTTAGGTTCCTACAATTACCTTGGCTTTGCTGCGGCAGATGAATACTGCACTCCTCGTGTTATTGAGTCA

upper sequence: GRMZM2G010202_T02 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA02G07250.1 (Glycine max), 3'ss of exon 3
-----------gtgtgttactcttacattgcatcctatagtaatttagcaatcgtctcagcgtggatgtcaacatctaacctggtgcatcttt--gatgcagTCGTACCACAGCAACAACCAAATGCCTTAACTTGGGTTCCTATAACTACCTTGGTTTTGCTGCGGCTGATGAGTACTGCACCCCTCGTGTTATTGAGTCA
            | | ||  |  || |||  |   || ||   || ||||   |    |     |||| | |  | | |     |   || |    |||||| || ||      || ||  | ||||||||| ||||| || || ||||| ||||||||||| || || ||||| |||||||| ||||| ||  ||||  | 
ttgaaatatatatatatttgttgtaaattttaatttagagc--ttcagcatgagaaatatatctgatgcctatttttcatactatttctcctcccaatgcagACGGACTGATAAAATAAGTAGATGCCTTAATTTGGGATCATACAACTATCTTGGTTTTGCGGCAGCAGATGAATACTGCACGCCTCGAGTAGTTGATACG

upper sequence: GRMZM2G010202_T02 (Zea mays), 3'ss of exon 3
lower sequence: Vv14s0068g01300.t01 (Vitis vinifera), 3'ss of exon 3
----------------gtgtgttactcttacattgcatcctatagt--aatttagcaatcgtctcagcgtggatgtcaacatctaacctggtgcatctttgatgcagTCGTACCA-CAGCAACAACCAAATGCCTTAACTTGGGTTCCTATAACTACCTTGGTTTTGCTGCGGCTGATGAGTACTGCACCCCTCGTGTTATTGAGTCA
                 | || |   | |   || ||| ||  |||  ||  ||  | || |       | |     | || |||| |         ||| |||||| || || | ||  | ||  | | |||||||||||||| || || ||||||||||| ||||||||  | ||||| |||||||| || ||||| ||||| |||
tatggtgcacaatgatttatggttgccctgatttacattctccagtgtaagctaaaactcataaatttttagtatctatcaactaatcga-------tttcatgcagACGAACTAGCAATATCAGTCGA-TGCCTTAACTTGGGATCATACAACTACCTTGGCTTTGCTGCATCGGATGAATACTGCACGCCACGTGTAATTGAATCA

upper sequence: GRMZM2G010202_T02 (Zea mays), 3'ss of exon 3
lower sequence: EFJ20689 (Selaginella moellendorffii), 3'ss of exon 3
-------------gtgtgttactcttacattgcatcctatagtaatttagcaatcgtctcagcgtggatgtcaacatctaacctggtgcatctttgatg-cagTCGTACCACAGCAACAACCAAATGCCTTAACTTGGGTTCCTATAACTACCTTGGTTTTGCTGCGGCTGATGAGTACTGCACCCCTCGTGTTATTGAGTCA
              | |||   |  ||| | | || ||   ||  ||| | ||   |||   || |    ||              |  || |||  ||  |||||  ||      |||   | ||| || ||| | || || || ||||||||||| |||||||| ||||| ||||||||||| || || || || ||||| 
gtaggtgataactttttgtgtttggtacttagaattctc--gtgcttttggaagtttcttttcgggagcttccctgatccttggattttattttttttgatagTCGGCCCTTCAAGACACGGAGATGTCTCAACCTTGGCTCTTACAACTACCTTGGATTTGCTGCCGCTGACGAGTACTGCACGCCCCGGGTGATCGAGTCT

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|26559603|gb|CA831838.1|CA831838
EST:     TGGTTCGATGTGGTTGAGCGCTACTCAAATGACTGCAACAAGACACTCCA                         TCGTACCACAGCAACAACCAAATGCCTTAACTTGGGTTCCTATAACTACCT
genomic: TGGTTCGATGTGGTTGAGCGCTACTCAAATGACTGCAACAAGACACTCCAgtgtgttact ... tttgatgcagTCGTACCACAGCAACAACCAAATGCCTTAACTTGGGTTCCTATAACTACCT
EST: gi|19821837|gb|BQ047861.1|BQ047861
EST:     TGGTTCGATGTGGTTGAGCGCTACTCAAATGACTGCAACAAGACACTCCA                         TCGTACCACAGCAACAACCAAATGCCTTAACTTGGGTTCCTATAACTACCT
genomic: TGGTTCGATGTGGTTGAGCGCTACTCAAATGACTGCAACAAGACACTCCAgtgtgttact ... tttgatgcagTCGTACCACAGCAACAACCAAATGCCTTAACTTGGGTTCCTATAACTACCT
EST: gi|22935830|gb|BU572105.1|BU572105
EST:     TGGTTCGATGTGGTTGAGCGCTACTCAAATGACTGCAACAAGACACTCCA                         TCGTACCACAGCAACAACCAAATGCCTTAACTTGGGTTCCTATAACTACCT
genomic: TGGTTCGATGTGGTTGAGCGCTACTCAAATGACTGCAACAAGACACTCCAgtgtgttact ... tttgatgcagTCGTACCACAGCAACAACCAAATGCCTTAACTTGGGTTCCTATAACTACCT
EST: gi|87151662|gb|DY396451.1|DY396451
EST:     TGGTTCGATGTGGTTGAGCGCTACTCAAATGACTGCAACAAGACACTCCA                         TCGTACCACAGCAACAACCAAATGCCTTAACTTGGGTTCCTATAACTACCT
genomic: TGGTTCGATGTGGTTGAGCGCTACTCAAATGACTGCAACAAGACACTCCAgtgtgttact ... tttgatgcagTCGTACCACAGCAACAACCAAATGCCTTAACTTGGGTTCCTATAACTACCT
EST: gi|20300198|gb|BQ163141.1|BQ163141
EST:     TGGTTCGATGTGGTTGAGCGCTACTCAAATGACTGCAACAAGACACTCCA                         TCGTACCACAGCAACAACCAAATGCCTTAACTTGGGTTCCTATAACTACCT
genomic: TGGTTCGATGTGGTTGAGCGCTACTCAAATGACTGCAACAAGACACTCCAgtgtgttact ... tttgatgcagTCGTACCACAGCAACAACCAAATGCCTTAACTTGGGTTCCTATAACTACCT
EST: gi|18964841|gb|BM661241.1|BM661241
EST:     TGGTTCGATGTGGTTGAGCGCTACTCAAATGACTGCAACAAGACACTCCA                         TCGTACCACAGCAACAACCAAATGCCTTAACTTGGGTTCCTATAACTACCT
genomic: TGGTTCGATGTGGTTGAGCGCTACTCAAATGACTGCAACAAGACACTCCAgtgtgttact ... tttgatgcagTCGTACCACAGCAACAACCAAATGCCTTAACTTGGGTTCCTATAACTACCT
EST: gi|87152364|gb|DY397153.1|DY397153
EST:     TGGTTCGATGTGGTTGAGCGCTACTCAAATGACTGCAACAAGACACTCCA                         TCGTACCACAGCAACAACCAAATGCCTTAACTTGGGTTCCTATAACTACCT
genomic: TGGTTCGATGTGGTTGAGCGCTACTCAAATGACTGCAACAAGACACTCCAgtgtgttact ... tttgatgcagTCGTACCACAGCAACAACCAAATGCCTTAACTTGGGTTCCTATAACTACCT
EST: gi|87156277|gb|DY401066.1|DY401066
EST:     TGGTTCGATGTGGTTGAGCGCTACTCAAATGACTGCAACAAGACACTCCA                         TCGTACCACAGCAACAACCAAATGCCTTAACTTGGGTTCCTATAACTACCT
genomic: TGGTTCGATGTGGTTGAGCGCTACTCAAATGACTGCAACAAGACACTCCAgtgtgttact ... tttgatgcagTCGTACCACAGCAACAACCAAATGCCTTAACTTGGGTTCCTATAACTACCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagcaatcgtctcagcgtggatgtcaacatctaacctggtgcatctttgatgcagTCGTACCACAGCAACAACCAAATGCCTTAACTTGGGTTCCTATAACTACCTTGGTTTTGCTGCGGCTGATGAGTACTGCACCCCTCGTGTTATTGAGTCA
                                         catcttt  CT-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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgtgttactcttacattgcatcctatagtaatttagcaatcgtctcagcgtggatgtcaacatctaacctggtgcatctttgatgcagTCGTACCACAGCAACAACCAAATGCCTTAACTTGGGTTCCTATAACTACCTTGGTTTTGCTGCGGCTGATGAGTACTGCACCCCTCGTGTTATTGAGTCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT