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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacagtcgacatgcctttttgtatatattgttcaatcttaggttcatttacagcactgataaatggctgtttaatatgaaagGTTCTTGATGACTGCCCTGGTGATCTGAATGACTGGTACCGCCACACATCTAAAGGTGCATGGCCATTCTCAACTGCTGATCATGGTTGGCCTATATCTG

Basic information

species Zea mays
transcript GRMZM2G023798_T01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G023798_T02 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os02g04710.2 (Oryza sativa), 3'ss of exon 9
----gtacagtcgacatgcctttttgta----tatattgttcaatcttaggttcatttacagcactgataaatggctgtttaatatgaaagGTTCTTGATGACTGCCCTGGTGATCTGAATGACTGGTACCGCCACACATCTAAAGGTGCATGGCCATTCTCAACTGCTGATCATGGTTGGCCTATATCTG
     | |      ||||     || ||    |||| |  ||||  ||     |  |  ||  ||| |    ||||| ||||   ||||||||| | |||||||||||||| ||||| | | | ||||||||||||| |||||||||||||||||| || || |||||||||||||||||||||||||| |
gtgcatgcctcatgcatgttcccttatacgattatactaatcaacatttcaagccatctcattacttacctgtggct-tttatcctgaaagGTTATCGATGACTGCCCTGGAGATCTTAGTCAGTGGTACCGCCACATATCTAAAGGTGCATGGCCCTTTTCTACTGCTGATCATGGTTGGCCTATATCAG

upper sequence: GRMZM2G023798_T02 (Zea mays), 3'ss of exon 7
lower sequence: AT2G07050.1 (Arabidopsis thaliana), 3'ss of exon 9
gtacagtcgacatgcctttttgtatatattgttcaatcttaggttcatttacagcactgataaatggctgttta-atatgaaagGTTCTTGATGACTGCCCTGGTGATCTGAATGACTGGTACCGCCACACATCTAAAGGTGCATGGCCATTCTCAACTGCTGATCATGGTTGGCCTATATCTG
||   |   |      |  |   |   |  ||      || | |    ||    | || || | ||  | |||  ||   | ||||  | || ||||||||||| ||||||||| ||||||| |||||||  |||||||| || ||||| ||||||||||| ||||| |||||||| || ||||
gtttgggataggcagttaatgaaaatcagcgtgttgctttggatgttcttttccctctcatgattgtttcttttcatggtatagGTGTTAGAAGACTGCCCTGGAGATCTGAATTACTGGTATCGCCACATTTCTAAAGGGGCTTGGCCTTTCTCAACTGCAGATCACGGTTGGCCCATCTCTG

upper sequence: GRMZM2G023798_T02 (Zea mays), 3'ss of exon 7
lower sequence: Vv09s0054g01090.t01 (Vitis vinifera), 3'ss of exon 10
-------gtacagtcgacatgcctttttgtatat-attgttcaatcttag-gttcatttacagcactgataaatggctgtt------taatatgaaagGTTCTTGATGACTGCCCTGGTGATCTGAATGACTGGTACCGCCACACATCTAAAGGTGCATGGCCATTCTCAACTGCTGATCATGGTTGGCCTATATCTG
        | |  | ||  |    | |  || || |    |  || ||||   |  |  | |    |  ||  |  || ||      |  | |  |||||  | || || || ||||| ||||||||    ||||| || ||||  || |||||||| |||||||||||||||||||||||||| ||||| || ||||
gttcatgttgctattgaagtttgatctcataaatcacctatgtatattagcagttttccataatgattttacttaactattcctactttgttttcaagGTCTTAGAAGATTGTCCTGGAGATCTGAAATTTTGGTATCGTCACATTTCCAAAGGTGCTTGGCCATTCTCAACTGCTGATCATGGATGGCCGATCTCTG

upper sequence: GRMZM2G023798_T02 (Zea mays), 3'ss of exon 7
lower sequence: Vv09s0054g01550.t01 (Vitis vinifera), 3'ss of exon 9
-------gtacagtcgacatgcctttttgtatatattgttca-atcttag-gttcatttacagcactgataaatggctgtt------taatatgaaagGTTCTTGATGACTGCCCTGGTGATCTGAATGACTGGTACCGCCACACATCTAAAGGTGCATGGCCATTCTCAACTGCTGATCATGGTTGGCCTATATCTG
        | |  | ||  |    | |  || ||    | |  || ||||   |  |  | |    |  ||  |  || ||      |  | |  |||||  | || || || ||||| ||||||||    ||||| || ||||  || |||||||| ||||||||||||||||||||||| || ||||| || ||||
gttcatgttgctattgaagtttgatctcataaatcacctacgtatattagcagttgtccataatgattttacctaactattcctactttgttttcaagGTCTTAGAAGATTGTCCTGGAGATCTGAAATTTTGGTATCGTCACATTTCCAAAGGTGCTTGGCCATTCTCAACTGCTGATCAGGGATGGCCGATCTCTG

upper sequence: GRMZM2G023798_T02 (Zea mays), 3'ss of exon 7
lower sequence: Vv09s0018g00630.t01 (Vitis vinifera), 3'ss of exon 9
-------gtacagtcgacatgcctttttgtatatattgttca-atcttag-----gttcat--ttacagcactgataaatggctgtttaatatgaaagGTTCTTGATGACTGCCCTGGTGATCTGAATGACTGGTACCGCCACACATCTAAAGGTGCATGGCCATTCTCAACTGCTGATCATGGTTGGCCTATATCTG
        | |  | ||  |    | |  || ||    | || || ||||     || |||  | |    ||| |   ||  ||  ||  | |  |||||  | || || || ||||| ||||||||    ||||| || ||||  || |||||||| |||||||||||||||||||||||||| ||| |  | ||||
gttcatgttgctattgaagtttgatctcataaatcacctacatatattagcagttgtccataatgattttacttaactattcctactttgttttcaagGTCTTAGAAGATTGTCCTGGAGATCTGAAATTTTGGTATCGTCACATTTCCAAAGGTGCTTGGCCATTCTCAACTGCTGATCATGGATGGGCGGTCTCTG

upper sequence: GRMZM2G023798_T02 (Zea mays), 3'ss of exon 7
lower sequence: Vv09s0054g01120.t01 (Vitis vinifera), 3'ss of exon 8
-------gtacagtcgacatgcctttttgtatatattgttca-atcttag-----gttcat--ttacagcactgataaatggctgtttaatatgaaagGTTCTTGATGACTGCCCTGGTGATCTGAATGACTGGTACCGCCACACATCTAAAGGTGCATGGCCATTCTCAACTGCTGATCATGGTTGGCCTATATCTG
        | |  | ||  |    | |  || ||    | || || ||||     || |||  | |    ||| |   ||  ||  ||  | |  |||||  | || || || ||||| ||||||||    ||||| || ||||  || |||||||| ||||||||||||||||||||| |||| ||||| |  ||||
gttcatgttgctattgaagtttgatgtcataaatcacctacatatgttagcagttgtccataatgattttactcaactattcctactttgttttcaagGTCTTAGAAGATTGTCCTGGAGATCTGAAATTTTGGTATCGTCACATTTCCAAAGGTGCTTGGCCATTCTCAACTGCTGATAATGGATGGCCCACCTCTG

upper sequence: GRMZM2G023798_T02 (Zea mays), 3'ss of exon 7
lower sequence: Vv09s0054g01110.t01 (Vitis vinifera), 3'ss of exon 11
-------gtacagtcgacatgcctttttgtatatattgttca-atcttag-----gttcat--ttacagcactgataaatggctgtttaatatgaaagGTTCTTGATGACTGCCCTGGTGATCTGAATGACTGGTACCGCCACACATCTAAAGGTGCATGGCCATTCTCAACTGCTGATCATGGTTGGCCTATATCTG
        | |  | ||  |    | |  || ||    | || || ||||     || |||  | |    ||| |   ||  ||  ||  | |  |||||  | || || || ||||| ||||| ||    ||||| || ||||  || |||||||| ||||||||||||||||||||| |||| ||||| |  ||||
gttcatgttgctattgaagtttgatctcataaatcacctacatatgttagcagttgtccataatgattttactcaactattcctactttgttttcaagGTCTTAGAAGATTGTCCTGGAGATCTCAAATTTTGGTATCGTCACATTTCCAAAGGTGCTTGGCCATTCTCAACTGCTGATAATGGATGGCCCACCTCTG

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|21331674|gb|BQ487055.1|BQ487055
EST:     AGTTTGGTCCTACCCTTAAACTAGCACACAACTATATCAAGAATTCACAG                         GTTCTTGATGACTGCCCTG
genomic: AGTTTGGTCCTACCCTTAAACTAGCACACAACTATATCAAGAATTCACAGgtacagtcga ... aatatgaaagGTTCTTGATGACTGCCCTG
EST: gi|23199794|gb|BU582359.1|BU582359
EST:     AGTTTGGTCCTACCCTTAAACTAGCACACAACTATATCAAGAATTCACAG                         GTTCTTGATGACTGCCCTGGTGATCTGAATGACTGGTACCGCCACACATCT
genomic: AGTTTGGTCCTACCCTTAAACTAGCACACAACTATATCAAGAATTCACAGgtacagtcga ... aatatgaaagGTTCTTGATGACTGCCCTGGTGATCTGAATGACTGGTACCGCCACACATCT
EST: gi|18659473|gb|BM500356.1|BM500356
EST:     GTTTGGTCCTACCCTTAAACTAGCACACAACTATATCAAGAATTCACAG                         GTTCTTGATGACTGCCCTGGTGATCTGAATGACTGGTACCGCCACACATCT
genomic: GTTTGGTCCTACCCTTAAACTAGCACACAACTATATCAAGAATTCACAGgtacagtcga ... aatatgaaagGTTCTTGATGACTGCCCTGGTGATCTGAATGACTGGTACCGCCACACATCT
EST: gi|87156285|gb|DY401074.1|DY401074
EST:     AGTTTGGTCCTACCCTTAAACTAGCACACAACTATATCAAGAATTCACAG                         GTTCTTGATGACTGCCCTGGTGATCTGAATGACTGGTACCGCCACACATCT
genomic: AGTTTGGTCCTACCCTTAAACTAGCACACAACTATATCAAGAATTCACAGgtacagtcga ... aatatgaaagGTTCTTGATGACTGCCCTGGTGATCTGAATGACTGGTACCGCCACACATCT
EST: gi|26560142|gb|CA832377.1|CA832377
EST:     AGTTTGGTCCTACCCTTAAACTAGCACACAACTATATCAAGAATTCACAG                         GTTCTTGATGACTGCCCTGGTGATCTGAATGACTGGTACCGCCACACATCT
genomic: AGTTTGGTCCTACCCTTAAACTAGCACACAACTATATCAAGAATTCACAGgtacagtcga ... aatatgaaagGTTCTTGATGACTGCCCTGGTGATCTGAATGACTGGTACCGCCACACATCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgttcaatcttaggttcatttacagcactgataaatggctgtttaatatgaaagGTTCTTGATGACTGCCCTGGTGATCTGAATGACTGGTACCGCCACACATCTAAAGGTGCATGGCCATTCTCAACTGCTGATCATGGTTGGCCTATATCTG
                                        tgtttaatatgaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacagtcgacatgcctttttgtatatattgttcaatcttaggttcatttacagcactgataaatggctgtttaatatgaaagGTTCTTGATGACTGCCCTGGTGATCTGAATGACTGGTACCGCCACACATCTAAAGGTGCATGGCCATTCTCAACTGCTGATCATGGTTGGCCTATATCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT