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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTTGTATTGCCAGAATGGTCTTGCTACTAAGGTTGAGAAGTCCCGCAAGCAAATGAAAGAGCGGAAGAACAGGGCCAAGAAGATCCGTGGTGTCAAGAAGgtgagctatctactgacatgcagtcctcttgtgaagtttatattacttactgtgccacgtgtgtaatacatgctttacgtcttttacag

Basic information

species Zea mays
transcript GRMZM2G151252_T02
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G151252_T02 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os01g52490.1 (Oryza sativa), 5'ss of exon 4
TTTGTATTGCCAGAATGGTCTTGCTACTAAGGTTGAGAAGTCCCGCAAGCAAATGAAAGAGCGGAAGAACAGGGCCAAGAAGATCCGTGGTGTCAAGAAGgtgagctatc---tactga---catgcagtcctcttgtgaagtttatattacttactgtgccacgtgtgtaatacatgctttacgtctt-ttacag
             |||||||||||||| ||||||||||| || ||||||||||||||||| || |||||||| || |||||||||||||||||||||||||||||||||    |||||    | |||  |    |  || || |||||||  || || ||  |      ||||       ||  || || || |||
-------------AATGGTCTTGCTACCAAGGTTGAGAAATCTCGCAAGCAAATGAAAGAACGCAAGAACAGAGCTAAGAAGATCCGTGGTGTCAAGAAGgtgagctattggttactggagtcctgccatttcttgatgcaggttatattggttgctttgtaatac---taatgggcatgttgggttttattgcag

upper sequence: GRMZM2G151252_T02 (Zea mays), 5'ss of exon 3
lower sequence: AT3G04920.1 (Arabidopsis thaliana), 5'ss of exon 4
TTTGTATTGCCAGAATGGTCTTGCTACTAAGGTTGAGAAGTCCCGCAAGCAAATGAAAGAGCGGAAGAACAGGGCCAAGAAGATCCGTGGTGTCAAGAAGgtgagctatctactgacatgcagtcctcttgtgaagtttatattacttactgtg-ccacgtgtgtaata-catgcttta--cgtcttttacag
             ||||| ||||  |||||| ||||||||||  | || ||||| || ||  ||||||||||||| ||||| ||||||||||| ||||||||    | | |||||   | |   |||||||  |   || | ||  | | |||| |      | ||| |   || |||   |    ||| |||
-------------AATGGACTTGACACTAAGATTGAGAAGTCAAGGAAACAAATTAAGGAAAGGAAGAACAGGGCGAAGAAAATCCGTGGTGTTAAGAAGgta---tgtatactggttttc---cctcttgctat-cttctgtttttgattgtgactgtagctttaagaatctgttttgatcaatgtttgcag

upper sequence: GRMZM2G151252_T02 (Zea mays), 5'ss of exon 3
lower sequence: AT5G28060.1 (Arabidopsis thaliana), 5'ss of exon 4
TTTGTATTGCCAGAATGGTCTTGCTACTAAGGTTGAGAAGTCCCGCAAGCAAATGAAAGAGCGGAAGAACAGGGCCAAGAAGATCCGTGGTGTCAAGAAGgt--gagctatc--tactgacatgcagtcctcttgtgaagtt--tatattacttactgtgccacgtgtgtaatacatgctttacgtcttt--tacag
             ||||| ||||  || ||| ||||||| ||  | || || || || ||| ||||||||||||| ||||||||||||||||| ||||||||  |||  | |   ||| ||  | | ||  | | ||   ||  ||| ||  |  ||||      |     |||  ||| ||   |  |   |  ||
-------------AATGGACTTGACACCAAGATTGAGAAATCAAGGAAACAGATCAAGGAGAGGAAGAACAGGGCGAAGAAGATCCGTGGTGTTAAGAAGgtaagagagaccaacactaaccagaaatctacatttgctattgttatgtttgtgcctgttttgtcttaacgatatttgcattgttttgtgagtgtag

upper sequence: GRMZM2G151252_T02 (Zea mays), 5'ss of exon 3
lower sequence: Vv07s0151g00900.t01 (Vitis vinifera), 5'ss of exon 4
TTTGTATTGCCAGAATGGTCTTGCTACTAAGGTTGAGAAGTCCCGCAAGCAAATGAAAGAGCGGAAGAACAGGGCCAAGAAGATCCGTGGTGTCAAGAAGgtgagctatctactgacatgcagtcctcttgtgaagtttatattacttactgtgccacgtgtgtaatacatgctttacgtcttttacag-----------------------------------------------------------------------------------------
             |||||  | | ||| ||||| || |||||  | ||||||||||| ||  |||||||||||||||||||| |||| || || |||||||| |   |   |    | |     |||  | ||  ||  |   ||   |  || ||| |  | | |       |||  |   |  || |                                                                                         
-------------AATGGATTGGATACCAAGGTGGAAAAGTCAAGGAAGCAAATGAAGGAAAGGAAGAACAGGGCCAAGAAGGTCCGAGGAGTGAAGAAGgtaaagaaatcatcttccttttaaccttgt-tggtgtgcactctagcaatagtaccaggcctttcaatttccttttttgctgtacactgggttactattgccattcccattagccatattatttgccttcaaagatttgggaccttcacgttcattgtactactcgttactcttgcag

upper sequence: GRMZM2G151252_T02 (Zea mays), 5'ss of exon 3
lower sequence: Vv14s0030g01620.t01 (Vitis vinifera), 5'ss of exon 4
TTTGTATTGCCAGAATGGTCTTGCTACTAAGGTTGAGAAGTCCCGCAAGCAAATGAAAGAGCGGAAGAACAGGGCCAAGAAGATCCGTGGTGTCAAGAAGgtgagctatctactgacatgcagtcct-cttgtgaagtttatattacttactgtgccacgtgtgtaatacatgctttacgtcttttacag
             |||||  | | ||| ||||| ||||||||  | ||||||||||| ||| ||||||| ||| |||||||| |||| ||||| |||||||| ||   |  |   |  ||||||  | | | |     | || | ||| | | |  ||| |   || | |    ||   |    | ||||
-------------AATGGATTGGATACCAAGGTCGAGAAGTCTAGGAAGCAAATGAAGGAGAGGAAGAATAGGTCCAAGAAGGTCCGAGGTGTAAAGAAGgtaagaagtgaataaatttgcagtggtacctttttctctcatttaactcattct--cacctccctatttcccatttcttgc---taacag

upper sequence: GRMZM2G151252_T02 (Zea mays), 5'ss of exon 3
lower sequence: PP1S204_49V6.1 (Physcomitrella patens), 5'ss of exon 4
TTTGTATTGCCAGAATGGTCTTGCTACTAAGGTTGAGAAGTCCCGCAAGCAAATGAAAGAGCGGAAGAACAGGGCCAAGAAGATCCGTGGTGTCAAGAAGgtgagc-tatctactgacatgcagtcctcttgtgaagtttatattacttactgtgc--cacgtgtgtaatacatgctttacgtcttttacag---------------------------------------------
             ||||| || || || ||||||||||||||| | |||||||| || ||||| |||||| |  ||||||||||| | ||||| ||||||||  || ||    ||||  || |    | | |   |||   |||  ||||   | |  ||  | |||  |  |   || |     |  |||                                              
-------------AATGGACTGGCGACCAAGGTTGAGAAGTCCAGGAAGCAAATTAAGGAGCGCAAGAACCGTTCCAAGAAGATCAGGGGTGTGAAGAAGgtatgcgtaatcgctgat-tgaa----tttggcagagtaactatctcttagaatccagcatatatgtcttttagatttcattaaatgcacaaatttaatgttttctgacgttattacacgtgattccttctctgcag

upper sequence: GRMZM2G151252_T02 (Zea mays), 5'ss of exon 3
lower sequence: EFJ29464 (Selaginella moellendorffii), 5'ss of exon 4
TTTGTATTGCCAGAATGGTCTTGCTACTAAGGTTGAGAAGTCCCGCAAGCAAATGAAAGAGCGGAAGAACAGGGCCAAGAAGATCCGTGGTGTCAAGAAGgtgagctatctactgacatgcagtcctcttgtgaagtttatattacttactgtgccacgtgtgtaatacatgctttacgtcttttacag
             || || ||||| || | ||   |||||||  | |||||  | || ||| ||||||||||||||||||||||||| || || ||||||||  ||| |||       |      ||||       | |   || ||| ||      |                               
-------------AACGGACTTGCAACCAGGGAGCAGAAGTCGAGGAAGCAGCTCAAGGAGAGGAAGAACAGGGCCAAGAAGATCCGCGGAGTGAAGAAGgtctgctttctctctctctctctctctctccattgatgtgc-ttgcttgctcccattcag-----------------------------

upper sequence: GRMZM2G151252_T02 (Zea mays), 5'ss of exon 3
lower sequence: EFJ28032 (Selaginella moellendorffii), 5'ss of exon 4
TTTGTATTGCCAGAATGGTCTTGCTACTAAGGTTGAGAAGTCCCGCAAGCAAATGAAAGAGCGGAAGAACAGGGCCAAGAAGATCCGTGGTGTCAAGAAGgtgagctatcta-ctgacatgcagtcctcttgtgaagtttatattacttactgtgccacgtgtgtaatacatgctttacgtcttttacag
             || || ||||| || | ||   |||||||  | |||||  | || ||| ||||||||||||||||||||||||| || || ||||||||  ||| |||  ||  |   |  ||    | |     ||    | ||| ||    | | |                             
-------------AACGGACTTGCAACCAGGGAGCAGAAGTCGAGGAAGCAGCTCAAGGAGAGGAAGAACAGGGCCAAGAAGATCCGCGGAGTGAAGAAGgtctgctctctctctctctctctctctctctctctccattgatgtgcttgcttgctcccattcag-------------------------

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|93017130|gb|EB642650.1|EB642650
EST:     AAATGAAAGAGCGGAAGAACAGGGCCAAGAAGATCCGTGGTGTCAAGAAG                         ACCAAGGCTGGTGACGCCAAGAAGAAGTAAACAGTCATTTATATTTCTGTA
genomic: AAATGAAAGAGCGGAAGAACAGGGCCAAGAAGATCCGTGGTGTCAAGAAGgtgagctatc ... tcttttacagACCAAGGCTGGTGACGCCAAGAAGAAGTAAACAGTCATTTATATTTCTGTA
EST: gi|32943820|gb|CF048639.1|CF048639
EST:     AAATGAAAGAGCGGAAGAACAGGGCCAAGAAGATCCGCGGTGTCAAGAAG                         ACCAAGGCTGGTGATGCCAAGAAGAAGTAAACAGTCATTTATATTTCTGTA
genomic: AAATGAAAGAGCGGAAGAACAGGGCCAAGAAGATCCGTGGTGTCAAGAAGgtgagctatc ... tcttttacagACCAAGGCTGGTGACGCCAAGAAGAAGTAAACAGTCATTTATATTTCTGTA
EST: gi|18650073|gb|BM498892.1|BM498892
EST:     CGTGGTGTCAAGAAG                         ACCAAGGCTGGTGACGCCAAGAAGAAGTAAACAGTCATTTATATTTCTGTA
genomic: CGTGGTGTCAAGAAGgtgagctatc ... tcttttacagACCAAGGCTGGTGACGCCAAGAAGAAGTAAACAGTCATTTATATTTCTGTA
EST: gi|32804188|gb|CD956424.1|CD956424
EST:     GATCCGTGGTGTCAAGAAG                         ACCAAGGCTGGTGATGCCAAGAAGAAGTAAACAGTCATTTATATTTCTGTA
genomic: GATCCGTGGTGTCAAGAAGgtgagctatc ... tcttttacagACCAAGGCTGGTGACGCCAAGAAGAAGTAAACAGTCATTTATATTTCTGTA
EST: gi|60397878|gb|DN230694.1|DN230694
EST:     AAATGAAAGAGCGGAAGAACAGGGCCAAGAAGATCCGTGGTGTCAAGAAG                         ACCAAGGCTGGTGACGCCAAGAAGAAGTAAACAGTCATTTATATTTCTGTA
genomic: AAATGAAAGAGCGGAAGAACAGGGCCAAGAAGATCCGTGGTGTCAAGAAGgtgagctatc ... tcttttacagACCAAGGCTGGTGACGCCAAGAAGAAGTAAACAGTCATTTATATTTCTGTA
EST: gi|14206819|gb|BG840497.1|BG840497
EST:     AAATGAAAGAGCGGAAGAACAGGGCCAAGAAGATCCGTGGTGTCAAGAAG                         ACCAA-GCTGGTGACGCCAAGAAGAAGTAAACAGTCATTTATATTTCTGTA
genomic: AAATGAAAGAGCGGAAGAACAGGGCCAAGAAGATCCGTGGTGTCAAGAAGgtgagctatc ... tcttttacagACCAAGGCTGGTGACGCCAAGAAGAAGTAAACAGTCATTTATATTTCTGTA
EST: gi|113789340|gb|DW909149.1|DW909149
EST:     GAAGATCCGTGGTGTCAAGAAG                         ACCAAGGCTGGTGACGCCAAGAAGAAGTAAACAGTCATTTATATTTCTGTA
genomic: GAAGATCCGTGGTGTCAAGAAGgtgagctatc ... tcttttacagACCAAGGCTGGTGACGCCAAGAAGAAGTAAACAGTCATTTATATTTCTGTA
EST: gi|14621547|gb|BI142308.1|BI142308
EST:     AAATGAAAGAGCGGAAGAACAGGGCCAAGAAGATCCGTGGTGTCAAGAAG                         ACCAAGGCTGGTGACGCCAAGAAGAAGTAAACAGTCATTTATATTTCTGTA
genomic: AAATGAAAGAGCGGAAGAACAGGGCCAAGAAGATCCGTGGTGTCAAGAAGgtgagctatc ... tcttttacagACCAAGGCTGGTGACGCCAAGAAGAAGTAAACAGTCATTTATATTTCTGTA
EST: gi|113615885|gb|DW781332.1|DW781332
EST:     GTGTCAAGAAG                         ACCAAGGCTGGTGACGCCAAGAAGAAGTAAACAGTCATTTATACTTTCTGT
genomic: GTGTCAAGAAGgtgagctatc ... tcttttacagACCAAGGCTGGTGACGCCAAGAAGAAGTAAACAGTCATTTATA-TTTCTGT
EST: gi|14244546|gb|BG840675.2|BG840675
EST:     AAATGAAAGAGCGGAAGAACAGGGCCAAGAAGATCCGTGGTGTCAAGAAG                         ACCAAGGCTGGTGACGCCAAGAAGAAGTAAACAGTCATTTATATTTCTGTA
genomic: AAATGAAAGAGCGGAAGAACAGGGCCAAGAAGATCCGTGGTGTCAAGAAGgtgagctatc ... tcttttacagACCAAGGCTGGTGACGCCAAGAAGAAGTAAACAGTCATTTATATTTCTGTA
EST: gi|93013351|gb|EB638871.1|EB638871
EST:     AAATGAAAGAGCGGAAGAACAGGGCCAAGAAGATCCGTGGTGTCAAGAAG                         ACCAAGGCTGGTGACGCCAAGAAGAAGTAAACAGTCATTTATATTTTTGTA
genomic: AAATGAAAGAGCGGAAGAACAGGGCCAAGAAGATCCGTGGTGTCAAGAAGgtgagctatc ... tcttttacagACCAAGGCTGGTGACGCCAAGAAGAAGTAAACAGTCATTTATATTTCTGTA
EST: gi|32864175|gb|CF003857.1|CF003857
EST:     AAATGAAAGAGCGGAAGAACAGGTCCAAGAAGATCCGTGGTGTCAAGAAG                         ACCAAGGCTGGTGATGCCAAGAAGAAGTAAACAGTCATTTATATTTCTGTA
genomic: AAATGAAAGAGCGGAAGAACAGGGCCAAGAAGATCCGTGGTGTCAAGAAGgtgagctatc ... tcttttacagACCAAGGCTGGTGACGCCAAGAAGAAGTAAACAGTCATTTATATTTCTGTA
EST: gi|37391783|gb|CF633135.1|CF633135
EST:     AAATGAAAGAGCGGAAGAACAGGGCCAAGAAGATCCGTGGTGTCAAGAAG                         ACCAAGGCTGGTGACGCCAAGAAGAAGTAAACAGTCATTTATATTTCTGTA
genomic: AAATGAAAGAGCGGAAGAACAGGGCCAAGAAGATCCGTGGTGTCAAGAAGgtgagctatc ... tcttttacagACCAAGGCTGGTGACGCCAAGAAGAAGTAAACAGTCATTTATATTTCTGTA
EST: gi|15499601|gb|BI596114.1|BI596114
EST:     AAATGAAAGAGCGGAAGAACAGGGCCAAGAAGATCCGTGGTGTCAAGAAG                         ACCAAGGCTGGTGACGCCAAGAAGAAGTAAACAGTCATTTATATTTCTGTA
genomic: AAATGAAAGAGCGGAAGAACAGGGCCAAGAAGATCCGTGGTGTCAAGAAGgtgagctatc ... tcttttacagACCAAGGCTGGTGACGCCAAGAAGAAGTAAACAGTCATTTATATTTCTGTA
EST: gi|166676541|gb|EG291966.1|EG291966
EST:     AGAAGATCCGTGGTGTCAAGAAG                         ACCAAGGCTGGTGACGCCAAGAAGAAGTAAACAGTCATTTATATTTCTGTA
genomic: AGAAGATCCGTGGTGTCAAGAAGgtgagctatc ... tcttttacagACCAAGGCTGGTGACGCCAAGAAGAAGTAAACAGTCATTTATATTTCTGTA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTTGTATTGCCAGAATGGTCTTGCTACTAAGGTTGAGAAGTCCCGCAAGCAAATGAAAGAGCGGAAGAACAGGGCCAAGAAGATCCGTGGTGTCAAGAAGgtgagctatctactgacatgcagtcctcttgtgaagtttatattacttactgtgccacgtgtgtaatacatgctttacgtcttttacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG