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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgtttgtttctctgcacatttgcttcatcacctgttctgtcctgtgtaaacatgggcttctgcagGTACTTCCTCAACGTCATATTCAACATCCTCAACAAGAAGATCTACAACTACTTCCCCTATCCATA

Basic information

species Zea mays
transcript GRMZM2G070605_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G070605_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os01g13770.3 (Oryza sativa), 3'ss of exon 1
---------------------------------------------------gtacgtttgtttctctgcacatttgcttcatcacctgttc-----tgtcctgtgtaaacatgggcttctgcagGTACTTCCTCAACGTCATATTCAACATCCTCAACAAGAAGATCTACAACTACTTCCCCTATCCATA
                                                    |   ||   ||   | ||||   | ||  ||| |||||      |  ||  | |   || | | |  || ||||||||| | ||||| ||||||||||||||||| |||||||| |||||||||||||||||||||||
gtatggttttctgccacaataatcgcgtgacctacacctctgcgttgtttattgaattgaattgatttcacagc-gattattcagctgtttgaagattgccattttgtgcaagtgatcttgtagGTACTTCTTGAACGTTATATTCAACATCCTCAATAAGAAGATATACAACTACTTCCCCTATCCATA

upper sequence: GRMZM2G070605_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA07G32190.1 (Glycine max), 3'ss of exon 2
---------------------------------gtacgtttgtttctctgcacatt---tgcttcatcacctgttctgtcctgtgtaaacatgggcttctgcagGTACTTCCTCAACGTCATATTCAACATCCTCAACAAGAAGATCTACAACTACTTCCCCTATCCATA
                                  ||||| ||  | |   | |      || |  |    |  || ||||||     |   |   ||  |||||||||||| | ||||| || ||||||||||||||||||||||||||||| |||||||||||||||||
tgtgttgtgtccatgaagaacagaaagactttattacgtgtggctgtgatcgccccgagtgttgaaattaccattttgtcct----tattcttttctgatgcagGTACTTCTTGAACGTGATTTTCAACATCCTCAACAAGAAGATCTACAATTACTTCCCCTATCCATA

upper sequence: GRMZM2G070605_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA13G24360.1 (Glycine max), 3'ss of exon 2
------------------------------------------------------------------------------------------------------------------------gtacgtttgtttctctgcacatttgcttcatcacctgttctgtcctgtg-taaacatgggcttctgcagGTACTTCCTCAACGTCATATTCAACATCCTCAACAAGAAGATCTACAACTACTTCCCCTATCCATA
                                                                                                                         | | | |||  || ||  | ||       |      | | ||  |||  |   | |   ||  |||||||||||| | ||||| || ||||||||||| ||||||||||||||||| |||||||||||||||||
gtacgtcacgtgactctgttcttattacacgcaaaaaacaacctatgattgtgtcgtgtgctcctgttctgtgtctcttacgttccctaagcttaaacttttaaccacttaacagatagacttcatgtgtggctgtgatcgttccgagtgttgaaattacggttttgtccttttccttttctgatgcagGTACTTCTTGAACGTGATTTTCAACATCCTTAACAAGAAGATCTACAATTACTTCCCCTATCCATA

upper sequence: GRMZM2G070605_T01 (Zea mays), 3'ss of exon 2
lower sequence: AT5G46110.1 (Arabidopsis thaliana), 3'ss of exon 2
-----------------------------------------------------gtacgtttgtttct-ctgcaca--tttgcttcatcacctgttctgtcctgtgtaaacatg-ggcttctgcagGTACTTCCTCAACGTCATATTCAACATCCTCAACAAGAAGATCTACAACTACTTCCCCTATCCATA
                                                      | | | || || | | ||  |  |||| || |   |   ||    | | | |   |||  ||  | | |||||||||| | || || || ||||||||||| |||||||||||||| || |||||||| ||||| ||
gtacgtatcattcacgcgcttttcttaaaacgttatcctgcgcactttagcagattcttatgattttaccgccaagttttggtttagtgcgaattgacgcttttatcctcatttggtatttacagGTACTTCTTGAATGTGATTTTCAACATCCTTAACAAGAAGATCTATAATTACTTCCCTTATCCCTA

upper sequence: GRMZM2G070605_T01 (Zea mays), 3'ss of exon 2
lower sequence: Vv10s0003g00300.t01 (Vitis vinifera), 3'ss of exon 2
-------------------------------------------------gtacgtttgtttctctgcacatt--tgcttca---tcacctgttctgt---cctgtgtaaacatgggcttctgcagGTACTTCCTCAACGTCATATTCAACATCCTCAACAAGAAGATCTACAACTACTTCCCCTATCCATA
                                                 ||  |   |  ||     | | |  || ||||   || |   |||||     || |   ||  ||  ||| | |||||| ||||||||||| ||||||||||||||||||||||||||||||||||||||||| ||||| ||
gtaggtcatcaccgttaccaactaacaacatctacaattctcttcaacggtcagaaagagtcaaaataaaatggtgattcaaaatccctgtttctgggtgtctttaccaaattgtactttttcagGTATTTCCTCAACGTTATATTCAACATCCTCAACAAGAAGATCTACAACTACTTCCCATATCCTTA

upper sequence: GRMZM2G070605_T01 (Zea mays), 3'ss of exon 2
lower sequence: PP1S450_22V6.1 (Physcomitrella patens), 3'ss of exon 2
--------------------------------------------------------------------------------------gtacgtttgtttctctgcacatttgcttcatcacctgttctgtcctgtgtaaa---catgggcttctgc-----agGTACTTCCTCAACGTCATATTCAACATCCTCAACAAGAAGATCTACAACTACTTCCCCTATCCATA
                                                                                       |  | |  | || ||||    |       |||   |||       |  ||||    |  |  |  ||      ||||||||| | |||||||| ||||||||| | |||||||||||||||||||| || ||||| || ||
gtacacattctactcttgtgcagtgctattgagccaaatgcaccgtctattctgtctcaacagctaagatgtctgaaaactgcgtcttgagatgatctccctgctttctgaggcagtcaggagtttcagggagattaaaatgtaatgcttgttgtgtattagGTACTTCTTGAACGTCATCTTCAACATCATGAACAAGAAGATCTACAACTATTTTCCCTACCCCTA

upper sequence: GRMZM2G070605_T01 (Zea mays), 3'ss of exon 2
lower sequence: PP1S450_17V6.1 (Physcomitrella patens), 3'ss of exon 2
-----------------------------gtacgtttgtttctctgcacatttgcttc-atcacctgttctgtcctgtgtaaacatgggct-tctg-cagGTACTTCCTCAACGTCATATTCAACATCCTCAACAAGAAGATCTACAACTACTTCCCCTATCCATA
                              | | ||   |||| |      |||  |  |    | |  || |  ||     |     | | | || |||||||||||| || || || ||||||||| | ||||||||||||||||||||||| ||||| || ||
ggctgcgctgtttgaatatgcatcatgagatgcattcccttctttttgtggttgtctagagtttcagggctatgatgccgtgatgcctgttgtgtgtcagGTACTTCCTGAATGTTATCTTCAACATCATGAACAAGAAGATCTACAACTACTTTCCCTACCCTTA

upper sequence: GRMZM2G070605_T01 (Zea mays), 3'ss of exon 2
lower sequence: EFJ15759 (Selaginella moellendorffii), 3'ss of exon 2
----gtacgtttgtttctctgcacatttgcttcatcacctgttctgtcctgtgtaaacatgggcttc-----tgcagGTACTTCCTCAACGTCATATTCAACATCCTCAACAAGAAGATCTACAACTACTTCCCCTATCCATA
    | | | || ||  ||    | | |  | | |  ||  || | ||   || |||   |  ||||     |||||||| || ||||| || || ||||||||||| ||||||||||||||||| || || || ||||||||
gtaggcatgctttttcttccttccttattttgcttttccacttttctctcttgcaaatgagatcttccttcttgcagGTATTTTCTCAATGTGATCTTCAACATCCTTAACAAGAAGATCTACAATTATTTTCCTTATCCATA

upper sequence: GRMZM2G070605_T01 (Zea mays), 3'ss of exon 2
lower sequence: EFJ38162 (Selaginella moellendorffii), 3'ss of exon 1
------gtacgtttgtttctctgcacatttgcttcatcacctgttctgtcctgtgta---aacatgggcttctgcagGTACTTCCTCAACGTCATATTCAACATCCTCAACAAGAAGATCTACAACTACTTCCCCTATCCATA
       | | |||  |||  | |   |||||||   ||| |||||| || ||   |    |  |    |  |||||||| || ||||| || || ||||||||||| ||||||||||||||||| || || || ||||||||
gtaggcatgctttttcttccttccttttttgcttttccac-tgttctctcttgcaaatgagatcttccttcttgcagGTATTTTCTCAATGTGATCTTCAACATCCTTAACAAGAAGATCTACAATTATTTTCCTTATCCATA

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|76914837|gb|DV165713.1|DV165713
EST:     TTCCTGGAGAAGTACCCGGCCCTGGTCACTGGCTTCTTCTTCTTCATGTG                         GTACTTCCTCAACGTCATATTCAACATCCTCAACAAGAAGATCTACAACTA
genomic: TTCCTGGAGAAGTACCCGGCCCTGGTCACTGGCTTCTTCTTCTTCATGTGgtacgtttgt ... gcttctgcagGTACTTCCTCAACGTCATATTCAACATCCTCAACAAGAAGATCTACAACTA
EST: gi|149013546|gb|EE043037.2|EE043037
EST:     TTCCTGGAGAAGTACCCGGCCCTGGTCACTGGCTTCTTCTTCTTCATGTG                         GTACTTCCTCAACGTCATATTCAACATCCTCAACAAGAAGATCTACAACTA
genomic: TTCCTGGAGAAGTACCCGGCCCTGGTCACTGGCTTCTTCTTCTTCATGTGgtacgtttgt ... gcttctgcagGTACTTCCTCAACGTCATATTCAACATCCTCAACAAGAAGATCTACAACTA
EST: gi|101394747|gb|EB819306.1|EB819306
EST:     TTCCTGGAGAAGTACCCGGCCCTGGTCACTGGCTTCTTCTTCTTCATGTG                         GTACTTCCTCAACGTCATATTCAACATCCTCAACAAGAAGATCTACAACTA
genomic: TTCCTGGAGAAGTACCCGGCCCTGGTCACTGGCTTCTTCTTCTTCATGTGgtacgtttgt ... gcttctgcagGTACTTCCTCAACGTCATATTCAACATCCTCAACAAGAAGATCTACAACTA
EST: gi|148966890|gb|EE018012.2|EE018012
EST:     TTCCTGGAGAAGTACCCGGCCCTGGTCACTGGCTTCTTCTTCTTCATGTG                         GTACTTCCTCAACGTCATATTCAACATCCTCAACAAGAAGATCTACAACTA
genomic: TTCCTGGAGAAGTACCCGGCCCTGGTCACTGGCTTCTTCTTCTTCATGTGgtacgtttgt ... gcttctgcagGTACTTCCTCAACGTCATATTCAACATCCTCAACAAGAAGATCTACAACTA
EST: gi|148986357|gb|EE030094.2|EE030094
EST:     TTCCTGGAGAAGTACCCGGCCCTGGTCACTGGCTTCTTCTTCTTCATGTG                         GTACTTCCTCAACGTCATATTCAACATCCTCAACAAGAAGATCTACAACTA
genomic: TTCCTGGAGAAGTACCCGGCCCTGGTCACTGGCTTCTTCTTCTTCATGTGgtacgtttgt ... gcttctgcagGTACTTCCTCAACGTCATATTCAACATCCTCAACAAGAAGATCTACAACTA
EST: gi|149075125|gb|EE163618.2|EE163618
EST:     TTCCTGGAGAAGTACCCGGCCCTGGTCACTGGCTTCTTCTTCTTCATGTG                         GTACTTCCTCAACGTCATATTCAACATCCTCAACAAGAAGATCTACAACTA
genomic: TTCCTGGAGAAGTACCCGGCCCTGGTCACTGGCTTCTTCTTCTTCATGTGgtacgtttgt ... gcttctgcagGTACTTCCTCAACGTCATATTCAACATCCTCAACAAGAAGATCTACAACTA
EST: gi|211407726|gb|FL367074.1|FL367074
EST:     TTCCTGGAGAAGTACCCGGCCCTGGTCACTGGCTTCTTCTTCTTCATGTG                         GTACTTCCTCAACGTCATATTCAACATCCTCAACAAGAGGATCTACAACTA
genomic: TTCCTGGAGAAGTACCCGGCCCTGGTCACTGGCTTCTTCTTCTTCATGTGgtacgtttgt ... gcttctgcagGTACTTCCTCAACGTCATATTCAACATCCTCAACAAGAAGATCTACAACTA
EST: gi|149112153|gb|EE191267.2|EE191267
EST:     TTCCTGGAGAAGTACCCGGCCCTGGTCACTGGCTTCTTCTTCTTCATGTG                         GTACTTCCTCAACGTCATATTCAACATCCTCAACAAGAAGATCTACAACTA
genomic: TTCCTGGAGAAGTACCCGGCCCTGGTCACTGGCTTCTTCTTCTTCATGTGgtacgtttgt ... gcttctgcagGTACTTCCTCAACGTCATATTCAACATCCTCAACAAGAAGATCTACAACTA
EST: gi|149026859|gb|EE046212.2|EE046212
EST:     TTCCTGGAGAAGTACCCGGCCCTGGTCACTGGCTTCTTCTTCTTCATGTG                         GTACTTCCTCAACGTCATATTCAACATCCTCAACAAGAAGATCTACAACTA
genomic: TTCCTGGAGAAGTACCCGGCCCTGGTCACTGGCTTCTTCTTCTTCATGTGgtacgtttgt ... gcttctgcagGTACTTCCTCAACGTCATATTCAACATCCTCAACAAGAAGATCTACAACTA
EST: gi|149097452|gb|EE183315.2|EE183315
EST:     TTCCTGGAGAAGTACCCGGCCCTGGTCACTGGCTTCTTCTTCTTCATGTG                         GTACTTCCTCAACGTCATATTCAACATCCTCAACAAGAAGATCTACAACTA
genomic: TTCCTGGAGAAGTACCCGGCCCTGGTCACTGGCTTCTTCTTCTTCATGTGgtacgtttgt ... gcttctgcagGTACTTCCTCAACGTCATATTCAACATCCTCAACAAGAAGATCTACAACTA
EST: gi|149095141|gb|EE180755.2|EE180755
EST:     TTCCTGGAGAAGTACCCGGCCCTGGTCACTGGCTTCTTCTTCTTCATGTG                         GTACTTCCTCAACGTCATATTCAACATCCTCAACAAGAAGATCTACAACTA
genomic: TTCCTGGAGAAGTACCCGGCCCTGGTCACTGGCTTCTTCTTCTTCATGTGgtacgtttgt ... gcttctgcagGTACTTCCTCAACGTCATATTCAACATCCTCAACAAGAAGATCTACAACTA
EST: gi|149015293|gb|EE045098.2|EE045098
EST:     TTCCTGGAGAAGTACCCGGCCCTGGTCACTGGCTTCTTCTTCTTCATGTG                         GTACTTCCTCAACGTCATATTCAACATCCTCAACAAGAAGATCTACAACTA
genomic: TTCCTGGAGAAGTACCCGGCCCTGGTCACTGGCTTCTTCTTCTTCATGTGgtacgtttgt ... gcttctgcagGTACTTCCTCAACGTCATATTCAACATCCTCAACAAGAAGATCTACAACTA
EST: gi|71766326|gb|DR964263.1|DR964263
EST:     TTCTTGGAGAAGTACCCGGCCCTGGTCACTGGCTTCTTCTTCTTCATGTG                         GTACTTCCTCAACGTCATATTCAACATCCTCAACAAGAAGATCTACAACTA
genomic: TTCCTGGAGAAGTACCCGGCCCTGGTCACTGGCTTCTTCTTCTTCATGTGgtacgtttgt ... gcttctgcagGTACTTCCTCAACGTCATATTCAACATCCTCAACAAGAAGATCTACAACTA
EST: gi|211475706|gb|FL352571.1|FL352571
EST:     TTCCTGGAGAAGTACCCGGCCCTGGTCACTGGCTTCTTCTTCTTCATGTG                         GTACTTCCTCAACGTCATATTCAACATCCTCAACAAGAAGATCTACAACTA
genomic: TTCCTGGAGAAGTACCCGGCCCTGGTCACTGGCTTCTTCTTCTTCATGTGgtacgtttgt ... gcttctgcagGTACTTCCTCAACGTCATATTCAACATCCTCAACAAGAAGATCTACAACTA
EST: gi|149075192|gb|EE163691.2|EE163691
EST:     TTCCTGGAGAAGTACCCGGCCCTGGTCACTGGCTTCTTCTTCTTCATGTG                         GTACTTCCTCAACGTCATATTCAACATCCTCAACAAGAAGATCTACAACTA
genomic: TTCCTGGAGAAGTACCCGGCCCTGGTCACTGGCTTCTTCTTCTTCATGTGgtacgtttgt ... gcttctgcagGTACTTCCTCAACGTCATATTCAACATCCTCAACAAGAAGATCTACAACTA
EST: gi|78077772|gb|DV506204.1|DV506204
EST:     TTCCTGGAGAAGTACCCGGCCCTGGTCACTGGCTTCTTCTTCTTCATGTG                         GTACTTCCTCAACGTCATATTCAACATCCTCAACAAGAAGATCTACAACTA
genomic: TTCCTGGAGAAGTACCCGGCCCTGGTCACTGGCTTCTTCTTCTTCATGTGgtacgtttgt ... gcttctgcagGTACTTCCTCAACGTCATATTCAACATCCTCAACAAGAAGATCTACAACTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctgcacatttgcttcatcacctgttctgtcctgtgtaaacatgggcttctgcagGTACTTCCTCAACGTCATATTCAACATCCTCAACAAGAAGATCTACAACTACTTCCCCTATCCATA
                                              cttctgc  CT-rich tract
                                    taaacat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgtttgtttctctgcacatttgcttcatcacctgttctgtcctgtgtaaacatgggcttctgcagGTACTTCCTCAACGTCATATTCAACATCCTCAACAAGAAGATCTACAACTACTTCCCCTATCCATA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG