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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaactgttcctctagtctgccgtgctccacttccactaccagccgccgctccggcctctgacgcgtgcgccgggctccggcgaggcactgcagCATCTACGGCCCCGTCCACGACGTGCGCATCCCGTACCAGCAGAAGCGCATGTTCGGGTTCGTCACCTTCGTGTACCCGGAGACGGTGAAGCTGATCCTG

Basic information

species Zea mays
transcript GRMZM2G311665_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G311665_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os07g48410.2 (Oryza sativa), 3'ss of exon 2
gtaactgttcctctagtctgccgtgctccacttccactaccagccgccgctccggcctctgacgcgtgcgccgggctccggcgaggca-ctgcagCATCTACGGCCCCGTCCACGACGTGCGCATCCCGTACCAGCAGAAGCGCATGTTCGGGTTCGTCACCTTCGTGTACCCGGAGACGGTGAAGCTGATCCTG
                  |    | ||  | | ||||  ||  ||| | |  |     |  | || |    | |     | |    ||  || |||||||||||||||||||||||||| |||||||||||||||||||||||||||||||| |||||||||||||| ||||||||||||||||||||||| || 
-----------------gtagtatactataatcccaccgcccaccgtcaccgccatgccata-gctttaatctgatgatgccctctcaattgaagCATCTACGGCCCCGTCCACGACGTTCGCATCCCGTACCAGCAGAAGCGCATGTTCGGCTTCGTCACCTTCGTCTACCCGGAGACGGTGAAGCTGATTCTC

upper sequence: GRMZM2G311665_T01 (Zea mays), 3'ss of exon 2
lower sequence: AT3G63450.1 (Arabidopsis thaliana), 3'ss of exon 2
gtaactgttcctctagtctgccgtgctccacttccactaccagccgccgctccggcctctgacgcgtgcgccgggctccggcga-ggcactgcagCATCTACGGCCCCGTCCACGACGTGCGCATCCCGTACCAGCAGAAGCGCATGTTCGGGTTCGTCACCTTCGTGTACCCGGAGACGGTGAAGCTGATCCTG
                      ||  | | |||    |   | ||     | |  | | |     ||  | |    |   || | ||   ||||| |  |  || || || || |||||| | || || |||||||||||| | ||||| |||||||| |||||| ||||||| ||||| ||||||   || |||
----------------------gtattactcttgt-ttggaacccattcattcttcttgttggatgt-tgtctacttaaagcaatggtggtgcagTACGTTTGGGCCAGTTCAGGACGTGAGGATACCTTACCAGCAGAAGAGGATGTTTGGGTTCGTGACCTTCATGTACCCAGAGACTGTGAAGAGCATTCTG

upper sequence: GRMZM2G311665_T01 (Zea mays), 3'ss of exon 2
lower sequence: Vv13s0158g00370.t01 (Vitis vinifera), 3'ss of exon 3
-------------------gtaactgttcctctagtctgccgtgctccacttccactaccagccgccgctccggcctctgacgcgtgcgccgggctccggcgaggcactgcagCATCTACGGCCCCGTCCACGACGTGCGCATCCCGTACCAGCAGAAGCGCATGTTCGGGTTCGTCACCTTCGTGTACCCGGAGACGGTGAAGCTGATCCTG
                     || |||| || | || |   |   |  | ||     |      |    | |||    |  |     ||| |   |  |    |    || ||||| | ||| || || || || ||| | ||||| || ||||||||| | ||||||||||| || |||||||| || || ||||| |||||||| ||  ||
gttttgaccacaattttcatgaattgtttct-tggttttgtgcaattgaattgtgggaagttgagagctttcggttggtttctaaatcgctg--ttttgttttgttgttgaagCATTTTCGGTCCAGTTCAAGATGTGAGGATCCCATATCAGCAGAAGAGGATGTTCGGGTTTGTAACCTTCGTTTATCCAGAGACAGTGAAGCTCATTTTG

upper sequence: GRMZM2G311665_T01 (Zea mays), 3'ss of exon 2
lower sequence: Vv06s0061g00150.t01 (Vitis vinifera), 3'ss of exon 2
gtaactgttcctctagtctgccgtgctccacttccactaccagccgccgctccggcctctgacgcgtgcgccgggctccggcgaggcactgcagCATCTACGGCCCCGTCCACGACGTGCGCATCCCGTACCAGCAGAAGCGCATGTTCGGGTTCGTCACCTTCGTGTACCCGGAGACGGTGAAGCTGATCCTG
|||| || | |    ||  |  |       |||| | |    |     | |  |   | |             ||||   | | |    || || || |  || || || || || ||| | || || |||||||||||| | |||||||| |||||||| ||||| ||||| ||||| |||||||| ||  | 
gtaattgctacgt--gttggttggaaatttcttcaatttggggttcgtgttgtgaaatttagttaacctagttggctt--gtgtgcttttgaagTATTTTTGGGCCAGTTCAAGATGTGAGGATTCCATACCAGCAGAAGAGGATGTTCGGATTCGTCACTTTCGTCTACCCCGAGACTGTGAAGCTCATTTTA

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|87157568|gb|DY402357.1|DY402357
EST:     TTCCCGGCAGACAGCACCTTCCGCGAGGAGGACGTGTCCAACTACTTCAG                         CATCTACGGCCCCGTCCACGACGTGCGCATCCCGTACCAGCAGAAGCGCAT
genomic: TTCCCGGCAGACAGCACCTTCCGCGAGGAGGACGTGTCCAACTACTTCAGgtaactgttc ... ggcactgcagCATCTACGGCCCCGTCCACGACGTGCGCATCCCGTACCAGCAGAAGCGCAT
EST: gi|149096961|gb|EE182760.2|EE182760
EST:     TTCCCGGCAGACAGCACCTTCCGCGAGGAGGACGTGTCCAACTACTTCAG                         CATCTACGGCCCCGTCCACGACGTGCGCATCCCGTACCAGCAGAAGCGCAT
genomic: TTCCCGGCAGACAGCACCTTCCGCGAGGAGGACGTGTCCAACTACTTCAGgtaactgttc ... ggcactgcagCATCTACGGCCCCGTCCACGACGTGCGCATCCCGTACCAGCAGAAGCGCAT
EST: gi|88756925|gb|DY541066.1|DY541066
EST:     TTCCCGGCAGACAGCACCTTCCGCGAGGAGGACGTGTCCAACTACTTCAG                         CATCTACGGCCCCGTCCACGACGTGCGCATCCCGTACCAGCAGAAGCGCAT
genomic: TTCCCGGCAGACAGCACCTTCCGCGAGGAGGACGTGTCCAACTACTTCAGgtaactgttc ... ggcactgcagCATCTACGGCCCCGTCCACGACGTGCGCATCCCGTACCAGCAGAAGCGCAT
EST: gi|148937220|gb|EC881402.2|EC881402
EST:     TTCCCGGCAGACAGCACCTTCCGCGAGGAGGACGTGTCCAACTACTTCAG                         CATCTACGGCCCCGTCCACGACGTGCGCATCCCGTACCAGCAGAAGCGCAT
genomic: TTCCCGGCAGACAGCACCTTCCGCGAGGAGGACGTGTCCAACTACTTCAGgtaactgttc ... ggcactgcagCATCTACGGCCCCGTCCACGACGTGCGCATCCCGTACCAGCAGAAGCGCAT
EST: gi|149088773|gb|EE177898.2|EE177898
EST:     TTCCCGGCAGACAGCACCTTCCGCGAGGAGGACGTGTCCAACTACTTCAG                         CATCTACGGCCCCGTCCACGACGTGCGCATCCCGTACCAGCAGAAGCGCAT
genomic: TTCCCGGCAGACAGCACCTTCCGCGAGGAGGACGTGTCCAACTACTTCAGgtaactgttc ... ggcactgcagCATCTACGGCCCCGTCCACGACGTGCGCATCCCGTACCAGCAGAAGCGCAT
EST: gi|22520971|gb|BU079782.1|BU079782
EST:     TTCCCGGCAGACAGCACCTTCCGCGAGGAGGACGTGTCCAACTACTTCAG                         CATCTACGGCCCCGTCCACGACGTGCGCATCCCGTACCAGCAGAAGCGCAT
genomic: TTCCCGGCAGACAGCACCTTCCGCGAGGAGGACGTGTCCAACTACTTCAGgtaactgttc ... ggcactgcagCATCTACGGCCCCGTCCACGACGTGCGCATCCCGTACCAGCAGAAGCGCAT
EST: gi|71771644|gb|DR969581.1|DR969581
EST:     GTCCAACTACTTCAG                         CATCTACGGCCCCGTCCACGACGTGCGCATCCCGTACCAGCAGAAGCGCAT
genomic: GTCCAACTACTTCAGgtaactgttc ... ggcactgcagCATCTACGGCCCCGTCCACGACGTGCGCATCCCGTACCAGCAGAAGCGCAT
EST: gi|148933685|gb|EC877585.2|EC877585
EST:     TTCCCGGCAGACAGCACCTTCCGCGAGGAGGACGTGTCCAACTACTTCAG                         CATCTACGGCCCCGTCCACGACGTGCGCATCCCGTACCAGCAGAAGCGCAT
genomic: TTCCCGGCAGACAGCACCTTCCGCGAGGAGGACGTGTCCAACTACTTCAGgtaactgttc ... ggcactgcagCATCTACGGCCCCGTCCACGACGTGCGCATCCCGTACCAGCAGAAGCGCAT
EST: gi|149072206|gb|EE160452.2|EE160452
EST:     TTCCCGGCAGACAGCACCTTCCGCGAGGAGGACGTGTCCAACTACTTCAG                         CATCTACGGCCCCGTCCACGACGTGCGCATCCCGTACCAGCAGAAGCGCAT
genomic: TTCCCGGCAGACAGCACCTTCCGCGAGGAGGACGTGTCCAACTACTTCAGgtaactgttc ... ggcactgcagCATCTACGGCCCCGTCCACGACGTGCGCATCCCGTACCAGCAGAAGCGCAT
EST: gi|149015392|gb|EE045235.2|EE045235
EST:     TTCCCGGCAGACAGCACCTTCCGCGAGGAGGACGTGTCCAACTACTTCAG                         CATCTACGGCCCCGTCCACGACGTGCGCATCCCGTACCAGCAGAAGCGCAT
genomic: TTCCCGGCAGACAGCACCTTCCGCGAGGAGGACGTGTCCAACTACTTCAGgtaactgttc ... ggcactgcagCATCTACGGCCCCGTCCACGACGTGCGCATCCCGTACCAGCAGAAGCGCAT
EST: gi|149082408|gb|EE171596.2|EE171596
EST:     TTCCCGGCAGACAGCACCTTCCGCGAGGAGGACGTGTCCAACTACTTCAG                         CATCTACGGCCCCGTCCACGACGTGCGCATCCCGTACCAGCAGAAGCGCAT
genomic: TTCCCGGCAGACAGCACCTTCCGCGAGGAGGACGTGTCCAACTACTTCAGgtaactgttc ... ggcactgcagCATCTACGGCCCCGTCCACGACGTGCGCATCCCGTACCAGCAGAAGCGCAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccagccgccgctccggcctctgacgcgtgcgccgggctccggcgaggcactgcagCATCTACGGCCCCGTCCACGACGTGCGCATCCCGTACCAGCAGAAGCGCATGTTCGGGTTCGTCACCTTCGTGTACCCGGAGACGGTGAAGCTGATCCTG
                 ctctgac  putative branch site (score: 3)
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaactgttcctctagtctgccgtgctccacttccactaccagccgccgctccggcctctgacgcgtgcgccgggctccggcgaggcactgcagCATCTACGGCCCCGTCCACGACGTGCGCATCCCGTACCAGCAGAAGCGCATGTTCGGGTTCGTCACCTTCGTGTACCCGGAGACGGTGAAGCTGATCCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT