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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtgaattattcaaaccttatgttgcttgaaataattattcggtttgatccccctcaaaagaactatacatgtattcagcttaagtgttctcttagattttacaaaaataaatgatttttgctaagtaggtttgaaattctttcttttcagatgaaaatcacagaatgctttgacactctaaattttcagGAGGACCAACTGCTGAAACACGTGCAATTCTGGACCTCAGTGTCCAGTATTGGACAAGTAGAGGGTGGGCATATGTCGATGTCAACTATGGAGGAAGCAC

Basic information

species Zea mays
transcript GRMZM2G120302_T02
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G120302_T02 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os06g11180.1 (Oryza sativa), 3'ss of exon 11
gtaagtgaattattcaaaccttatgttgcttgaaataattattcggtttgatccccctcaaaagaactatacatgtattcagcttaagtgttctcttagattttacaaaaataaatgatttttgctaagtaggtt-tgaaattctttcttttca-gatgaaaatcacagaatgc-----tttgacactctaaat---tttcagGAGGACCAACTGCTGAAACACGTGCAATTCTGGACCTCAGTGTCCAGTATTGGACAAGTAGAGGGTGGGCATATGTCGATGTCAACTATGGAGGAAGCAC
                                                                                                       |             | ||| | |   |||||| |   || |||  ||| || ||| | |||||  | |  |     ||||| | ||   |    |||||||||||||||| || |||||||||| |||||||||||| ||||| ||||||||||||||| |||| ||||||||| | ||||| |||||||| ||||||||
-------------------------------------------------------------------------------------------------------tgtggtttctgtctaatttggttcgttaggttattgcatccttcttttccatgatcacaatcatggcaatcgcatatttgatattccccacatctttcagGAGGACCAACAGCAGAAACACGTGGAATTCTGGACCTGAGTGTTCAGTATTGGACAAGTCGAGGATGGGCATATCTTGATGTTAACTATGGGGGAAGCAC

upper sequence: GRMZM2G120302_T02 (Zea mays), 3'ss of exon 11
lower sequence: GLYMA08G42730.1 (Glycine max), 3'ss of exon 11
gtaagtgaattattcaaaccttatgttgcttgaaataattattcggtttgatccccctcaaaagaactatacatgtattcagcttaagtgttctcttagattttacaaaaataaatgatttttgctaagtaggtttgaaattctttcttttcagatgaaaatcacagaatgctttgacactctaaattttcagGAGGACCAACTGCTGAAACACGTGCAATTCTGGACCTCAGTGTCCAGTATTGGACAAGTAGAGGGTGGGCATATGTCGATGTCAACTATGGAGGAAGCAC
                                                                                    ||| |||| |   | | |||  |    |  |||  || |  ||| |  ||    | ||| | |    ||  |  | ||     | |  ||||    |  ||  ||||||| |||||||||||||||||||||| |||| |  || | ||  | ||||| ||||| ||| | || |||||||  || ||||| || ||||| ||||||||
------------------------------------------------------------------------------------taattgttttggcaaacttttta----tgcatgggttctcttaa-tgagtaatgacttcatacaacgcacttttatatt-ttcattattttg---tttgaatatttcagGTGGACCAACTGCTGAAACACGTGGAATTTTAAACTTGAGCATTCAGTACTGGACTAGTCGGGGTTGGGCATTCGTTGATGTTAATTATGGTGGAAGCAC

upper sequence: GRMZM2G120302_T02 (Zea mays), 3'ss of exon 11
lower sequence: Vv18s0001g11140.t01 (Vitis vinifera), 3'ss of exon 11
gtaagtgaattattcaaaccttatgttgcttgaaataattattcggtttgatccccctcaaaagaactatacatgtattcagcttaagtgttctcttagattttacaaaaataaatgatttttgctaagtaggtttgaaattctttcttttcagatgaaaatcacagaatgctttgacactctaaatttt-cagGAGGACCAACTGCTGAAACACGTGCAATTCTGGACCTCAGTGTCCAGTATTGGACAAGTAGAGGGTGGGCATATGTCGATGTCAACTATGGAGGAAGCAC
                                                                ||  || |||| |||    |||    |||||| | ||      ||||   |  |||| | ||||                    | |   ||    ||  || |    | |||      |||| || ||||||| || ||   ||||||||||| |||| |  |  | ||| ||||||||||||| ||| |||| ||||||| ||| ||||| || ||||| ||||||||
----------------------------------------------------------------aaagatccatg-attagctttatacattctctgaaat-----gaaaaggtagaatttcttctaa--------------------tattgaattgggatagcata----tgtgatgtgtgaaatattgcagGAGGGCCTACAAGTGAAACACGTGGAATTTTAAATTTGAGTATCCAGTATTGGACTAGTCGAGGTTGGGCATTTGTGGATGTGAATTATGGTGGAAGCAC

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|32931835|gb|CF036647.1|CF036647
EST:     TTTTCAAGGTTTGCCCGATGAAAAGCCTCCTTTGCTTGTCAAAACACATG                         GAGGACCAACTGCTGAAACACGTGCAATTCTGGACCTCAGTGTCCAGTATT
genomic: TTTTCAAGGTTTGCCTGATGAAAAGCCTCCTTTGCTTGTCAAAACACATGgtaagtgaat ... aaattttcagGAGGACCAACTGCTGAAACACGTGCAATTCTGGACCTCAGTGTCCAGTATT
EST: gi|211313026|gb|FL032573.1|FL032573
EST:     TTTTCAAGGTTTGCCTGATGAAAAGCCTCCTTTGCTTGTCAAAACACATG                         GAGGACCAACTGCTGAAACACGTGCAATTCTGGACCTCAGTGTCCAGTATT
genomic: TTTTCAAGGTTTGCCTGATGAAAAGCCTCCTTTGCTTGTCAAAACACATGgtaagtgaat ... aaattttcagGAGGACCAACTGCTGAAACACGTGCAATTCTGGACCTCAGTGTCCAGTATT
EST: gi|166449944|gb|EG144966.1|EG144966
EST:     TTCTAAGGTTTGCCTGATGAAAAGACCTCCTTTGCTTGTCAAAACACATG                         GAGGACCAACTGCTGAAACACGTGCAATTCTGGACC
genomic: TTC-AAGGTTTGCCTGATGAAAAG-CCTCCTTTGCTTGTCAAAACACATGgtaagtgaat ... aaattttcagGAGGACCAACTGCTGAAACACGTGCAATTCTGGACC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aattctttcttttcagatgaaaatcacagaatgctttgacactctaaattttcagGAGGACCAACTGCTGAAACACGTGCAATTCTGGACCTCAGTGTCCAGTATTGGACAAGTAGAGGGTGGGCATATGTCGATGTCAACTATGGAGGAAGCAC
                                         ctctaaa  putative branch site (score: 3)
                                                ttttc  CT-rich tract
                                          tctaaatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtgaattattcaaaccttatgttgcttgaaataattattcggtttgatccccctcaaaagaactatacatgtattcagcttaagtgttctcttagattttacaaaaataaatgatttttgctaagtaggtttgaaattctttcttttcagatgaaaatcacagaatgctttgacactctaaattttcagGAGGACCAACTGCTGAAACACGTGCAATTCTGGACCTCAGTGTCCAGTATTGGACAAGTAGAGGGTGGGCATATGTCGATGTCAACTATGGAGGAAGCAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA