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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaatgttgtgctcacctgtttcttttatccatgctcgatgctgatcactatagttcttatacgagcaaatgttggtctgaatatagTTGTGGAGCAAATCAGTGGGAGGGACAACATTTTAAATCACCTAAGCATCCCAGCTGCTTGTTTCACTCACCCTGAGATCAGTATGGTTGGCTTGACAGA

Basic information

species Zea mays
transcript GRMZM2G145595_T01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G145595_T01 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os01g23610.1 (Oryza sativa), 3'ss of exon 10
-------gtaaatgttgtgctcacctgtttcttttatc------catgctcgatgct--------gatcactatagttcttatacgagcaaatgttggtctgaatatagTTGTGGAGCAAATCAGTGGGAGGGACAACATTTTAAATCACCTAAGCATCCCAGCTGCTTGTTTCACTCACCCTGAGATCAGTATGGTTGGCTTGACAGA
          |||  | || ||||   ||| || ||        |||  |    | |         |  | | ||||||||  |  |  || |  | |||||||||||||||| |||| ||||  |||||  ||||||||  ||||||| ||||||||||| ||||| ||||||||||| || ||||| |||||||||||  | |||||
gtagatacagaataatttgttcactgttttattgtacttcagcgcatatttcgggttttgctttgaactagtgtagttctttgataactaatttcttgtctgaatatagTTGTTGAGCGAATCTCTGGGAAAGACAACATCCTAAATCATCTAAGCATCCCGGCTGCCTGTTTCACTCATCCGGAGATTAGTATGGTTGGGCTAACAGA

upper sequence: GRMZM2G145595_T01 (Zea mays), 3'ss of exon 10
lower sequence: GLYMA09G04270.1 (Glycine max), 3'ss of exon 5
gtaaatgttgtgctcacctgtttcttttatccatgctcgatgctgatcactatagttcttatacgagcaaatgttggtctgaatatagTTGTGGAGCAAATCAGTGGGAGGGACAACATTTTAAATCACCTAAGCATCCCAGCTGCTTGTTTCACTCACCCTGAGATCAGTATGGTTGGCTTGACAGA
||||       | | |  |  || |  ||   ||  | || |    |  ||    |||   ||   | |||| ||| | |    | ||| || || ||| ||| ||| || ||  || |  | |||||  ||||||| |||||||||||||||||||| ||||| ||||| |||||||| ||||| ||
gtaagaagcaag-taatgtaattttgctactaatatttga-gtcatttgcttccattcactta-atgaaaatattgttgttggaa-agTGGTTGAACAAGTCACTGGAAGAGATCACGTGCTCAATCATTTAAGCATACCAGCTGCTTGTTTCACTCATCCTGAAATCAGCATGGTTGGATTGACTGA

upper sequence: GRMZM2G145595_T01 (Zea mays), 3'ss of exon 10
lower sequence: GLYMA17G03560.1 (Glycine max), 3'ss of exon 10
gtaaatgttgtgctcacctgtttcttttatccatgctcgatgctgatcactatagttcttatacgagcaaatgttggtctgaatatagTTGTGGAGCAAATCAGTGGGAGGGACAACATTTTAAATCACCTAAGCATCCCAGCTGCTTGTTTCACTCACCCTGAGATCAGTATGGTTGGCTTGACAGA
||||     ||| | ||   | |   || ||||   |  |   |   ||  |   |  ||  | ||  ||||    |||| |    ||| || || ||| ||| ||| |  ||  || |  | |||||  |||||||||||||||||||||||||||| |||||  | || |||||||| || |||||
gtaa-----gtggtaactgatgtaacttttccaaaatttagtttatgcagcaatatcatttgatgaaaaaatt---gtctaa---cagTGGTTGAACAAGTCACTGGAAAAGATCACGTGCTCAATCATTTAAGCATCCCAGCTGCTTGTTTCACTCATCCTGAACTTAGCATGGTTGGATTAACAGA

upper sequence: GRMZM2G145595_T01 (Zea mays), 3'ss of exon 10
lower sequence: GLYMA15G15310.1 (Glycine max), 3'ss of exon 10
gtaaatgttgtgctcacctgtttcttttatccatgctcgatgctgatcactatagttcttatacgagcaaatgttggtctgaatatagTTGTGGAGCAAATCAGTGGGAGGGACAACATTTTAAATCACCTAAGCATCCCAGCTGCTTGTTTCACTCACCCTGAGATCAGTATGGTTGGCTTGACAGA
||||       | | |  |  || |  ||   ||  | || |    |  ||    |  |||    |  ||| | | ||  ||   |||| || || ||| | |  || || ||  || |  | |||||  ||||||| |||||||||||||||||||| ||||| ||||| |||||||| ||||||||
gtaagaagca-ggtaatgtaattttgctactaatttttga-gtcatttgcttccat--ttacttaatgaaaagattgttgga---tagTGGTTGAACAAGTGACCGGAAGAGATCACGTGCTCAATCATTTAAGCATACCAGCTGCTTGTTTCACTCATCCTGAAATCAGCATGGTTGGATTGACAGA

upper sequence: GRMZM2G145595_T01 (Zea mays), 3'ss of exon 10
lower sequence: GLYMA07G37050.1 (Glycine max), 3'ss of exon 10
gtaaatgttgtgctcacctgtttcttttatccatgctcgatgctgatcactatagttcttatacgagcaaatgttggtctgaatatagTTGTGGAGCAAATCAGTGGGAGGGACAACATTTTAAATCACCTAAGCATCCCAGCTGCTTGTTTCACTCACCCTGAGATCAGTATGGTTGGCTTGACAGA
|||| || |   ||||  |  || |   |   ||  | | |  || |  | |||    | ||  ||  |||   | |||| |    ||| || || ||| ||| ||| || ||   | |  | |||||  |||||||||||||||||||||||||||| ||||| ||||| |||||||| ||||||||
gtaagtggta-actcatgtaattttcccaaaaattttagtttttgct-gcaata----tcatttgatgaaaaaattgtctaa---cagTGGTTGAACAAGTCACTGGAAGAGATCTCGTGCTCAATCATTTAAGCATCCCAGCTGCTTGTTTCACTCATCCTGAAATCAGCATGGTTGGATTGACAGA

upper sequence: GRMZM2G145595_T01 (Zea mays), 3'ss of exon 10
lower sequence: AT4G16155.1 (Arabidopsis thaliana), 3'ss of exon 10
--------------------------gtaaatgttgtgctcacctgtttctt-ttatccatgctcgatgctgatcact-atagttcttatac---gagcaaatgttggtctgaatatagTTGTGGAGCAAATCAGTGGGAGGGACAACATTTTAAATCACCTAAGCATCCCAGCTGCTTGTTTCACTCACCCTGAGATCAGTATGGTTGGCTTGACAGA
                            |||||      ||   ||||| |  || || |  ||  || |     | | |   || ||| ||     |||  |  | || |     |||| ||||||||| |||  || || ||  |  |  | ||||| || |||||||||||||||||||| ||||| ||||| || |||||||| || ||||||||
gtaaatggttttatcaatatttcactccaaatgcatctttcttttgtttttccttttctacactgaatacgttagattgacctttattaaactctatgcatctacttgtgttggc-tagTGGTGGAGCAAGTCACAGGTAGAGATCATGTGCTTAATCATCTTAGCATCCCAGCTGCTTGTTTTACTCATCCTGAAATAAGTATGGTGGGATTGACAGA

upper sequence: GRMZM2G145595_T01 (Zea mays), 3'ss of exon 10
lower sequence: AT3G16950.2 (Arabidopsis thaliana), 3'ss of exon 10
gtaaatgttgtgctcacctgtttcttttatccatgc---------tcgatgctgatcactatagttcttatacgagc-----aaatgttggtctgaatatagTTGTGGAGCAAATCAGTGGGAGGGACAACATTTTAAATCACCTAAGCATCCCAGCTGCTTGTTTCACTCACCCTGAGATCAGTATGGTTGGCTTGACAGA
|||||||   |        |   ||  || | ||||         |      |  ||    |    ||| ||  |       |  | ||  ||||    |||| || |||||| |||| || || ||  |  |  | ||||| || ||||||||||||||||| || ||||| ||||| ||||| ||||| || || |||||
gtaaatggcttatcagtaggaggctactaacaatgcaataatattttcccttttttcttcttgagccttgtattaaactctgagctcttactctgtggctagTGGTCGAGCAAGTCAGCGGCAGAGATCATGTGCTTAATCATCTTAGCATCCCAGCTGCTTGCTTTACTCATCCTGAAATCAGCATGGTGGGATTAACAGA

upper sequence: GRMZM2G145595_T01 (Zea mays), 3'ss of exon 10
lower sequence: Vv14s0060g01330.t01 (Vitis vinifera), 3'ss of exon 10
gtaaatgttgtgctcac-----ctgtttcttttatccatgctcgatgctgatca-ctatagttcttatacgag---caaatgttggtctg--aatatagTTGTGGAGCAAATCAGTGGGAGGGACAACATTTTAAATCACCTAAGCATCCCAGCTGCTTGTTTCACTCACCCTGAGATCAGTATGGTTGGCTTGACAGA
|||| |    || |        || | ||| |  | |||| |   ||    |||  | || |   ||   ||      | | ||  | ||   | |||||||| || ||||| ||||| | ||||||  |  | |||||  | ||||||||||| || |||||||| || ||||||||||||||||| ||  |||||||
gtaattaccttgtttgttgccactctctctctactacatggtttttgtcattcagttttaatatctacttgaaacctgacttttcttttgtcgacatagTTGTTGAACAAATTAGTGGAAAGGACAATGTGCTGAATCATTTGAGCATCCCAGCAGCGTGTTTCACCCATCCTGAGATCAGTATGGTGGGGCTGACAGA

upper sequence: GRMZM2G145595_T01 (Zea mays), 3'ss of exon 10
lower sequence: Vv05s0077g01210.t01 (Vitis vinifera), 3'ss of exon 10
gtaaatgttgtgctcacc-tgtttcttttatccatgctcgatgctgatcactatagt-tcttatacgagcaaatgttggtctgaatatagTTGTGGAGCAAATCAGTGGGAGGGACAACATTTTAAATCACCTAAGCATCCCAGCTGCTTGTTTCACTCACCCTGAGATCAGTATGGTTGGCTTGACAGA
|| | || |     |  | | |||   |  |  |   |  |   || |   || |   ||||           ||    |    ||  |||||| |||||| | |  || | |||  |  |  | |||||  | ||||||||||| |||||||||||||| || || |||||||||||||| ||||| ||
gttagtggtaactacctcatattttgctgttttacctttaaaaatgctacttaaaccatcttcattttttgcttggctcttgtgatgcagTTGTTGAGCAAGTTACCGGAAAGGATCATGTGCTCAATCATTTGAGCATCCCAGCAGCTTGTTTCACTCATCCAGAAATCAGTATGGTTGGATTGACTGA

upper sequence: GRMZM2G145595_T01 (Zea mays), 3'ss of exon 10
lower sequence: PP1S112_186V6.1 (Physcomitrella patens), 3'ss of exon 10
-----------------------------------------gtaaatgttgtgctcacctgtttcttttat-ccatgctcgatgctgatcactatagttcttatacgagcaaatgttggtctgaatatagTTGTGGAGCAAATCAGTGGGAGGGACAACATTTTAAATCACCTAAGCATCCCAGCTGCTTGTTTCACTCACCCTGAGATCAGTATGGTTGGCTTGACAGA
                                          || ||  |   |     || || ||   |  | | ||||   ||| ||  ||| ||   || |   ||   |     |      | |||  | ||||| |||  |||| ||||||||||||| || ||    ||| | ||||| ||||||||||| |||||||||||||| ||||| |||||||| ||
gtgaatcattctactgtgttcctcgaattgaagcatttacattagatccttgccattgttggttattgagtgtcgtactcggcactgttccttat-gtcgataaatttgcgt-taccttttcatgaacagTGATTGAGCAGATCGCTGGGCGGGACAACATTTTGAACCATAATAGCGTACCAGCGGCTTGTTTCACGCACCCTGAGATCAGCATGGTCGGCTTGACTGA

upper sequence: GRMZM2G145595_T01 (Zea mays), 3'ss of exon 10
lower sequence: PP1S352_68V6.1 (Physcomitrella patens), 3'ss of exon 10
-----------------------------------------------------------------------------------gtaaatgttgtgctcacctgtttcttttatccatgct-cgatgctgatcactatagttcttatacgagcaaatgttggtctgaatatagTTGTGGAGCAAATCAGTGGGAGGGACAACATTTTAAATCACCTAAGCATCCCAGCTGCTTGTTTCACTCACCCTGAGATCAGTATGGTTGGCTTGACAGA
                                                                                     |  | ||        |       || ||  ||  |  |||  |      |  ||| ||||  ||||  ||||    |||   || |||  | ||||| ||   |||| | || ||  || | |||||    ||| | ||||| ||||||||||| |||||||| ||||| ||||||||  | || ||
gtatgtcaattggctctaagacaaataaatgaagtatttatttatatatttattgatttttatcctcaatgctccaatgcttcaaagctattcgatggttccacgcaattgataaattttatgatattttagtttgaagtccttac-cgagttaatgactttcttt-tacagTCATTGAGCAGATTGCTGGGCGAGATAATGTTCTGAATCATAACAGCGTTCCAGCAGCTTGTTTCACACACCCTGAAATCAGCATGGTTGGACTTACTGA

upper sequence: GRMZM2G145595_T01 (Zea mays), 3'ss of exon 10
lower sequence: PP1S35_94V6.1 (Physcomitrella patens), 3'ss of exon 10
-------------------------------------------------gtaaatgttgtgctcacctgtttctt-ttatccatgctcgatgctgatcactatagttctt---atacgagcaa---atgttggtct---gaatatagTTGTGGAGCAAATCAGTGGGAGGGACAACATTTTAAATCACCTAAGCATCCCAGCTGCTTGTTTCACTCACCCTGAGATCAGTATGGTTGGCTTGACAGA
                                                    ||  || |  |||  | | | || ||    |||  | ||     ||     ||||  |   |||  | | |     |||||| |       | |||  | ||||| ||   |||  | || |||||||| || ||    ||| | || || || |||||||| |||||||||||||| |||||||||||||| ||
gtgggtcatacgaccctgttcctcgggattgaagcgctaacattggattcataacattatattcatatttattttattgattatgggcaatctcactcgtcccagtttctcacataaaatcgatatgcgttggttttttatgaacagTAATTGAGCAGATTGCTGGCCGAGATAACATTTTGAACCATAATAGCGTGCCCGCGGCCTGTTTCACGCACCCTGAGATCAGCATGGTTGGCTTGACTGA

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|32830615|gb|CD970293.1|CD970293
EST:     CTCATGC-TGCT-ATGCAGCCAGCGCACAA-GAATCTCAG                         TT-TGGAGCAAATCAGTGGGAGGGACAACATTTTAAATCACCTAAGCATCC
genomic: CTCATGCTTGCTCATGCAGCCAGCGCACAAGGAATCTCAGgtaaatgttg ... ctgaatatagTTGTGGAGCAAATCAGTGGGAGGGACAACATTTTAAATCACCTAAGCATCC
EST: gi|26456706|gb|CA828289.1|CA828289
EST:     CAATGGTAAGCTCATGCTTGCTCATGCAGCCAGCGCACAAGGAATCTCAG                         TTGTGGAGCAAATCAG-GGGAGGGACAACATTTTAAATCACCTAAGCATCC
genomic: CAATGGTAAGCTCATGCTTGCTCATGCAGCCAGCGCACAAGGAATCTCAGgtaaatgttg ... ctgaatatagTTGTGGAGCAAATCAGTGGGAGGGACAACATTTTAAATCACCTAAGCATCC
EST: gi|32830552|gb|CD970230.1|CD970230
EST:     GTAAGCTCATGC-TGCTCATGCAGCCAGCGCAC-AGG-ATCCTCAG                         -TGTGGAGCAAATCAGT-GGAGGGAC-ACATTTTTAAATCACCTAAGCAT
genomic: GTAAGCTCATGCTTGCTCATGCAGCCAGCGCACAAGGAAT-CTCAGgtaaatgttg ... ctgaatatagTTGTGGAGCAAATCAGTGGGAGGGACAACA-TTTTAAATCACCTAAGCAT
EST: gi|32831600|gb|CD971278.1|CD971278
EST:     CTCATGCAGCCAGCGCACAAGGAATCTCAG                         TTGTGGAGCAAATCAGTGGGAGGGACAACATTTTAAATCACCTAAGCATCC
genomic: CTCATGCAGCCAGCGCACAAGGAATCTCAGgtaaatgttg ... ctgaatatagTTGTGGAGCAAATCAGTGGGAGGGACAACATTTTAAATCACCTAAGCATCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgctcgatgctgatcactatagttcttatacgagcaaatgttggtctgaatatagTTGTGGAGCAAATCAGTGGGAGGGACAACATTTTAAATCACCTAAGCATCCCAGCTGCTTGTTTCACTCACCCTGAGATCAGTATGGTTGGCTTGACAGA
       tgctgat  putative branch site (score: 3)
                      ttcttata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaatgttgtgctcacctgtttcttttatccatgctcgatgctgatcactatagttcttatacgagcaaatgttggtctgaatatagTTGTGGAGCAAATCAGTGGGAGGGACAACATTTTAAATCACCTAAGCATCCCAGCTGCTTGTTTCACTCACCCTGAGATCAGTATGGTTGGCTTGACAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA