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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtctcacctctttatgcatggtcatgtttgtcatagttttactgttatattggtaaactgatggccggcagtgtgatggactgatggtcatgctccacagGCAGAAAAGGAACCTATTTTGAGTAGCTTCTTGTATGCCAGTGTGCTGTCTCATGATTGCCTAGAGCGTGCATTGAGCTTCGTCCTTGCAAATAGGCTTG

Basic information

species Zea mays
transcript GRMZM2G048740_T03
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G048740_T03 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os03g04140.1 (Oryza sativa), 3'ss of exon 1
---gtctcacct-ctttatgcatggtcatgtttgtcatagttttactgttatattggtaaactgatggccggcagtgtgatggactgatggtcatgctccacagGCAGAAAAGGAACCTATTTTGAGTAGCTTCTTGTATGCCAGTGTGCTGTCTCATGATTGCCTAGAGCGTGCATTGAGCTTCGTCCTTGCAAATAGGCTTG
      | | || | | || | |||| |  | || | |  |  |  | |  |  || || |    | |       | |  | | ||  |    |   | |||||||||| |||||||||||||| |||||||||||||| ||||| || || |||||||| || || ||| | || ||||| |||||||||||||| ||||| |
taaacatgagctacatcatacgtggttaaatatgactttatggttttttatttatgatagagctttagtt--ttatattgttgcctctta--tactgttcacagGCAGAGAAGGAACCTATTTTAAGTAGCTTCTTGTACGCCAGCGTACTATCTCATGACTGTCTCGAGAGGGCGTTGAGTTTCGTCCTTGCAAACAGGCTCG

upper sequence: GRMZM2G048740_T03 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA16G22630.1 (Glycine max), 3'ss of exon 2
------gtctcacctctttatgcatggt-catgtttgtcatagttttactgttatattggtaaactgatggccggcagtgtgatggactgatggtcatgctccacagGCAGAAAAGGAACCTATTTTGAGTAGCTTCTTGTATGCCAGTGTGCTGTCTCATGATTGCCTAGAGCGTGCATTGAGCTTCGTCCTTGCAAATAGGCTTG
       |         | || |||  | ||| ||||    ||| |||  |  | |||   |   |  |     |||   ||||  ||   |  |  ||     |||||||||||||| || ||||||||||||||||| ||||||| | | ||||||||||||||| | ||||  ||||||   || |  ||||| ||  | ||  
tgaaatatgcagttagatgattcattttgcatatttgatg-agtgttagaga-acatttacatgtt--tcatatgcatcatgatataccattatttgtgt---gcagGCAGAAAAGGAGCCAATTTTGAGTAGCTTCTTCTATGCCACTATTCTGTCTCATGATTGCTTGGAGCAAGCATTGGCTTTTGCTCTTGCCAACCGACTCC

upper sequence: GRMZM2G048740_T03 (Zea mays), 3'ss of exon 1
lower sequence: AT2G17640.1 (Arabidopsis thaliana), 3'ss of exon 1
-gtctcacctctttatgcatggtcatgtttgtcatagttttactgttata-ttggtaaactgatggccggcagtgtgatggactgatggtcatgctccacagGCAGAAAAGGAACCTATTTTGAGTAGCTTCTTGTATGCCAGTGTGCTGTCTCATGATTGCCTAGAGCGTGCATTGAGCTTCGTCCTTGCAAATAGGCTTG
 | ||      || || ||     |  |  | ||      |     || | || || || || ||      |   || || |    | ||  |||    |||||||| || || ||||||||||||||||||||||||||  || |  |  | ||||||||  ||||||  || ||  | || || || || ||  | ||  
agccttgatatttaatccaaccaaacataggacaagaaagtttgagtacagtttgtgaaatgttgaatcttataatggtgaatc--ttgttgtgcgtttcagGCAGAGAAAGAGCCTATTTTGAGTAGCTTCTTGTATGCTGGTATCTTAGCACATGATTGTTTAGAGCAAGCTTTAGGGTTTGTTCTAGCCAACCGTCTCC

upper sequence: GRMZM2G048740_T03 (Zea mays), 3'ss of exon 1
lower sequence: AT4G35640.1 (Arabidopsis thaliana), 3'ss of exon 1
-gtctcacctctttatgcatggtcatgtttgtcatagttttactgttata--ttg-gtaaactgatgg-ccggcagtgtgatggactgatggtcatgctccacagGCAGAAAAGGAACCTATTTTGAGTAGCTTCTTGTATGCCAGTGTGCTGTCTCATGATTGCCTAGAGCGTGCATTGAGCTTCGTCCTTGCAAATAGGCTTG
 |  |||  | || ||   |    |        | |  || |     | |  ||| ||    | |||  ||   | ||      | || ||    || |  |||||||||| |||| ||  |||||||||||||||||||||| ||| |  |||| ||||| ||  ||||||  |||||||| || || || || ||  | ||  
agcgtcaatttttcat---taactacacgaaggacaagttaaggaacagagtttgtgtgtgtttatgttcctttaatggtgaatattgttg--tgtgttttacagGCAGAAGAGGAGCCGGTTTTGAGTAGCTTCTTGTATGCTAGTATCTTGTCGCATGACTGTTTAGAGCAAGCATTGAGTTTTGTTCTAGCTAACCGTCTCC

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|76291950|gb|DV031518.1|DV031518
EST:     CCCCCGAGGACCCCATATGGGTTGCCGTCAAGGCGGAGGCCAAGTCTGAG                         GCAGAAAAGGAACCTATTTTGAGTAGCTTCTTGTATGCCAGTGTGCTGTCT
genomic: CCCCCGAGGACCCCATATGGGTTGCCGTCAAGGCGGAGGCCAAGTCTGAGgtgagtatgc ... tgctccacagGCAGAAAAGGAACCTATTTTGAGTAGCTTCTTGTATGCCAGTGTGCTGTCT
EST: gi|71320313|gb|DR796903.1|DR796903
EST:     CCCCCGAGGACCCCATATGGGTTGCCGTCAAGGCGGAGGCCAAGTCTGAG                         GCAGAAAAGGAACCTATTTTGAGTAGCTTCTTGTATGCCAGTGTGCTGTCT
genomic: CCCCCGAGGACCCCATATGGGTTGCCGTCAAGGCGGAGGCCAAGTCTGAGgtgagtatgc ... tgctccacagGCAGAAAAGGAACCTATTTTGAGTAGCTTCTTGTATGCCAGTGTGCTGTCT
EST: gi|149108314|gb|EE292652.2|EE292652
EST:     CCCCCGAGGACCCCATATGGGTTGCCGTCAAGGCGGAGGCCAAGTCTGAG                         GCAGAAAAGGAACCTATTTTGAGTAGCTTCTTGTATGCCAGTGTGCTGTCT
genomic: CCCCCGAGGACCCCATATGGGTTGCCGTCAAGGCGGAGGCCAAGTCTGAGgtgagtatgc ... tgctccacagGCAGAAAAGGAACCTATTTTGAGTAGCTTCTTGTATGCCAGTGTGCTGTCT
EST: gi|149078416|gb|EE167191.2|EE167191
EST:     CCCCCGAGGACCCCATATGGGTTGCCGTCAAGGCGGAGGCCAAGTCTGAG                         GCAGAAAAGGAACCTATTTTGAGTAGCTTCTTGTATGCCAGTGTGCTGTCT
genomic: CCCCCGAGGACCCCATATGGGTTGCCGTCAAGGCGGAGGCCAAGTCTGAGgtgagtatgc ... tgctccacagGCAGAAAAGGAACCTATTTTGAGTAGCTTCTTGTATGCCAGTGTGCTGTCT
EST: gi|93012509|gb|EB638029.1|EB638029
EST:     CCCCCGAGGACCCCATATGGGTTGCCGTCAAGGCGGAGGCCAAGTCTGAG                         GCAGAAAAGGAACCTATTTTGAGTAGCTTCTTGTATGCCAGTGTGCTGTCT
genomic: CCCCCGAGGACCCCATATGGGTTGCCGTCAAGGCGGAGGCCAAGTCTGAGgtgagtatgc ... tgctccacagGCAGAAAAGGAACCTATTTTGAGTAGCTTCTTGTATGCCAGTGTGCTGTCT
EST: gi|71434262|gb|DR815312.1|DR815312
EST:     CCCCCGAGGACCCCATATGGGTTGCCGTCAAGGCGGAGGCCAAGTCTGAG                         GCAGAAAAGGAACCTATTTTGAGTAGCTTCTTGTATGCCAGTGTGCTGTCT
genomic: CCCCCGAGGACCCCATATGGGTTGCCGTCAAGGCGGAGGCCAAGTCTGAGgtgagtatgc ... tgctccacagGCAGAAAAGGAACCTATTTTGAGTAGCTTCTTGTATGCCAGTGTGCTGTCT
EST: gi|211068411|gb|FL280203.1|FL280203
EST:     CCCCCGAGGACCC-ATATGGGTTGCCGTCAAGGCGGAGGCCAAGTCTGAG                         GCAGAAAAGGAACCTATTTTGAGTAGCTTCTT
genomic: CCCCCGAGGACCCCATATGGGTTGCCGTCAAGGCGGAGGCCAAGTCTGAGgtgagtatgc ... tgctccacagGCAGAAAAGGAACCTATTTTGAGTAGCTTCTT
EST: gi|71771744|gb|DR969681.1|DR969681
EST:     CCCCCGAGGACCCCATATGGGTTGCCGTCAAGGCGGAGGCCAAGTCTGAG                         GCAGAAAAGGAACCTATTTTGAGTAGCTTCTTGTATGCCAGTGTGCTGTCT
genomic: CCCCCGAGGACCCCATATGGGTTGCCGTCAAGGCGGAGGCCAAGTCTGAGgtgagtatgc ... tgctccacagGCAGAAAAGGAACCTATTTTGAGTAGCTTCTTGTATGCCAGTGTGCTGTCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatattggtaaactgatggccggcagtgtgatggactgatggtcatgctccacagGCAGAAAAGGAACCTATTTTGAGTAGCTTCTTGTATGCCAGTGTGCTGTCTCATGATTGCCTAGAGCGTGCATTGAGCTTCGTCCTTGCAAATAGGCTTG
                                 gactgat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtctcacctctttatgcatggtcatgtttgtcatagttttactgttatattggtaaactgatggccggcagtgtgatggactgatggtcatgctccacagGCAGAAAAGGAACCTATTTTGAGTAGCTTCTTGTATGCCAGTGTGCTGTCTCATGATTGCCTAGAGCGTGCATTGAGCTTCGTCCTTGCAAATAGGCTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - tgcatgg
- - - - - - - - - - - - tgtttgt
- - - - - - - - - - - - - - - - - - -tttactg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - actgatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgatgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gccggca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtgatg