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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttacccgtaagtgccataatatcctttcatacttcgtacatttttttctaacaatcaaacccggacaaagcttgttttaagtgaagcgaactgacatcagGTTGCAGAACCTCTGAGGGCTATGGTTATGGGAGCTCCTTTGGAGGATGCTCGCCACCTTGCTCAAAGGTACGACAGAATGCGTCAAGAAGCTGAAGCGC

Basic information

species Zea mays
transcript GRMZM2G002859_T02
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G002859_T03 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os10g36870.1 (Oryza sativa), 3'ss of exon 4
ttacccgtaagtgccataatatcctttcatacttcgtacatttttttctaac--aatcaaacccggacaaagcttgttttaagtgaagcgaactgacatcagGTTGCAGAACCTCTGAGGGCTATGGTTATGGGAGCTCCTTTGGAGGATGCTCGCCACCTTGCTCAAAGGTACGACAGAATGCGTCAAGAAGCTGAAGCGC
    |  | | |||||||||  |||| || | |     | | |   | ||    | ||||| | | |  |  ||  | | |  |   |   | |  ||| |||| ||||||||  ||||||||||||| ||||||||||||||||| ||||||||||| ||||| ||||| |||||||| |||||||| ||||| ||||| |
--tgcaatgaatgccataatgcccttgcaaattgtaatcttgtgcatatattttactcaaatctgcatgagactgttctgacatatggattaatatcattagGTGGCAGAACCGTTGAGGGCTATGGTGATGGGAGCTCCTTTGGAAGATGCTCGCCATCTTGCCCAAAGATACGACAGGATGCGTCAGGAAGCCGAAGCAC

upper sequence: GRMZM2G002859_T03 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA12G04210.1 (Glycine max), 3'ss of exon 4
ttacccgtaagtgccataatatcctttcat-acttcgtacatttttttctaacaatcaaacccggacaaagcttgttttaagtgaagcgaactgac-atcagGTTGCAGAACCTCTGAGGGCTATGGTTATGGGAGCTCCTTTGGAGGATGCTCGCCACCTTGCTCAAAGGTACGACAGAATGCGTCAAGAAGCTGAAGCGC
    |  |   | |       || | |  |   ||     | | | |  |  ||    | ||     |     || || |||| | |   | ||   || |||||||||| ||  | ||||| |||||  |||||||||| |||||||||||||| || ||||||||| | || ||||||||||| || ||||||||||| |
--ctctatctatactggtggctcatattgttgatttacctagtgtgtgttgccatcttagcctaataattatgtgattgaagtcatggtcaatgctgattagGTTGCAGAGCCATTAAGGGCAATGGTGGTGGGAGCTCCATTGGAGGATGCTCGGCATCTTGCTCAACGTTATGACAGAATGCGACAGGAAGCTGAAGCCC

upper sequence: GRMZM2G002859_T03 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA11G11950.3 (Glycine max), 3'ss of exon 4
ttacccgtaagtgccataatatcctttcat-acttcgtacatttttttctaacaatcaaacccggacaaagcttgttttaagtgaagcgaactgac-atcagGTTGCAGAACCTCTGAGGGCTATGGTTATGGGAGCTCCTTTGGAGGATGCTCGCCACCTTGCTCAAAGGTACGACAGAATGCGTCAAGAAGCTGAAGCGC
    |  |   | |       || | | ||   ||     | | | |  |  ||    | ||     |     || || |||| | |   | || | || |||||||||| ||  | ||||| |||||  |||||||||| |||||||||||| | || ||||||||| | || ||||||||||| || ||||| ||||| |
--cgctatctatactggtggctcatattattgatttacctagtgtgtgttgccatcttagcctaataactatgtgattgaagtcatggtcaatgccgattagGTTGCAGAGCCATTAAGGGCAATGGTGGTGGGAGCTCCATTGGAGGATGCTAGGCATCTTGCTCAACGTTATGACAGAATGCGACAGGAAGCGGAAGCCC

upper sequence: GRMZM2G002859_T03 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA04G01100.2 (Glycine max), 3'ss of exon 4
-ttacccg-taagtgccataatatcct-ttcatacttcgtacatttttttctaacaatcaaacccggacaaagcttgttttaagtgaagcgaactgacatcagGTTGCAGAACCTCTGAGGGCTATGGTTATGGGAGCTCCTTTGGAGGATGCTCGCCACCTTGCTCAAAGGTACGACAGAATGCGTCAAGAAGCTGAAGCGC
  | |  | | | || ||   |||||  ||  | |||  |   ||||| |||  ||        | |  |  |    ||||||||   ||    ||   | |||||||||| ||  |||| || ||||| ||||||||||| ||||||||||| || || ||||||||| | || ||||||||||| || ||||| ||||| |
tatgctggctcattgtcaatttatccaatttgtgcttgat-tttttttatctggcataatgtttctgcgagtgaacattttaagtattgcttgatgc--ttagGTTGCAGAGCCCTTGAGAGCAATGGTGATGGGAGCTCCATTGGAGGATGCCCGGCATCTTGCTCAACGTTATGACAGAATGCGGCAGGAAGCCGAAGCAC

upper sequence: GRMZM2G002859_T03 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA06G01120.2 (Glycine max), 3'ss of exon 4
--ttacccg-taagtgccataatatcct-ttcatacttcgtacatttttttctaacaatcaaacccggacaaagcttgttttaagtgaagcgaactgacatcagGTTGCAGAACCTCTGAGGGCTATGGTTATGGGAGCTCCTTTGGAGGATGCTCGCCACCTTGCTCAAAGGTACGACAGAATGCGTCAAGAAGCTGAAGCGC
   | |  | | | || ||   |||||  ||  | |||  |   ||||| ||| |||        | |  |  |    |||||||    ||    ||   | |||||||||| ||  | || || ||||| ||||||||||| ||||||||||| || || ||||||||| | || ||||||||||| || ||||| ||||| |
atatgctggctcattgtcaatttatccagtttgtgcttgatt--tttttatctgacataatgtttctgcgagtgaacattttaagaattgcttgatgc--ttagGTTGCAGAGCCCTTAAGAGCAATGGTGATGGGAGCTCCATTGGAGGATGCCCGGCATCTTGCTCAACGTTATGACAGAATGCGGCAGGAAGCCGAAGCCC

upper sequence: GRMZM2G002859_T03 (Zea mays), 3'ss of exon 3
lower sequence: AT4G34660.2 (Arabidopsis thaliana), 3'ss of exon 4
---ttacccgtaagtgcca--taatatcctttcat--acttcgtacatttttttctaacaatcaaacccggacaaagcttgttttaagtgaagcgaactgacatcagGTTGCAGAACCTCTGAGGGCTATGGTTATGGGAGCTCCTTTGGAGGATGCTCGCCACCTTGCTCAAAGGTACGACAGAATGCGTCAAGAAGCTGAAGCGC
   |   |  |||  | ||  |||| || |    |  |||| || | ||| ||| |  |  |    |    ||||  | | | | ||       ||| |    | ||||||| || ||  |  |||| |||||| |||||||||| |||||||||||| | || ||||||||| | || ||||||||||| |||||||||||||| |
acatactctttaaaagtcaattaatgtcatggtgttcacttggttc-tttctttattgcggtttggctactacaat-catatgtcaatcc---tgaatt--tgttagGTTGCTGAGCCATTACGGGCAATGGTTTTGGGAGCTCCATTGGAGGATGCTAGACATCTTGCTCAACGCTATGACAGAATGCGCCAAGAAGCTGAAGCTC

upper sequence: GRMZM2G002859_T03 (Zea mays), 3'ss of exon 3
lower sequence: Vv18s0001g13530.t01 (Vitis vinifera), 3'ss of exon 4
-ttacccgtaagtgccataatatcctttcatacttcgtacatttttttctaacaatcaaacccggacaaagc----ttgttttaagtgaagcgaactgacatcagGTTGCAGAACCTCTGAGGGCTATGGTTATGGGAGCTCCTTTGGAGGATGCTCGCCACCTTGCTCAAAGGTACGACAGAATGCGTCAAGAAGCTGAAGCGC
 | |  | ||  |   | | |||| ||  | | |   | |||||  |  | |   |   |||   | || |     || |     ||         |     ||||||| ||||||  | || || ||||| ||||||||||| |||||||||||||| || ||||||||| | || || ||||||||    ||||||||||| |
ttaagacatattt---acattatcattctaaattc--tccatttaatagtcagtttttcacctttataatgtgtagttatccagtgtttgattctttatttccagGTTGGAGAACCCTTAAGAGCAATGGTAATGGGAGCTCCCTTGGAGGATGCTCGACATCTTGCTCAACGATATGAGAGAATGCGAATGGAAGCTGAAGCTC

upper sequence: GRMZM2G002859_T03 (Zea mays), 3'ss of exon 3
lower sequence: Vv03s0038g00460.t01 (Vitis vinifera), 3'ss of exon 4
ttacccgtaagtgccataatatcctttcatact-tcgtacatttttttctaacaatcaaacccggacaaagcttgtttt--aagtgaagcgaactgacat------cagGTTGCAGAACCTCTGAGGGCTATGGTTATGGGAGCTCCTTTGGAGGATGCTCGCCACCTTGCTCAAAGGTACGACAGAATGCGTCAAGAAGCTGAAGCGC
          ||||||   | || |||   | | | |  | | |  |  |  | |||| |  ||    || | |||  |  | |||  ||  | || | |       |||||||||| ||  | || || ||||| ||||||||||| |||||||||||||| || ||||||||| | || || |||||||| |||||||||||||| |
---------cgtgccactttttcattttcaattattgctcctctcctatttgctatcacaggcgttgtaatcatgtgctcgatgtggtgctgaatgccttgatttctagGTTGCAGAGCCATTAAGAGCGATGGTAATGGGAGCTCCATTGGAGGATGCTCGACATCTTGCTCAACGCTATGAAAGAATGCGACAAGAAGCTGAAGCTC

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|148932010|gb|EC875305.2|EC875305
EST:     CCATGATGGAAAAGGAAAGGGGTAACCTGCTGAAAGCCCTTGGCACACAG                         GTTGCAGAACCTCTGAGGGCTATGGTTATGGGAGCTCCTTTGGAGGATGCT
genomic: CCATGATGGAAAAGGAAAGGGGTAACCTGCTGAAAGCCCTTGGCACACAGgtattagtca ... ctgacatcagGTTGCAGAACCTCTGAGGGCTATGGTTATGGGAGCTCCTTTGGAGGATGCT
EST: gi|50324117|gb|CO519243.1|CO519243
EST:     CCATGATGGAAAAGGAAAGGGGTAACCTGCTGAAAGCCCTTGGCACACAG                         GTTGCAGAACCTCTGAGGGCTATGGTTATGGGAGCTCCTTTGGAGGATGCT
genomic: CCATGATGGAAAAGGAAAGGGGTAACCTGCTGAAAGCCCTTGGCACACAGgtattagtca ... ctgacatcagGTTGCAGAACCTCTGAGGGCTATGGTTATGGGAGCTCCTTTGGAGGATGCT
EST: gi|71307048|gb|DR789679.1|DR789679
EST:     CCATGATGGAAAAGGAAAGGGGTAACCTGCTGAAAGCCCTTGGCACACAG                         GTTGCAGAACCTCTGAGGGCTATGGTTATGGGAGCTCCTTTGGAGGATGCT
genomic: CCATGATGGAAAAGGAAAGGGGTAACCTGCTGAAAGCCCTTGGCACACAGgtattagtca ... ctgacatcagGTTGCAGAACCTCTGAGGGCTATGGTTATGGGAGCTCCTTTGGAGGATGCT
EST: gi|148959420|gb|EC905446.2|EC905446
EST:     CCATGATGGAAAAGGAAAGGGGTAACCTGCTGAAAGCCCTTGGCACACAG                         GTTGCAGAACCTCTGAGGGCTATGGTTATGGGAGCTCCTTTGGAGGATGCT
genomic: CCATGATGGAAAAGGAAAGGGGTAACCTGCTGAAAGCCCTTGGCACACAGgtattagtca ... ctgacatcagGTTGCAGAACCTCTGAGGGCTATGGTTATGGGAGCTCCTTTGGAGGATGCT
EST: gi|148986437|gb|EE030179.2|EE030179
EST:     CCATGATGGAAAAGGAAAGGGGTAACCTGCTGAAAGCCCTTGGCACACAG                         GTTGCAGAACCTCTGAGGGCTATGGTTATGGGAGCTCCTTTGGAGGATGCT
genomic: CCATGATGGAAAAGGAAAGGGGTAACCTGCTGAAAGCCCTTGGCACACAGgtattagtca ... ctgacatcagGTTGCAGAACCTCTGAGGGCTATGGTTATGGGAGCTCCTTTGGAGGATGCT
EST: gi|21987351|gb|BQ778879.1|BQ778879
EST:     CCATGATGGAAAAGGAAAGGGGTAACCTGCTGAAAG-CCTTGGCACACAG                         GTTGCAGAACCTCTGAGGGCTATGGTTATGGGAGCTCCTTTGGAGGATGCT
genomic: CCATGATGGAAAAGGAAAGGGGTAACCTGCTGAAAGCCCTTGGCACACAGgtattagtca ... ctgacatcagGTTGCAGAACCTCTGAGGGCTATGGTTATGGGAGCTCCTTTGGAGGATGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctaacaatcaaacccggacaaagcttgttttaagtgaagcgaactgacatcagGTTGCAGAACCTCTGAGGGCTATGGTTATGGGAGCTCCTTTGGAGGATGCTCGCCACCTTGCTCAAAGGTACGACAGAATGCGTCAAGAAGCTGAAGCGC
                          ttgttttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttacccgtaagtgccataatatcctttcatacttcgtacatttttttctaacaatcaaacccggacaaagcttgttttaagtgaagcgaactgacatcagGTTGCAGAACCTCTGAGGGCTATGGTTATGGGAGCTCCTTTGGAGGATGCTCGCCACCTTGCTCAAAGGTACGACAGAATGCGTCAAGAAGCTGAAGCGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC