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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttgtgtaatcgtacaggcgtgcttttttgaaaattggccacctagtcagacttgtaagtatataatgttactgcattttaatggttgtcgttttggtagGTGAACAAGGCATGGTTGATGAAGCTCAAAAAGCTTTGGAAGAGGCAGAAGCTCTGAAAAAG

Basic information

species Zea mays
transcript GRMZM2G069916_T04
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G069916_T04 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os03g62640.2 (Oryza sativa), 3'ss of exon 6
tttgtgtaatcgtacag-gcgtgcttttttgaaaattggccacctagtcagacttgtaagtatataatg---ttactgcattttaat---ggttgtcgttttggtagGTGAACAAGGCATGGTTGATGAAGCTCAAAAAGCTTTGGAAGAGGCAGAAGCTCTGAAAAAG
       | | | |  | | | || |||       ||      ||||| ||  || |||  | |||| |   ||  ||   | ||||   | |  || ||||| ||||||||||||| ||||| |||||||| || |||| | ||||||| ||||| ||| ||||||||
------gagtgggatggagggagcatttgcattggttatggtgctagt-agttttttaatgacataaagaagtttatgtgatataatcttgctcatccttttgttagGTGAACAAGGGATGGTAGATGAAGCACAGAAAGTTATGGAAGAAGCAGAGGCTTTGAAAAAG

upper sequence: GRMZM2G069916_T04 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA09G38430.1 (Glycine max), 3'ss of exon 6
tttgtgtaatcgtacaggcgtgcttttttgaaaattggccacctagtcagacttgtaagtatataa--tgttactgcatttta-atggttgtcgttttggtagGTGAACAAGGCATGGTTGATGAAGCTCAAAAAGCTTTGGAAGAGGCAGAAGCTCTGAAAAAG
  |   | ||     |              ||| || | |   |   |   ||  || |    | |  | ||| |  ||  ||  |  || | |  |    |||||| ||||| ||||||||||| ||||||||||| ||||||||||| ||||| || || |||
-cttaatgataagcaaatttcaagagccacaaactttgtcctttg--cgttctcctaggctctttactttttatttaatgatatgtattttttgaatgaacagGTGAGCAAGGAATGGTTGATGAGGCTCAAAAAGCATTGGAAGAGGCTGAAGCACTTAAGAAG

upper sequence: GRMZM2G069916_T04 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA18G47910.1 (Glycine max), 3'ss of exon 6
tttgtgtaatcgtacaggcgtgcttttttgaaaattggccacctagtcagacttgtaagtat--ataatgttactgcatttta-atggttgtcgttttggtagGTGAACAAGGCATGGTTGATGAAGCTCAAAAAGCTTTGGAAGAGGCAGAAGCTCTGAAAAAG
  |||||  |  |       |   | |   | ||||| |  |    |   | |  | | | |  |||   ||  |  ||  ||  |  || | |  |    |||||| ||||| ||||||||||| |||||||||||  |||||||||| ||||| || || |||
aatgtgttttaatgtcaatatcgatat---ataattgactgctgcatggtaatcatgactcttgatagcattttttaatgatatgtattttttgaataaacagGTGAGCAAGGAATGGTTGATGAGGCTCAAAAAGCACTGGAAGAGGCTGAAGCACTTAAGAAG

upper sequence: GRMZM2G069916_T04 (Zea mays), 3'ss of exon 6
lower sequence: AT5G17440.1 (Arabidopsis thaliana), 3'ss of exon 6
---tttgtgtaatcgtacaggcgtgcttttttgaaaattggccacctagtcagacttgtaagtatataatgttactgcattttaatggttgt-cgttt-tggtagGTGAACAAGGCATGGTTGATGAAGCTCAAAAAGCTTTGGAAGAGGCAGAAGCTCTGAAAAAG
      |     |  |     | | | |   | |||| ||   || |  |||   ||| ||  |    |   ||| |  || | ||   ||| ||||| |   |||||||||||| |||||||||||||| || |||||  | |||||||| |||||||| || |||
gaagaagacagtttatggttacatacatacataaaaactga--actttttcaatgttggaaaca-gccacagtacag--ttatgatatctgtacgtttatttcagGTGAACAAGGGATGGTTGATGAAGCGCAGAAAGCACTAGAAGAGGCGGAAGCTCTTAAGAAG

upper sequence: GRMZM2G069916_T04 (Zea mays), 3'ss of exon 6
lower sequence: AT3G03340.1 (Arabidopsis thaliana), 3'ss of exon 6
tttgtgtaatcgtacaggcgtgcttttttgaaaattggccacctagtcagacttgtaagtatataatgttactgcattttaatggttgtc-gttttggtagGTGAACAAGGCATGGTTGATGAAGCTCAAAAAGCTTTGGAAGAGGCAGAAGCTCTGAAAAAG
 |   | |||          ||  | ||   | ||          |  | ||| |     |   | | |||      ||  |||||| |  | | |  ||||||||||||| |||||||||||||| || |||||  |||||||||| |||||||| || |||
-taaggaaatttcttcccgttgtatgttactatatctatgttaaggaaacactggacttcacgaagttttatatagattgtatggttatttgatattttagGTGAACAAGGAATGGTTGATGAAGCCCAGAAAGCCCTGGAAGAGGCTGAAGCTCTTAAGAAG

upper sequence: GRMZM2G069916_T04 (Zea mays), 3'ss of exon 6
lower sequence: EFJ11722 (Selaginella moellendorffii), 3'ss of exon 6
tttgtgtaatcgtacaggcgtgcttttttgaaaattggccacctagtcagacttgtaagtatataatgttactgcattttaatggttgtcgttttggt--agGTGAACAAGGCATGGTTGATGAAGCTCAAAAAGCTTTGGAAGAGGCAGAAGCTCTGAAAAAG
                                           ||   | | || |   || | | ||||      |  | |  | | | | | || |  |||||| |||||| |||| |||||||| |||||  | |||||||||||||||||  ||||||||
------------------------------------------gtaaatatatttcttt-tagagattgttgtgttttcctcactggtttggatgtgatctagGTGAGCAAGGCTTGGTGGATGAAGCGCAAAAGACCTTGGAAGAGGCAGAAGCGTTGAAAAAG

upper sequence: GRMZM2G069916_T04 (Zea mays), 3'ss of exon 6
lower sequence: EFJ22509 (Selaginella moellendorffii), 3'ss of exon 6
tttgtgtaatcgtacaggcgtgcttttttgaaaattggccacctagtcagacttgtaagtatataatgttactgcattttaatggttgtcgttttggt--agGTGAACAAGGCATGGTTGATGAAGCTCAAAAAGCTTTGGAAGAGGCAGAAGCTCTGAAAAAG
                                           ||   | | ||     || | | ||||      |  | |  | | | | |  | |  |||||| |||||| |||| |||||||| ||||| ||  ||||||||||||||||  ||||||||
------------------------------------------gtaaatatattt-cgtttagagattgttgtgttttcctcactggttttgatgcgatctagGTGAGCAAGGCTTGGTGGATGAAGCGCAAAAGGCCCTGGAAGAGGCAGAAGCGTTGAAAAAG

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|67033512|gb|CO462261.1|CO462261
EST:     TCGTACTCAAGAAATTATCAACGAAAAGCTTAAGAAAGCTGAAGAGCTTG                         GTGAACA-GGCATGGTTGATGAAGCTCAAAAAGCTTTGGAAGAGGCAGAAG
genomic: TCGTACTCAAGAAATTATCAACGAAAAGCTTAAGAAAGCTGAAGAGCTTGgtatggaaag ... gttttggtagGTGAACAAGGCATGGTTGATGAAGCTCAAAAAGCTTTGGAAGAGGCAGAAG
EST: gi|32832751|gb|CD972429.1|CD972429
EST:     TACTCAAGAAATTATCAACGAAAAGCTTAAGAAAGCTGAAGAGCTTG                         GTGAACAAGGCATGGTTGATGAAGCTCAAAAAGCTTTGGAAGAGGCAGAAG
genomic: TACTCAAGAAATTATCAACGAAAAGCTTAAGAAAGCTGAAGAGCTTGgtatggaaag ... gttttggtagGTGAACAAGGCATGGTTGATGAAGCTCAAAAAGCTTTGGAAGAGGCAGAAG
EST: gi|149000973|gb|EE038213.2|EE038213
EST:     TCGTACTCAAGAAATTATCACCGAAAAGCTTAAGAAAGCTGAAGAGCTTG                         GTGAACCAGG-ATGGTTGATGAAGCTCAAAAAGCTT
genomic: TCGTACTCAAGAAATTATCAACGAAAAGCTTAAGAAAGCTGAAGAGCTTGgtatggaaag ... gttttggtagGTGAACAAGGCATGGTTGATGAAGCTCAAAAAGCTT
EST: gi|76920400|gb|DV168155.1|DV168155
EST:     TCGTACTCAAGAAATTATCAACGAAAAGCTTAAGAAAGCTGAAGAGCTTG                         GTGAACAAGGCATGGTTGATGAAGCTCAAAAAGCTTTGGAAGAGGCAGAAG
genomic: TCGTACTCAAGAAATTATCAACGAAAAGCTTAAGAAAGCTGAAGAGCTTGgtatggaaag ... gttttggtagGTGAACAAGGCATGGTTGATGAAGCTCAAAAAGCTTTGGAAGAGGCAGAAG
EST: gi|148952947|gb|EE152420.2|EE152420
EST:     TCGTACTCAAGAAATTATCAACGAAAAGCTTAAGAAAGCTGAAGAGCTTG                         GTGAAACA-GGCATGGTTGATGAAGCTCAAAAAGCTTTGGAAGAGGCAGAA
genomic: TCGTACTCAAGAAATTATCAACGAAAAGCTTAAGAAAGCTGAAGAGCTTGgtatggaaag ... gttttggtagGTGAA-CAAGGCATGGTTGATGAAGCTCAAAAAGCTTTGGAAGAGGCAGAA
EST: gi|71312972|gb|DR793008.1|DR793008
EST:     TCGTACTCAAGAAATTATCAACGAAAAGCTTAAGAAAGCTGAAGAGCTTG                         GTGAACAAGGCATGGTTGATGAAGCTCAAAAAGCTTTGGAAGAGGCAGAAG
genomic: TCGTACTCAAGAAATTATCAACGAAAAGCTTAAGAAAGCTGAAGAGCTTGgtatggaaag ... gttttggtagGTGAACAAGGCATGGTTGATGAAGCTCAAAAAGCTTTGGAAGAGGCAGAAG
EST: gi|87157020|gb|DY401809.1|DY401809
EST:     TCGTACTCAAGAAATTATCAACGAAAAGCTTAAGAAAGCTGAAGAGCTTG                         GTGAACAAGGCATGGTTGATGAAGCTCAAAAAGCTTTGGAAGAGGCAGAAG
genomic: TCGTACTCAAGAAATTATCAACGAAAAGCTTAAGAAAGCTGAAGAGCTTGgtatggaaag ... gttttggtagGTGAACAAGGCATGGTTGATGAAGCTCAAAAAGCTTTGGAAGAGGCAGAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtcagacttgtaagtatataatgttactgcattttaatggttgtcgttttggtagGTGAACAAGGCATGGTTGATGAAGCTCAAAAAGCTTTGGAAGAGGCAGAAGCTCTGAAAAAG
                               ttttaat  putative branch site (score: 3)
                                           tcgtttt  putative PPT
          taagtatataatgtta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttgtgtaatcgtacaggcgtgcttttttgaaaattggccacctagtcagacttgtaagtatataatgttactgcattttaatggttgtcgttttggtagGTGAACAAGGCATGGTTGATGAAGCTCAAAAAGCTTTGGAAGAGGCAGAAGCTCTGAAAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC