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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttagttcctgtttttgtaaaatataatattgaattagtagagtactagtagaattcattgcattacctgcttgtgtaactgacaaatgataaaaatgcagTTCCCCGAAACTTCAGGCTATTAGAGGAGCTCGAGCGTGGAGAGAAGGGCATTGGTGATGGAACAGTGAGCTATGGAATGGATGATGCCGATGACATCTA

Basic information

species Zea mays
transcript GRMZM2G071010_T03
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G071010_T03 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA10G09280.2 (Glycine max), 3'ss of exon 1
---ttagt-tcctgtttttgtaaaatataatattgaattagtagagtactagtagaattcattgcattacctgcttgtgtaactgacaaatgataaaaatgcagTTCCCCGAAACTTCAGGCTATTAGAGGAGCTCGAGCGTGGAGAGAAGGGCATTGGTGATGGAACAGTGAGCTATGGAATGGATGATGCCGATGACATCTA
   | | | |    |   |  |    | |||    | |||  |  ||  || |  |||  |     ||   |  ||||  ||       ||| ||||  |||||||||  | ||||||||  |  | |||||||| || |||||||| || || ||||| ||||| ||||| |||||||||||||||||||  |||||||| ||
ttatcaatatgtcatgcattgatcccacaatggctagtta-cattgtgttattcaaataaaaaagtttgtgt-tttgttaaatatttgtatgttaaa--tgcagTTCCTAGGAACTTCAGATTGCTGGAGGAGCTTGAACGTGGAGAAAAAGGAATTGGAGATGGCACAGTTAGCTATGGAATGGATGATGGTGATGACATTTA

upper sequence: GRMZM2G071010_T03 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA02G35990.1 (Glycine max), 3'ss of exon 1
ttagttcctgtttttgtaaa---atataatattgaattagtagagtactagtagaattcattgcattacctgcttgtgtaactgacaaatgataaaaatgcagTTCCCCGAAACTTCAGGCTATTAGAGGAGCTCGAGCGTGGAGAGAAGGGCATTGGTGATGGAACAGTGAGCTATGGAATGGATGATGCCGATGACATCTA
 ||| |  | || |  | ||   ||   | | ||   ||||    |  |   | |||  |     ||       |||  ||       ||| | ||| |||||||||  | ||||||||  |  | |||||||| || ||||| || || || ||||| ||||| ||||| |||||||||||||||||||  |||||||| ||
gtagatattcttgtcatgaattgatcccacaatgg-ctagttacatgttttca-aataaaaaatgtttgtgttctgttaaatatttgtatgtttaaa-tgcagTTCCTAGGAACTTCAGATTGCTGGAGGAGCTTGAACGTGGTGAAAAAGGAATTGGAGATGGCACAGTTAGCTATGGAATGGATGATGGTGATGACATTTA

upper sequence: GRMZM2G071010_T03 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA03G35790.1 (Glycine max), 3'ss of exon 1
ttagttcctgtttttgtaaaatataatattgaattagtagag-tactagtagaattcattgcattacc-tgcttgtgtaactga---caaatg-ataaaaatgcagTTCCCCGAAACTTCAGGCTATTAGAGGAGCTCGAGCGTGGAGAGAAGGGCATTGGTGATGGAACAGTGAGCTATGGAATGGATGATGCCGATGACATCTA
        | |  ||| |  ||   ||||  |   | |   | || |  | |||   |     ||| | ||  | ||||  | |   ||  || |    |||||||||||  | ||||||||  |  | |||||||| |||   ||||| || || || || ||||||||||| |||||||||||||||||||  || ||||| ||
------aatttggttgaaggattacatatgtagccattcttgatatttattgaagatacaatgttagcatgagtatgtagttaaaggcatttgtactttaatgcagTTCCAAGGAACTTCAGATTGCTGGAGGAGCTTGAGAAGGGAGAAAAAGGAATCGGAGATGGAACAGTTAGCTATGGAATGGATGATGGTGACGACATTTA

upper sequence: GRMZM2G071010_T03 (Zea mays), 3'ss of exon 1
lower sequence: AT3G52560.4 (Arabidopsis thaliana), 3'ss of exon 1
ttagttcctgtttttgtaaaatataatattgaattagtagagtactagtaga-attcattg-cattacctgcttgtgtaactgacaaatgataaaaatgcagTTCCCCGAAACTTCAGGCTATTAGAGGAGCTCGAGCGTGGAGAGAAGGGCATTGGTGATGGAACAGTGAGCTATGGAATGGATGATGCCGATGACATCTA
 ||     |||| |  |      |   ||| ||  |   || | || ||    ||| | ||  || |  || || ||| ||   |   | ||   |||  ||||||  | || ||  || | || |||||||| || ||||| ||||| || ||||| |||||||| ||||||||||||||||||||||  |||||||||||
atatgatatgttctgttctctgctttgattaaaaaaagtgattgcttgttttcatttactgatatgaattgtttttgttac--gcttgttattgcaatatagTTCCGAGGAATTTTCGGTTGTTGGAGGAGCTTGAACGTGGGGAGAAAGGTATTGGGGATGGAACTGTGAGCTATGGAATGGATGATGGAGATGACATCTA

upper sequence: GRMZM2G071010_T03 (Zea mays), 3'ss of exon 1
lower sequence: AT2G36060.3 (Arabidopsis thaliana), 3'ss of exon 1
ttagttcctgtttttgtaaaatataatattgaattagtagagtactagtagaattcattgcattacctgcttgtgtaactgacaaatgataaaaatgca--gTTCCCCGAAACTTCAGGCTATTAGAGGAGCTCGAGCGTGGAGAGAAGGGCATTGGTGATGGAACAGTGAGCTATGGAATGGATGATGCCGATGACATCTA
 ||| |  | ||   |   | |    |  | |     |||||   || | |  ||  || | ||  ||     |  | |||    ||| |   |||| |  |||||  | || ||| || |  | |||||||| || ||||||||||| || ||||| |||||||| ||||||||||||||||||||||  |||||||| ||
-tagattgttttcaagctcagtgctttgcttagaatatagagc-ttatttgtgttagtttccttcactaaaaattgagctgtttgatgttgttaatgtaaagTTCCGAGGAATTTCCGGTTGCTGGAGGAGCTTGAACGTGGAGAGAAAGGTATTGGAGATGGAACTGTGAGCTATGGAATGGATGATGGAGATGACATTTA

upper sequence: GRMZM2G071010_T03 (Zea mays), 3'ss of exon 1
lower sequence: Vv06s0080g01080.t01 (Vitis vinifera), 3'ss of exon 1
ttagttcctgtttttgtaaaatataatattgaatt---agtagagtactagtagaattcattgcattacctgcttgtgtaactgacaaatgataaaaatgcagTTCCCCGAAACTTCAGGCTATTAGAGGAGCTCGAGCGTGGAGAGAAGGGCATTGGTGATGGAACAGTGAGCTATGGAATGGATGATGCCGATGACATCTA
  |   |  |  || | ||    |  |||    |    |||  |    |  |||| |  |    |  |  |   |||||   || |      | |   |||||| || || ||||||||  |  | ||||| || || ||||| |||||||| ||||| ||||| || ||||| ||||||||||||||||  |||||||| ||
--acaactggagttggaaatgcttggtatcttgtctcaagtgaaactatcttaga-tggaagttacaaggtatgtgtgtttttgtctttatgttatcttgcagTCCCTCGCAACTTCAGATTGCTGGAGGAACTTGAACGTGGGGAGAAGGGTATTGGAGATGGTACTGTGAGTTATGGAATGGATGATGGAGATGACATATA

upper sequence: GRMZM2G071010_T03 (Zea mays), 3'ss of exon 1
lower sequence: Vv08s0007g02580.t01 (Vitis vinifera), 3'ss of exon 1
-----ttagttcctgtttttgtaaaatataatattgaattagtagagtactagtagaattcattgcattacctgcttgtgtaactgacaaatgataaaaatgcagTTCCCCGAAACTTCAGGCTATTAGAGGAGCTCGAGCGTGGAGAGAAGGGCATTGGTGATGGAACAGTGAGCTATGGAATGGATGATGCCGATGACATCTA
     | |      |  ||||  |  ||         |||   | | |  || ||   ||||  |  || |   ||| |    ||    | |   |    |||||| || |||||||||||  |  | ||||| || || |||||||| ||||| ||||| ||||| || || |||||||||||||||||||  |||||||| ||
tggtctgaagcttagcctttgatatttaaggcgccttattcagacaattttattaattttcaa-gatttgcgcacttttaagtctctgcatttcca----tgcagTCCCTCGAAACTTCAGATTGCTTGAGGAACTTGAACGTGGAGAAAAGGGTATTGGAGATGGTACTGTCAGCTATGGAATGGATGATGGAGATGACATTTA

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|32923039|gb|CF027851.1|CF027851
EST:     TCCAGGGGCGATGACGCTGGGTAGCTCCGGCGCCGGATCGAGCGTCGTCG                         TTCCCCGAAACTTCAGGCTATTAGAGGAGCTCGAGCGTGGAGAGAAGGGCA
genomic: TCCAGGGGCGATGACGCTGGGTAGCTCCGGCGCCGGATCGAGCGTCGTCGgtaagtaacc ... aaaaatgcagTTCCCCGAAACTTCAGGCTATTAGAGGAGCTCGAGCGTGGAGAGAAGGGCA
EST: gi|33095289|gb|CF055283.1|CF055283
EST:     TCCAGGGGCGATGACGCTGGGTAGCTCCGGCGCCGGATCGAGCGTCGTCG                         TTCCCCGAAACTTCAGGCTATTATTGGAGCTCGAGCGTGGAGAGAAGGGCA
genomic: TCCAGGGGCGATGACGCTGGGTAGCTCCGGCGCCGGATCGAGCGTCGTCGgtaagtaacc ... aaaaatgcagTTCCCCGAAACTTCAGGCTATTAGAGGAGCTCGAGCGTGGAGAGAAGGGCA
EST: gi|211256805|gb|FL058291.1|FL058291
EST:     TCCAGGGGCGATGACGCTGGGTAGCTCCGGCGCCGGATCGAGCGTCGTCG                         TTCCCCGAAACTTCAGGCTATTAGAGGAGCTCGAGCGTGGAGAAAAGGGCA
genomic: TCCAGGGGCGATGACGCTGGGTAGCTCCGGCGCCGGATCGAGCGTCGTCGgtaagtaacc ... aaaaatgcagTTCCCCGAAACTTCAGGCTATTAGAGGAGCTCGAGCGTGGAGAGAAGGGCA
EST: gi|71437348|gb|DR818398.1|DR818398
EST:     TCCAGGGGCGATGACGCTGGGTAGCTCCGGCGCCGGATCGAGCGTCGTCG                         TTCCCCGAAACTTCAGGCTATTAGAGGAGCTCGAGCGTGGAGAGAAGGGCA
genomic: TCCAGGGGCGATGACGCTGGGTAGCTCCGGCGCCGGATCGAGCGTCGTCGgtaagtaacc ... aaaaatgcagTTCCCCGAAACTTCAGGCTATTAGAGGAGCTCGAGCGTGGAGAGAAGGGCA
EST: gi|211040687|gb|FL105663.1|FL105663
EST:     TCCAGGGGCGATGACGCTGGGTAGCTCCGGCGCCGGATCGAGCGTCGTCG                         TTCCCCGAAACTTCAGGCTATTAGAGGAGCTCGAGCGTG
genomic: TCCAGGGGCGATGACGCTGGGTAGCTCCGGCGCCGGATCGAGCGTCGTCGgtaagtaacc ... aaaaatgcagTTCCCCGAAACTTCAGGCTATTAGAGGAGCTCGAGCGTG
EST: gi|211055493|gb|FL105750.1|FL105750
EST:     TCCAGGGGCGATGACGCTGGGTAGCTCCGGCGCCGGATCGAGCGTCGTCG                         TTCCCCGAAACTTCAGGCTATTA
genomic: TCCAGGGGCGATGACGCTGGGTAGCTCCGGCGCCGGATCGAGCGTCGTCGgtaagtaacc ... aaaaatgcagTTCCCCGAAACTTCAGGCTATTA
EST: gi|32929652|gb|CF034464.1|CF034464
EST:     TCCAGGGGCGATGACGCTGGGTAGCTCCGGCGCCGGATCGAGCGTCGTCG                         TTCCCCGAAACTTCAGGCTATTAGAGGAGCTCGAGCGTGGAGAGAAGGGCA
genomic: TCCAGGGGCGATGACGCTGGGTAGCTCCGGCGCCGGATCGAGCGTCGTCGgtaagtaacc ... aaaaatgcagTTCCCCGAAACTTCAGGCTATTAGAGGAGCTCGAGCGTGGAGAGAAGGGCA
EST: gi|211437842|gb|FL105651.1|FL105651
EST:     TCCAGGGGCGATSACGCTGGGTAGCTCCGGCGCCGGATCGAGCGTCGTCG                         TTCCCCGAAACTTCAGGCTATTAGAGGAGCTCGAGCGTGGAGAGAAGGGCA
genomic: TCCAGGGGCGATGACGCTGGGTAGCTCCGGCGCCGGATCGAGCGTCGTCGgtaagtaacc ... aaaaatgcagTTCCCCGAAACTTCAGGCTATTAGAGGAGCTCGAGCGTGGAGAGAAGGGCA
EST: gi|33104245|gb|CF064205.1|CF064205
EST:     TCCAGGGGCGATGACGCTGGGTAGCTCCGGCGCCGGATCGAGCGTCGTCGG                         TTCCCCGAAACTTCAGGCTATTAGAGGAGCTCGAGCGTGGAGAGAAGGGC
genomic: TCCAGGGGCGATGACGCTGGGTAGCTCCGGCGCCGGATCGAGCGTCGTC-Ggtaagtaacc ... aaaaatgcagTTCCCCGAAACTTCAGGCTATTAGAGGAGCTCGAGCGTGGAGAGAAGGGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagtagaattcattgcattacctgcttgtgtaactgacaaatgataaaaatgcagTTCCCCGAAACTTCAGGCTATTAGAGGAGCTCGAGCGTGGAGAGAAGGGCATTGGTGATGGAACAGTGAGCTATGGAATGGATGATGCCGATGACATCTA
                               aactgac  putative branch site (score: 2)
                                    acaaatgataaaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttagttcctgtttttgtaaaatataatattgaattagtagagtactagtagaattcattgcattacctgcttgtgtaactgacaaatgataaaaatgcagTTCCCCGAAACTTCAGGCTATTAGAGGAGCTCGAGCGTGGAGAGAAGGGCATTGGTGATGGAACAGTGAGCTATGGAATGGATGATGCCGATGACATCTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA