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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcgaattccttcctgctcagttgctctgacgcctgcctagtttgttaccctcttcgtgtcctcagttgctcatttgttcttcttctggccttaattgcagACCATCAGTTACATGGCAGAACGTGTCGTGGGTACGGGCTCATTTGGGATCGTCTTCCAG

Basic information

species Zea mays
transcript GRMZM2G472625_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G472625_T02 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA12G33950.1 (Glycine max), 3'ss of exon 2
tcgaattccttcctgctcagttgctctgacgcctgcctagtttgttaccc-----tcttcgtgtcctcagttgctcatttgttcttcttctggccttaattgcagACCATCAGTTACATGGCAGAACGTGTCGTGGGTACGGGCTCATTTGGGATCGTCTTCCAG
   | ||         |    ||||   | |  ||   |   ||  | ||     | |   | || |   ||  ||||   ||  |  |||        ||||||||||||||||||||||| |||||||| || || || || |||||||| || || ||||||
---attttgaataaaattgactgctt--aagattgatgatgatggcatccacgggtttcaatttcttttattcttcataaatttgtgctctaatgcctcttgcagACCATCAGTTACATGGCCGAACGTGTTGTTGGCACTGGATCATTTGGCATTGTTTTCCAG

upper sequence: GRMZM2G472625_T02 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA06G42840.1 (Glycine max), 3'ss of exon 2
--tcgaattccttcctgctcagttgctctgacgcctgcctagtttgttaccctcttcgtgtcctcagttgctcatttgttcttcttctggccttaattgcagACCATCAGTTACATGGCAGAACGTGTCGTGGGTACGGGCTCATTTGGGATCGTCTTCCAG
  |  |||  |||     |  ||     || |    |  |  ||  ||   ||       |      ||  | ||   ||| |   |||     |  ||||||||||||||||||||||||||||||| || || || || ||||||||  | || ||||||
ggttcaataactttaaaattggtgatattgtc-tgagtttcattatttgttcttcgtaaataacttatttgttatg-attccttccctgataccacctgcagACCATCAGTTACATGGCAGAACGTGTTGTTGGCACTGGATCATTTGGAGTTGTTTTCCAG

upper sequence: GRMZM2G472625_T02 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA13G36570.1 (Glycine max), 3'ss of exon 1
tcgaattccttcctgc-tcagttgctctgacgcctgcctagtttgttaccctcttcgtgtcctcagttgctcatttgttcttcttctggccttaattgcagACCATCAGTTACATGGCAGAACGTGTCGTGGGTACGGGCTCATTTGGGATCGTCTTCCAG
  |||||          | |  ||||            ||   |       | |   | || ||  ||  ||||   ||  |  ||       | ||||||||||||||||||||||| |||||||| || || || || ||||| || || || ||||||
-agaattttgaataaaattaaatgcttgagattgatgataacatccacgggtttcaatttcttctattcttcataaatttgtgctcgaatgccacttgcagACCATCAGTTACATGGCTGAACGTGTTGTTGGCACTGGATCATTCGGAATTGTTTTCCAG

upper sequence: GRMZM2G472625_T02 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA12G15470.2 (Glycine max), 3'ss of exon 2
tcgaattccttcctgctcagttgctctgacgcctgcctagtttgttaccctcttcgtgtcctcagttgctcatttgtt----cttcttc--tggccttaattgcagACCATCAGTTACATGGCAGAACGTGTCGTGGGTACGGGCTCATTTGGGATCGTCTTCCAG
    || | ||  |    | |  || ||  | |     |      ||   | |     || | | |  || |||||||     | ||||  ||     |  ||||||||||||||||||||||||||||||| || || || || ||||||||  | || || |||
----atgcattaatatatattatctttggagtccaaaaaa--aaataaaatttattcttcgtaaataacttatttgttatgattacttccatgataccacctgcagACCATCAGTTACATGGCAGAACGTGTTGTTGGCACTGGATCATTTGGAGTTGTTTTTCAG

upper sequence: GRMZM2G472625_T02 (Zea mays), 3'ss of exon 2
lower sequence: Vv10s0003g01480.t01 (Vitis vinifera), 3'ss of exon 2
-tcgaattccttcctgctcagttgctctgacgcctgcctagtttgttaccctcttcgtgtcctcagttgctcatttgttcttcttctggccttaattgcagACCATCAGTTACATGGCAGAACGTGTCGTGGGTACGGGCTCATTTGGGATCGTCTTCCAG
 |  || | |||      |       |     |    | |  |||| |         ||         | |  | | |  ||||| ||    | | ||||||||||||||||||||||||| ||||| |||||||| || |||||||| || || || |||
gtataactactttgaatgcccacaagcaatttctcttccaaattgtgagtggaaatatgattgtcaacggttttatatatttcttgtgatgcttactgcagACCATCAGTTACATGGCAGAGCGTGTTGTGGGTACCGGGTCATTTGGAATTGTTTTTCAG

upper sequence: GRMZM2G472625_T02 (Zea mays), 3'ss of exon 2
lower sequence: Vv12s0028g01810.t01 (Vitis vinifera), 3'ss of exon 2
-tcgaattccttcctgctcagttgctctgacgcctgcctagtttgttaccctcttcgtgtcctcagttgctcatttgttcttcttctggccttaattgcagACCATCAGTTACATGGCAGAACGTGTCGTGGGTACGGGCTCATTTGGGATCGTCTTCCAG
 | |||        |  |   |||   |   |  | |   ||||  |    | ||| |  |   |      | |  |    |||| ||    |  |||||||||||||||||||||||||| ||  | || || || || || ||||| || || || |||
tttgaaaagtagaattgtttattggattcgtgaat-ctgtgtttcctgatttgttcttcccagtaaaaatgcttaggcctctcttgtgatgcttcttgcagACCATCAGTTACATGGCAGAGCGCATTGTAGGCACTGGATCGTTTGGAATTGTTTTTCAG

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|211126298|gb|FL137999.1|FL137999
EST:     GCCACATCATCTCCACCACCATCGGTGGGAAGAACGGCGAGCCGAAGCGG                         ACCATCAGTTACATGGCAGAACGTGTCGTGGGTACGGGCTCATTTGGGATC
genomic: GTCACATCATCTCCACCACCATCGGTGGGAAGAACGGCGAGCCGAAGCGGgtaaagctac ... ttaattgcagACCATCAGTTACATGGCAGAACGTGTCGTGGGTACGGGCTCATTTGGGATC
EST: gi|211127223|gb|FL138012.1|FL138012
EST:     GCCACATCATCTCCACCACCATCGGTGGGAAGAACGGCGAGCCGAAGCGG                         ACCATCAGTTACATGGCAGAACGTGTCGTGGGTACGGGCTCATTTGGGATC
genomic: GTCACATCATCTCCACCACCATCGGTGGGAAGAACGGCGAGCCGAAGCGGgtaaagctac ... ttaattgcagACCATCAGTTACATGGCAGAACGTGTCGTGGGTACGGGCTCATTTGGGATC
EST: gi|211126301|gb|FL138002.1|FL138002
EST:     GCCACATCATCTCCACCACCATCGGTGGGAAGAACGGCGAGCCGAAGCGG                         ACCATCAGTTACATGGCAGAACGTGTCGTGGGTACGGGCTCATTTGGGATC
genomic: GTCACATCATCTCCACCACCATCGGTGGGAAGAACGGCGAGCCGAAGCGGgtaaagctac ... ttaattgcagACCATCAGTTACATGGCAGAACGTGTCGTGGGTACGGGCTCATTTGGGATC

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 293

AAGAAGGAAGGGGAAGGGGGAGACACTGTTACGGGTCACATCATCTCCACCACCATCGGTGGGAAGAACGGCGAGCCGAAGCGGgtaaagctac ... ttaattgcagACCATCAGTTACATGGCAGAACGTGTCGTGGGTACGGGCTCATTTGGGATCGTCTTCCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 90

AAGAAGGAAGGGGAAGGGGGAGACACTGTTACGGGTCACATCATCTCCACCACCATCGGTGGGAAGAACGGCGAGCCGAAGCGGgtaaagctac ... ttaattgcagACCATCAGTTACATGGCAGAACGTGTCGTGGGTACGGGCTCATTTGGGATCGTCTTCCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 122

AAGAAGGAAGGGGAAGGGGGAGACACTGTTACGGGTCACATCATCTCCACCACCATCGGTGGGAAGAACGGCGAGCCGAAGCGGgtaaagctac ... ttaattgcagACCATCAGTTACATGGCAGAACGTGTCGTGGGTACGGGCTCATTTGGGATCGTCTTCCAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 103

AAGAAGGAAGGGGAAGGGGGAGACACTGTTACGGGTCACATCATCTCCACCACCATCGGTGGGAAGAACGGCGAGCCGAAGCGGgtaaagctac ... ttaattgcagACCATCAGTTACATGGCAGAACGTGTCGTGGGTACGGGCTCATTTGGGATCGTCTTCCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taccctcttcgtgtcctcagttgctcatttgttcttcttctggccttaattgcagACCATCAGTTACATGGCAGAACGTGTCGTGGGTACGGGCTCATTTGGGATCGTCTTCCAG
                                           ccttaat  putative branch site (score: 103)
                               ttcttcttctggcctt  CT-rich tract
                                             ttaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcgaattccttcctgctcagttgctctgacgcctgcctagtttgttaccctcttcgtgtcctcagttgctcatttgttcttcttctggccttaattgcagACCATCAGTTACATGGCAGAACGTGTCGTGGGTACGGGCTCATTTGGGATCGTCTTCCAG

- - - - - -cctgctc
- - - - - - - - - -gttgctc
- - - - - - - - - - - - - - - gcctgcc