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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttcgtgaatttttcccgagctataacatacgtactacttttgcgagactaagaaaatagaaaacgaaagatttgacacttttgatatcgcatttcccagGTCAGGGTGAGCGAGTCTTACGGGCTGAAATTTCCTCGGGAGTTTGCTCTTCTCATGAAGCAGCTGCTGTATTTTGATCGCTACACAAGACTGCTGGCTC

Basic information

species Zea mays
transcript GRMZM2G031780_T02
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G031780_T02 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os07g12530.1 (Oryza sativa), 3'ss of exon 10
--------------------------------------------------------------------tttcgtgaatttttcccg--agctataacatac------gtactacttttgcgagactaagaaaatagaaaacgaaagat----ttgacacttttgatatc--gcatttcccagGTCAGGGTGAGCGAGTCTTACGGGCTGAAATTTCCTCGGGAGTTTGCTCTTCTCATGAAGCAGCTGCTGTATTTTGATCGCTACACAAGACTGCTGGCTC
                                                                        ||   || ||   |  |  | |  | | |      ||| |  |||  ||| |  |   | ||     |  ||| |      ||||| || || |     || | | |||||| ||||| |||||||| || ||  ||||||||||||| || || |||||||| ||||||||||| |||||||||||||||||||||||| || ||||||
gtgagctactttcttttctctctcggttagaacaaggtagagagaacttctaccttatacattcgtatcactgtatgttcttgttggtaaatgttgcctgccagcgtgtattgttttcacgaaagaagagagatgagggaaaaaaaacaatgctgacaattctgttgctctgcgtcttccagGTGAGGGTCAGCGAGTCGTATGGATTGAAATTTCCTCGCGAATTCGCTCTTCTGATGAAGCAGCTTCTGTATTTTGATCGCTACACAAGATTGTTGGCTC

upper sequence: GRMZM2G031780_T02 (Zea mays), 3'ss of exon 8
lower sequence: Vv13s0067g03210.t01 (Vitis vinifera), 3'ss of exon 10
tttcgtgaatttttcccgagctataacatacgtactacttttgcgagactaagaaaatagaaaacgaaagatttgacacttttgatatcgcatttcc----cagGTCAGGGTGAGCGAGTCTTACGGGCTGAAATTTCCTCGGGAGTTTGCTCTTCTCATGAAGCAGCTGCTGTATTTTGATCGCTACACAAGACTGCTGGCTC
   |      |  || | |  | |  |  |  |  ||  | |    || |    |  | ||     ||| |||    | | |  ||     |||||     |||||  |||| || || || || || |||| |||||||||||||||||| ||||||||||| ||||| ||||||||||| || || ||||| ||| | ||||
--cccaagggtgatcacaaatttt--ctcagtttttaagtctttttgattgctcattttgaggggcaaacattcctgattatgcattctctatttcttctacagGTTCGGGTTAGTGAATCCTATGGACTGAGATTTCCTCGGGAGTTTGCACTTCTCATGAAACAGCTTCTGTATTTTGACCGATATACAAGGCTGTTAGCTC
















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|67025107|gb|CO453856.1|CO453856
EST:     CTAATGTTGTCCTTGATGAGAGGCAGATGAATGCTCTATTTCTTGATCTG                         GTCAGGGTGAGCGAGTCTTACGGGCTGAAGTTTCCTCGGGAGTTTGCTCTT
genomic: CTAATGTTGTCCTTGATGAGAGGCAGATGAATGCTCTTTTTCTTGATCTGgtgagttact ... catttcccagGTCAGGGTGAGCGAGTCTTACGGGCTGAAATTTCCTCGGGAGTTTGCTCTT
EST: gi|211023728|gb|FL449217.1|FL449217
EST:     CTAATGTTGTCCTTGATGAGAGGCAGATGAATGCTCTATTTCTTGATCTG                         GTCAGGGTGAGCGAGTCTTACGGGCTGAAGTTTCCTCGGGAGTTTGCTCTT
genomic: CTAATGTTGTCCTTGATGAGAGGCAGATGAATGCTCTTTTTCTTGATCTGgtgagttact ... catttcccagGTCAGGGTGAGCGAGTCTTACGGGCTGAAATTTCCTCGGGAGTTTGCTCTT
EST: gi|211125159|gb|FL454370.1|FL454370
EST:     CTAATGTTGTCCTTGATGAGAGGCAGATGAATGCTCTTTTTCTTGATCTG                         GTCAGGGTGAGCGAGTCTTACGGGCTGAAATTTCCTCGGGAGTTTGCTCTT
genomic: CTAATGTTGTCCTTGATGAGAGGCAGATGAATGCTCTTTTTCTTGATCTGgtgagttact ... catttcccagGTCAGGGTGAGCGAGTCTTACGGGCTGAAATTTCCTCGGGAGTTTGCTCTT
EST: gi|78089905|gb|DV518279.1|DV518279
EST:     CTAATGTTGTCCTTGATGAGAGGCAGATGAATGCTCTTTTTCTTGATCTG                         GTCAGGGTGAGCGAGTCTTACGGGCTGAAATTTCCTCGGGAGTTTGCTCTT
genomic: CTAATGTTGTCCTTGATGAGAGGCAGATGAATGCTCTTTTTCTTGATCTGgtgagttact ... catttcccagGTCAGGGTGAGCGAGTCTTACGGGCTGAAATTTCCTCGGGAGTTTGCTCTT
EST: gi|94475889|gb|EB704847.1|EB704847
EST:     TTAATGTTGTCCTTGATGAGAGGCAGATGAATGCTCTTTTTCTTGATCTG                         GTCAGGGTGAGCGAGTCTTACGGGCTGAAATTTCCTCGGGAGTTTGCTCTT
genomic: CTAATGTTGTCCTTGATGAGAGGCAGATGAATGCTCTTTTTCTTGATCTGgtgagttact ... catttcccagGTCAGGGTGAGCGAGTCTTACGGGCTGAAATTTCCTCGGGAGTTTGCTCTT
EST: gi|24934308|gb|CA452526.1|CA452526
EST:     CTAATGTTGTCCTTGATGAGAGGCAGATGAATGCTCTTTTTCTTGATCTG                         GTCAGGGTGAGCGAGTCTTACGGGCTGAAATTTCCTCGGGAGTTTGCTCTT
genomic: CTAATGTTGTCCTTGATGAGAGGCAGATGAATGCTCTTTTTCTTGATCTGgtgagttact ... catttcccagGTCAGGGTGAGCGAGTCTTACGGGCTGAAATTTCCTCGGGAGTTTGCTCTT

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: 44 (upstream exon), 49 (downstream exon)
Score: 127

TGAAATCATAGTGGCAACAGCAAGGACCCCTGATGCTACAGCAGTATCTGCTAATGTTGTCCTTGATGAGAGGCAGATGAATGCTCTTTTTCTTGATCTGgtgagttact ... catttcccagGTCAGGGTGAGCGAGTCTTACGGGCTGAAATTTCCTCGGGAGTTTGCTCTTCTCATGAAGCAGCTGCTGTATTTTGATCGCTACACAAGACTGCTGGCTC


Block sizes: 43 (upstream exon), 49 (downstream exon)
Score: 57

TGAAATCATAGTGGCAACAGCAAGGACCCCTGATGCTACAGCAGTATCTGCTAATGTTGTCCTTGATGAGAGGCAGATGAATGCTCTTTTTCTTGATCTGgtgagttact ... catttcccagGTCAGGGTGAGCGAGTCTTACGGGCTGAAATTTCCTCGGGAGTTTGCTCTTCTCATGAAGCAGCTGCTGTATTTTGATCGCTACACAAGACTGCTGGCTC


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 45

TGAAATCATAGTGGCAACAGCAAGGACCCCTGATGCTACAGCAGTATCTGCTAATGTTGTCCTTGATGAGAGGCAGATGAATGCTCTTTTTCTTGATCTGgtgagttact ... catttcccagGTCAGGGTGAGCGAGTCTTACGGGCTGAAATTTCCTCGGGAGTTTGCTCTTCTCATGAAGCAGCTGCTGTATTTTGATCGCTACACAAGACTGCTGGCTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 72

TGAAATCATAGTGGCAACAGCAAGGACCCCTGATGCTACAGCAGTATCTGCTAATGTTGTCCTTGATGAGAGGCAGATGAATGCTCTTTTTCTTGATCTGgtgagttact ... catttcccagGTCAGGGTGAGCGAGTCTTACGGGCTGAAATTTCCTCGGGAGTTTGCTCTTCTCATGAAGCAGCTGCTGTATTTTGATCGCTACACAAGACTGCTGGCTC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agactaagaaaatagaaaacgaaagatttgacacttttgatatcgcatttcccagGTCAGGGTGAGCGAGTCTTACGGGCTGAAATTTCCTCGGGAGTTTGCTCTTCTCATGAAGCAGCTGCTGTATTTTGATCGCTACACAAGACTGCTGGCTC
                                  ttttgat  putative branch site (score: 72)
                                             catttccc  putative PPT
     aagaaaatagaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttcgtgaatttttcccgagctataacatacgtactacttttgcgagactaagaaaatagaaaacgaaagatttgacacttttgatatcgcatttcccagGTCAGGGTGAGCGAGTCTTACGGGCTGAAATTTCCTCGGGAGTTTGCTCTTCTCATGAAGCAGCTGCTGTATTTTGATCGCTACACAAGACTGCTGGCTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - -cttttgc
- - - - - - - - - - - - - - - - - - - - - - - - - aagaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaacgaa