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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...actgaaaaggggccattgatgggtggtcgggaggagcttattactacctttgaacttttcttatcgactccatttgcatgttataatgttcgttctgtagGGAGGAGCTTGAGAAACAAAAAGCTCATGAACGTTATATGAAACTTCAGGAGCAAGGAAAAACAGAACAAGCACGGAAAGATTTGG

Basic information

species Zea mays
transcript GRMZM2G093535_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G093535_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os01g54920.1 (Oryza sativa), 3'ss of exon 5
actgaaaaggggccattgatgggt--ggtcgGGAGGAGCTTATTACTACCTTTGAACTTTTCTTATCGACTCCATTTGCATGTTATAATGTTCGTTCTGTAGGGAGGAGCTTGAGAAACAAAAAGCTCATGAACGTTATATGAAACTTCAGGAGCAAGGAAAAACAGAACAAGCACGGAAAGATTTGG
         |  || ||  |   |   |||         |  |||     |  | |   || | |   ||   | || ||  |    ||||| |   | ||| |||||| | |||||||| ||||||||||| || |||||||| |||||||||||||||||||||||||||||  ||||||||||||
---------gtaccttttcttatttcagtccatgcattgtgtttagctgttcaggaaaattttaaggtacaatactt-caaat----atgtttgaattatagAGAGGAGATCGAGAAACAGAAAGCTCATGAGCGCTATATGAAGCTTCAGGAGCAAGGAAAAACAGAACAAGCTAGGAAAGATTTGG

upper sequence: GRMZM2G093535_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA13G21760.1 (Glycine max), 3'ss of exon 5
actgaaaaggggccattgatgggtggtcgGGAGGAGCTTATTACTACCTTTGAACTTTTCTTATCGACTCCATTTGCATGTTATAATGTTCGTTC-----TGTAGGGAGGAGCTTGAGAAACAAAAAGCTCATGAACGTTATATGAAACTTCAGGAGCAAGGAAAAACAGAACAAGCACGGAAAGATTTGG
  |  ||  |   || |    | |       ||| |  | ||   |    ||||  ||    | |   |   ||   || || |||| | | | |     || ||||||||| | |||||||| | ||| ||||| || |||||||  || || ||||||||||||||||||||||||  ||| ||||| |
--tctaactgtttcagtttgagttctatattaggggaatgttgaaag---tgaaacttctgaaacatgttttttaatatattttaatttccatgcctgtgtgcagGGAGGAGATAGAGAAACAGAGAGCCCATGAGCGCTATATGAGGCTGCAAGAGCAAGGAAAAACAGAACAAGCAAAGAAGGATTTAG

upper sequence: GRMZM2G093535_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA10G07980.4 (Glycine max), 3'ss of exon 3
----actgaaaaggggccattgatgggtggtcgGGAGGAGCTTATTACTACCTTTGAACTTTTCTTATCGACTCCATTTGCATGTTATAATGTTCGTTCTGTAGGGAGGAGCTTGAGAAACAAAAAGCTCATGAACGTTATATGAAACTTCAGGAGCAAGGAAAAACAGAACAAGCACGGAAAGATTTGG
    |||      |   || |  |   |    || |       | |   || | ||||   |  || |  |    || |  |  || | |||   ||| || || |||||| | |||||||| | ||| ||||| || |||||||  || || ||||||||||||||||||||||||  ||| ||||| |
tctaactatttcagtttcagttctatattaggggaattttgaaagtgaaacttctgaaacatgttttttaat---atatttaaattttcatgcctgtt-tgcagAGAGGAGATAGAGAAACAGAGAGCCCATGAGCGCTATATGAGGCTGCAAGAGCAAGGAAAAACAGAACAAGCAAAGAAGGATTTAG

upper sequence: GRMZM2G093535_T01 (Zea mays), 3'ss of exon 1
lower sequence: EFJ15319 (Selaginella moellendorffii), 3'ss of exon 5
actgaaaaggggccattgatgggtggtcgGGAGGAGCTTATTACTACCTTTGAACTTTTCTTATCGACTCCATTTGCATGTTATAATGTTCGTTCTGTAGGGAGGAGCTTGAGAAACAAAAAGCTCATGAACGTTATATGAAACTTCAGGAGCAAGGAAAAACAGAACAAGCACGGAAAGATTTGG
                         ||   ||  | ||| |||  | || ||||        |   |||  | ||    |||     | ||| ||   ||||||||||||||||| |||| ||| |||||||| ||| | ||||| ||||||||||||||||| || ||||| || || ||| | |
-------------------------gtgaagacaaccttcttagaatctatgaaa-------aaaaactaaacttttgcgtt-----gatcgatc---agGGAGGAGCTTGAGAAGCAAAGAGCGCATGAACGCTATCTCAAACTCCAGGAGCAAGGAAAAACTGAGCAAGCTCGAAAGGATCTTG

upper sequence: GRMZM2G093535_T01 (Zea mays), 3'ss of exon 1
lower sequence: EFJ09898 (Selaginella moellendorffii), 3'ss of exon 5
actgaaaaggggccattgatgggtggtcgGGAGGAGCTTATTACTACCTTTGAACTTTTCTTATCGACTCCATTTGCATGTTATAATGTTCGTTCTGTAGGGAGGAGCTTGAGAAACAAAAAGCTCATGAACGTTATATGAAACTTCAGGAGCAAGGAAAAACAGAACAAGCACGGAAAGATTTGG
                         ||   ||| |  || |||  | |||||||        |  ||||   ||||| |       || ||| ||   ||||||||||||||||| |||| ||| |||||||| ||| | ||||| ||||||||||||||||| || ||||| || || ||| | |
-------------------------gtaaagagaacttttttagaatctttgaaaaa---aaactgact---tttgcgt-------tgatcgatc---agGGAGGAGCTTGAGAAGCAAAGAGCACATGAACGCTATCTCAAACTCCAGGAGCAAGGAAAAACTGAGCAAGCTCGAAAGGATCTTG

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|211192189|gb|FL404823.1|FL404823
EST:     CTTGGAAAGACAACTGAACTCTCAAGGCGTGAAAG                         GGAGGAGCTTGAGAAACAAAAAGCTCAGGAACGTTATATGAAACTTCAGGA
genomic: CTTGGAAAGACAACTGAACTCTCAAGGCGTGAAAGgtgcacttcc ... cgttctgtagGGAGGAGCTTGAGAAACAAAAAGCTCATGAACGTTATATGAAACTTCAGGA
EST: gi|211213892|gb|FL469120.1|FL469120
EST:     CTTGGAAAGACAACTGAACTCTCAAGGCGTGAAAG                         GGAGGAGCTTGAGAAACAAAAAGCTCATGAACGTTATATGAAACTTCAGGA
genomic: CTTGGAAAGACAACTGAACTCTCAAGGCGTGAAAGgtgcacttcc ... cgttctgtagGGAGGAGCTTGAGAAACAAAAAGCTCATGAACGTTATATGAAACTTCAGGA
EST: gi|32837519|gb|CD977197.1|CD977197
EST:     CTTGGAAAGACAACTGAACTCTCAAGGCGTTAAAG                         GGAGGAGCTTGAGAAACAAAAAGCTCATGAACGTTATATGGAACTTCAGGA
genomic: CTTGGAAAGACAACTGAACTCTCAAGGCGTGAAAGgtgcacttcc ... cgttctgtagGGAGGAGCTTGAGAAACAAAAAGCTCATGAACGTTATATGAAACTTCAGGA
EST: gi|211273115|gb|FL373254.1|FL373254
EST:     CTTGGAAAGACAACTGAACTCTCAAGGCGTGAAAG                         GGAGGAGCTTGAGAAACAAAAAGCTCAGGAACGTTATATGAAACTTCAGGA
genomic: CTTGGAAAGACAACTGAACTCTCAAGGCGTGAAAGgtgcacttcc ... cgttctgtagGGAGGAGCTTGAGAAACAAAAAGCTCATGAACGTTATATGAAACTTCAGGA
EST: gi|32937462|gb|CF042281.1|CF042281
EST:     CTTGGAAAGACAACTGAACTCTCAAGGCGTGAAAG                         GGAGGAGCTTGAGAAACAAAAAGCTCATGAACGTTATATGAAACTTCAGGA
genomic: CTTGGAAAGACAACTGAACTCTCAAGGCGTGAAAGgtgcacttcc ... cgttctgtagGGAGGAGCTTGAGAAACAAAAAGCTCATGAACGTTATATGAAACTTCAGGA
EST: gi|32944737|gb|CF049556.1|CF049556
EST:     CTTGGAAAGACAACTGAACTCTCAAGGCGTGAAAG                         GGAGGAGCTTGAGAAACAAAAAGCTCATGAACGTTATATGAAACTTCAGGA
genomic: CTTGGAAAGACAACTGAACTCTCAAGGCGTGAAAGgtgcacttcc ... cgttctgtagGGAGGAGCTTGAGAAACAAAAAGCTCATGAACGTTATATGAAACTTCAGGA

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: 38 (upstream exon), 49 (downstream exon)
Score: 361

AGCTTGGAAAGACAACTGAACTCTCAAGGCGTGAAAGgtgcacttcc ... cgttctgtagGGAGGAGCTTGAGAAACAAAAAGCTCATGAACGTTATATGAAACTTCAGGAGCAAGGAAAAACAGAACAAGCACGGAAAGATTTGG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 276

AGCTTGGAAAGACAACTGAACTCTCAAGGCGTGAAAGgtgcacttcc ... cgttctgtagGGAGGAGCTTGAGAAACAAAAAGCTCATGAACGTTATATGAAACTTCAGGAGCAAGGAAAAACAGAACAAGCACGGAAAGATTTGG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 299

AGCTTGGAAAGACAACTGAACTCTCAAGGCGTGAAAGgtgcacttcc ... cgttctgtagGGAGGAGCTTGAGAAACAAAAAGCTCATGAACGTTATATGAAACTTCAGGAGCAAGGAAAAACAGAACAAGCACGGAAAGATTTGG


Block sizes: 38 (upstream exon), 49 (downstream exon)
Score: 171

AGCTTGGAAAGACAACTGAACTCTCAAGGCGTGAAAGgtgcacttcc ... cgttctgtagGGAGGAGCTTGAGAAACAAAAAGCTCATGAACGTTATATGAAACTTCAGGAGCAAGGAAAAACAGAACAAGCACGGAAAGATTTGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acctttgaacttttcttatcgactccatttgcatgttataatgttcgttctgtagGGAGGAGCTTGAGAAACAAAAAGCTCATGAACGTTATATGAAACTTCAGGAGCAAGGAAAAACAGAACAAGCACGGAAAGATTTGG
                                           ttcgttct  CT-rich tract
                                atgttataat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
actgaaaaggggccattgatgggtggtcgggaggagcttattactacctttgaacttttcttatcgactccatttgcatgttataatgttcgttctgtagGGAGGAGCTTGAGAAACAAAAAGCTCATGAACGTTATATGAAACTTCAGGAGCAAGGAAAAACAGAACAAGCACGGAAAGATTTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - attgatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgcatgt