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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CATATCTGCAGAGGAGTTGCCACCTATGGACATTGGTGGCAAGGCTGACCCATTTGTGGTCCTGTACTTAAAGAAGGGAGAAACCAAAAAGAAGACAAGGgtttttatctttcccaatctcagagttctgtagggccatatacttttttcaaggctctcatagttcagtattgttgcag

Basic information

species Zea mays
transcript GRMZM2G049347_T01
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G049347_T01 (Zea mays), 5'ss of exon 11
lower sequence: LOC_Os08g20544.1 (Oryza sativa), 5'ss of exon 10
CATATCTGCAGAGGAGTTGCCACCTATGGACATTGGTGGCAAGGCTGACCCATTTGTGGTCCTGTACTTAAAGAAGGGAGAAACCAAAAAGAAGACAAGGgtttttatctttcccaatctcagag-----ttctgtagggccatatactt-ttttcaaggctctcatagttcagtattgttgcag--------------------
 || || |||||||| |||||||| |||||  |    |||||||||||||||||||| ||||||||| | ||||||||||||||||||||||||||||||||| || ||| ||   ||||  |       |  | |  |    ||   || || |  ||||| |  |  |  | | || || ||                     
TATCTCAGCAGAGGACTTGCCACCAATGGATGTGATGGGCAAGGCTGACCCATTTGTAGTCCTGTACCTGAAGAAGGGAGAAACCAAAAAGAAGACAAGGgttattctctctctttatcttgggaccttttcttttgtgatggtagctttgttcttgaggctgttttgttatattgtttttccatactcatgattatgtttgcag
















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|94478713|gb|EB707671.1|EB707671
EST:     CATTTGTGGTCCTGTACTTAAAGAAGGGAGAAACCAAAAAGAAGACAAGG                         GTTGTGACAGACACGCTAAATCCAATATGGAACCAGACATTTGATTTCATG
genomic: CATTTGTGGTCCTGTACTTAAAGAAGGGAGAAACCAAAAAGAAGACAAGGgtttttatct ... attgttgcagGTTGTGACAGACACGCTAAATCCAATATGGAACCAGACATTTGATTTCATG
EST: gi|6403329|gb|AW171804.1|AW171804
EST:     CATTTGTGGTCCTGTACTTAAAGAAGGGAGAAACCAAAAAGAAGACGAGG                         GTTGTGACAGACACGTTAAATCCAATATGGAACCAGACATTTGATTTCATG
genomic: CATTTGTGGTCCTGTACTTAAAGAAGGGAGAAACCAAAAAGAAGACAAGGgtttttatct ... attgttgcagGTTGTGACAGACACGCTAAATCCAATATGGAACCAGACATTTGATTTCATG
EST: gi|78025577|gb|DV493964.1|DV493964
EST:     CATTTGTGGTCCTGTACTTAAAGAAGGGAGAAACCAAAAAGAAGACGAGG                         GTTGTGACAGACACGTTAAATCCAATATGGAACCAGACATTTGATTTCATG
genomic: CATTTGTGGTCCTGTACTTAAAGAAGGGAGAAACCAAAAAGAAGACAAGGgtttttatct ... attgttgcagGTTGTGACAGACACGCTAAATCCAATATGGAACCAGACATTTGATTTCATG
EST: gi|211290677|gb|FL187015.1|FL187015
EST:     CATTTGTGGTCCTGTACTTAAAGAAGGGAGAAACCAAAAAGAAGACGAGG                         GTTGTGACAGACACGTTAAATCCAATATGGAACCAGACATTTGATTTCATG
genomic: CATTTGTGGTCCTGTACTTAAAGAAGGGAGAAACCAAAAAGAAGACAAGGgtttttatct ... attgttgcagGTTGTGACAGACACGCTAAATCCAATATGGAACCAGACATTTGATTTCATG
EST: gi|149000006|gb|EE037097.2|EE037097
EST:     CATTTGTGGTCCTGTACTTAAAGAAGGGAGAAACCAAAAAGAAGACAAGG                         GTTGTGACAGACACGCTAAATCCAATATGGAACCAGACATTTGATTTCATG
genomic: CATTTGTGGTCCTGTACTTAAAGAAGGGAGAAACCAAAAAGAAGACAAGGgtttttatct ... attgttgcagGTTGTGACAGACACGCTAAATCCAATATGGAACCAGACATTTGATTTCATG
EST: gi|60398772|gb|DN231588.1|DN231588
EST:     CATTTGTGGTCCTGTACTTAAAGAAGGGAGAAACCAAAAAGAAGACGAGG                         GTTGTGACAGACACGTTAAATCCAATATGGAACCAGACATTTGATTTCATG
genomic: CATTTGTGGTCCTGTACTTAAAGAAGGGAGAAACCAAAAAGAAGACAAGGgtttttatct ... attgttgcagGTTGTGACAGACACGCTAAATCCAATATGGAACCAGACATTTGATTTCATG
EST: gi|148933621|gb|EC877504.2|EC877504
EST:     CATTTGTGGTCCTGTACTTAAAGAAGGGAGAAACCAAAAAGAAGACAAGG                         GTTGTGACAGACACGCTAAATCCAATATGGAACCAGACATTTGATTTCATG
genomic: CATTTGTGGTCCTGTACTTAAAGAAGGGAGAAACCAAAAAGAAGACAAGGgtttttatct ... attgttgcagGTTGTGACAGACACGCTAAATCCAATATGGAACCAGACATTTGATTTCATG
EST: gi|78027134|gb|DV495521.1|DV495521
EST:     CATTTGTGGTCCTGTACTTAAAGAAGGGAGAAACCAAAAAGAAGACGAGG                         GTTGTGACAGACACGTTAAATCCAATATGGAACCAGACATTTGATTTCATG
genomic: CATTTGTGGTCCTGTACTTAAAGAAGGGAGAAACCAAAAAGAAGACAAGGgtttttatct ... attgttgcagGTTGTGACAGACACGCTAAATCCAATATGGAACCAGACATTTGATTTCATG
EST: gi|211233131|gb|FL455332.1|FL455332
EST:     CATTTGTGGTCCTGTACTTAAAGAAGGGAGAAACCAAAAAGAAGACAAGG                         GTTGTGACAGACACGCTAAATCCAATATGGAACCAGACATTTGATTTCATG
genomic: CATTTGTGGTCCTGTACTTAAAGAAGGGAGAAACCAAAAAGAAGACAAGGgtttttatct ... attgttgcagGTTGTGACAGACACGCTAAATCCAATATGGAACCAGACATTTGATTTCATG
EST: gi|60354039|gb|DN221012.1|DN221012
EST:     CATTTGTGGTCCTGTACTTAAAGAAGGGAGAAACCAAAAAGAAGACAAGG                         GTTGTGACAGACACGCTAAATCCAATATGGAACCAGACATTTGATTTCATG
genomic: CATTTGTGGTCCTGTACTTAAAGAAGGGAGAAACCAAAAAGAAGACAAGGgtttttatct ... attgttgcagGTTGTGACAGACACGCTAAATCCAATATGGAACCAGACATTTGATTTCATG
EST: gi|211392050|gb|FL249966.1|FL249966
EST:     CATTTGTGGTCCTGTACTTAAAGAAGGGAGAAACCAAAAAGAAGACGAGG                         GTTGTGACAGACACGTTAAATCCAATATGG
genomic: CATTTGTGGTCCTGTACTTAAAGAAGGGAGAAACCAAAAAGAAGACAAGGgtttttatct ... attgttgcagGTTGTGACAGACACGCTAAATCCAATATGG
EST: gi|148971874|gb|EE022636.2|EE022636
EST:     CATTTGTGGTCCTGTACTTAAAGAAGGGAGAAACCAAAAAGAAGACAAGG                         GTTGTGACAGACACGCTAAATCCAATATGGAACCAGACATTTGATTTCATG
genomic: CATTTGTGGTCCTGTACTTAAAGAAGGGAGAAACCAAAAAGAAGACAAGGgtttttatct ... attgttgcagGTTGTGACAGACACGCTAAATCCAATATGGAACCAGACATTTGATTTCATG
EST: gi|18659840|gb|BM500549.1|BM500549
EST:     CATTTGTGGTCCTGTACTTAAAGAAGGGAGAAACCAAAAAGAAGACAAGG                         GTTGTGACAGACACGCTAAATCCAATATGGAACCAGACATTTGATTTCATG
genomic: CATTTGTGGTCCTGTACTTAAAGAAGGGAGAAACCAAAAAGAAGACAAGGgtttttatct ... attgttgcagGTTGTGACAGACACGCTAAATCCAATATGGAACCAGACATTTGATTTCATG
EST: gi|149060777|gb|EE157227.2|EE157227
EST:     CATTTGTGGTCCTGTACTTAAAGAAGGGAGAAACCAAAAAGAAGACAAGG                         GTTGTGACAGACACGCTAAATCCAATATGGAACCAGACATTTGATTTCATG
genomic: CATTTGTGGTCCTGTACTTAAAGAAGGGAGAAACCAAAAAGAAGACAAGGgtttttatct ... attgttgcagGTTGTGACAGACACGCTAAATCCAATATGGAACCAGACATTTGATTTCATG

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: 49 (upstream exon), 49 (downstream exon)
Score: 107

CATATCTGCAGAGGAGTTGCCACCTATGGACATTGGTGGCAAGGCTGACCCATTTGTGGTCCTGTACTTAAAGAAGGGAGAAACCAAAAAGAAGACAAGGgtttttatct ... attgttgcagGTTGTGACAGACACGCTAAATCCAATATGGAACCAGACATTTGATTTCATGGTAGAAGATGCACTGCATGATTTGCTCATGGTGGAAGTATGGGACCATG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 170

CATATCTGCAGAGGAGTTGCCACCTATGGACATTGGTGGCAAGGCTGACCCATTTGTGGTCCTGTACTTAAAGAAGGGAGAAACCAAAAAGAAGACAAGGgtttttatct ... attgttgcagGTTGTGACAGACACGCTAAATCCAATATGGAACCAGACATTTGATTTCATGGTAGAAGATGCACTGCATGATTTGCTCATGGTGGAAGTATGGGACCATG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 176

CATATCTGCAGAGGAGTTGCCACCTATGGACATTGGTGGCAAGGCTGACCCATTTGTGGTCCTGTACTTAAAGAAGGGAGAAACCAAAAAGAAGACAAGGgtttttatct ... attgttgcagGTTGTGACAGACACGCTAAATCCAATATGGAACCAGACATTTGATTTCATGGTAGAAGATGCACTGCATGATTTGCTCATGGTGGAAGTATGGGACCATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 172

CATATCTGCAGAGGAGTTGCCACCTATGGACATTGGTGGCAAGGCTGACCCATTTGTGGTCCTGTACTTAAAGAAGGGAGAAACCAAAAAGAAGACAAGGgtttttatct ... attgttgcagGTTGTGACAGACACGCTAAATCCAATATGGAACCAGACATTTGATTTCATGGTAGAAGATGCACTGCATGATTTGCTCATGGTGGAAGTATGGGACCATG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CATATCTGCAGAGGAGTTGCCACCTATGGACATTGGTGGCAAGGCTGACCCATTTGTGGTCCTGTACTTAAAGAAGGGAGAAACCAAAAAGAAGACAAGGgtttttatctttcccaatctcagagttctgtagggccatatacttttttcaaggctctcatagttcagtattgttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG