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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCAATAAGCTCTATGAAGCTAAGGTCTGGGAGAAGCCATGGGAGAACTTCAAGCAGCTGCAGGAATTCAAGCCTGTTGAAGAGGGTGCTAGCGCCTAAGgtagaattatgcatatttacgtactgtctgaaactatgtttatatttttacatccttagaccttactagcttagtgatgacacattgaaatcttgccata...

Basic information

species Zea mays
transcript GRMZM2G438551_T02
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G438551_T02 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os01g58890.4 (Oryza sativa), 5'ss of exon 1
GTCAATAAGCTCTATGAAGCTAAGGTCTGGGAGAAGCCATGGGAGAACTTCAAGCAGCTGCAGGAATTCAAGCCTGTTGAAGAGGGTGCTAGCGCCTAAGgtagaattatgcata-tttacgtactgtctgaaactatgtttatattt-ttacatccttagaccttactagcttagtgatgacacattgaaatcttgccata
| ||| ||||||||||||||||||||||||||||| ||||||  | |||||||| |||| ||||| ||||||||||| || |   |||| |  |||||||||  |   |||  |  ||||  |||   |  |||| |  |||  |  | || ||| | |   | |   ||   ||   || | | ||  | || |    |||
GCCAAGAAGCTCTATGAAGCTAAGGTCTGGGAGAAACCATGGATGGACTTCAAGGAGCTCCAGGAGTTCAAGCCTGTCGATGCCAGTGCAAATGCCTAAGgtctagacatgtttggtttagatacccgcc-aaacaaaattttcacctgttccatgcattaccatgtataatatatatat-atatatatatatatatatata

upper sequence: GRMZM2G438551_T02 (Zea mays), 5'ss of exon 2
lower sequence: PP1S66_209V6.2 (Physcomitrella patens), 5'ss of exon 2
GTCAATAAGCTCTATGAAGCTAAGGTCTGGGAGAAGCCATGGGAGAACTTCAAGCAGCTGCAGGAATTCAAGCCTGTTGAAGAGGGTG---------CTAGCGCCTAAGgta--gaattatgcatattt-acgtactgtctgaaactatgtttatatttttacatccttagaccttact----agcttagtgatgacacattg--aaa---tcttgccata
                     ||||| |||| ||||||||||||||| |||||| || || |||| ||||||||    ||  | |  |         ||   | ||  |||     |  | |   ||   | || |  ||     |||  |||  | |  ||  ||  |     | |||    ||||   | |  ||| |  |   ||   |||| || | 
---------------------AAGGTGTGGGTGAAGCCATGGGAGAATTTCAAGAAGTTGGAGGACTTCAAGCCCAAAGAGCAAGAAGTGTTTACTTCTGCTGACTTGGGTGTCAGACCAGgttgatacgatgtgccctcgctccctactttttgactcatatttctatgcgtttcactgtcgagctctttaacaacaaacagccgaacgttcttcccttc
















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|74035349|gb|DT535838.1|DT535838
EST:     CAAGCAGCTGCAGGAATTCAAGCCTGTTGAAGAGGGTGCTAGCGCCTAAG                         GTTGTGGCCACAGCCCCGGCTCTCGCAG
genomic: CAAGCAGCTGCAGGAATTCAAGCCTGTTGAAGAGGGTGCTAGCGCCTAAGgtagaattat ... gccctgacagGTTGTGGCCACAGCCC-GGCTCTCGCAG
EST: gi|211035017|gb|FL300564.1|FL300564
EST:     CAAGCAGCTGCAGGAATTCAAGCCTGTTGAAGAGGGTGCTAGCGCCTAAG                         GTTGTGGCCACAGCCCGGCTCTCGCAG
genomic: CAAGCAGCTGCAGGAATTCAAGCCTGTTGAAGAGGGTGCTAGCGCCTAAGgtagaattat ... gccctgacagGTTGTGGCCACAGCCCGGCTCTCGCAG
EST: gi|211037457|gb|FL300576.1|FL300576
EST:     CAAGCAGCTGCAGGAATTCAAGCCTGTTGAAGAGGGTGCTAGCGCCTAAG                         GTTGTKGCCACAGCCCGGCTCTCGCA
genomic: CAAGCAGCTGCAGGAATTCAAGCCTGTTGAAGAGGGTGCTAGCGCCTAAGgtagaattat ... gccctgacagGTTGTGGCCACAGCCCGGCTCTCGCA
EST: gi|71595831|gb|DR906582.1|DR906582
EST:     CAAGCAGCTGCAGGAATTCAAGCCTGTTGAAGAGGGTGCTAGCGCCTAAG                         GTTGTGGCCACAGCCCGGCTCTCGCAG
genomic: CAAGCAGCTGCAGGAATTCAAGCCTGTTGAAGAGGGTGCTAGCGCCTAAGgtagaattat ... gccctgacagGTTGTGGCCACAGCCCGGCTCTCGCAG
EST: gi|74237713|gb|DT645627.1|DT645627
EST:     CAAGCAGCTGCAGGAATTCAAGCCTGTTGAAGAGGGTGCTAGCGCCTAAG                         GTTGTGGCCACAGCCCGGCTCTCGCAG
genomic: CAAGCAGCTGCAGGAATTCAAGCCTGTTGAAGAGGGTGCTAGCGCCTAAGgtagaattat ... gccctgacagGTTGTGGCCACAGCCCGGCTCTCGCAG
EST: gi|211030097|gb|FL300540.1|FL300540
EST:     CAAGCAGCTGCAGGAATTCAAGCCTGTTGAAGAGGGTGCTAGCGCCTAAG                         GTTTTGGCCACAGCCCGGCTCTCGCAG
genomic: CAAGCAGCTGCAGGAATTCAAGCCTGTTGAAGAGGGTGCTAGCGCCTAAGgtagaattat ... gccctgacagGTTGTGGCCACAGCCCGGCTCTCGCAG
EST: gi|21621004|gb|BQ619010.1|BQ619010
EST:     CAAGCAGCTGCAGGAATTCAAGCCTGTTGAAGAGGGTGCTAGCGCCTAAG                         GTTGTGGCCACAGCCCGGCTCTCGCAG
genomic: CAAGCAGCTGCAGGAATTCAAGCCTGTTGAAGAGGGTGCTAGCGCCTAAGgtagaattat ... gccctgacagGTTGTGGCCACAGCCCGGCTCTCGCAG
EST: gi|71596322|gb|DR907073.1|DR907073
EST:     CAAGCAGCTGCAGGAATTCAAGCCTGTTGAAGAGGGTGCTAGCGCCTAAG                         GTTGTGGCCACAGCCCGGCTCTCGCAG
genomic: CAAGCAGCTGCAGGAATTCAAGCCTGTTGAAGAGGGTGCTAGCGCCTAAGgtagaattat ... gccctgacagGTTGTGGCCACAGCCCGGCTCTCGCAG

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

GTCAATAAGCTCTATGAAGCTAAGGTCTGGGAGAAGCCATGGGAGAACTTCAAGCAGCTGCAGGAATTCAAGCCTGTTGAAGAGGGTGCTAGCGCCTAAGgtagaattat ... gccctgacagGTTGTGGCCACAGCCCGGCTCTCGCAG


Block sizes: 38 (upstream exon), 49 (downstream exon)
Score: 89

GTCAATAAGCTCTATGAAGCTAAGGTCTGGGAGAAGCCATGGGAGAACTTCAAGCAGCTGCAGGAATTCAAGCCTGTTGAAGAGGGTGCTAGCGCCTAAGgtagaattat ... gccctgacagGTTGTGGCCACAGCCCGGCTCTCGCAG


Block sizes: 27 (upstream exon), 49 (downstream exon)
Score: 54

GTCAATAAGCTCTATGAAGCTAAGGTCTGGGAGAAGCCATGGGAGAACTTCAAGCAGCTGCAGGAATTCAAGCCTGTTGAAGAGGGTGCTAGCGCCTAAGgtagaattat ... gccctgacagGTTGTGGCCACAGCCCGGCTCTCGCAG


Block sizes: 27 (upstream exon), 49 (downstream exon)
Score: 41

GTCAATAAGCTCTATGAAGCTAAGGTCTGGGAGAAGCCATGGGAGAACTTCAAGCAGCTGCAGGAATTCAAGCCTGTTGAAGAGGGTGCTAGCGCCTAAGgtagaattat ... gccctgacagGTTGTGGCCACAGCCCGGCTCTCGCAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTCAATAAGCTCTATGAAGCTAAGGTCTGGGAGAAGCCATGGGAGAACTTCAAGCAGCTGCAGGAATTCAAGCCTGTTGAAGAGGGTGCTAGCGCCTAAGgtagaattatgcatatttacgtactgtctgaaactatgtttatatttttacatccttagaccttactagcttagtgatgacacattgaaatcttgccata

- - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG