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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CATCCTCACCAGCGCGGTCCCAAAGATGAAACCGGGGTTTGATCCTAGCAAAGGGGGGCGCCCTGAGTTTTACTTTGAAGAAGGGAGTTATCCTGAGCAGgtgcctgaaattattcgatatacagtgctcttacagtatttatctaaaatacgtggtgctcttacggtagctgtatgtgtcaattcccaaatttgtttggaattgatgttctatgttgtttgtctctgtttcaag

Basic information

species Zea mays
transcript GRMZM2G047219_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G047219_T03 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os05g01970.1 (Oryza sativa), 5'ss of exon 2
CATCCTCACCAGCGCGGTCCCAAAGATGAAACCGGGGTTTGATCCTAGCAAAGGGGGGCGCCCTGAGTTTTACTTTGAAGAAGGGAGTTATCCTGAGCAGgtgcctgaaattattcgatatacagtgctcttacagtatttatctaaaatacgtggtgctcttacggtagctgtatgtgtcaattcccaaatttgtttggaattgatgttctatgttgtttgtctctgtttcaag
|||||||||||| ||||| || || ||||| || ||||||||||| ||||| ||||| ||||| ||||| |||||||| || ||   ||||||||||||||||  | ||  ||||   | |      | || ||| | | |                                   || |||| |      ||  |||| |||||||||| | || | ||||   || ||| |||
CATCCTCACCAGTGCGGTTCCGAAAATGAAGCCTGGGTTTGATCCCAGCAAGGGGGGACGCCCAGAGTTCTACTTTGAGGATGGCTCTTATCCTGAGCAGgtgattaaatgtattttgtgt------cactcacattttct-----------------------------------gtatcaacttgtgccttcatttgaaattgatgttttctgctatttgctactctttgaag

upper sequence: GRMZM2G047219_T03 (Zea mays), 5'ss of exon 2
lower sequence: EFJ09978 (Selaginella moellendorffii), 5'ss of exon 2
CATCCTCACCAGCGCGGTCCCAAAGATGAAACCGGGGTTTGATCCTAGCAAAGGGGGGCGCCCTGAGTTTTACTTTGAAGAAGGGAGTTATCCTGAGCAGgtgcctgaaattattcgatatacagtgctcttacagtatttatctaaaatacgtggtgctcttacggtagctgtatgtgtcaattcccaaatttgtttggaattgatgttctatgttgtttgtctctgtttcaag
||| || |||||||| || || ||||| || || ||||||||||| |||||||| || ||||| |||||||||||||| || ||   || ||||||||||||      || | || | ||        | || || |  |    |||| |  |  |    ||  | |                                                                    
CATTCTTACCAGCGCCGTGCCCAAGATAAAGCCCGGGTTTGATCCGAGCAAAGGTGGTCGCCCCGAGTTTTACTTTGAGGATGGTGCTTTTCCTGAGCAGgt------aactctttgttacttttgcttttttcactgctggagtaaactgtgatgcttgctctcag--------------------------------------------------------------------

upper sequence: GRMZM2G047219_T03 (Zea mays), 5'ss of exon 2
lower sequence: EFJ23715 (Selaginella moellendorffii), 5'ss of exon 2
CATCCTCACCAGCGCGGTCCCAAAGATGAAACCGGGGTTTGATCCTAGCAAAGGGGGGCGCCCTGAGTTTTACTTTGAAGAAGGGAGTTATCCTGAGCAGgtgcctgaaattattcgatatacagtgctcttacagtatttatctaaaatacgtggtgctcttacggtagctgtatgtgtcaattcccaaatttgtttggaattgatgttctatgttgtttgtctctgtttcaag
 || || |||||||| || || ||||| || || ||||||||||| |||||||| || ||||| |||||||||||||| || ||   || ||||||||||||      || | || | ||     |  | || || |  |    |||| |  |  |    ||  | |                                                                    
TATTCTTACCAGCGCCGTGCCCAAGATAAAGCCCGGGTTTGATCCGAGCAAAGGTGGTCGCCCCGAGTTTTACTTTGAGGATGGTGCTTTTCCTGAGCAGgt------aactctttgttactttttcttttttcactgctggagtaaactctgatgcttgctctcag--------------------------------------------------------------------

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|50331999|gb|CO527125.1|CO527125
EST:     AAGGGGGGCGCCCTGAGTTTTACTTTGAAGAAGGGAGTTATCCTGAGCAG                         GTGGATTGGATTGGCCAAAAGAATCAAATTGATGCTG
genomic: AAGGGGGGCGCCCTGAGTTTTACTTTGAAGAAGGGAGTTATCCTGAGCAGgtgcctgaaa ... ctgtttcaagGTGGATTGGATTGGCCAAAAGAATCAAATTGATGCTG
EST: gi|211142589|gb|FL359509.1|FL359509
EST:     AAGGGGGGCGCCCTGAGTTTTACTTTGAAGAAGGGAGTTATCCTGAGCAG                         GTGGATTGGATTGGCCAAAAGAATCAAATTGATGCTG
genomic: AAGGGGGGCGCCCTGAGTTTTACTTTGAAGAAGGGAGTTATCCTGAGCAGgtgcctgaaa ... ctgtttcaagGTGGATTGGATTGGCCAAAAGAATCAAATTGATGCTG
EST: gi|211529297|gb|FL356731.1|FL356731
EST:     AAGGGGGGCGCCCTGAGTTTTACTTTGAAGAAGGGAGTTATCCTGAGCAG                         GTGGATTGGATTGGCCAAAAGAATCAAATTGATGCTG
genomic: AAGGGGGGCGCCCTGAGTTTTACTTTGAAGAAGGGAGTTATCCTGAGCAGgtgcctgaaa ... ctgtttcaagGTGGATTGGATTGGCCAAAAGAATCAAATTGATGCTG
EST: gi|17931616|gb|BM268576.1|BM268576
EST:     AAGGGGGGCGCCCTGAGTTTTACTTTGAAGAAGGGAGTTATCCTGAGCAG                         GTGGATTGGATTGGCCAAAAGAATCAAATTGATGCTG
genomic: AAGGGGGGCGCCCTGAGTTTTACTTTGAAGAAGGGAGTTATCCTGAGCAGgtgcctgaaa ... ctgtttcaagGTGGATTGGATTGGCCAAAAGAATCAAATTGATGCTG
EST: gi|149015400|gb|EE045246.2|EE045246
EST:     AAGGGGGGCGCCCTGAGTTTTACTTTGAAGAAGGGAGTTATCCTGAGCAG                         GTGGATTGGATTGGCCAAAAGAATCAAATTGATGCTG
genomic: AAGGGGGGCGCCCTGAGTTTTACTTTGAAGAAGGGAGTTATCCTGAGCAGgtgcctgaaa ... ctgtttcaagGTGGATTGGATTGGCCAAAAGAATCAAATTGATGCTG
EST: gi|211267296|gb|FL319984.1|FL319984
EST:     AGGGGGGCGCCCTGAGTTTTACTTTGAAGAAGGGAGTTATCCTGNAGCAG                         -TGGATTGGATTGGCCAAAAGAATCAA-TTGATGCTG
genomic: AGGGGGGCGCCCTGAGTTTTACTTTGAAGAAGGGAGTTATCCTG-AGCAGgtgcctgaaa ... ctgtttcaagGTGGATTGGATTGGCCAAAAGAATCAAATTGATGCTG
EST: gi|148966373|gb|EE017367.2|EE017367
EST:     AAGGGGGGCGCCCTGAGTTTTACTTTGAAGAAGGGAGTTATCCTTAGCAG                         GTGGATTGGATTGGCCAAAAGAATCAAATTGATGCTG
genomic: AAGGGGGGCGCCCTGAGTTTTACTTTGAAGAAGGGAGTTATCCTGAGCAGgtgcctgaaa ... ctgtttcaagGTGGATTGGATTGGCCAAAAGAATCAAATTGATGCTG
EST: gi|12045929|gb|BF728159.1|BF728159
EST:     AAGGGGGGCGCCCTGAGTTTTACTTTGAAGAAGGGAGTTATCCTGAGCAG                         GTGGATTGGATTGGCCAAAAGAATCAAATTGATGCTG
genomic: AAGGGGGGCGCCCTGAGTTTTACTTTGAAGAAGGGAGTTATCCTGAGCAGgtgcctgaaa ... ctgtttcaagGTGGATTGGATTGGCCAAAAGAATCAAATTGATGCTG
EST: gi|211072521|gb|FL326767.1|FL326767
EST:     AAGGGGGGCGCCCTGAGTTTTACTTTGAAGAAGGGAGTTATCCTGAGCAG                         GTGGATTGGATTGGCCAAAAGAATCAAATTGATGCTG
genomic: AAGGGGGGCGCCCTGAGTTTTACTTTGAAGAAGGGAGTTATCCTGAGCAGgtgcctgaaa ... ctgtttcaagGTGGATTGGATTGGCCAAAAGAATCAAATTGATGCTG
EST: gi|148996959|gb|EE035773.2|EE035773
EST:     AAGGGGGGCGCCCTGAGTTTTACTTTGAAGAAGGGAGTTATCCTGAGCAG                         GTGGATTGGATTGGCCAAAAGAATCAAATTGATGCTG
genomic: AAGGGGGGCGCCCTGAGTTTTACTTTGAAGAAGGGAGTTATCCTGAGCAGgtgcctgaaa ... ctgtttcaagGTGGATTGGATTGGCCAAAAGAATCAAATTGATGCTG
EST: gi|74243388|gb|DT651302.1|DT651302
EST:     AAGGGGGGCGCCCTGAGTTTTACTTTGAAGAAGGGAGTTATCCTGAGCAG                         GTGGATTGGATTGGCCAAAAGAATCAAATTGATGCTG
genomic: AAGGGGGGCGCCCTGAGTTTTACTTTGAAGAAGGGAGTTATCCTGAGCAGgtgcctgaaa ... ctgtttcaagGTGGATTGGATTGGCCAAAAGAATCAAATTGATGCTG
EST: gi|89251955|gb|DY623741.1|DY623741
EST:     AAGGGGGGCGCCCTGAGTTTTACTTTGAAGAAGGGAGTTATCCTGAGCAG                         GTGGATTGGATTGGCCAAAAGAATCAAATTGATGCTG
genomic: AAGGGGGGCGCCCTGAGTTTTACTTTGAAGAAGGGAGTTATCCTGAGCAGgtgcctgaaa ... ctgtttcaagGTGGATTGGATTGGCCAAAAGAATCAAATTGATGCTG
EST: gi|76293497|gb|DV033065.1|DV033065
EST:     AAGGGGGGCGCCCTGAGTTTTACTTTGAAGAAGGGAGTTATCCTGAGCAG                         GTGGATTGGATTGGCCAAAAGAATCAAATTGATGCTG
genomic: AAGGGGGGCGCCCTGAGTTTTACTTTGAAGAAGGGAGTTATCCTGAGCAGgtgcctgaaa ... ctgtttcaagGTGGATTGGATTGGCCAAAAGAATCAAATTGATGCTG
EST: gi|78180658|gb|DV550986.1|DV550986
EST:     AAGGGGGGCGCCCTGAGTTTTACTTTGAAGAAGGGAGTTATCCTGAGCAG                         GTGGATTGGATTGGCCAAAAGAATCAAATTGATGCTG
genomic: AAGGGGGGCGCCCTGAGTTTTACTTTGAAGAAGGGAGTTATCCTGAGCAGgtgcctgaaa ... ctgtttcaagGTGGATTGGATTGGCCAAAAGAATCAAATTGATGCTG
EST: gi|32848760|gb|CD988441.1|CD988441
EST:     AAGGGGGGCGCCCTGAGTTTTACTTTGAAGAAGGGAGTTATCCTGAGCAG                         GTGGATTGGATTGGCCAAAAGAATCAAATTGATGCTG
genomic: AAGGGGGGCGCCCTGAGTTTTACTTTGAAGAAGGGAGTTATCCTGAGCAGgtgcctgaaa ... ctgtttcaagGTGGATTGGATTGGCCAAAAGAATCAAATTGATGCTG
EST: gi|211394348|gb|FL351051.1|FL351051
EST:     AAGGGGGGCGCCCTGAGTTTTACTTTGAAGAAGGGAGTTATCCTGAGCAG                         GTGGATTGGATTGGCCAAAAGAATCAAATTGATGCTG
genomic: AAGGGGGGCGCCCTGAGTTTTACTTTGAAGAAGGGAGTTATCCTGAGCAGgtgcctgaaa ... ctgtttcaagGTGGATTGGATTGGCCAAAAGAATCAAATTGATGCTG
EST: gi|148966374|gb|EE017368.2|EE017368
EST:     AAGGGGGGCGCCCTGAGTTTTACTTTGAAGAAGGGAGTTATCCTTACCAG                         GTGGATTGGATTGGCCAAAAGAATCAAATTGATGCTG
genomic: AAGGGGGGCGCCCTGAGTTTTACTTTGAAGAAGGGAGTTATCCTGAGCAGgtgcctgaaa ... ctgtttcaagGTGGATTGGATTGGCCAAAAGAATCAAATTGATGCTG
EST: gi|89762676|gb|DY690164.1|DY690164
EST:     AAGGGGGGCGCCCTGAGTTTTACTTTGAAGAAGGGAGTTATCCTGAGCAG                         GTGGATTGGATTGGCCAAAAGAATCAAATTGATGCTG
genomic: AAGGGGGGCGCCCTGAGTTTTACTTTGAAGAAGGGAGTTATCCTGAGCAGgtgcctgaaa ... ctgtttcaagGTGGATTGGATTGGCCAAAAGAATCAAATTGATGCTG
EST: gi|6742502|gb|AW313317.1|AW313317
EST:     AAGGGGGGCGCCCTGAGTTTTACTTTGAAGAAGGGAGTTATCCTGAGCAG                         GTGGATTGGATTGGCCAAAAGAATCAAATTGATGCTG
genomic: AAGGGGGGCGCCCTGAGTTTTACTTTGAAGAAGGGAGTTATCCTGAGCAGgtgcctgaaa ... ctgtttcaagGTGGATTGGATTGGCCAAAAGAATCAAATTGATGCTG
EST: gi|71774203|gb|DR972081.1|DR972081
EST:     AAGGGGGGCGCCCTGAGTTTTACTTTGAAGAAGGGAGTTATCCTGAGCAG                         GTGGATTGGATTGGCCAAAAGAATCAAATTGATGCTG
genomic: AAGGGGGGCGCCCTGAGTTTTACTTTGAAGAAGGGAGTTATCCTGAGCAGgtgcctgaaa ... ctgtttcaagGTGGATTGGATTGGCCAAAAGAATCAAATTGATGCTG
EST: gi|148935909|gb|EC879959.2|EC879959
EST:     AAGGGGGGCGCCCTGAGTTTTACTTTGAAGAAGGGAGTTATCCTGAGCAG                         GTGGATTGGATTGGCCAAAAGAATCAAATTGATGCTGC
genomic: AAGGGGGGCGCCCTGAGTTTTACTTTGAAGAAGGGAGTTATCCTGAGCAGgtgcctgaaa ... ctgtttcaagGTGGATTGGATTGGCCAAAAGAATCAAATTGATGCTGC
EST: gi|91055640|gb|EB166058.1|EB166058
EST:     AAGGGGGGCGCCCTGAGTTTTACTTTGAAGAAGGGAGTTATCCTGAGCAG                         GTGGATTGGATTGGCCAAAAGAATCAAATTGATGCTG
genomic: AAGGGGGGCGCCCTGAGTTTTACTTTGAAGAAGGGAGTTATCCTGAGCAGgtgcctgaaa ... ctgtttcaagGTGGATTGGATTGGCCAAAAGAATCAAATTGATGCTG

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: 121

CATCCTCACCAGCGCGGTCCCAAAGATGAAACCGGGGTTTGATCCTAGCAAAGGGGGGCGCCCTGAGTTTTACTTTGAAGAAGGGAGTTATCCTGAGCAGgtgcctgaaa ... ctgtttcaagGTGGATTGGATTGGCCAAAAGAATCAAATTGATGCTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 454

CATCCTCACCAGCGCGGTCCCAAAGATGAAACCGGGGTTTGATCCTAGCAAAGGGGGGCGCCCTGAGTTTTACTTTGAAGAAGGGAGTTATCCTGAGCAGgtgcctgaaa ... ctgtttcaagGTGGATTGGATTGGCCAAAAGAATCAAATTGATGCTG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 30

CATCCTCACCAGCGCGGTCCCAAAGATGAAACCGGGGTTTGATCCTAGCAAAGGGGGGCGCCCTGAGTTTTACTTTGAAGAAGGGAGTTATCCTGAGCAGgtgcctgaaa ... ctgtttcaagGTGGATTGGATTGGCCAAAAGAATCAAATTGATGCTG


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 242

CATCCTCACCAGCGCGGTCCCAAAGATGAAACCGGGGTTTGATCCTAGCAAAGGGGGGCGCCCTGAGTTTTACTTTGAAGAAGGGAGTTATCCTGAGCAGgtgcctgaaa ... ctgtttcaagGTGGATTGGATTGGCCAAAAGAATCAAATTGATGCTG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CATCCTCACCAGCGCGGTCCCAAAGATGAAACCGGGGTTTGATCCTAGCAAAGGGGGGCGCCCTGAGTTTTACTTTGAAGAAGGGAGTTATCCTGAGCAGgtgcctgaaattattcgatatacagtgctcttacagtatttatctaaaatacgtggtgctcttacggtagctgtatgtgtcaattcccaaatttgtttggaattgatgttctatgttgtttgtctctgtttcaag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG