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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTCCTGTCCTGGAGACACCTGATGGTCCTGTCTTTGAGAGCAATGCAATAGCAAGATATGgtaatttaaatgttgcaacaattggtttgtttagtcttttgtttgcatttatttgattgagcaccgaattctgtcatctccctgaag

Basic information

species Zea mays
transcript GRMZM2G029559_T02
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G029559_T02 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os02g12794.3 (Oryza sativa), 5'ss of exon 3
---------------------------------------GTTCCTGTCCTGGAGACACCTGATGGTCCTGTCTTTGAGAGCAATGCAATAGCAAGATATGgtaatttaaatgttgcaac-aattgg--tttgtttagtcttttgtttgcatttatttgattgagcaccgaatt-ctgtcatctccctgaag
                                        ||||||| || ||||| |||||||||||||| |||||||||||||| || ||| |||||||||| | | |  | ||||  ||||||  ||   ||| ||||||  |  |||  || ||||| ||  |  | |  ||||||| | |||||||
CATTCGCACAGAATCTTATTTGGACACGTTTTCTTTCAGATTCCTGTTCTAGAGACTCCTGATGGTCCTGTTTTTGAGAGCAATGCGATTGCACGATATGgtaagtgatacatagcaaggaattggagttctcttaatctttttctatcat--atctgatttagttctaagtcactgtcattttcctgaag

upper sequence: GRMZM2G029559_T02 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os02g12800.3 (Oryza sativa), 5'ss of exon 1
---------------------------------------GTTCCTGTCCTGGAGACACCTGATGGTCCTGTCTTTGAGAGCAATGCAATAGCAAGATATGgtaatttaaatgttgcaacaattg-gtttgtttagtcttttgtttgcatttatttgattgagcaccgaattc-tgtcatctccctgaag
                                       || ||| | || ||||| |||||||||||||| ||||| |||||||| || ||| |||||||||| | | |  | ||||  |||  |||  |||| || |||  |  |  ||  |||||| ||  |  | ||| | |||| | |||||||
CATTTGCACAGAATCTGATTTGGACACGTTTCCTTTCAGGTCCCTATTCTAGAGACTCCTGATGGTCCTGTTTTTGAAAGCAATGCGATTGCACGATATGgtaagtgatacatagcaaggattccgttcttttaatccttttctctctattgcttgatttagttctaagttcctctcattttcctgaag

upper sequence: GRMZM2G029559_T02 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os02g12800.2 (Oryza sativa), 5'ss of exon 3
GTTCCTGTCCTGGAGACACCTGATGGTCCTGTCTTTGAGAGCAATGCAATAGCAAGATATGgtaatttaaatgttgcaacaattg-gtttgtttagtcttttgtttgcatttatttgattgagcaccgaattc-tgtcatctccctgaag
|| ||| | || ||||| |||||||||||||| ||||| |||||||| || ||| |||||||||| | | |  | ||||  |||  |||  |||| || |||  |  |  ||  |||||| ||  |  | ||| | |||| | |||||||
GTCCCTATTCTAGAGACTCCTGATGGTCCTGTTTTTGAAAGCAATGCGATTGCACGATATGgtaagtgatacatagcaaggattccgttcttttaatccttttctctctattgcttgatttagttctaagttcctctcattttcctgaag

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|211045449|gb|FL056742.1|FL056742
EST:     GGAGACACCTGATGGTCCTGTCTTTGAGAGCAATGCAATAGCAAGATATG                         TTACTCGCTTGAAGGCTAACAACCCACTTTACGGATCTTCACTGATTGATT
genomic: GGAGACACCTGATGGTCCTGTCTTTGAGAGCAATGCAATAGCAAGATATGgtaatttaaa ... ctccctgaagTTACTCGCTTGAAGGCTAACAACCCACTTTACGGATCTTCACTGATTGATT
EST: gi|17921484|gb|BM259135.1|BM259135
EST:     GGAGACACCTGATGGTCCTGTCTTTGAGAGCAATGCAATAGCAAGATATG                         TTACTCGCTTGAAGGCTAACAACCCACTTTACGGATCTTCACTGATTGATT
genomic: GGAGACACCTGATGGTCCTGTCTTTGAGAGCAATGCAATAGCAAGATATGgtaatttaaa ... ctccctgaagTTACTCGCTTGAAGGCTAACAACCCACTTTACGGATCTTCACTGATTGATT
EST: gi|15426721|gb|BI542543.1|BI542543
EST:     GGAGACACCTGATGGTCCTGTCTTTGAGAGCAATGCAATAGCAAGATATG                         TTACTCGCTTGAAGGCTAACAACCCACTTTACGGATCTTCACTGATTGATT
genomic: GGAGACACCTGATGGTCCTGTCTTTGAGAGCAATGCAATAGCAAGATATGgtaatttaaa ... ctccctgaagTTACTCGCTTGAAGGCTAACAACCCACTTTACGGATCTTCACTGATTGATT
EST: gi|17921811|gb|BM259462.1|BM259462
EST:     GGAGACACCTGATGGTCCTGTCTTTGAGAGCAATGCAATAGCAAGATATG                         TTACTCGCTTGAAGGCTAACAACCCACTTTACGGATCTTCACTGATTGATT
genomic: GGAGACACCTGATGGTCCTGTCTTTGAGAGCAATGCAATAGCAAGATATGgtaatttaaa ... ctccctgaagTTACTCGCTTGAAGGCTAACAACCCACTTTACGGATCTTCACTGATTGATT
EST: gi|56382464|gb|CV985133.1|CV985133
EST:     GGAGACACCTGATGGTCCTGTCTTTGAGAGCAATGCAATAGCAAGATATG                         TTACTCGCTTGAAGGCTAACAACCCACTTTACGGATCTTCACTGATTGATT
genomic: GGAGACACCTGATGGTCCTGTCTTTGAGAGCAATGCAATAGCAAGATATGgtaatttaaa ... ctccctgaagTTACTCGCTTGAAGGCTAACAACCCACTTTACGGATCTTCACTGATTGATT
EST: gi|33100592|gb|CF060552.1|CF060552
EST:     GGAGACACCTGATGGTCCTGTCTTTGAGAGCAATGCAATAGCAAGATATG                         TTACTCGCTTGAAGGCTAACAACCCACTTTACGGATCTTCACTGATTGATT
genomic: GGAGACACCTGATGGTCCTGTCTTTGAGAGCAATGCAATAGCAAGATATGgtaatttaaa ... ctccctgaagTTACTCGCTTGAAGGCTAACAACCCACTTTACGGATCTTCACTGATTGATT
EST: gi|211045448|gb|FL056741.1|FL056741
EST:     GGAGACACCTGATGGTCCTGTCTTTGAGAGCAATGCAATAGCAAGATATG                         TTACTCGCTTGAAGGCTAACAACCCACTTTACGGATCTTCACTGATTGATT
genomic: GGAGACACCTGATGGTCCTGTCTTTGAGAGCAATGCAATAGCAAGATATGgtaatttaaa ... ctccctgaagTTACTCGCTTGAAGGCTAACAACCCACTTTACGGATCTTCACTGATTGATT
EST: gi|21987889|gb|BQ779417.1|BQ779417
EST:     GGAGACACCTGATGGTCCTGTCTTTGAGAGCAATGCAATAGCAAGATATG                         TTACTCGCTTGAAGGCTAACAACCCACTTTACGGATCTTCACTGATTGATT
genomic: GGAGACACCTGATGGTCCTGTCTTTGAGAGCAATGCAATAGCAAGATATGgtaatttaaa ... ctccctgaagTTACTCGCTTGAAGGCTAACAACCCACTTTACGGATCTTCACTGATTGATT
EST: gi|32942861|gb|CF047680.1|CF047680
EST:     GGAGACACCTGATGGTCCTGTCTTTGAGAGCAATGCAATAGCAAGATATG                         TTACTCGCTTGAAGGCTAACAACCCACTTTACGGATCTTCACTGATTGATT
genomic: GGAGACACCTGATGGTCCTGTCTTTGAGAGCAATGCAATAGCAAGATATGgtaatttaaa ... ctccctgaagTTACTCGCTTGAAGGCTAACAACCCACTTTACGGATCTTCACTGATTGATT
EST: gi|211045450|gb|FL056743.1|FL056743
EST:     GGAGACACCTGATGGTCCTGTCTTTGAGAGCAATGCAATAGCAAGATATG                         TTACTCGCTTGAAGGCTAACAACCCACTTTACGGATCTTCACTGATTGATT
genomic: GGAGACACCTGATGGTCCTGTCTTTGAGAGCAATGCAATAGCAAGATATGgtaatttaaa ... ctccctgaagTTACTCGCTTGAAGGCTAACAACCCACTTTACGGATCTTCACTGATTGATT
EST: gi|30087596|gb|CB885802.1|CB885802
EST:     GGAGACACCTGATGGTCCTGTCTTTGAGAGCAATGCAATAGCAAGATATG                         TTACTCGCTTGAAGGCTAACAACCCACTTTACGGATCTTCACTGATTGATT
genomic: GGAGACACCTGATGGTCCTGTCTTTGAGAGCAATGCAATAGCAAGATATGgtaatttaaa ... ctccctgaagTTACTCGCTTGAAGGCTAACAACCCACTTTACGGATCTTCACTGATTGATT
EST: gi|32908341|gb|CF013154.1|CF013154
EST:     GGAGACACCTGATGGTCCTGTCTTTGAGAGCAATGCAATAGCAAGATATG                         TTACTCGCTTGAAGGCTAACAACCCACTTTACGGATCTTCACTGATTGATT
genomic: GGAGACACCTGATGGTCCTGTCTTTGAGAGCAATGCAATAGCAAGATATGgtaatttaaa ... ctccctgaagTTACTCGCTTGAAGGCTAACAACCCACTTTACGGATCTTCACTGATTGATT
EST: gi|211045447|gb|FL056740.1|FL056740
EST:     GGAGACACCTGATGGTCCTGTCTTTGAGAGCAATGCAATAGCAAGATATG                         TTACTCGCTTGAAGGCTAACAACCCACTTTACGGATCTTCACTGATTGATT
genomic: GGAGACACCTGATGGTCCTGTCTTTGAGAGCAATGCAATAGCAAGATATGgtaatttaaa ... ctccctgaagTTACTCGCTTGAAGGCTAACAACCCACTTTACGGATCTTCACTGATTGATT
EST: gi|26456546|gb|CA828129.1|CA828129
EST:     GGAGACACCTGATGGTCCTGTCTTTGAGAGCAATGCAATAGCAAGATATG                         TTACTCGCTTGAAGGCTAACAACCCACTTTACGGATCTTCACTGATTGATT
genomic: GGAGACACCTGATGGTCCTGTCTTTGAGAGCAATGCAATAGCAAGATATGgtaatttaaa ... ctccctgaagTTACTCGCTTGAAGGCTAACAACCCACTTTACGGATCTTCACTGATTGATT
EST: gi|211045445|gb|FL056738.1|FL056738
EST:     GGAGACACCTGATGGTCCTGTCTTT-AGAGCAATGCAATAGCAAGATATG                         TTACTCGCTTGAAGGCTAACAACCCACTTTACGGATCTTCACTGATTGATT
genomic: GGAGACACCTGATGGTCCTGTCTTTGAGAGCAATGCAATAGCAAGATATGgtaatttaaa ... ctccctgaagTTACTCGCTTGAAGGCTAACAACCCACTTTACGGATCTTCACTGATTGATT
EST: gi|20301474|gb|BQ164417.1|BQ164417
EST:     GGAGACACCTGATGGTCCTGTCTTTGAGAGCAATGCAATAGCAAGATATG                         TTACTCGCTTGAAGGCTAACAACCCACTTTACGGATCTTCACTGATTGATT
genomic: GGAGACACCTGATGGTCCTGTCTTTGAGAGCAATGCAATAGCAAGATATGgtaatttaaa ... ctccctgaagTTACTCGCTTGAAGGCTAACAACCCACTTTACGGATCTTCACTGATTGATT
EST: gi|211045441|gb|FL056734.1|FL056734
EST:     GGAGACACCTGATGGTCCTGTCTTTGAGAGCAATGCAATAGCAAGATATG                         TTACTCGCTTGAAGGCTAACAACCCACTTTACGGATCTTCACTGATTGATT
genomic: GGAGACACCTGATGGTCCTGTCTTTGAGAGCAATGCAATAGCAAGATATGgtaatttaaa ... ctccctgaagTTACTCGCTTGAAGGCTAACAACCCACTTTACGGATCTTCACTGATTGATT
EST: gi|31406016|gb|CD484748.1|CD484748
EST:     GGAGACACCTGATGGTCCTGTCTTTGAGAGCAATGCAATAGCAAGATATG                         TTACTCGCTTGAAGGCTAACAACCCACTTTACGGATCTTCACTGATTGATT
genomic: GGAGACACCTGATGGTCCTGTCTTTGAGAGCAATGCAATAGCAAGATATGgtaatttaaa ... ctccctgaagTTACTCGCTTGAAGGCTAACAACCCACTTTACGGATCTTCACTGATTGATT
EST: gi|74237946|gb|DT645860.1|DT645860
EST:     GGAGACACCTGATGGTCCTGTCTTTGAGAGCAATGCAATAGCAAGATATG                         TTACTCGCTTGAAGGCTAACAACCCACTTTACGGATCTTCACTGATTGATT
genomic: GGAGACACCTGATGGTCCTGTCTTTGAGAGCAATGCAATAGCAAGATATGgtaatttaaa ... ctccctgaagTTACTCGCTTGAAGGCTAACAACCCACTTTACGGATCTTCACTGATTGATT
EST: gi|33093176|gb|CF053170.1|CF053170
EST:     GGAGACACCTGATGGTCCTGTCTTTGAGAGCAATGCAATAGCAAGATATG                         TTACTCGCTTGAAGGCTAACAACCCACTTTACGGATCTTCACTGATTGATT
genomic: GGAGACACCTGATGGTCCTGTCTTTGAGAGCAATGCAATAGCAAGATATGgtaatttaaa ... ctccctgaagTTACTCGCTTGAAGGCTAACAACCCACTTTACGGATCTTCACTGATTGATT
EST: gi|31359821|gb|CD444178.1|CD444178
EST:     GGAGACACCTGATGGTCCTGTCTTTGAGAGCAATGCAATAGCAAGATATG                         TTACTCGCTTGAAGGCTAACAACCCACTTTACGGATCTTCACTGATTGATT
genomic: GGAGACACCTGATGGTCCTGTCTTTGAGAGCAATGCAATAGCAAGATATGgtaatttaaa ... ctccctgaagTTACTCGCTTGAAGGCTAACAACCCACTTTACGGATCTTCACTGATTGATT
EST: gi|21331579|gb|BQ486960.1|BQ486960
EST:     GGAGACACCTGATGGTCCTGTCTTTGAGAGCAATGCAATAGCAAGATATG                         TTACTCGCTTGAAGGCTAACAACCCACTTTACGGATCTTCACTGATTGATT
genomic: GGAGACACCTGATGGTCCTGTCTTTGAGAGCAATGCAATAGCAAGATATGgtaatttaaa ... ctccctgaagTTACTCGCTTGAAGGCTAACAACCCACTTTACGGATCTTCACTGATTGATT
EST: gi|548017|gb|T25217.1|T25217
EST:     GGAGACACCTGATGGTCCTGTCTTTGAGAGCAATGCAATAGCAAGATATG                         TTACTCGCTTGAAGGCTAACAACCCACTTTACGGATCTTCACTGATTGATT
genomic: GGAGACACCTGATGGTCCTGTCTTTGAGAGCAATGCAATAGCAAGATATGgtaatttaaa ... ctccctgaagTTACTCGCTTGAAGGCTAACAACCCACTTTACGGATCTTCACTGATTGATT
EST: gi|211045444|gb|FL056737.1|FL056737
EST:     GGAGACACCTGATGGTCCTGTCTTTGAGAGCAATGCAATAGCAAGATATG                         TTACTCGCTTGAAGGCTAACAACCCACTTTACGGATCTTCACTGATTGATT
genomic: GGAGACACCTGATGGTCCTGTCTTTGAGAGCAATGCAATAGCAAGATATGgtaatttaaa ... ctccctgaagTTACTCGCTTGAAGGCTAACAACCCACTTTACGGATCTTCACTGATTGATT

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: 646

GTTCCTGTCCTGGAGACACCTGATGGTCCTGTCTTTGAGAGCAATGCAATAGCAAGATATGgtaatttaaa ... ctccctgaagTTACTCGCTTGAAGGCTAACAACCCACTTTACGGATCTTCACTGATTGATTAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 431

GTTCCTGTCCTGGAGACACCTGATGGTCCTGTCTTTGAGAGCAATGCAATAGCAAGATATGgtaatttaaa ... ctccctgaagTTACTCGCTTGAAGGCTAACAACCCACTTTACGGATCTTCACTGATTGATTAT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 288

GTTCCTGTCCTGGAGACACCTGATGGTCCTGTCTTTGAGAGCAATGCAATAGCAAGATATGgtaatttaaa ... ctccctgaagTTACTCGCTTGAAGGCTAACAACCCACTTTACGGATCTTCACTGATTGATTAT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 254

GTTCCTGTCCTGGAGACACCTGATGGTCCTGTCTTTGAGAGCAATGCAATAGCAAGATATGgtaatttaaa ... ctccctgaagTTACTCGCTTGAAGGCTAACAACCCACTTTACGGATCTTCACTGATTGATTAT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTCCTGTCCTGGAGACACCTGATGGTCCTGTCTTTGAGAGCAATGCAATAGCAAGATATGgtaatttaaatgttgcaacaattggtttgtttagtcttttgtttgcatttatttgattgagcaccgaattctgtcatctccctgaag

- - - - - - - - - - - - - - - - - -  AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA