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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatacttctaataacgccaacgtgcagcgtctcgcttttattacagtcttgcttttagtctgtgtggcacagttttggtaacatgtttcgtggatcctgtacagGTACGTTATTTTGGGAGATGGCTGCCAAATGGAGGGTATTGCTAATGAAGCTTGCTCCTTGGCTGGACACTGGGGTCTTGGCAAGCTGATTGCTTTCTAC

Basic information

species Zea mays
transcript GRMZM2G033208_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G033208_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os06g04270.1 (Oryza sativa), 3'ss of exon 3
gtaatacttctaataacgccaacgtgcagcgtctcgcttttattacagtcttgcttttagtctgtgtggcacagttttggtaacatgtttcgtggatcctgtacagGTACGTTATTTTGGGAGATGGCTGCCAAATGGAGGGTATTGCTAATGAAGCTTGCTCCTTGGCTGGACACTGGGGTCTTGGCAAGCTGATTGCTTTCTAC
|||||  || |  || |   ||       | | | | ||| | |  |||  ||            ||||  ||   ||||||||||| ||| |||||  ||| ||| |||  ||||||||||||||| ||||| |||||||||||  | |||||||||||||| |||||||| || ||||||||||||||||||||||| ||||| 
gtaattttttttttatcatgaata-----cctttagttttcactttagttatg------------gtggtgcaaccttggtaacatgattcatggattttgtgcagCTACTGTATTTTGGGAGATGGGTGCCAGATGGAGGGTATCTCCAATGAAGCTTGCTCGTTGGCTGGCCATTGGGGTCTTGGCAAGCTGATTGCATTCTAT

upper sequence: GRMZM2G033208_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA10G43990.1 (Glycine max), 3'ss of exon 3
-----gtaat-acttctaataacgccaacgtgcagcgtctcgcttttattacagtcttgc---ttttagtctgtgtggcacagttttggtaacatgtttcgtggatcctgtacagGTACGTTATTTTGGGAGATGGCTGCCAAATGGAGGGTATTGCTAATGAAGCTTGCTCCTTGGCTGGACACTGGGGTCTTGGCAAGCTGATTGCTTTCTAC
      ||||  | |||  |   |    | | |  |    |  | | ||    |||||||   |  | || | |    ||      | ||    |  || ||    |   |  || || ||||| ||||| ||||| || ||||||||||| ||| | |||||||| |||||  | || || ||||||||||| || ||||| |||||||| || 
gtaggataattgcatcttgttttgttctcattct-ctctacattgtgatctacgtcttgcaattcctggtgttttacccatgagaattgtttttttctttgttttactcttgtagATATGTTATATTGGGTGATGGTTGTCAAATGGAGGGAATTTCAAATGAAGCATGCTCACTTGCCGGTCACTGGGGTCTAGGAAAGCTCATTGCTTTATAT

upper sequence: GRMZM2G033208_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA03G03200.1 (Glycine max), 3'ss of exon 3
gtaatacttctaataacgccaacgtgcagcgtctcgcttttattacagtcttgcttttagtctgtgtggcacagttttggtaacatgtttcgtggatcctgtacagGTACGTTATTTTGGGAGATGGCTGCCAAATGGAGGGTATTGCTAATGAAGCTTGCTCCTTGGCTGGACACTGGGGTCTTGGCAAGCTGATTGCTTTCTAC
             |||    ||| |  | | |       ||   | | | | | | || ||            |||||| |||       |||   |  | | |||||| | |||| |||| ||||| || ||||||||||| ||||| |||||||| |||||  | ||||| |||||||| || || |||||||| || || || 
------------gtaaaaataac-taaatcatacacaacttgcaagactttagttgttggt------------gttttgctaatgg----cgtttgttttatgcagGTATGCTATTCTGGGTGATGGTTGTCAAATGGAGGGAATTGCAAATGAAGCATGCTCACTTGCTGGCCACTGGGGACTGGGGAAGCTGATAGCATTTTAT

upper sequence: GRMZM2G033208_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA20G38720.1 (Glycine max), 3'ss of exon 3
gtaatacttctaataacgccaacgtgcagcgtctcgcttt-tattacagtct---tgcttttagtct---gtgtggcac-agttttggtaacatgtttcgtggat---cctgtacagGTACGTTATTTTGGGAGATGGCTGCCAAATGGAGGGTATTGCTAATGAAGCTTGCTCCTTGGCTGGACACTGGGGTCTTGGCAAGCTGATTGCTTTCTAC
|||  |   ||||  |        ||       || || |  |||    |||   | |||  | |     ||||   || |||     |    | |||| | | |   |   |  || || ||||| ||||| ||||| || ||||||||||| ||| | |||||||| |||||  | || || ||||||||||| || ||||| |||||||| || 
gtaggataactaa--atcttgttttgttttcattctctctacattgtgatctatgtacttgcaattcctggtgttttaccagtgagaattgtttttttctttgttttactcttgtagATATGTTATATTGGGTGATGGTTGTCAAATGGAGGGAATTTCAAATGAAGCATGCTCACTTGCCGGTCACTGGGGTCTAGGGAAGCTTATTGCTTTATAT

upper sequence: GRMZM2G033208_T01 (Zea mays), 3'ss of exon 3
lower sequence: AT3G60750.1 (Arabidopsis thaliana), 3'ss of exon 3
gtaatacttctaataacgccaacgtgcagcgtctcgcttttattacagtcttgcttttagtctgtgtggcacagttttggtaacatgtttcgtggatcctgtacagGTACGTTATTTTGGGAGATGGCTGCCAAATGGAGGGTATTGCTAATGAAGCTTGCTCCTTGGCTGGACACTGGGGTCTTGGCAAGCTGATTGCTTTCTAC
             |||     |  |  | |   | | | |  |  |  ||||| |||   | |   |   | | |     ||   | |||  | |||  |||  || || |  ||  | |||||||| || || |||||||||||| ||||||||||||||||  | ||||| || ||||| ||||| ||||| ||||||||||||
------------gtaat----atatataacccatagttatgttgtcgttcttggtttgtatatagctctgataatagaaatactgtttttgattgat--tgtctagATATGCGATCCTTGGAGATGGTTGTCAGATGGAGGGTATTTCTAATGAAGCTTGCTCTCTAGCTGGCCATTGGGGACTTGGAAAGCTCATTGCTTTCTAC

upper sequence: GRMZM2G033208_T01 (Zea mays), 3'ss of exon 3
lower sequence: Vv15s0048g00370.t01 (Vitis vinifera), 3'ss of exon 3
gtaatacttctaat--aacgccaacgtgcagcgtctcgcttttattacagtcttgcttttagtctgtg-tggcacagttttggtaacatgtttcgtggatcctgtacagGTACGTTATTTTGGGAGATGGCTGCCAAATGGAGGGTATTGCTAATGAAGCTTGCTCCTTGGCTGGACACTGGGGTCTTGGCAAGCTGATTGCTTTCTAC
|||| ||  || ||  || |     |||         ||| ||   | ||   ||   |     | || |   | | | || |   |||   |  |||    |    || ||||| ||  |||| ||||| || |||||||||||| ||||  |||||||||| ||  | |||||||| ||||||||||| |||||||| ||||| || 
gtaa-acagcttatcaaatgttgttgtgtttttcagtgctctttagatagatctgaaatgtacgtatgctcttatattgtttggctcattggtattggcatttccttagATACGTGATACTGGGGGATGGTTGTCAAATGGAGGGTGTTGCACATGAAGCTTGTTCACTTGCTGGACATTGGGGTCTTGGGAAGCTGATAGCTTTGTAT

upper sequence: GRMZM2G033208_T01 (Zea mays), 3'ss of exon 3
lower sequence: Vv16s0022g01440.t01 (Vitis vinifera), 3'ss of exon 3
gtaatacttctaataacgccaacgtgcagcgtctcgcttttattacagtcttgcttttagtctgtgtggcacagttttggtaacatgtttcgtggatcctgtacagGTACGTTATTTTGGGAGATGGCTGCCAAATGGAGGGTATTGCTAATGAAGCTTGCTCCTTGGCTGGACACTGGGGTCTTGGCAAGCTGATTGCTTTCTAC
||||  | ||    |        || |    |||   |  |||  || | |      |  | || |    ||   ||||||    || |   | |||  |    ||||| || ||  | || ||||| || |||||||| || ||| | ||||||| ||| ||| | ||||| |||||||| ||||| ||||||||||| || || 
gtaaatcctc----attcttggtgttcttgttctgtttcctatctcaatgtatacaatcatttg-gccttacttgtttggttttttgat--attgattattcttagGTATGTGATACTTGGTGATGGATGTCAAATGGAAGGAATTTCAAATGAAGTTTGTTCCCTTGCTGGGCACTGGGGGCTTGGGAAGCTGATTGCATTTTAT

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|211471115|gb|FL255208.1|FL255208
EST:     CTGGCTGCCCGCTTCAACAAGCCTGACAGTGAGATCGTCGACCACTACAC                         GTACGTTATTTTGGGAGATGGCTGCCAAATGGAGGGTATTGCTAATGAAGC
genomic: CTGGCTGCCCGCTTCAACAAGCCTGACAGTGAGATCGTCGACCACTACACgtaatacttc ... tcctgtacagGTACGTTATTTTGGGAGATGGCTGCCAAATGGAGGGTATTGCTAATGAAGC
EST: gi|6952400|gb|AW424468.1|AW424468
EST:     CAACAAGCCTGACAGTGAGATCG-C-ACCACTACAC                         GTACGTTATTTTGGGAGATGGCTGCCAAATGGAGGGTATTGCTAATGAAGC
genomic: CAACAAGCCTGACAGTGAGATCGTCGACCACTACACgtaatacttc ... tcctgtacagGTACGTTATTTTGGGAGATGGCTGCCAAATGGAGGGTATTGCTAATGAAGC
EST: gi|149086592|gb|EE176136.2|EE176136
EST:     CTGGCTGCCCGCTTCAACAAGCCTGACAGTGAGATCGTCGACCACTACAC                         GTACGTTATTTTGGGAGATGGCTGCCAAATGGAGGGTATTGCTAATGAAGC
genomic: CTGGCTGCCCGCTTCAACAAGCCTGACAGTGAGATCGTCGACCACTACACgtaatacttc ... tcctgtacagGTACGTTATTTTGGGAGATGGCTGCCAAATGGAGGGTATTGCTAATGAAGC
EST: gi|71311290|gb|DR791959.1|DR791959
EST:     CTGGCTGCCCGCTTCAACAAGCCTGACAGTGAGATCGTCGACCACTACAC                         GTACGTTATTTTGGGAGATGGCTGCCAAATGGAGGGTATTGCTAATGAAGC
genomic: CTGGCTGCCCGCTTCAACAAGCCTGACAGTGAGATCGTCGACCACTACACgtaatacttc ... tcctgtacagGTACGTTATTTTGGGAGATGGCTGCCAAATGGAGGGTATTGCTAATGAAGC
EST: gi|78083762|gb|DV512155.1|DV512155
EST:     CTGGCTGCCCGCTTCAACAAGCCTGACAGTGAGATCGTCGACCACTACAC                         GTACGTTATTTTGGGAGATGGCTGCCAAATGGAGGGTATTGCTAATGAAGC
genomic: CTGGCTGCCCGCTTCAACAAGCCTGACAGTGAGATCGTCGACCACTACACgtaatacttc ... tcctgtacagGTACGTTATTTTGGGAGATGGCTGCCAAATGGAGGGTATTGCTAATGAAGC
EST: gi|148999663|gb|EE036652.2|EE036652
EST:     CTGGCTGCCCGCTTCAACAAGCCTGACAGTGAGATCGTCGACCACTACAC                         GTACGTTATTTTGGGAGATGGCTGCCAAATGGAGGGTATTGCTAATGAAGC
genomic: CTGGCTGCCCGCTTCAACAAGCCTGACAGTGAGATCGTCGACCACTACACgtaatacttc ... tcctgtacagGTACGTTATTTTGGGAGATGGCTGCCAAATGGAGGGTATTGCTAATGAAGC
EST: gi|148938610|gb|EC882938.2|EC882938
EST:     CTGGCTGCCCGCTTCAACAAGCCTGACAGTGAGATCGTCGACCACTACAC                         GTACGTTATTTTGGGAGATGGCTGCCAAATGGAGGGTATTGCTAATGAAGC
genomic: CTGGCTGCCCGCTTCAACAAGCCTGACAGTGAGATCGTCGACCACTACACgtaatacttc ... tcctgtacagGTACGTTATTTTGGGAGATGGCTGCCAAATGGAGGGTATTGCTAATGAAGC
EST: gi|149074164|gb|EE162522.2|EE162522
EST:     CTGGCTGCCCGCTTCAACAAGCCTGACAGTGAGATCGTCGACCACTACAC                         GTACGTTATTTTGGGAGATGGCTGCCAAATGGAGGGTATTGCTAATGAAGC
genomic: CTGGCTGCCCGCTTCAACAAGCCTGACAGTGAGATCGTCGACCACTACACgtaatacttc ... tcctgtacagGTACGTTATTTTGGGAGATGGCTGCCAAATGGAGGGTATTGCTAATGAAGC
EST: gi|148950704|gb|EC896296.2|EC896296
EST:     CTGGCTGCCCGCTTCAACAAGCCTGACAGTGAGATCGTCGACCACTACAC                         GTACGTTATTTTGGGAGATGGCTGCCAAATGGAGGGTATTGCTAATGAAGC
genomic: CTGGCTGCCCGCTTCAACAAGCCTGACAGTGAGATCGTCGACCACTACACgtaatacttc ... tcctgtacagGTACGTTATTTTGGGAGATGGCTGCCAAATGGAGGGTATTGCTAATGAAGC
EST: gi|8383193|gb|BE056136.1|BE056136
EST:     CTGGCTGCCCGCTTCAACAAGCCTGACAGTGAGATCGTCGACCACTACAC                         GTACGTTATTTTGGGAGATGGCTGCCAAATGGAGGGTATTGCTAATGAAGC
genomic: CTGGCTGCCCGCTTCAACAAGCCTGACAGTGAGATCGTCGACCACTACACgtaatacttc ... tcctgtacagGTACGTTATTTTGGGAGATGGCTGCCAAATGGAGGGTATTGCTAATGAAGC
EST: gi|149004965|gb|EE039481.2|EE039481
EST:     CTGGCTGCCCGCTTCAACAAGCCTGACAGTGAGATCGTCGACCACTACAC                         GTACGTTATTTTGGGAGATGGCTGCCAAATGGAGGGTATTGCTAATGAAGC
genomic: CTGGCTGCCCGCTTCAACAAGCCTGACAGTGAGATCGTCGACCACTACACgtaatacttc ... tcctgtacagGTACGTTATTTTGGGAGATGGCTGCCAAATGGAGGGTATTGCTAATGAAGC
EST: gi|76281986|gb|DV021554.1|DV021554
EST:     CTGGCTGCCCGCTTCAACAAGCCTGACAGTGAGATCGTCGACCACTACAC                         GTACGTTATTTTGGGAGATGGCTGCCAAATGGAGGGTATTGCTAATGAAGC
genomic: CTGGCTGCCCGCTTCAACAAGCCTGACAGTGAGATCGTCGACCACTACACgtaatacttc ... tcctgtacagGTACGTTATTTTGGGAGATGGCTGCCAAATGGAGGGTATTGCTAATGAAGC
EST: gi|76285424|gb|DV024992.1|DV024992
EST:     CTGGCTGCCCGCTTCAACAAGCCTGACAGTGAGATCGTCGACCACTACAC                         GTACGTTATTTTGGGAGATGGCTGCCAAATGGAGGGTATTGCTAATGAAGC
genomic: CTGGCTGCCCGCTTCAACAAGCCTGACAGTGAGATCGTCGACCACTACACgtaatacttc ... tcctgtacagGTACGTTATTTTGGGAGATGGCTGCCAAATGGAGGGTATTGCTAATGAAGC
EST: gi|8318856|gb|BE025496.1|BE025496
EST:     CTGGCTGCCCGCTTCAACAAGCCTGACAGTGAGATCGTCGACCACTACAC                         GTACGTTATTTTGGGAGATGGCTGCCAAATGGAGGGTATTGCTAATGAAGC
genomic: CTGGCTGCCCGCTTCAACAAGCCTGACAGTGAGATCGTCGACCACTACACgtaatacttc ... tcctgtacagGTACGTTATTTTGGGAGATGGCTGCCAAATGGAGGGTATTGCTAATGAAGC
EST: gi|78079231|gb|DV507643.1|DV507643
EST:     CTGGCTGCCCGCTTCAACAAGCCTGACAGTGAGATCGTCGACCACTACAC                         GTACGTTATTTTGGGAGATGGCTGCCAAATGGAGGGTATTGCTAATGAAGC
genomic: CTGGCTGCCCGCTTCAACAAGCCTGACAGTGAGATCGTCGACCACTACACgtaatacttc ... tcctgtacagGTACGTTATTTTGGGAGATGGCTGCCAAATGGAGGGTATTGCTAATGAAGC
EST: gi|71311289|gb|DR791958.1|DR791958
EST:     CTGGCTGCCCGCTTCAACAAGCCTGACAGTGAGATCGTCGACCACTACAC                         GTACGTTATTTTGGGAGATGGCTGCCAAATGGAGGGTATTGCTAATGAAGC
genomic: CTGGCTGCCCGCTTCAACAAGCCTGACAGTGAGATCGTCGACCACTACACgtaatacttc ... tcctgtacagGTACGTTATTTTGGGAGATGGCTGCCAAATGGAGGGTATTGCTAATGAAGC
EST: gi|8318855|gb|BE025495.1|BE025495
EST:     CTGGCTGCCCGCTTCAACAAGCCTGACAGTGAGATCGTCGACCACTACAC                         GTACGTTATTTTGGGAGATGGCTGCCAAATGGAGGGTATTGCTAATGAAGC
genomic: CTGGCTGCCCGCTTCAACAAGCCTGACAGTGAGATCGTCGACCACTACACgtaatacttc ... tcctgtacagGTACGTTATTTTGGGAGATGGCTGCCAAATGGAGGGTATTGCTAATGAAGC

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), 47 (downstream exon)
Score: 295

TTGGTCAGGGTATCGCCAATGCCGTTGGGTTGGCACTTGCTGAGAAGCACCTGGCTGCCCGCTTCAACAAGCCTGACAGTGAGATCGTCGACCACTACACgtaatacttc ... tcctgtacagGTACGTTATTTTGGGAGATGGCTGCCAAATGGAGGGTATTGCTAATGAAGCTTGCTCCTTGGCTGGACACTGGGGTCTTGGCAAGCTGATTGCTTTCTAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1070

TTGGTCAGGGTATCGCCAATGCCGTTGGGTTGGCACTTGCTGAGAAGCACCTGGCTGCCCGCTTCAACAAGCCTGACAGTGAGATCGTCGACCACTACACgtaatacttc ... tcctgtacagGTACGTTATTTTGGGAGATGGCTGCCAAATGGAGGGTATTGCTAATGAAGCTTGCTCCTTGGCTGGACACTGGGGTCTTGGCAAGCTGATTGCTTTCTAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 529

TTGGTCAGGGTATCGCCAATGCCGTTGGGTTGGCACTTGCTGAGAAGCACCTGGCTGCCCGCTTCAACAAGCCTGACAGTGAGATCGTCGACCACTACACgtaatacttc ... tcctgtacagGTACGTTATTTTGGGAGATGGCTGCCAAATGGAGGGTATTGCTAATGAAGCTTGCTCCTTGGCTGGACACTGGGGTCTTGGCAAGCTGATTGCTTTCTAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1195

TTGGTCAGGGTATCGCCAATGCCGTTGGGTTGGCACTTGCTGAGAAGCACCTGGCTGCCCGCTTCAACAAGCCTGACAGTGAGATCGTCGACCACTACACgtaatacttc ... tcctgtacagGTACGTTATTTTGGGAGATGGCTGCCAAATGGAGGGTATTGCTAATGAAGCTTGCTCCTTGGCTGGACACTGGGGTCTTGGCAAGCTGATTGCTTTCTAC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcttttagtctgtgtggcacagttttggtaacatgtttcgtggatcctgtacagGTACGTTATTTTGGGAGATGGCTGCCAAATGGAGGGTATTGCTAATGAAGCTTGCTCCTTGGCTGGACACTGGGGTCTTGGCAAGCTGATTGCTTTCTAC
                          tggtaac  putative branch site (score: 1195)
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatacttctaataacgccaacgtgcagcgtctcgcttttattacagtcttgcttttagtctgtgtggcacagttttggtaacatgtttcgtggatcctgtacagGTACGTTATTTTGGGAGATGGCTGCCAAATGGAGGGTATTGCTAATGAAGCTTGCTCCTTGGCTGGACACTGGGGTCTTGGCAAGCTGATTGCTTTCTAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT