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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAACCGTCCCTGTTAGAACTGTCAACCGCCAGTGTTCATCTGGGCTACAGGCAGTAGCTGATGTCGCAGCTGCTATAAAGGCTGGTTACTATGACATAGgtacttagtatctgaatatacatgctactttcgctcttgtgctttagtttggctgctgaatcgctgctctccctctaaacag

Basic information

species Zea mays
transcript GRMZM5G848768_T04
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G848768_T02 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os02g57260.1 (Oryza sativa), 5'ss of exon 5
AAACCGTCCCTGTTAGAACTGTCAACCGCCAGTGTTCATCTGGGCTACAGGCAGTAGCTGATGTCGCAGCTGCTATAAAGGCTGGTTACTATGACATAGgtacttag-----tatctg--------aatata--catgctactttcgct-cttg--tgctttagtttg-gctgctgaatcgctgctctccctctaaa-cag
||| ||| |||||||||||||||||||| || ||||| |||||  |||||||||| |||||||| || || || || || ||||| | ||| |||||||||| |||      ||   |        |||||    ||||||  |  ||| | ||  ||||| | ||   | |||| | | |    | ||| || ||| |||
AAAACGTTCCTGTTAGAACTGTCAACCGGCAATGTTCCTCTGGATTACAGGCAGTGGCTGATGTTGCCGCGGCCATTAAAGCTGGGTTCTACGACATAGgtaattaactagttactcgttctagacaatatggttatgctaactctgctacatggttgcttcatttaaaggtgctaatttgtctttttccatcaaaaacag

upper sequence: GRMZM5G848768_T02 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA20G18980.1 (Glycine max), 5'ss of exon 5
AAACCGTCCCTGTTAGAACTGTCAACCGCCAGTGTTCATCTGGGCTACAGGCAGTAGCTGATGTCGCAGCTGCTATAAAGGCTGGTTACTATGACATAGgtacttagtatctgaatatacatgctactttcgctcttgtgctttagtttggctgctgaatcgctgctctccctctaaacag---------
|||| || |||||||| ||||| ||  | || |||||||||||||| ||||| || |||||||| || |||||||||| |||||| | ||||||||| |||| |   |  || || ||   ||||  ||||  ||||||| ||   | || ||  |       |    | ||| |||  |          
AAACTGTGCCTGTTAGGACTGTTAATAGGCAATGTTCATCTGGGCTCCAGGCTGTTGCTGATGTAGCTGCTGCTATAAGGGCTGGGTTCTATGACATTGgtaatggatgcctcaa-at---tgcttttttc-ttcttgtgatt-gctatgacttttagtatcttatgttacctttaattattttgtttag

upper sequence: GRMZM5G848768_T02 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA10G24590.3 (Glycine max), 5'ss of exon 5
AAACCGTCCCTGTTAGAACTGTCAACCGCCAGTGTTCATCTGGGCTACAGGCAGTAGCTGATGTCGCAGCTGCTATAAAGGCTGGTTACTATGACATAGgtacttagtatctgaatatacatgctactttcgctcttgtgctttagtttggctgctgaatcgctgctctccctctaaacag---------
|||| || |||||||| || || ||  | || |||||||||||||| ||||| || |||||||| || |||||||||| |||||| | ||||||||| ||||   || ||  | ||  |  ||||  ||||  ||||||| ||   | || ||  |       |    | ||| |||  |          
AAACTGTGCCTGTTAGGACCGTTAATAGGCAATGTTCATCTGGGCTCCAGGCTGTCGCTGATGTAGCTGCTGCTATAAGGGCTGGGTTCTATGACATTGgtaa--aggat--gcatcaaattgctgttttc-ttcttgtgatt-gatatgacttttagtatcttatgttgcctttaattattttgtttag

upper sequence: GRMZM5G848768_T02 (Zea mays), 5'ss of exon 5
lower sequence: AT1G04710.1 (Arabidopsis thaliana), 5'ss of exon 5
AAACCGTCCCTGTTAGAACTGTCAACCGCCAGTGTTCATCTGGGCTACAGGCAGTAGCTGATGTCGCAGCTGCTATAAAGGCTGGTTACTATGACATAGgtact-tagtatctgaatatacatgctactttcgctcttgtgctttagtttggctgctgaatcgctgctctccctctaaacag
|||| || ||  | ||||| || ||| | ||||||||||||||||| ||||| || |||||||| || ||||| ||||| |||||||  |||||||| ||||   ||||| ||   | |    | ||| |    | |  |   || |  ||     |  | |     |  |  |  | ||||
AAACTGTTCCCATCAGAACCGTGAACAGACAGTGTTCATCTGGGCTTCAGGCTGTTGCTGATGTTGCCGCTGCCATAAAAGCTGGTTTTTATGACATTGgtaagatagtaactatctttg---gttacataaattgtcttatcttggcatgaagaattgagctgaaattacgttgaatacag

upper sequence: GRMZM5G848768_T02 (Zea mays), 5'ss of exon 5
lower sequence: Vv05s0051g00720.t01 (Vitis vinifera), 5'ss of exon 5
AAACCGTCCCTGTTAGAACTGTCAACCGCCAGTGTTCATCTGGGCTACAGGCAGTAGCTGATGTCGCAGCTGCTATAAAGGCTGGTTACTATGACATAGgtacttagtatctgaatatacatgctactttcg--ctcttgtgctttagtttggctgctgaatcgctgctctccctctaaacag
|||| || ||||| |||||||| ||| | || ||||||||||| || |||||||| |||||||| || ||||| || || ||||| |  |||||||| ||||   |    |  | | |||     | |  |   ||  | |   | |          | ||    |  | ||   ||    ||
AAACTGTGCCTGTCAGAACTGTGAACAGGCAATGTTCATCTGGTCTTCAGGCAGTTGCTGATGTAGCTGCTGCAATTAAAGCTGGGTTTTATGACATTGgtaagaatgtacatattttaccgaggagtcccatacttctatatgtgaacaaaatacattaaagtttaatatcttcctgtttag

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|213184067|gb|FM191388.1|FM191388
EST:     GGCAGTAGCCGATGTCGCAGCTGCTATAAAGGCTGGTTACTATGACATAG                         GGATTGGTGCTGGTTTGGAATCCATGTCCATAAATTCCATTGCTTGGGAAG
genomic: GGCAGTAGCTGATGTCGCAGCTGCTATAAAGGCTGGTTACTATGACATAGgtacttagta ... ctctaaacagGGATTGGTGCTGGTTTGGAATCCATGTCCATAAATTCCATTGCTTGGGAAG
EST: gi|148952059|gb|EC897848.2|EC897848
EST:     GGCAGTAGCTGATGTCGCAGCTGCTATAAAGGCTGGTTACTATGACATAG                         GGATTGGTGCTGGTTTGGAATCCATGTCCATAAATTCCATTGCTTGGGAAG
genomic: GGCAGTAGCTGATGTCGCAGCTGCTATAAAGGCTGGTTACTATGACATAGgtacttagta ... ctctaaacagGGATTGGTGCTGGTTTGGAATCCATGTCCATAAATTCCATTGCTTGGGAAG
EST: gi|32859848|gb|CD999529.1|CD999529
EST:     GCAGTAGCCGATGTCGCAGCTGCTATAAAGGCTGGTTACTATGACATAG                         GGATTGGTGCTGGTTTGGAATCCATGTCCATAAATTCCATTGCTTGGGAAG
genomic: GCAGTAGCTGATGTCGCAGCTGCTATAAAGGCTGGTTACTATGACATAGgtacttagta ... ctctaaacagGGATTGGTGCTGGTTTGGAATCCATGTCCATAAATTCCATTGCTTGGGAAG
EST: gi|6012216|gb|AW061758.1|AW061758
EST:     GATGTCGCAGCTGCTATAAAGGCTGGNTACTATGACATAG                         GGATTGGTGCTGGTTTGGAATCCATGTCCATAAATTCCATTGCTTGGGAAG
genomic: GATGTCGCAGCTGCTATAAAGGCTGGTTACTATGACATAGgtacttagta ... ctctaaacagGGATTGGTGCTGGTTTGGAATCCATGTCCATAAATTCCATTGCTTGGGAAG

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: 311

AAACCGTCCCTGTTAGAACTGTCAACCGCCAGTGTTCATCTGGGCTACAGGCAGTAGCTGATGTCGCAGCTGCTATAAAGGCTGGTTACTATGACATAGgtacttagta ... ctctaaacagGGATTGGTGCTGGTTTGGAATCCATGTCCATAAATTCCATTGCTTGGGAAGGACAAGTTAACCCAAAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1064

AAACCGTCCCTGTTAGAACTGTCAACCGCCAGTGTTCATCTGGGCTACAGGCAGTAGCTGATGTCGCAGCTGCTATAAAGGCTGGTTACTATGACATAGgtacttagta ... ctctaaacagGGATTGGTGCTGGTTTGGAATCCATGTCCATAAATTCCATTGCTTGGGAAGGACAAGTTAACCCAAAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 772

AAACCGTCCCTGTTAGAACTGTCAACCGCCAGTGTTCATCTGGGCTACAGGCAGTAGCTGATGTCGCAGCTGCTATAAAGGCTGGTTACTATGACATAGgtacttagta ... ctctaaacagGGATTGGTGCTGGTTTGGAATCCATGTCCATAAATTCCATTGCTTGGGAAGGACAAGTTAACCCAAAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 834

AAACCGTCCCTGTTAGAACTGTCAACCGCCAGTGTTCATCTGGGCTACAGGCAGTAGCTGATGTCGCAGCTGCTATAAAGGCTGGTTACTATGACATAGgtacttagta ... ctctaaacagGGATTGGTGCTGGTTTGGAATCCATGTCCATAAATTCCATTGCTTGGGAAGGACAAGTTAACCCAAAA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAACCGTCCCTGTTAGAACTGTCAACCGCCAGTGTTCATCTGGGCTACAGGCAGTAGCTGATGTCGCAGCTGCTATAAAGGCTGGTTACTATGACATAGgtacttagtatctgaatatacatgctactttcgctcttgtgctttagtttggctgctgaatcgctgctctccctctaaacag

- - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT