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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaagcgagcttcgggcactcttttatttgaagacgatgtactgtggcctccttcaccaggcactaattgtgttttcgtcttcttctgtatctcagACTGGAGTCAATAAGCTTGCAGACCTAGTTGGAGTTACACTCGGACCGAAGGGAAGGAATGTCGTTTTGGAGAGCAAGTACGGCTCTCCCAAGATTGTTA

Basic information

species Zea mays
transcript GRMZM2G083716_T04
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G083716_T04 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os06g02380.1 (Oryza sativa), 3'ss of exon 2
gtgaag--cgagcttcgggcactcttttatttgaagacgatgtactgtggcct----ccttcaccaggcactaattgtgttttcgtcttcttctgtatctcagACTGGAGTCAATAAGCTTGCAGACCTAGTTGGAGTTACACTCGGACCGAAGGGAAGGAATGTCGTTTTGGAGAGCAAGTACGGCTCTCCCAAGATTGTTA
||||    | |  |||  | || | | |  |  ||        ||| ||        |||| |||||||||| |||  ||| |       ||||  || |||||||||||| || |||||||| ||||| |||||||||||||| ||||| |||||||||||||| ||||||||||||||||| || || || | |||||| |
gtgagctccaaagttcttggacacatcttatcaaattttggtcactatgattcttagccttgaccaggcactcatta-gttat-------ttctacatgtcagACTGGAGTAAACAAGCTTGCTGACCTTGTTGGAGTTACACTGGGACCAAAGGGAAGGAATGTTGTTTTGGAGAGCAAGTATGGGTCCCCTAGGATTGTCA

upper sequence: GRMZM2G083716_T04 (Zea mays), 3'ss of exon 2
lower sequence: Vv06s0004g00240.t01 (Vitis vinifera), 3'ss of exon 2
-------------------------gtgaagcgagcttcgggcactcttttatttgaagacgatgtactgtggcctcct--tcaccaggcactaa-ttgtgttttcgtcttcttctgtatctcagACTGGAGTCAATAAGCTTGCAGACCTAGTTGGAGTTACACTCGGACCGAAGGGAAGGAATGTCGTTTTGGAGAGCAAGTACGGCTCTCCCAAGATTGTTA
                         |   |    | |  |  || | | ||  ||     | ||||| |  | | | ||  |||  |     ||| |  |    || |    ||   | | |||||||||||| ||||| ||||| || ||||| |||||||| || || || || || |||||||| ||  | ||||||||||| ||||| || || |||||||
gtgagtttgtgtgtaaaacacttttgatcaatatgttctgaacattttgttgattc----ctatgtatta-gactttctgatcattatctcttaagtcctaacatctttcaatttcctttttcagACTGGAGTAAATAAACTTGCTGATCTAGTGGGAGTTACTCTTGGTCCAAAAGGCAGGAATGTTGTCCTAGAGAGCAAGTATGGCTCCCCAAAAATTGTTA
















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|148983129|gb|EE029060.2|EE029060
EST:     CTAAGGAGCTGTACTTCAACAAGGATGGGTCAGCTATCAAGAAGCTCCAG                         ACTGGAGTCAATAAGCTTGCAGACCTAGTTGGAGTTACACTCGGACCGAAG
genomic: CTAAGGAGCTGTACTTCAACAAGGATGGGTCAGCTATCAAGAAGCTCCAGgtgaagcgag ... tgtatctcagACTGGAGTCAATAAGCTTGCAGACCTAGTTGGAGTTACACTCGGACCGAAG
EST: gi|148983089|gb|EE029008.2|EE029008
EST:     CTAAGGAGCTGTACTTCAACAAGGATGGGTCAGCTATCAAGAAGCTCCAG                         ACTGGAGTCAATAAGCTTGCAGACCTAGTTGGAGTTACACTCGGACCGAAG
genomic: CTAAGGAGCTGTACTTCAACAAGGATGGGTCAGCTATCAAGAAGCTCCAGgtgaagcgag ... tgtatctcagACTGGAGTCAATAAGCTTGCAGACCTAGTTGGAGTTACACTCGGACCGAAG
EST: gi|149009207|gb|EE041320.2|EE041320
EST:     CTAAGGAGCTGTACTTCAACAAGGATGGGTCAGCTATCAAGAAGCTCCAG                         ACTGGAGTCAATAAGCTTGCAGACCTAGTTGGAGTTACACTCGGACCGAAG
genomic: CTAAGGAGCTGTACTTCAACAAGGATGGGTCAGCTATCAAGAAGCTCCAGgtgaagcgag ... tgtatctcagACTGGAGTCAATAAGCTTGCAGACCTAGTTGGAGTTACACTCGGACCGAAG
EST: gi|148963973|gb|EE015101.2|EE015101
EST:     CTAAGGAGCTGTACTTCAACAAGGATGGGTCAGCTATCAAGAAGCTCCAG                         ACTGGAGTCAATAAGCTTGCAGACCTAGTTGGAGTTACACTCGGACCGAAG
genomic: CTAAGGAGCTGTACTTCAACAAGGATGGGTCAGCTATCAAGAAGCTCCAGgtgaagcgag ... tgtatctcagACTGGAGTCAATAAGCTTGCAGACCTAGTTGGAGTTACACTCGGACCGAAG
EST: gi|149080249|gb|EE169273.2|EE169273
EST:     CTAAGGAGCTGTACTTCAACAAGGATGGGTCAGCTATCAAGAAGCTCCAG                         ACTGGAGTCAATAAGCTTGCAGACCTAGTTGGAGTTACACTCGGACCGAAG
genomic: CTAAGGAGCTGTACTTCAACAAGGATGGGTCAGCTATCAAGAAGCTCCAGgtgaagcgag ... tgtatctcagACTGGAGTCAATAAGCTTGCAGACCTAGTTGGAGTTACACTCGGACCGAAG
EST: gi|149099158|gb|EE185183.2|EE185183
EST:     CTAAGGAGCTGTACTTCAACAAGGATGGGTCAGCTATCAAGAAGCTCCAG                         ACTGGAGTCAATAAGCTTGCAGACCTAGTTGGAGTTACACTCGGACCGAAG
genomic: CTAAGGAGCTGTACTTCAACAAGGATGGGTCAGCTATCAAGAAGCTCCAGgtgaagcgag ... tgtatctcagACTGGAGTCAATAAGCTTGCAGACCTAGTTGGAGTTACACTCGGACCGAAG
EST: gi|148941096|gb|EC885959.2|EC885959
EST:     CTAAGGAGCTGTACTTCAACAAGGATGGGTCAGCTATCAAGAAGCTCCAG                         ACTGGAGTCAATAAGCTTGCAGACCTAGTTGGAGTTACACTCGGACCGAAG
genomic: CTAAGGAGCTGTACTTCAACAAGGATGGGTCAGCTATCAAGAAGCTCCAGgtgaagcgag ... tgtatctcagACTGGAGTCAATAAGCTTGCAGACCTAGTTGGAGTTACACTCGGACCGAAG
EST: gi|211393798|gb|FL326098.1|FL326098
EST:     CTAAGGAGCTGTACTTCAACAAGGATGGGTCAGCTATCAAGAAGCTCCAG                         ACTGGAGTCAATAAGCTTGCAGACCTAGTTGGAGTTACACTCGGACCGAAG
genomic: CTAAGGAGCTGTACTTCAACAAGGATGGGTCAGCTATCAAGAAGCTCCAGgtgaagcgag ... tgtatctcagACTGGAGTCAATAAGCTTGCAGACCTAGTTGGAGTTACACTCGGACCGAAG
EST: gi|148940496|gb|EC885295.2|EC885295
EST:     CTAAGGAGCTGTACTTCAACAAGGATGGGTCAGCTATCAAGAAGCTCCAG                         ACTGGAGTCAATAAGCTTGCAGACCTAGTTGGAGTTACACTCGGACCGAAG
genomic: CTAAGGAGCTGTACTTCAACAAGGATGGGTCAGCTATCAAGAAGCTCCAGgtgaagcgag ... tgtatctcagACTGGAGTCAATAAGCTTGCAGACCTAGTTGGAGTTACACTCGGACCGAAG
EST: gi|78080918|gb|DV509330.1|DV509330
EST:     CTAAGGAGCTGTACTTCAACAAGGATGGGTCAGCTATCAAGAAGCTCCAG                         ACTGGAGTCAATAAGCTTGCAGACCTAGTTGGAGTTACACTCGGACCGAAG
genomic: CTAAGGAGCTGTACTTCAACAAGGATGGGTCAGCTATCAAGAAGCTCCAGgtgaagcgag ... tgtatctcagACTGGAGTCAATAAGCTTGCAGACCTAGTTGGAGTTACACTCGGACCGAAG
EST: gi|148961770|gb|EE012547.2|EE012547
EST:     CTAAGGAGCTGTACTTCAACAAGGATGGGTCAGCTATCAAGAAGCTCCAG                         ACTGGAGTCAATAAGCTTGCAGACCTAGTTGGAGTTACACTCGGACCGAAG
genomic: CTAAGGAGCTGTACTTCAACAAGGATGGGTCAGCTATCAAGAAGCTCCAGgtgaagcgag ... tgtatctcagACTGGAGTCAATAAGCTTGCAGACCTAGTTGGAGTTACACTCGGACCGAAG
EST: gi|149075815|gb|EE164351.2|EE164351
EST:     CTAAGGAGCTGTACTTCAACAAGGATGGGTCAGCTATCAAGAAGCTCCAG                         ACTGGAGTCAATAAGCTTGCAGACCTAGTTGGAGTTACACTCGGACCGAAG
genomic: CTAAGGAGCTGTACTTCAACAAGGATGGGTCAGCTATCAAGAAGCTCCAGgtgaagcgag ... tgtatctcagACTGGAGTCAATAAGCTTGCAGACCTAGTTGGAGTTACACTCGGACCGAAG
EST: gi|71764884|gb|DR962821.1|DR962821
EST:     CTAAGGAGCTGTACTTCAACAAGGATGGGTCAGCTATCAAGAAGCTCCAG                         ACTGGAGTCAATAAGCTTGCAGACCTAGTTGGAGTTACACTCGGACCGAAG
genomic: CTAAGGAGCTGTACTTCAACAAGGATGGGTCAGCTATCAAGAAGCTCCAGgtgaagcgag ... tgtatctcagACTGGAGTCAATAAGCTTGCAGACCTAGTTGGAGTTACACTCGGACCGAAG

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), 46 (downstream exon)
Score: 373

GGGGAAGAATGTGCGCCTTCAGAGGAGGGCTAACTTCAGAGTAAAAGCGGCTAAGGAGCTGTACTTCAACAAGGATGGGTCAGCTATCAAGAAGCTCCAGgtgaagcgag ... tgtatctcagACTGGAGTCAATAAGCTTGCAGACCTAGTTGGAGTTACACTCGGACCGAAGGGAAGGAATGTCGTTTTGGAGAGCAAGTACGGCTCTCCCAAGATTGTTA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1299

GGGGAAGAATGTGCGCCTTCAGAGGAGGGCTAACTTCAGAGTAAAAGCGGCTAAGGAGCTGTACTTCAACAAGGATGGGTCAGCTATCAAGAAGCTCCAGgtgaagcgag ... tgtatctcagACTGGAGTCAATAAGCTTGCAGACCTAGTTGGAGTTACACTCGGACCGAAGGGAAGGAATGTCGTTTTGGAGAGCAAGTACGGCTCTCCCAAGATTGTTA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 148

GGGGAAGAATGTGCGCCTTCAGAGGAGGGCTAACTTCAGAGTAAAAGCGGCTAAGGAGCTGTACTTCAACAAGGATGGGTCAGCTATCAAGAAGCTCCAGgtgaagcgag ... tgtatctcagACTGGAGTCAATAAGCTTGCAGACCTAGTTGGAGTTACACTCGGACCGAAGGGAAGGAATGTCGTTTTGGAGAGCAAGTACGGCTCTCCCAAGATTGTTA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 657

GGGGAAGAATGTGCGCCTTCAGAGGAGGGCTAACTTCAGAGTAAAAGCGGCTAAGGAGCTGTACTTCAACAAGGATGGGTCAGCTATCAAGAAGCTCCAGgtgaagcgag ... tgtatctcagACTGGAGTCAATAAGCTTGCAGACCTAGTTGGAGTTACACTCGGACCGAAGGGAAGGAATGTCGTTTTGGAGAGCAAGTACGGCTCTCCCAAGATTGTTA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgtggcctccttcaccaggcactaattgtgttttcgtcttcttctgtatctcagACTGGAGTCAATAAGCTTGCAGACCTAGTTGGAGTTACACTCGGACCGAAGGGAAGGAATGTCGTTTTGGAGAGCAAGTACGGCTCTCCCAAGATTGTTA
                    cactaat  putative branch site (score: 657)
                               ttttcgtcttcttctg  putative PPT
                     actaatt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgaagcgagcttcgggcactcttttatttgaagacgatgtactgtggcctccttcaccaggcactaattgtgttttcgtcttcttctgtatctcagACTGGAGTCAATAAGCTTGCAGACCTAGTTGGAGTTACACTCGGACCGAAGGGAAGGAATGTCGTTTTGGAGAGCAAGTACGGCTCTCCCAAGATTGTTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG