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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgattacatctttatatgctcttattaccttttgcttgtattatagacaattggtcctatatgtatgtgtgtgtatttccgttttgatattatgtgactttgcagGTTTAAGGACATTTTCCAGGAGGTCTATGAAGCTGACTGGAAGTCCAAATTTGAGGCTGCTGGAATATG

Basic information

species Zea mays
transcript GRMZM2G432128_T01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G432128_T01 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os01g46610.1 (Oryza sativa), 3'ss of exon 9
---------------gtgattacatct-ttatatgctcttattaccttttgcttg-------tattatagacaattggtcctatatgtatgtgtg---tgtatttccgttttgatattatgt-gactttgcagGTTTAAGGACATTTTCCAGGAGGTCTATGAAGCTGACTGGAAGTCCAAATTTGAGGCTGCTGGAATATG
                   || || ||  ||| |  ||  ||     |||   |        ||| || |   ||  | |  || | |    |||   | |||  | | | | ||||| | | ||   |||||||| ||||| |||||||||||||||||||||||||  ||||| ||||| ||||||||||| ||||||||
gtagtacatttttgcacatttgcacctactatttattcaaatcttggtttatgtatccaggctatgattgtgtatctgactaatcttttcaggtgacatatataactggtgtaatatttttttgatgatgcagGTTCAAGGATATTTTCCAGGAGGTCTATGAAGCTGGGTGGAAATCCAAGTTTGAGGCTGCCGGAATATG
















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|211440945|gb|FL371134.1|FL371134
EST:     CCACTCTACCTTAGCACCAAAAACACAATCCTGAAAAAATATGATGGCAG                         GTTTAAGGACATTTTCCAGGAGGTCTATGAAGCTGACTGGAAGTCCAAATT
genomic: CCACTCTACCTTAGCACCAAAAACACAATCCTGAAAAAATATGATGGCAGgtgattacat ... gactttgcagGTTTAAGGACATTTTCCAGGAGGTCTATGAAGCTGACTGGAAGTCCAAATT
EST: gi|211423961|gb|FL408856.1|FL408856
EST:     CCACTCTACCTTAGCACCAAAAACACAATCCTGAAAAAATATGATGGCAG                         GTTTAAGGACATTTTCCAGGAGGTCTATGAAGCTGACTGGAAGTCCAAATT
genomic: CCACTCTACCTTAGCACCAAAAACACAATCCTGAAAAAATATGATGGCAGgtgattacat ... gactttgcagGTTTAAGGACATTTTCCAGGAGGTCTATGAAGCTGACTGGAAGTCCAAATT
EST: gi|148957374|gb|EC903424.2|EC903424
EST:     CCACTCTACCTTAGCACCAAAAACACAATCCTGAAAAAATATGATGGCAG                         GTTTAAGGACATTTTCCAGGAGGTCTATGAAGCTAACTGG
genomic: CCACTCTACCTTAGCACCAAAAACACAATCCTGAAAAAATATGATGGCAGgtgattacat ... gactttgcagGTTTAAGGACATTTTCCAGGAGGTCTATGAAGCTGACTGG
EST: gi|32844962|gb|CD984643.1|CD984643
EST:     CCACTCTACCTTAGCACCAAAAACACAATCCTGAAAAAATATGATGCCAG                         GTTTAAGGACATTTTCCAGGAGGTCTATGAAGCTGACTGGAAGTCCAAATT
genomic: CCACTCTACCTTAGCACCAAAAACACAATCCTGAAAAAATATGATGGCAGgtgattacat ... gactttgcagGTTTAAGGACATTTTCCAGGAGGTCTATGAAGCTGACTGGAAGTCCAAATT
EST: gi|6695772|gb|AW288850.1|AW288850
EST:     CCACTCTACCTTAGCACCAAAAACACAATCCTGAAAAAATATGATGGCAG                         GTTTAAGGACATTTTCCAG
genomic: CCACTCTACCTTAGCACCAAAAACACAATCCTGAAAAAATATGATGGCAGgtgattacat ... gactttgcagGTTTAAGGACATTTTCCAG
EST: gi|149110655|gb|EE190535.2|EE190535
EST:     CCACTCTACCTTAGCACCAAAAACACAATCCTGAAAAAATATGATGGCAG                         GTTTAAGGACATTTTCCAGGAGGTCTATGAAGCTGAC
genomic: CCACTCTACCTTAGCACCAAAAACACAATCCTGAAAAAATATGATGGCAGgtgattacat ... gactttgcagGTTTAAGGACATTTTCCAGGAGGTCTATGAAGCTGAC
EST: gi|21760011|gb|BQ635552.1|BQ635552
EST:     CCGCTCTACCTTAGCACCAAAAACACAATCCTGAAAAAATATGATGGCAG                         GTTTAAGGACATTTTCCAGGAGGTCTATGAAGCTGACTGGAAGTCCAAATT
genomic: CCACTCTACCTTAGCACCAAAAACACAATCCTGAAAAAATATGATGGCAGgtgattacat ... gactttgcagGTTTAAGGACATTTTCCAGGAGGTCTATGAAGCTGACTGGAAGTCCAAATT
EST: gi|211106972|gb|FL115259.1|FL115259
EST:     ACAATCCTGAAAAAATATGATGGCAG                         GTTTAAGGACATTTTCCAGGAGGTCTATGAAGCTGACTGGAAGTCCAAATT
genomic: ACAATCCTGAAAAAATATGATGGCAGgtgattacat ... gactttgcagGTTTAAGGACATTTTCCAGGAGGTCTATGAAGCTGACTGGAAGTCCAAATT
EST: gi|67031198|gb|CO459947.1|CO459947
EST:     CCACTCTACCTTAGCACCAAAAACACAATCCTGAAAAAATATGATGGCAG                         GTTTAAGGACATTTTCCAGGAGGTCTATGAAGCTGACTGGAAGTCCAAATT
genomic: CCACTCTACCTTAGCACCAAAAACACAATCCTGAAAAAATATGATGGCAGgtgattacat ... gactttgcagGTTTAAGGACATTTTCCAGGAGGTCTATGAAGCTGACTGGAAGTCCAAATT
EST: gi|149031177|gb|EE286335.2|EE286335
EST:     CCACTCTACCTTAGCACCAAAAACACAATCCTGAAAAAATATGATGGCAG                         GTTTAAGGACATTTTCCAGGAGGTCTATGAAGCTGACTGGAAGTCCAAATT
genomic: CCACTCTACCTTAGCACCAAAAACACAATCCTGAAAAAATATGATGGCAGgtgattacat ... gactttgcagGTTTAAGGACATTTTCCAGGAGGTCTATGAAGCTGACTGGAAGTCCAAATT
EST: gi|32844138|gb|CD983819.1|CD983819
EST:     CCACTCTACCTTAGCACCAAAAACACAATCCTGAAAAAATATGATGGCAG                         GTTTAAGGACATTTTCCAGGAGGTCTACGAAGCTGACTGGAAGTCCAAATT
genomic: CCACTCTACCTTAGCACCAAAAACACAATCCTGAAAAAATATGATGGCAGgtgattacat ... gactttgcagGTTTAAGGACATTTTCCAGGAGGTCTATGAAGCTGACTGGAAGTCCAAATT
EST: gi|5915562|gb|AW053203.1|AW053203
EST:     AAACACAATCCTGAAAAAATATGATGGCAG                         GTTTAAGGACATTTTCCAGGAGGTCTATGAAGCTGACTGGAAGTCCAAATT
genomic: AAACACAATCCTGAAAAAATATGATGGCAGgtgattacat ... gactttgcagGTTTAAGGACATTTTCCAGGAGGTCTATGAAGCTGACTGGAAGTCCAAATT
EST: gi|67010786|gb|CO439535.1|CO439535
EST:     CACTCTACCTTAGCACCAAAAACACAANTCCTGAAAAAATATGATGGCAG                         GTTTAAGGACATTTTCCAGGAGGTCTATGAAGCTGACTGGAAGTCCAAATT
genomic: CACTCTACCTTAGCACCAAAAACACAA-TCCTGAAAAAATATGATGGCAGgtgattacat ... gactttgcagGTTTAAGGACATTTTCCAGGAGGTCTATGAAGCTGACTGGAAGTCCAAATT
EST: gi|32846488|gb|CD986169.1|CD986169
EST:     CCACTCTACCTTAGCACCAAAAACACAATCCTGAAAAAATATGATGGCAG                         GTTTAAGGACATTTTCCAGGAGGTCTATGAAGCTGACTGGAAGTCCAAATT
genomic: CCACTCTACCTTAGCACCAAAAACACAATCCTGAAAAAATATGATGGCAGgtgattacat ... gactttgcagGTTTAAGGACATTTTCCAGGAGGTCTATGAAGCTGACTGGAAGTCCAAATT
EST: gi|31356012|gb|CD440369.1|CD440369
EST:     CCGCTCTACCTTAGCACCAAAAACACAATCCTGAAAAAATATGATGGCAG                         GTTTAAGGACATTTTCCAGGAGGTCTATGAAGCTGACTGGAAGTCCAAATT
genomic: CCACTCTACCTTAGCACCAAAAACACAATCCTGAAAAAATATGATGGCAGgtgattacat ... gactttgcagGTTTAAGGACATTTTCCAGGAGGTCTATGAAGCTGACTGGAAGTCCAAATT
EST: gi|74237580|gb|DT645494.1|DT645494
EST:     CCACTCTACCTTAGCACCAAAAACACAATCCTGAAAAAATATGATGGCAG                         GTTTAAGGACATTTTTCAGGAGGTCTATGAAGCTGACTGGAAGTCCAA-TT
genomic: CCACTCTACCTTAGCACCAAAAACACAATCCTGAAAAAATATGATGGCAGgtgattacat ... gactttgcagGTTTAAGGACATTTTCCAGGAGGTCTATGAAGCTGACTGGAAGTCCAAATT
EST: gi|76286556|gb|DV026124.1|DV026124
EST:     CCACTCTACCTTAGCAC-AAAAACACAATCCTGAAAAAATATGATGGCAG                         GTTTAAGGACATTTTTCCAGGAGGTCTATGAAGCTGACTGGAAG
genomic: CCACTCTACCTTAGCACCAAAAACACAATCCTGAAAAAATATGATGGCAGgtgattacat ... gactttgcagGTTTAAGGACATTTT-CCAGGAGGTCTATGAAGCTGACTGGAAG
EST: gi|60352979|gb|DN219952.1|DN219952
EST:     CCACTCTACCTTAGCACCAAAAACACAATCCTGAAAAAATATGATGGCAG                         GTTTAAGGACATTTTCCAGGAGGTCTATGAAGCTGACTGGAAGTCCAAATT
genomic: CCACTCTACCTTAGCACCAAAAACACAATCCTGAAAAAATATGATGGCAGgtgattacat ... gactttgcagGTTTAAGGACATTTTCCAGGAGGTCTATGAAGCTGACTGGAAGTCCAAATT
EST: gi|60343928|gb|DN210901.1|DN210901
EST:     CCACTCTACCTTAGCACCAAAAACACAATCCTGAAAAAATATGATGGCAG                         GTTTAAGGACATTTTCCAGGAGGTCTATGAAGCTGACTGGAAGTCCAAATT
genomic: CCACTCTACCTTAGCACCAAAAACACAATCCTGAAAAAATATGATGGCAGgtgattacat ... gactttgcagGTTTAAGGACATTTTCCAGGAGGTCTATGAAGCTGACTGGAAGTCCAAATT
EST: gi|67023195|gb|CO451944.1|CO451944
EST:     CCACTCTACCTTAGCACCAAAAACACAATCCTGAAAAAATATGATGGCAG                         GTTTAAGGACATTTTCCAGGAGGTCTATGAAGCTGACTGGAAGTCCAAATT
genomic: CCACTCTACCTTAGCACCAAAAACACAATCCTGAAAAAATATGATGGCAGgtgattacat ... gactttgcagGTTTAAGGACATTTTCCAGGAGGTCTATGAAGCTGACTGGAAGTCCAAATT
EST: gi|148961311|gb|EE012038.2|EE012038
EST:     CCACTCTACCTTAGCACCAAAAACACAATCCTGAAAAAATATGATGGCAG                         GTTTAAGGACATTTTCCCAG-AGGTCTATGAAGCTGACTGGAAGTCCAAAT
genomic: CCACTCTACCTTAGCACCAAAAACACAATCCTGAAAAAATATGATGGCAGgtgattacat ... gactttgcagGTTTAAGGACATTTTCC-AGGAGGTCTATGAAGCTGACTGGAAGTCCAAAT
EST: gi|211392274|gb|FL373436.1|FL373436
EST:     CCACTCTACCNTAGCACCAAAA-CACA-TCCTGAAAAAATATGATGGCAG                         GTTTAAG-ACATTTTCCCAGGAG-TCTATGAAGCTGACTGGAAGTCCAA-T
genomic: CCACTCTACCTTAGCACCAAAAACACAATCCTGAAAAAATATGATGGCAGgtgattacat ... gactttgcagGTTTAAGGACATTTTCC-AGGAGGTCTATGAAGCTGACTGGAAGTCCAAAT
EST: gi|13198145|gb|BG354175.1|BG354175
EST:     CCACTCTACCTTAGCACCAAAAACACAATCCTGAAAAAATATGATGGCAG                         GTTTAAGGACATTTTCCAGGAGGTCTATGAAGCTGACTGGAAGTCCAAATT
genomic: CCACTCTACCTTAGCACCAAAAACACAATCCTGAAAAAATATGATGGCAGgtgattacat ... gactttgcagGTTTAAGGACATTTTCCAGGAGGTCTATGAAGCTGACTGGAAGTCCAAATT
EST: gi|74237579|gb|DT645493.1|DT645493
EST:     TGAAAAAATATGATGACAG                         GTTTAAGGACATTTTCCAGGAGGTCTATGAAGCTGACTGGAAGTCCAAATT
genomic: TGAAAAAATATGATGGCAGgtgattacat ... gactttgcagGTTTAAGGACATTTTCCAGGAGGTCTATGAAGCTGACTGGAAGTCCAAATT
EST: gi|21891602|gb|BQ744815.1|BQ744815
EST:     CCGCTCTACCTTAGCACCAAAAACACAATCCTGAAAAAATATGATGGCAG                         GTTTAAGGACATTTTCCAGGAGGTCTATGAAGCTGACTGGAAGTCCAAATT
genomic: CCACTCTACCTTAGCACCAAAAACACAATCCTGAAAAAATATGATGGCAGgtgattacat ... gactttgcagGTTTAAGGACATTTTCCAGGAGGTCTATGAAGCTGACTGGAAGTCCAAATT
EST: gi|67019645|gb|CO448394.1|CO448394
EST:     CCACTCTACCTTAGCACCAAAAACACAATCCTGAAAAAATATGATGGCAG                         GTTTAAGGACATTTTCCAGGAGGTCTATGAAGCTGACTGGAAGTCCAAATT
genomic: CCACTCTACCTTAGCACCAAAAACACAATCCTGAAAAAATATGATGGCAGgtgattacat ... gactttgcagGTTTAAGGACATTTTCCAGGAGGTCTATGAAGCTGACTGGAAGTCCAAATT
EST: gi|211197469|gb|FL425784.1|FL425784
EST:     CCACTCTACCTTAGCACCAAAAACACAATCCTGAAAAAATATGATGGCAG                         GTTTAAGGACATTTTCCAGGAGGTCTATGAAGCTGACTGGAAGTCCAAATT
genomic: CCACTCTACCTTAGCACCAAAAACACAATCCTGAAAAAATATGATGGCAGgtgattacat ... gactttgcagGTTTAAGGACATTTTCCAGGAGGTCTATGAAGCTGACTGGAAGTCCAAATT

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: 219

TCCGAGCTTTTGCTGAGGCTTCTATGACAACTGCTTATGAGAAGAAATGGCCACTCTACCTTAGCACCAAAAACACAATCCTGAAAAAATATGATGGCAGgtgattacat ... gactttgcagGTTTAAGGACATTTTCCAGGAGGTCTATGAAGCTGACTGGAAGTCCAAATTTGAGGCTGCTGGAATATG


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

TCCGAGCTTTTGCTGAGGCTTCTATGACAACTGCTTATGAGAAGAAATGGCCACTCTACCTTAGCACCAAAAACACAATCCTGAAAAAATATGATGGCAGgtgattacat ... gactttgcagGTTTAAGGACATTTTCCAGGAGGTCTATGAAGCTGACTGGAAGTCCAAATTTGAGGCTGCTGGAATATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 677

TCCGAGCTTTTGCTGAGGCTTCTATGACAACTGCTTATGAGAAGAAATGGCCACTCTACCTTAGCACCAAAAACACAATCCTGAAAAAATATGATGGCAGgtgattacat ... gactttgcagGTTTAAGGACATTTTCCAGGAGGTCTATGAAGCTGACTGGAAGTCCAAATTTGAGGCTGCTGGAATATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 764

TCCGAGCTTTTGCTGAGGCTTCTATGACAACTGCTTATGAGAAGAAATGGCCACTCTACCTTAGCACCAAAAACACAATCCTGAAAAAATATGATGGCAGgtgattacat ... gactttgcagGTTTAAGGACATTTTCCAGGAGGTCTATGAAGCTGACTGGAAGTCCAAATTTGAGGCTGCTGGAATATG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttggtcctatatgtatgtgtgtgtatttccgttttgatattatgtgactttgcagGTTTAAGGACATTTTCCAGGAGGTCTATGAAGCTGACTGGAAGTCCAAATTTGAGGCTGCTGGAATATG
                               ttttgat  putative branch site (score: 764)
                               ttttgatattatgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgattacatctttatatgctcttattaccttttgcttgtattatagacaattggtcctatatgtatgtgtgtgtatttccgttttgatattatgtgactttgcagGTTTAAGGACATTTTCCAGGAGGTCTATGAAGCTGACTGGAAGTCCAAATTTGAGGCTGCTGGAATATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA