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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acatatttataaacttgctttggaattttcactcatattggagcttcattttgttagtcccaatcaatgaattgaaaacaaaaacactattcttttacagATGCTTCCATCCAAAGATGCAAACTTTGTTGGGTATACGTACAAGAACTTTGAAATTGTGAATGATGATGAAGTGGCAGGAATTG

Basic information

species Zea mays
transcript GRMZM2G375904_T01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G375904_T02 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os05g43570.3 (Oryza sativa), 3'ss of exon 11
acatatttataaacttgctttggaattttcactcatattggagcttcattttgttagt----cccaatcaatgaattgaaaacaaaaacactatt-cttttacagATGCTTCCATCCAAAGATGCAAACTTTGTTGGGTATACGTACAAGAACTTTGAAATTGTGAATGATGATGAAGTGGCAGGAATTG
   | ||   |  |     ||   ||  | | | | |  |  | ||||||||  || |    |  |  ||||||| | |||  || | ||||  |  |||| ||||||||||| ||||| ||||||||||||||||| ||||| || ||||| ||||||||||| ||||||||||| || ||||||||||
---ttttaggaggcagaaattaacatgcttaattaga--gatgtttcattttcgtattgcctcttagccaatgaactaaaacgaagagcactgctatttttgcagATGCTTCCGTCCAAGGATGCAAACTTTGTTGGCTATACATATAAGAATTTTGAAATTGTAAATGATGATGAGGTTGCAGGAATTG

upper sequence: GRMZM2G375904_T02 (Zea mays), 3'ss of exon 11
lower sequence: Vv10s0003g05720.t01 (Vitis vinifera), 3'ss of exon 11
acatatttataaacttgctttggaatttt--cactcatattggagcttcattttgttagtcccaatcaatgaattgaaaaca----aaaacactattcttttacagATGCTTCCATCCAAAGATGCAAACTTTGTTGGGTATACGTACAAGAACTTTGAAATTGTGAATGATGATGAAGTGGCAGGAATTG
       || |  |||    ||   ||||   ||| |  |      ||  || |  |||||   ||| |  | |||| ||       |  |  ||||   || ||||||||||||||||| |||| ||| || ||||| ||||| |||||||| ||||||||||| || ||  || | ||| | || ||||
------atacagccttttggtgagtttttgctacttagctcatcttttatttctagtagtctgtatctagaatttgagaattctttgattccttatttcattgcagATGCTTCCATCCAAGGATGTAAATTTCGTTGGTTATACATACAAGAATTTTGAAATTGTCAACGAGCATCATGTGCCTGGCATTG
















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|5895617|gb|AW036863.1|AW036863
EST:     ATTGGAACTCAAATTCAAAGTTCATCCAAGTCAGGCCCTTGGAGAAAG                         ATGCTTCCATCCAAAGATGCAAACTTTGTTGGGTATACGTACAAGAACTTT
genomic: ATTGGAACTCAAATTCAAAGTTCATCCAAGTCAGGCCCTTGGAGAAAGgtatgcatga ... tcttttacagATGCTTCCATCCAAAGATGCAAACTTTGTTGGGTATACGTACAAGAACTTT
EST: gi|28187719|gb|CB179329.1|CB179329
EST:     ATTGGAACTCAAATTCAAAGTTCATCCAAGTCAGGCCCTTGGAGAAAG                         ATGCTTCCATCCAAAGATGCAAACTTTGTTGGGTATACGTACAAGAACTTT
genomic: ATTGGAACTCAAATTCAAAGTTCATCCAAGTCAGGCCCTTGGAGAAAGgtatgcatga ... tcttttacagATGCTTCCATCCAAAGATGCAAACTTTGTTGGGTATACGTACAAGAACTTT
EST: gi|5901099|gb|AW042199.1|AW042199
EST:     ATTGGAACTCAAATTCAAAGTTCATCCAAGTCAGGCCCTTGGAGAAAG                         ATGCTTCCATCCAAAGATGCAAACTTTGTTGGGTATACGTACAAGAACTTT
genomic: ATTGGAACTCAAATTCAAAGTTCATCCAAGTCAGGCCCTTGGAGAAAGgtatgcatga ... tcttttacagATGCTTCCATCCAAAGATGCAAACTTTGTTGGGTATACGTACAAGAACTTT
EST: gi|33285627|gb|CF075422.1|CF075422
EST:     ATTGGAACTCAAATTCAAAGTTCATCCAAGTCAGGCCCTTGGAGAAAG                         ATGCTTCCATCCAAAGATGCAAACTTTGTTGGGTATACGTACAAGAACTTT
genomic: ATTGGAACTCAAATTCAAAGTTCATCCAAGTCAGGCCCTTGGAGAAAGgtatgcatga ... tcttttacagATGCTTCCATCCAAAGATGCAAACTTTGTTGGGTATACGTACAAGAACTTT
EST: gi|211195854|gb|FL001022.1|FL001022
EST:     ATTGGAACTCAAATTCAAAGTTCATCCAAGTCAGGCCCTTGGAGAAAG                         ATGCTTCCATCCAAAGATGCAAACTTTGTTGGGTATACGTACAAGAACTTT
genomic: ATTGGAACTCAAATTCAAAGTTCATCCAAGTCAGGCCCTTGGAGAAAGgtatgcatga ... tcttttacagATGCTTCCATCCAAAGATGCAAACTTTGTTGGGTATACGTACAAGAACTTT
EST: gi|32934179|gb|CF038991.1|CF038991
EST:     GGAACTCAAATTCAAAGTTCATCCAAGTCAGGCCCATGGAGAAAG                         ATGCTTCCATCCAAAGATGCAAACTTTGTTGGGTATACGTACAAGAACTTT
genomic: GGAACTCAAATTCAAAGTTCATCCAAGTCAGGCCCTTGGAGAAAGgtatgcatga ... tcttttacagATGCTTCCATCCAAAGATGCAAACTTTGTTGGGTATACGTACAAGAACTTT
EST: gi|149049839|gb|EE048526.2|EE048526
EST:     ATTGGAACTCAAATTCAAAGTTCATCCAAGTCAGGCCCTTGGAGAAAG                         ATGCTTCCATCCAAAGATGCAAACTTTGTTGGGTATACGTACAAGAACTTT
genomic: ATTGGAACTCAAATTCAAAGTTCATCCAAGTCAGGCCCTTGGAGAAAGgtatgcatga ... tcttttacagATGCTTCCATCCAAAGATGCAAACTTTGTTGGGTATACGTACAAGAACTTT
EST: gi|32870336|gb|CF010018.1|CF010018
EST:     ATTGGAACTCAAATTCAAAGTTCATCCAAGTCAGGCCCTTGGAGAAAG                         ATGCTTCCATCCAAAGATGCAAACTTTGTTGGGTATACGTACAAGAACTTT
genomic: ATTGGAACTCAAATTCAAAGTTCATCCAAGTCAGGCCCTTGGAGAAAGgtatgcatga ... tcttttacagATGCTTCCATCCAAAGATGCAAACTTTGTTGGGTATACGTACAAGAACTTT
EST: gi|32928081|gb|CF032893.1|CF032893
EST:     ATTGGAACTCAAATTCAAAGTTCATCCAAGTCAGGCCCTTGGAGAAAG                         ATGCTTCCATCCAAAGATGCAAACTTTGTTGGGTATACGT
genomic: ATTGGAACTCAAATTCAAAGTTCATCCAAGTCAGGCCCTTGGAGAAAGgtatgcatga ... tcttttacagATGCTTCCATCCAAAGATGCAAACTTTGTTGGGTATACGT

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: 47 (upstream exon), 45 (downstream exon)
Score: 216

ATTGGAACTCAAATTCAAAGTTCATCCAAGTCAGGCCCTTGGAGAAAGgtatgcatga ... tcttttacagATGCTTCCATCCAAAGATGCAAACTTTGTTGGGTATACGTACAAGAACTTTGAAATTGTGAATGATGATGAAGTGGCAGGAATTG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 280

ATTGGAACTCAAATTCAAAGTTCATCCAAGTCAGGCCCTTGGAGAAAGgtatgcatga ... tcttttacagATGCTTCCATCCAAAGATGCAAACTTTGTTGGGTATACGTACAAGAACTTTGAAATTGTGAATGATGATGAAGTGGCAGGAATTG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 453

ATTGGAACTCAAATTCAAAGTTCATCCAAGTCAGGCCCTTGGAGAAAGgtatgcatga ... tcttttacagATGCTTCCATCCAAAGATGCAAACTTTGTTGGGTATACGTACAAGAACTTTGAAATTGTGAATGATGATGAAGTGGCAGGAATTG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 355

ATTGGAACTCAAATTCAAAGTTCATCCAAGTCAGGCCCTTGGAGAAAGgtatgcatga ... tcttttacagATGCTTCCATCCAAAGATGCAAACTTTGTTGGGTATACGTACAAGAACTTTGAAATTGTGAATGATGATGAAGTGGCAGGAATTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcattttgttagtcccaatcaatgaattgaaaacaaaaacactattcttttacagATGCTTCCATCCAAAGATGCAAACTTTGTTGGGTATACGTACAAGAACTTTGAAATTGTGAATGATGATGAAGTGGCAGGAATTG
                                         ctattctttt  CT-rich tract
                        aattgaaaacaaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acatatttataaacttgctttggaattttcactcatattggagcttcattttgttagtcccaatcaatgaattgaaaacaaaaacactattcttttacagATGCTTCCATCCAAAGATGCAAACTTTGTTGGGTATACGTACAAGAACTTTGAAATTGTGAATGATGATGAAGTGGCAGGAATTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - -tgctttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccaatca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgaattg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaacaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aacacta