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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtgtaacaatgttcaaatttaaacccattgctcacgaaagtaagaaatcaagacaggaaactgcaccttgcagaactgtcagggttaattttgattggctttgtgtttgtagGGTCTGAATGTAAACCAAGTCCTTACAAGGTGTCTTTTCGCTGGACTGTGTTTCCATGCATACCAACAG

Basic information

species Zea mays
transcript GRMZM2G174107_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G174107_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os08g25624.2 (Oryza sativa), 3'ss of exon 6
gtaagtgtaacaatgttcaaatttaaacccattgctcac--gaaagtaagaaatcaagacaggaaact---gcaccttgcagaactgtcagggttaattttgattggctttgtgtt------tgtagGGTCTGAATGTAAACCAAGTCCTTACAAGGTGTCTTTTCGCTGGACTGTGTTTCCATGCATACCAACAG
|| |||   |||    ||||  || |   || || | |   |||| ||  ||| ||| | | | | ||    |||||| ||  |   | | |   | || ||| ||  ||  ||        ||||||||||||||||||| || || |||||||||| | |  | |||| ||| |||||||| || |||||||||
gtgagtaatacacaactcaa--ttcatttcactggttattagaaaatacaaaaacaaaataagcacctttctcacctttcatgatcctaatgaa-atttctgactgatttcctgacacatgatgtagggtctgaatgtaaaacagGTGCTTACAAGGTCTTTACTTGCTGCACTTTGTTTCCACGCGTACCAACAG
















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|32842413|gb|CD982094.1|CD982094
EST:     CCTTCTTTACAGAAGGTGTCAAAATTACTCCTACATTTTTGCAATCTGCT                         GGTCTGAATGTAAACCAAGTCCTTACAAGGTGTCTTTTCGCTGGACTGTGT
genomic: CCTTCTTTACAGAAGGTGTCAAAATTACTCCTACATTTTTGCAATCTGCTgtaagtgtaa ... gtgtttgtagGGTCTGAATGTAAACCAAGTCCTTACAAGGTGTCTTTTCGCTGGACTGTGT
EST: gi|60351427|gb|DN218400.1|DN218400
EST:     CCTTCTTTACAGAAGGTGTCAAAATTACTCCTACATTTTTGCAATCTGCT                         GGTCTGAATGTAAACCAAGTCCTTACAAGGTGTCTTTTCGCTGGACTGTGT
genomic: CCTTCTTTACAGAAGGTGTCAAAATTACTCCTACATTTTTGCAATCTGCTgtaagtgtaa ... gtgtttgtagGGTCTGAATGTAAACCAAGTCCTTACAAGGTGTCTTTTCGCTGGACTGTGT
EST: gi|60354172|gb|DN221145.1|DN221145
EST:     CCTTCTTTACAGAAGGTGTCAAAATTACTCCTACATTTTTGCAATCTGCT                         GGTCTGAATGTAAACCAAGTCCTTACAAGGTGTCTTTTCGCTGGACTGTGT
genomic: CCTTCTTTACAGAAGGTGTCAAAATTACTCCTACATTTTTGCAATCTGCTgtaagtgtaa ... gtgtttgtagGGTCTGAATGTAAACCAAGTCCTTACAAGGTGTCTTTTCGCTGGACTGTGT
EST: gi|16378321|gb|BI992391.1|BI992391
EST:     CCTTCTTTACAGAAGGTGTCAAAATTACTCCTACATTTTTGCAATCTGCT                         GGTCTGAATGTAAACCAAGTCCTTACAAGGTGTCTTTTCGCTGGACTGTGT
genomic: CCTTCTTTACAGAAGGTGTCAAAATTACTCCTACATTTTTGCAATCTGCTgtaagtgtaa ... gtgtttgtagGGTCTGAATGTAAACCAAGTCCTTACAAGGTGTCTTTTCGCTGGACTGTGT
EST: gi|16377738|gb|BI992093.1|BI992093
EST:     CCTTCTTTACAGAAGGTGTCAAAATTACTCCTACATTTTTGCAATCTGCT                         GGTCTGAATGTAAACCAAGTCCTTACAAGGTGTCTTTTCGCTGGACTGTGT
genomic: CCTTCTTTACAGAAGGTGTCAAAATTACTCCTACATTTTTGCAATCTGCTgtaagtgtaa ... gtgtttgtagGGTCTGAATGTAAACCAAGTCCTTACAAGGTGTCTTTTCGCTGGACTGTGT
EST: gi|13177801|gb|BG349164.1|BG349164
EST:     CTTCTTTACAGAAGGTGTCAAAATTACTCCTACATTTTTGCAATCTGCT                         GGTCTGAATGTAAACCAAGTCCTTACAAGGTGTCTTTTCGCTGGACTGTGT
genomic: CTTCTTTACAGAAGGTGTCAAAATTACTCCTACATTTTTGCAATCTGCTgtaagtgtaa ... gtgtttgtagGGTCTGAATGTAAACCAAGTCCTTACAAGGTGTCTTTTCGCTGGACTGTGT
EST: gi|13178610|gb|BG349868.1|BG349868
EST:     CCTTCTTTACAGAAGGTGTCAAAATTACTCCTACATTTTTGCAATCTGCT                         GGTCTGAATGTAAACCAAGTCCTTACAAGGTGTCTTTTCGCTGGACTGTGT
genomic: CCTTCTTTACAGAAGGTGTCAAAATTACTCCTACATTTTTGCAATCTGCTgtaagtgtaa ... gtgtttgtagGGTCTGAATGTAAACCAAGTCCTTACAAGGTGTCTTTTCGCTGGACTGTGT
EST: gi|32941693|gb|CF046512.1|CF046512
EST:     CCTTCTTTACAGAAGGTGTCAAAATTACTCCTACATTTTTGCAATCTGCT                         GGTCTGAATGTAAACCAAGTCCTTACAAGGTGTCTTTTCGCTGGACTGTGT
genomic: CCTTCTTTACAGAAGGTGTCAAAATTACTCCTACATTTTTGCAATCTGCTgtaagtgtaa ... gtgtttgtagGGTCTGAATGTAAACCAAGTCCTTACAAGGTGTCTTTTCGCTGGACTGTGT
EST: gi|13150806|gb|BG321128.1|BG321128
EST:     CTTCTTTACAGAAGGTGTCAWAATTTACTCCTACATTTTTGCAATCTGCT                         GGTCTGAATGTAAACCAAGTCCTTACAAGGTGTCTTTTCGCTGGACTGTGT
genomic: CTTCTTTACAGAAGGTGTCA-AAATTACTCCTACATTTTTGCAATCTGCTgtaagtgtaa ... gtgtttgtagGGTCTGAATGTAAACCAAGTCCTTACAAGGTGTCTTTTCGCTGGACTGTGT
EST: gi|32842414|gb|CD982095.1|CD982095
EST:     AAATTACTCCTACATTTTTGCAATCTGCT                         GGTCTGAATGTAAACCAAGTCCTTACAAGGTGTCTTTTCGCTGGACTGTGT
genomic: AAATTACTCCTACATTTTTGCAATCTGCTgtaagtgtaa ... gtgtttgtagGGTCTGAATGTAAACCAAGTCCTTACAAGGTGTCTTTTCGCTGGACTGTGT
EST: gi|32940452|gb|CF045271.1|CF045271
EST:     CCTTCTTTACAGAAGGTGTCAAAATTACTCCTACATTTTTGCAATCTGCT                         GGTCTGAATGTAAACCAAGTCCTTACAAGGTGTCTTTTCGCTGGACTGTGT
genomic: CCTTCTTTACAGAAGGTGTCAAAATTACTCCTACATTTTTGCAATCTGCTgtaagtgtaa ... gtgtttgtagGGTCTGAATGTAAACCAAGTCCTTACAAGGTGTCTTTTCGCTGGACTGTGT
EST: gi|148937400|gb|EC881580.2|EC881580
EST:     CCTTCTTTACAGAAGGTGTCAAAATTACTCCTACATTTTTGCAATCTGCT                         GGTCTGAATGTAAACCAAGTCCTTACAAGGTGTCTTTTCGCTGGACTGTGT
genomic: CCTTCTTTACAGAAGGTGTCAAAATTACTCCTACATTTTTGCAATCTGCTgtaagtgtaa ... gtgtttgtagGGTCTGAATGTAAACCAAGTCCTTACAAGGTGTCTTTTCGCTGGACTGTGT
EST: gi|5688709|gb|AI941724.1|AI941724
EST:     CCTTCTTTACAGAAGGTGTCAAAATTACTCCTACATTTTTGCAATCTGCT                         GGTCTGAATGTAAACCAAGTCCTTACAAGGTGTCTTTTCGCTGGACTGTGT
genomic: CCTTCTTTACAGAAGGTGTCAAAATTACTCCTACATTTTTGCAATCTGCTgtaagtgtaa ... gtgtttgtagGGTCTGAATGTAAACCAAGTCCTTACAAGGTGTCTTTTCGCTGGACTGTGT
EST: gi|15313742|gb|BI478935.1|BI478935
EST:     CCTTCTTTACAGAAGGTGTCAAAATTACTCCTACATTTTTGCAATCTGCT                         GGTCTGAATGTAAACCAAGTCCTTACAAGGGGTCTTTTCGCTGGACTG
genomic: CCTTCTTTACAGAAGGTGTCAAAATTACTCCTACATTTTTGCAATCTGCTgtaagtgtaa ... gtgtttgtagGGTCTGAATGTAAACCAAGTCCTTACAAGGTGTCTTTTCGCTGGACTG
EST: gi|211517932|gb|FL479804.1|FL479804
EST:     CCTTCTTTACAGAAGGTGTCAAAATTACTCCTACATTTTTGCAATCTGCT                         GGTCTGAATGTAAACCAAGTCCTTACAAGGTGTCTTTTCGCTGGACTGTGT
genomic: CCTTCTTTACAGAAGGTGTCAAAATTACTCCTACATTTTTGCAATCTGCTgtaagtgtaa ... gtgtttgtagGGTCTGAATGTAAACCAAGTCCTTACAAGGTGTCTTTTCGCTGGACTGTGT
EST: gi|7227535|gb|AW566176.1|AW566176
EST:     CCTTCTTTACAGAAGGTGTCAAAATTACTCCTACATTTTTGCAATCTGCT                         GGTCTGAATGTAAACCAAGTCCTTACAAGGTGTCTTTTCGCTGGACTGTGT
genomic: CCTTCTTTACAGAAGGTGTCAAAATTACTCCTACATTTTTGCAATCTGCTgtaagtgtaa ... gtgtttgtagGGTCTGAATGTAAACCAAGTCCTTACAAGGTGTCTTTTCGCTGGACTGTGT
EST: gi|148940598|gb|EC885404.2|EC885404
EST:     CCTTCTTTACAGAAGGTGTCAAAATTACTCCTACATTTTTGCAATCTGCT                         GGTCTGAATGTAAACCAAGTCCTTACAAGGTGTCTTTTCGCTGGACTGTGT
genomic: CCTTCTTTACAGAAGGTGTCAAAATTACTCCTACATTTTTGCAATCTGCTgtaagtgtaa ... gtgtttgtagGGTCTGAATGTAAACCAAGTCCTTACAAGGTGTCTTTTCGCTGGACTGTGT
EST: gi|83279370|gb|DV943378.1|DV943378
EST:     CCTTCTTTACAGAAGGTGTCAAAATTACTCCTACATTTTTGCAATCTGCT                         GGTCTGAATGTAAACCAAGTCCTTACAAGGTGTCTTTTCGCTGGACTGTGT
genomic: CCTTCTTTACAGAAGGTGTCAAAATTACTCCTACATTTTTGCAATCTGCTgtaagtgtaa ... gtgtttgtagGGTCTGAATGTAAACCAAGTCCTTACAAGGTGTCTTTTCGCTGGACTGTGT
EST: gi|15427333|gb|BI543155.1|BI543155
EST:     CCTTCTTTACAGAAGGTGTCAAAATTACTCCTACATTTTTGCAATCTGCT                         GGTCTGAATGTAAACCAAGTCCTTACAAGGTGTCTTTTCGCTGGACTGTGT
genomic: CCTTCTTTACAGAAGGTGTCAAAATTACTCCTACATTTTTGCAATCTGCTgtaagtgtaa ... gtgtttgtagGGTCTGAATGTAAACCAAGTCCTTACAAGGTGTCTTTTCGCTGGACTGTGT
EST: gi|56462047|gb|CK986345.1|CK986345
EST:     CCTTCTTTACAGAAGGTGTCAAAATTACTCCTACATTTTTGCAATCTGCT                         GGTCTGAATGTAAACCAAGTCCTTACAAGGTGTCTTTTCGCTGGACTGTGT
genomic: CCTTCTTTACAGAAGGTGTCAAAATTACTCCTACATTTTTGCAATCTGCTgtaagtgtaa ... gtgtttgtagGGTCTGAATGTAAACCAAGTCCTTACAAGGTGTCTTTTCGCTGGACTGTGT
EST: gi|24934366|gb|CA452584.1|CA452584
EST:     CCTTCTTTACAGAAGGTGTCAAAATTACTCCTACATTTTTGCAATCTGCT                         GGTCTGAATGTAAACCAAGTCCTTACAAGGTGTCTTTTCGCTGGACTGTGT
genomic: CCTTCTTTACAGAAGGTGTCAAAATTACTCCTACATTTTTGCAATCTGCTgtaagtgtaa ... gtgtttgtagGGTCTGAATGTAAACCAAGTCCTTACAAGGTGTCTTTTCGCTGGACTGTGT
EST: gi|13126160|gb|BG316730.1|BG316730
EST:     CCTTCTTTACAGAAGGTGTCAAAATTACTCCTACATTTTTGCAATCTGCT                         GGTCTGAATGTAAACCAAGTCCTTACAAGGTGTCTTTTCGCTGGACTGTGT
genomic: CCTTCTTTACAGAAGGTGTCAAAATTACTCCTACATTTTTGCAATCTGCTgtaagtgtaa ... gtgtttgtagGGTCTGAATGTAAACCAAGTCCTTACAAGGTGTCTTTTCGCTGGACTGTGT
EST: gi|4624425|gb|AI615258.1|AI615258
EST:     CCTTCTTTACAGAAGGTGTCAAAATTACTCCTACATTTTTGCAATCTGCT                         GGTCTGAATGTAAACCAAGTCCTTACAAGGTGTCTTTTCGCTGGACTGTGT
genomic: CCTTCTTTACAGAAGGTGTCAAAATTACTCCTACATTTTTGCAATCTGCTgtaagtgtaa ... gtgtttgtagGGTCTGAATGTAAACCAAGTCCTTACAAGGTGTCTTTTCGCTGGACTGTGT

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), 48 (downstream exon)
Score: 35

TCTCTTCTCTATCATTACAGTGATGTCATTTTTCCTTTTGGCCCCTGTTACCTTCTTTACAGAAGGTGTCAAAATTACTCCTACATTTTTGCAATCTGCTgtaagtgtaa ... gtgtttgtagGGTCTGAATGTAAACCAAGTCCTTACAAGGTGTCTTTTCGCTGGACTGTGTTTCCATGCATACCAACAG


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

TCTCTTCTCTATCATTACAGTGATGTCATTTTTCCTTTTGGCCCCTGTTACCTTCTTTACAGAAGGTGTCAAAATTACTCCTACATTTTTGCAATCTGCTgtaagtgtaa ... gtgtttgtagGGTCTGAATGTAAACCAAGTCCTTACAAGGTGTCTTTTCGCTGGACTGTGTTTCCATGCATACCAACAG


Block sizes: 36 (upstream exon), 43 (downstream exon)
Score: 7

TCTCTTCTCTATCATTACAGTGATGTCATTTTTCCTTTTGGCCCCTGTTACCTTCTTTACAGAAGGTGTCAAAATTACTCCTACATTTTTGCAATCTGCTgtaagtgtaa ... gtgtttgtagGGTCTGAATGTAAACCAAGTCCTTACAAGGTGTCTTTTCGCTGGACTGTGTTTCCATGCATACCAACAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 226

TCTCTTCTCTATCATTACAGTGATGTCATTTTTCCTTTTGGCCCCTGTTACCTTCTTTACAGAAGGTGTCAAAATTACTCCTACATTTTTGCAATCTGCTgtaagtgtaa ... gtgtttgtagGGTCTGAATGTAAACCAAGTCCTTACAAGGTGTCTTTTCGCTGGACTGTGTTTCCATGCATACCAACAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaactgcaccttgcagaactgtcagggttaattttgattggctttgtgtttgtagGGTCTGAATGTAAACCAAGTCCTTACAAGGTGTCTTTTCGCTGGACTGTGTTTCCATGCATACCAACAG
                               ttttgat  putative branch site (score: 226)
                           ttaattttgatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtgtaacaatgttcaaatttaaacccattgctcacgaaagtaagaaatcaagacaggaaactgcaccttgcagaactgtcagggttaattttgattggctttgtgtttgtagGGTCTGAATGTAAACCAAGTCCTTACAAGGTGTCTTTTCGCTGGACTGTGTTTCCATGCATACCAACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA