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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttcccccctattttagaatataagaatgttgagggaattttggccttgttgtcgcgttgatttctcgctcgttccttttttttccccctcattctcgcagTCGAGACAAAGAAGCAGATCTCGTGCTCTATGCAGTTGACAAACCGAACAGATGACTACATCGGCTTTAAG

Basic information

species Zea mays
transcript GRMZM2G155543_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G155543_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os04g45190.1 (Oryza sativa), 3'ss of exon 1
-ttcccccctattttagaatataagaatgttgagggaattttggccttgttgtcgc----gttgatttctcgctcgttccttttttttccccctcattctcgcagTCGAGACAAAGAAGCAGATCTCGTGCTCTATGCAGTTGACAAACCGAACAGATGACTACATCGGCTTTAAG
 | |       |    | | ||       ||| |  | |   |  |    || |||    |||   ||     | | |  || |||| |    |   |   ||||||||||| |||||||||||||| ||||| |||||| |||| ||| |||||||||||||||||| |||||||
gtacggtttcctcgccggaaattccctgcttgtgaaattccggagccacatgccgctggggttttgtttgtttttgctgattcttttgctgtttggattgagcagTCGAGACGAAGAAGCAGATCTCATGCTCCATGCAGCTGACGAACAGAACAGATGACTACATCGCCTTTAAG
















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|211414035|gb|FK970738.1|FK970738
EST:     TCACTCCAAGGA-NTGCTCGAGATCGAGCCCCTCGAGCTCCGATTCCCAT                         TCGAGACAAAGAAGCAGATCTCGTGCTCTATGCAGTTGACAAACCGAACAG
genomic: TCACTCCAAGGACTTGCTCGAGATCGAGCCCCTCGAGCTCCGATTCCCATgtacggttcc ... attctcgcagTCGAGACAAAGAAGCAGATCTCGTGCTCTATGCAGTTGACAAACCGAACAG
EST: gi|211416583|gb|FK970749.1|FK970749
EST:     TCACTCCAAGGACTTGCTCGAGATCGAGCCCCTCGAGCTCCGATTCCCAT                         TCGAGACAAAGAAGCAGATCTCGTGCTCTATGCAGTTGACAAACCGAACAG
genomic: TCACTCCAAGGACTTGCTCGAGATCGAGCCCCTCGAGCTCCGATTCCCATgtacggttcc ... attctcgcagTCGAGACAAAGAAGCAGATCTCGTGCTCTATGCAGTTGACAAACCGAACAG
EST: gi|211419127|gb|FK970761.1|FK970761
EST:     TCACTCCAAGGACTTGCTCGAGATCGAGCCCCTCGAGCTCCGATTCCCAT                         TCGAGACAAAGAAGCAGATCTCGTGCTCTATGCAGTTGACAAACCGAACAG
genomic: TCACTCCAAGGACTTGCTCGAGATCGAGCCCCTCGAGCTCCGATTCCCATgtacggttcc ... attctcgcagTCGAGACAAAGAAGCAGATCTCGTGCTCTATGCAGTTGACAAACCGAACAG
EST: gi|211416592|gb|FK970758.1|FK970758
EST:     TCACTCCAAGGACTTGCTCGAGATCGAGCCCCTCGAGCTCCGATTCCCAT                         TCGAGACAAAGAAGCAGATCTCGTGCTCTATGCAGTTGACAAACCGAACAG
genomic: TCACTCCAAGGACTTGCTCGAGATCGAGCCCCTCGAGCTCCGATTCCCATgtacggttcc ... attctcgcagTCGAGACAAAGAAGCAGATCTCGTGCTCTATGCAGTTGACAAACCGAACAG
EST: gi|93281412|gb|EB673676.1|EB673676
EST:     TCACTCCAAGGACTTGCTCGAGATCGATCCCCTCGAGCTCCGATTCCCAT                         TCGAGAAAAAGAAACACATCTCGTGCTCTATGCAGTTGACAAACCGAACAC
genomic: TCACTCCAAGGACTTGCTCGAGATCGAGCCCCTCGAGCTCCGATTCCCATgtacggttcc ... attctcgcagTCGAGACAAAGAAGCAGATCTCGTGCTCTATGCAGTTGACAAACCGAACAG
EST: gi|211416589|gb|FK970755.1|FK970755
EST:     TCACTCCAAGGACTTGCTCGAGATCGAGCCCCTCGAGCTCCGATTCCCAT                         TCGAGACAAAGAAGCAGATCTCGTGCTCTATGCAGTTGACAAACCGAACAG
genomic: TCACTCCAAGGACTTGCTCGAGATCGAGCCCCTCGAGCTCCGATTCCCATgtacggttcc ... attctcgcagTCGAGACAAAGAAGCAGATCTCGTGCTCTATGCAGTTGACAAACCGAACAG
EST: gi|211414037|gb|FK970740.1|FK970740
EST:     TCACTCCAAGGACTTGCTCGAGATCGAGCCCCTCGAGCTCCGATTCCCAT                         TCGAGACAAAGAAGCAGATCTCGTGCTCTATGCAGTTGACAAACCGAACAG
genomic: TCACTCCAAGGACTTGCTCGAGATCGAGCCCCTCGAGCTCCGATTCCCATgtacggttcc ... attctcgcagTCGAGACAAAGAAGCAGATCTCGTGCTCTATGCAGTTGACAAACCGAACAG
EST: gi|211414040|gb|FK970743.1|FK970743
EST:     TCACTCCAAGGACTTGCTCGAGATCGAGCCCCTCGAGCTCCGATTCCCAT                         TCGAGACAAAGAAGCAGATCTCGTGCTCTATGCAGTTGACAAACCGAACAG
genomic: TCACTCCAAGGACTTGCTCGAGATCGAGCCCCTCGAGCTCCGATTCCCATgtacggttcc ... attctcgcagTCGAGACAAAGAAGCAGATCTCGTGCTCTATGCAGTTGACAAACCGAACAG
EST: gi|76935292|gb|DV174281.1|DV174281
EST:     TCACTCCAAGGACTTGCTCGAGATCGAGCCCCTCGAGCTCCGATTCCCAT                         TCGAGACAAAGAAGCAGATCTCGTGCTCTATGCAGTTGACAAACCGAACAG
genomic: TCACTCCAAGGACTTGCTCGAGATCGAGCCCCTCGAGCTCCGATTCCCATgtacggttcc ... attctcgcagTCGAGACAAAGAAGCAGATCTCGTGCTCTATGCAGTTGACAAACCGAACAG
EST: gi|211416580|gb|FK970746.1|FK970746
EST:     TCACTCCAAGGACTTGCTCGAGATCGATCCCCTCGAGCTCCGATTCCCAT                         TCGAGACAAAGAAGCAGATCTCGTGCTCTATGCAGTTGACAAACCGAACAG
genomic: TCACTCCAAGGACTTGCTCGAGATCGAGCCCCTCGAGCTCCGATTCCCATgtacggttcc ... attctcgcagTCGAGACAAAGAAGCAGATCTCGTGCTCTATGCAGTTGACAAACCGAACAG
EST: gi|211416586|gb|FK970752.1|FK970752
EST:     TCACTCCAAGGACTTGCTCGAGATCGAGCCCCTCGAGCTCCGATTCCCAT                         TCGAGACAAAGAAGCAGATCTCGTGCTCTATGCAGTTGACAAACCGAACAG
genomic: TCACTCCAAGGACTTGCTCGAGATCGAGCCCCTCGAGCTCCGATTCCCATgtacggttcc ... attctcgcagTCGAGACAAAGAAGCAGATCTCGTGCTCTATGCAGTTGACAAACCGAACAG
EST: gi|211416590|gb|FK970756.1|FK970756
EST:     TCACTCCAAGGACTTGCTCGAGATCGAGCCCCTCGAGCTCCGATTCCCAT                         TCGAGACAAAGAAGCAGATCTCGTGCTCTATGCAGTTGACAAACCGAACAG
genomic: TCACTCCAAGGACTTGCTCGAGATCGAGCCCCTCGAGCTCCGATTCCCATgtacggttcc ... attctcgcagTCGAGACAAAGAAGCAGATCTCGTGCTCTATGCAGTTGACAAACCGAACAG
EST: gi|89252124|gb|DY623910.1|DY623910
EST:     TCACTCCAAGGACTTGCTCGAGATCGAGCCCCTCGAGCTCCGATTCCCAT                         TCGAGACAAAGAAGCAGATCTCGTGCTCCATGCAGTTGACAAACCGAACAG
genomic: TCACTCCAAGGACTTGCTCGAGATCGAGCCCCTCGAGCTCCGATTCCCATgtacggttcc ... attctcgcagTCGAGACAAAGAAGCAGATCTCGTGCTCTATGCAGTTGACAAACCGAACAG
EST: gi|211414038|gb|FK970741.1|FK970741
EST:     TCACTCCAAGGACTTGCTCGAGATCGAGCCCCTCGAGCTCCGATTCCCAT                         TCGAGACAAAGAAGCAGATCTCGTGCTCTATGCAGTTGACAAACCGAACAG
genomic: TCACTCCAAGGACTTGCTCGAGATCGAGCCCCTCGAGCTCCGATTCCCATgtacggttcc ... attctcgcagTCGAGACAAAGAAGCAGATCTCGTGCTCTATGCAGTTGACAAACCGAACAG
EST: gi|211416582|gb|FK970748.1|FK970748
EST:     TCACTCCAAGGACTTGCTCGAGATCGAGCCCCTCGAGCTCCGATTCCCAT                         TCGAGACAAAGAAGCAGATCTCGTGCTCTATGCAGTTGACAAACCGAACAG
genomic: TCACTCCAAGGACTTGCTCGAGATCGAGCCCCTCGAGCTCCGATTCCCATgtacggttcc ... attctcgcagTCGAGACAAAGAAGCAGATCTCGTGCTCTATGCAGTTGACAAACCGAACAG
EST: gi|211419126|gb|FK970760.1|FK970760
EST:     TCACTCCAAGGACTTGCTCGAGATCGAGCCCCTCGAGCTCCGATTCCCAT                         TCGAGACAAAGAAGCAGATCTCGTGCTCTATGCAGTTGACAAACCGAACAG
genomic: TCACTCCAAGGACTTGCTCGAGATCGAGCCCCTCGAGCTCCGATTCCCATgtacggttcc ... attctcgcagTCGAGACAAAGAAGCAGATCTCGTGCTCTATGCAGTTGACAAACCGAACAG
EST: gi|29543772|gb|CB604152.1|CB604152
EST:     TCACTCCAAGGACTTGCTCGAGATCGAGCCCCTCGAGCTCCGATTCCCAT                         TCGAGACAAAGAAGCAGATCTCGTGCTCTATGCAGTTGACAAACCGAACAG
genomic: TCACTCCAAGGACTTGCTCGAGATCGAGCCCCTCGAGCTCCGATTCCCATgtacggttcc ... attctcgcagTCGAGACAAAGAAGCAGATCTCGTGCTCTATGCAGTTGACAAACCGAACAG
EST: gi|149109099|gb|EE190008.2|EE190008
EST:     TCACTCCAAGGACTTGCTCGAGATCGAGCCCCTCGAGCTCCGATTCCCAT                         TCGAGACAAAGAAGCAGATCTCGTGCTCTATGCAGTTGACAAACCGAACAG
genomic: TCACTCCAAGGACTTGCTCGAGATCGAGCCCCTCGAGCTCCGATTCCCATgtacggttcc ... attctcgcagTCGAGACAAAGAAGCAGATCTCGTGCTCTATGCAGTTGACAAACCGAACAG
EST: gi|211414039|gb|FK970742.1|FK970742
EST:     TCACTCCAAGGACTTGCTCGAGATCGAGCCCCTCGAGCTCCGATTCCCAT                         TCGAGACAAAGAAGCAGATCTCGTGCTCTATGCAGTTGACAAACCGAACAG
genomic: TCACTCCAAGGACTTGCTCGAGATCGAGCCCCTCGAGCTCCGATTCCCATgtacggttcc ... attctcgcagTCGAGACAAAGAAGCAGATCTCGTGCTCTATGCAGTTGACAAACCGAACAG
EST: gi|94478824|gb|EB707782.1|EB707782
EST:     TCACTCCAAGGACTTGCTCGAGATCGAGCCCCTCGAGCTCCGATTCCCAT                         TCGAGACAAAGAAGCAGATCTCGTGCTCTATGCAGTTGACAAACCCAACAG
genomic: TCACTCCAAGGACTTGCTCGAGATCGAGCCCCTCGAGCTCCGATTCCCATgtacggttcc ... attctcgcagTCGAGACAAAGAAGCAGATCTCGTGCTCTATGCAGTTGACAAACCGAACAG
EST: gi|149104621|gb|EE290069.2|EE290069
EST:     TCACTCCAAGGACTTGCTCGAGATCGAGCCCCTCGAGCTCCGATTCCCAT                         TCGAGACAAAGAAGCAGATCTCGTGCTCTATGCAGTTGACAAACCGAACAG
genomic: TCACTCCAAGGACTTGCTCGAGATCGAGCCCCTCGAGCTCCGATTCCCATgtacggttcc ... attctcgcagTCGAGACAAAGAAGCAGATCTCGTGCTCTATGCAGTTGACAAACCGAACAG
EST: gi|211416578|gb|FK970744.1|FK970744
EST:     TCACTCCAAGGACTTGCTCGAGATCGAGCCCCTCGAGCTCCGATTCCCAT                         TCGAGACAAAGAAGCAGATCTCGTGCTCTATGCAGTTGACAAACCGAACAG
genomic: TCACTCCAAGGACTTGCTCGAGATCGAGCCCCTCGAGCTCCGATTCCCATgtacggttcc ... attctcgcagTCGAGACAAAGAAGCAGATCTCGTGCTCTATGCAGTTGACAAACCGAACAG

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), 49 (downstream exon)
Score: 326

CGTACAGCGTGCCTCCGCCTCCCGGACTCCAGCGGCGGCGGGATGTGGTCTCACTCCAAGGACTTGCTCGAGATCGAGCCCCTCGAGCTCCGATTCCCATgtacggttcc ... attctcgcagTCGAGACAAAGAAGCAGATCTCGTGCTCTATGCAGTTGACAAACCGAACAGATGACTACATCGGCTTTAAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 128

CGTACAGCGTGCCTCCGCCTCCCGGACTCCAGCGGCGGCGGGATGTGGTCTCACTCCAAGGACTTGCTCGAGATCGAGCCCCTCGAGCTCCGATTCCCATgtacggttcc ... attctcgcagTCGAGACAAAGAAGCAGATCTCGTGCTCTATGCAGTTGACAAACCGAACAGATGACTACATCGGCTTTAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 177

CGTACAGCGTGCCTCCGCCTCCCGGACTCCAGCGGCGGCGGGATGTGGTCTCACTCCAAGGACTTGCTCGAGATCGAGCCCCTCGAGCTCCGATTCCCATgtacggttcc ... attctcgcagTCGAGACAAAGAAGCAGATCTCGTGCTCTATGCAGTTGACAAACCGAACAGATGACTACATCGGCTTTAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 223

CGTACAGCGTGCCTCCGCCTCCCGGACTCCAGCGGCGGCGGGATGTGGTCTCACTCCAAGGACTTGCTCGAGATCGAGCCCCTCGAGCTCCGATTCCCATgtacggttcc ... attctcgcagTCGAGACAAAGAAGCAGATCTCGTGCTCTATGCAGTTGACAAACCGAACAGATGACTACATCGGCTTTAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgttgtcgcgttgatttctcgctcgttccttttttttccccctcattctcgcagTCGAGACAAAGAAGCAGATCTCGTGCTCTATGCAGTTGACAAACCGAACAGATGACTACATCGGCTTTAAG
         cgttgat  putative branch site (score: 223)
               tttctcgctcgttcct  CT-rich tract
                              tttttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttcccccctattttagaatataagaatgttgagggaattttggccttgttgtcgcgttgatttctcgctcgttccttttttttccccctcattctcgcagTCGAGACAAAGAAGCAGATCTCGTGCTCTATGCAGTTGACAAACCGAACAGATGACTACATCGGCTTTAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG