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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttttgcatctgttttaatggaagaagactatgtttttttattgttcccactatcattgaagcctaacataagtttattattgtgctggataaaaaatcagGTTGACACATTGCTAGACAGTGTGAAGTGGGACAGCAAAGGGTTGGCTGTTGCCATTGCACAAAATGTGGATACTGGAGCCATTCTTATGCAGGGTTTTG

Basic information

species Zea mays
transcript GRMZM2G082214_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G082214_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os01g16940.1 (Oryza sativa), 3'ss of exon 1
-ttttgcatctgttttaatggaagaagactatgtttttttattgttcccactatcattgaagcctaacataagtttattattgtgctggataaaaaatcagGTTGACACATTGCTAGACAGTGTGAAGTGGGACAGCAAAGGGTTGGCTGTTGCCATTGCACAAAATGTGGATACTGGAGCCATTCTTATGCAGGGTTTTG
  |      |  |||||||        ||| | | |   |  | | |  | |   ||   | | || |  || |||||| |  | |||||  ||   | |||| ||  || | ||||||||||||||||||||||| ||||| ||||||||||| ||||| |||||||||||||||||||||||||| |||||||||||||
gatgcaatacaattttaatcatcatgtactgtatgtgactggtttgcttagttatatcatatcttacctaaattttattttcattctggacgaatt-ttagGTCGAAGCAATACTAGACAGTGTGAAGTGGGACAGTAAAGGCTTGGCTGTTGCTATTGCCCAAAATGTGGATACTGGAGCCATTCTCATGCAGGGTTTTG

upper sequence: GRMZM2G082214_T01 (Zea mays), 3'ss of exon 1
lower sequence: Vv14s0068g00910.t01 (Vitis vinifera), 3'ss of exon 1
----ttttgcatctgttttaatggaagaagactatgtttttttattgttcccactatcattgaagcctaacataagtttattattgtgctggataaaaaatcagGTTGACACATTGCTAGACAGTGTGAAGTGGGACAGCAAAGGGTTGGCTGTTGCCATTGCACAAAATGTGGATACTGGAGCCATTCTTATGCAGGGTTTTG
    |||  | ||||||| |    |  |      |    || | |||||||   |   ||  || |   |    |||    |||    | ||||| |   | ||||||| |||||| |||||||||||||||||||   |||||| ||||| || || || || |||||||| || || |||||  || | ||||| || ||||
ataatttgtcctctgtttcatc--accattttccttcccttcttttgttccttttggtatacaaacaagatg-gagtaaggtatctgacaggatatatt-ttagGTTGAAACATTGTTAGACAGTGTGAAGTGGGATGACAAAGGTTTGGCAGTGGCAATAGCCCAAAATGTCGACACAGGAGCAGTTTTAATGCAAGGCTTTG
















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|211369336|gb|FK959536.1|FK959536
EST:     TGTCGAGCTCCCCGCAGTCTGTGGCAGGAGCTATAACCGTCGACACCGAG                         GTTGACACATTGCTAGACAGTGTGAAGTGGGACAGCAAAGGGTTGGCTGTT
genomic: TGTCGAGCTCCCCGCAGTCTGTGGCAGGAGCTATAACCGTCGACACCGAGgtttggagtt ... aaaaaatcagGTTGACACATTGCTAGACAGTGTGAAGTGGGACAGCAAAGGGTTGGCTGTT
EST: gi|211366679|gb|FK959524.1|FK959524
EST:     TGTCGAGCTCCCCGCAGTCTGTGCCAGGAGCTATAACTGTCGACACCGAG                         GTTGACACATTGCTAGACAGTGTGAAGTGGGACAGCAAAGGGTTGGCTGTT
genomic: TGTCGAGCTCCCCGCAGTCTGTGGCAGGAGCTATAACCGTCGACACCGAGgtttggagtt ... aaaaaatcagGTTGACACATTGCTAGACAGTGTGAAGTGGGACAGCAAAGGGTTGGCTGTT
EST: gi|101400862|gb|EB822128.1|EB822128
EST:     TGTCCAGCTCCCCGCAGTCTGTGGCAGGAGCTATAACCGTCGACACCGAG                         GTTGACACATTGCTACACAGTGTGAAGTGGGACAGCAAAGGGTTGGCTGTT
genomic: TGTCGAGCTCCCCGCAGTCTGTGGCAGGAGCTATAACCGTCGACACCGAGgtttggagtt ... aaaaaatcagGTTGACACATTGCTAGACAGTGTGAAGTGGGACAGCAAAGGGTTGGCTGTT
EST: gi|211366684|gb|FK959529.1|FK959529
EST:     TGTCGAGCTCCCCGCAGTCTGTGGCAGGAGCTATAACCGTCGACACCGAG                         GTTGACACATTGCTAGACAGTGTGAAGTGGGACAGCAAAGGGTTGGCTGTT
genomic: TGTCGAGCTCCCCGCAGTCTGTGGCAGGAGCTATAACCGTCGACACCGAGgtttggagtt ... aaaaaatcagGTTGACACATTGCTAGACAGTGTGAAGTGGGACAGCAAAGGGTTGGCTGTT
EST: gi|211366675|gb|FK959520.1|FK959520
EST:     TGTCGAGCTCCCCGCAGTCTGTGGCAGGAGCTATAACCGTCGACACCGAG                         GTTGACACATTGCTAGACAGTGTGAAGTGGGACAGCAAAGGGTTGGCTGTT
genomic: TGTCGAGCTCCCCGCAGTCTGTGGCAGGAGCTATAACCGTCGACACCGAGgtttggagtt ... aaaaaatcagGTTGACACATTGCTAGACAGTGTGAAGTGGGACAGCAAAGGGTTGGCTGTT
EST: gi|211369332|gb|FK959532.1|FK959532
EST:     TGTCGAGCTCCCCGCAGTCTGTGGCAGGAGCTATAACCGTCGACACCGAG                         GTTGACACATTGCTAGACAGTGTGAAGTGGGACAGCAAAGGGTTGGCTGTT
genomic: TGTCGAGCTCCCCGCAGTCTGTGGCAGGAGCTATAACCGTCGACACCGAGgtttggagtt ... aaaaaatcagGTTGACACATTGCTAGACAGTGTGAAGTGGGACAGCAAAGGGTTGGCTGTT
EST: gi|32935051|gb|CF039863.1|CF039863
EST:     TGTCGAGCTCCCCGCAGTCTGTGGCAGGAGCTATAACCGTCGACACCGAG                         GTTGACACATTGCTAGACAGTGTGAAGTGGGACAGCAAAGGGTTGGCTGTT
genomic: TGTCGAGCTCCCCGCAGTCTGTGGCAGGAGCTATAACCGTCGACACCGAGgtttggagtt ... aaaaaatcagGTTGACACATTGCTAGACAGTGTGAAGTGGGACAGCAAAGGGTTGGCTGTT
EST: gi|211366680|gb|FK959525.1|FK959525
EST:     TGTCGAGCTCCCCGCAGTCTGTGGCAGGAGCTATAACCGTCGACACCGAG                         GTTGACACATTGCTAGACAGTGTGAAGTGGGACAGCAAAGGGTTGGCTGTT
genomic: TGTCGAGCTCCCCGCAGTCTGTGGCAGGAGCTATAACCGTCGACACCGAGgtttggagtt ... aaaaaatcagGTTGACACATTGCTAGACAGTGTGAAGTGGGACAGCAAAGGGTTGGCTGTT
EST: gi|148987058|gb|EE030883.2|EE030883
EST:     TGTCGAGCTCCCCGCAGTCTGTGGCAGGAGCTATAACCGTCGACACCGAG                         GTTGACACATTGCTAGACAGTGTGAAGTGGGACAGCAAAGGGTTGGCTGTT
genomic: TGTCGAGCTCCCCGCAGTCTGTGGCAGGAGCTATAACCGTCGACACCGAGgtttggagtt ... aaaaaatcagGTTGACACATTGCTAGACAGTGTGAAGTGGGACAGCAAAGGGTTGGCTGTT
EST: gi|211366676|gb|FK959521.1|FK959521
EST:     TGTCGAGCTCCCCGCAGTCTGTGCCAGGAGCTATAACTGTCGACACCGAG                         GTTGACACATTGCTAGACAGTGTGAAGTGGGACAGCAAAGGGTTGGCTGTT
genomic: TGTCGAGCTCCCCGCAGTCTGTGGCAGGAGCTATAACCGTCGACACCGAGgtttggagtt ... aaaaaatcagGTTGACACATTGCTAGACAGTGTGAAGTGGGACAGCAAAGGGTTGGCTGTT
EST: gi|211366678|gb|FK959523.1|FK959523
EST:     TGTCGAGCTCCCCGCAGTCTGTGGCAGGAGCTATAACCGTCGACACCGAG                         GTTGACACATTGCTAGACAGTGTGAAGTGGGACAGCAAAGGGTTGGCTGTT
genomic: TGTCGAGCTCCCCGCAGTCTGTGGCAGGAGCTATAACCGTCGACACCGAGgtttggagtt ... aaaaaatcagGTTGACACATTGCTAGACAGTGTGAAGTGGGACAGCAAAGGGTTGGCTGTT
EST: gi|211366685|gb|FK959530.1|FK959530
EST:     TGTCGAGCTCCCCGCAGTCTGTGCCAGGAGCTATAACTGTCGACACCGAG                         GTTGACACATTGCTAGACAGTGTGAAGTGGGACAGCAAAGGGTTGGCTGTT
genomic: TGTCGAGCTCCCCGCAGTCTGTGGCAGGAGCTATAACCGTCGACACCGAGgtttggagtt ... aaaaaatcagGTTGACACATTGCTAGACAGTGTGAAGTGGGACAGCAAAGGGTTGGCTGTT
EST: gi|20811241|gb|BQ295719.1|BQ295719
EST:     TGTCGAGCTCCCCGCAGTCTGTGGCAGGAGCTATAACCGTCGACACCGAG                         GTTGACACATTGCTAGACAGTGTGAAGTGGGACAGCAAAGGGTTGGTTGTT
genomic: TGTCGAGCTCCCCGCAGTCTGTGGCAGGAGCTATAACCGTCGACACCGAGgtttggagtt ... aaaaaatcagGTTGACACATTGCTAGACAGTGTGAAGTGGGACAGCAAAGGGTTGGCTGTT
EST: gi|61118955|gb|DN559916.1|DN559916
EST:     TGTCGAGCTCCCCGCAGTCTGTGGCAGGAGCTATAACTGTCGACACCGAG                         GTTGACACATTGCTAGACAGTGTGAAGTGGGACAGCAAAGGGTTGGCTGTT
genomic: TGTCGAGCTCCCCGCAGTCTGTGGCAGGAGCTATAACCGTCGACACCGAGgtttggagtt ... aaaaaatcagGTTGACACATTGCTAGACAGTGTGAAGTGGGACAGCAAAGGGTTGGCTGTT
EST: gi|26457028|gb|CA828611.1|CA828611
EST:     TCGAGCTCCCCGCAGTCTGTGGCAGGAGCTATAACCGTCGACACCGAG                         GTTGACACATTGCTAGACAGTGTGAAGTGGGACAGCAAAGGGTTGGCTGTT
genomic: TCGAGCTCCCCGCAGTCTGTGGCAGGAGCTATAACCGTCGACACCGAGgtttggagtt ... aaaaaatcagGTTGACACATTGCTAGACAGTGTGAAGTGGGACAGCAAAGGGTTGGCTGTT
EST: gi|37425598|gb|CF650545.1|CF650545
EST:     TGTCGAGCTCCCCGCAGTCTGTGGCAGGAGCTATAACCGTCGACACCGAG                         GTTGACACATTGCTAGACAGTGTGAAGTGGGACAGCAAAGGGTTGGCTGTT
genomic: TGTCGAGCTCCCCGCAGTCTGTGGCAGGAGCTATAACCGTCGACACCGAGgtttggagtt ... aaaaaatcagGTTGACACATTGCTAGACAGTGTGAAGTGGGACAGCAAAGGGTTGGCTGTT

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: 69

TTCGGCCCCTGGGTGGCGGCGCAGGGAGCCGTACCCGGCAGTCTCCGTAGTGTCGAGCTCCCCGCAGTCTGTGGCAGGAGCTATAACCGTCGACACCGAGgtttggagtt ... aaaaaatcagGTTGACACATTGCTAGACAGTGTGAAGTGGGACAGCAAAGGGTTGGCTGTTGCCATTGCACAAAATGTGGATACTGGAGCCATTCTTATGCAGGGTTTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 117

TTCGGCCCCTGGGTGGCGGCGCAGGGAGCCGTACCCGGCAGTCTCCGTAGTGTCGAGCTCCCCGCAGTCTGTGGCAGGAGCTATAACCGTCGACACCGAGgtttggagtt ... aaaaaatcagGTTGACACATTGCTAGACAGTGTGAAGTGGGACAGCAAAGGGTTGGCTGTTGCCATTGCACAAAATGTGGATACTGGAGCCATTCTTATGCAGGGTTTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 57

TTCGGCCCCTGGGTGGCGGCGCAGGGAGCCGTACCCGGCAGTCTCCGTAGTGTCGAGCTCCCCGCAGTCTGTGGCAGGAGCTATAACCGTCGACACCGAGgtttggagtt ... aaaaaatcagGTTGACACATTGCTAGACAGTGTGAAGTGGGACAGCAAAGGGTTGGCTGTTGCCATTGCACAAAATGTGGATACTGGAGCCATTCTTATGCAGGGTTTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 32

TTCGGCCCCTGGGTGGCGGCGCAGGGAGCCGTACCCGGCAGTCTCCGTAGTGTCGAGCTCCCCGCAGTCTGTGGCAGGAGCTATAACCGTCGACACCGAGgtttggagtt ... aaaaaatcagGTTGACACATTGCTAGACAGTGTGAAGTGGGACAGCAAAGGGTTGGCTGTTGCCATTGCACAAAATGTGGATACTGGAGCCATTCTTATGCAGGGTTTTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cccactatcattgaagcctaacataagtttattattgtgctggataaaaaatcagGTTGACACATTGCTAGACAGTGTGAAGTGGGACAGCAAAGGGTTGGCTGTTGCCATTGCACAAAATGTGGATACTGGAGCCATTCTTATGCAGGGTTTTG
               gcctaac  putative branch site (score: 32)
                  taacataagtttatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttttgcatctgttttaatggaagaagactatgtttttttattgttcccactatcattgaagcctaacataagtttattattgtgctggataaaaaatcagGTTGACACATTGCTAGACAGTGTGAAGTGGGACAGCAAAGGGTTGGCTGTTGCCATTGCACAAAATGTGGATACTGGAGCCATTCTTATGCAGGGTTTTG

- - gcatctg
- - - - - - - - - -gaagaaga
- - - - - - - - - - - - - - - tgttttt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aacataa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtgctgg