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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ataactgaagacttattttgtcttccttttgtctaaaaggacttatcagctctggttctaggagattgatcactctatactaactttgtctcgtgcacagTGTTTGTTGAAACATTGGACAGATGCTTCAAGAATGTATGCGAGCTTGACATCGTATTTAACTTCAACAAG

Basic information

species Zea mays
transcript GRMZM2G177914_T03
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G177914_T03 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os03g12710.1 (Oryza sativa), 3'ss of exon 5
ataactgaagacttattttgtcttccttttgtctaaaaggacttatcagctctggttctaggagattgatcactctatactaa-ctttgtctcgtgcacagTGTTTGTTGAAACATTGGACAGATGCTTCAAGAATGTATGCGAGCTTGACATCGTATTTAACTTCAACAAG
|   ||    |||| | ||   |||  |||  ||    |   ||||||||  || ||  || ||||  || | ||| ||  || |||| ||| ||||||||| ||||||||||||||||||||||||||||||||||| || ||||||||||||||||||||||||||||||
agctcttttcacttctgttaagttcactttaactccccgt-tttatcagccatgattgcagcagatcaattaatctgtagaaaactttatcttgtgcacagTTTTTGTTGAAACATTGGACAGATGCTTCAAGAATGTGTGTGAGCTTGACATCGTATTTAACTTCAACAAG

upper sequence: GRMZM2G177914_T03 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os01g25110.1 (Oryza sativa), 3'ss of exon 4
--ataactgaagacttattttgtcttccttttgtctaaaaggacttatcagctctggttctaggagattgatcactctatactaactttgtctcgtgcacagTGTTTGTTGAAACATTGGACAGATGCTTCAAGAATGTATGCGAGCTTGACATCGTATTTAACTTCAACAAG
  | | |   |     | |     | |  ||        |    ||||||||  || ||   | ||||  || | ||| ||  |||||| ||| ||||||||| ||||||||||||||||||||||||||||||||||| || |||||| |||| ||||||||||||||||||
gcacagcctcaaggacagtaaaaatgctcttaactctccat--tttatcagccatgattgcggcagatcaattaatctgtagaaactttatcttgtgcacagTTTTTGTTGAAACATTGGACAGATGCTTCAAGAATGTGTGTGAGCTTCACATTGTATTTAACTTCAACAAG

upper sequence: GRMZM2G177914_T03 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA16G25400.1 (Glycine max), 3'ss of exon 5
-ataactgaagacttattttgtcttccttttgtctaaaaggacttat-cagctctggttctaggagattgatcactctatactaactttgtctcgtgcacagTGTTTGTTGAAACATTGGACAGATGCTTCAAGAATGTATGCGAGCTTGACATCGTATTTAACTTCAACAAG
      ||   |  | |  |  |     ||| | |  |    ||||    | | |   | |    |||||||     ||   |     | ||| |    |||||||||||||||||||||||| ||||||||  |||||||| |||||||| ||||| || ||||  |  |||
ggcttttgtgtagatgtgctaacagttgtttat-tgcagcctcttacattgttgttaattttatggattgatttgcttactttgttcctttct-gccttcagTGTTTGTTGAAACATTGGACAAATGCTTCAGAAATGTATGTGAGCTTGATATCGTGTTCAACTATAGTAAG

upper sequence: GRMZM2G177914_T03 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA02G06350.2 (Glycine max), 3'ss of exon 5
-ataactgaagacttattttgtcttccttttgtctaaaaggacttat-cagctctggttctaggagattgatcactctatactaactttgtctcgtgcacagTGTTTGTTGAAACATTGGACAGATGCTTCAAGAATGTATGCGAGCTTGACATCGTATTTAACTTCAACAAG
    | ||   |  | |  |  |     ||| | ||      ||||    | | |   | | |  | |||||     ||   |  |  | ||| |    ||||| |||| ||||||||||||| ||||||||  |||||||| |||||||| ||||| || ||||  |  |||
ggctattgtgcaaatgtgctaacagttgtttat-tactgcctcttacattgttgttaattttgtggtttgatttgcttactttgtccctttct-gccttcagTGCTTGTGGAAACATTGGACAAATGCTTCAGAAATGTATGTGAGCTTGATATCGTGTTCAACTATAGTAAG

upper sequence: GRMZM2G177914_T03 (Zea mays), 3'ss of exon 4
lower sequence: Vv04s0023g01770.t01 (Vitis vinifera), 3'ss of exon 4
ataactgaagacttattttgtcttc-cttttgtctaaaaggacttatcagctctggttctaggagattgatcactctatactaactttgtctcgtgcacagTGTTTGTTGAAACATTGGACAGATGCTTCAAGAATGTATGCGAGCTTGACATCGTATTTAACTTCAACAAG
|  |    |   | || |    |   ||    |  || ||  ||| | |  | || |  | |     | ||   | ||  ||    |  ||| |    ||||  | || |||||||||||||  |||||||| |||||||||||||||||||| || || || |  | ||||
agcatatcatcttcatatcaaataagctaaaatacaacagtgcttttgatatttgttaatggtcatatcatttgtttactcttgactcttct-gccttcagTTCTGGTGGAAACATTGGACAAGTGCTTCAAAAATGTATGCGAGCTTGACATAGTGTTCAATTATAGCAAG

upper sequence: GRMZM2G177914_T03 (Zea mays), 3'ss of exon 4
lower sequence: PP1S128_112V6.1 (Physcomitrella patens), 3'ss of exon 4
---------------------------------------------------ataactgaagacttattttgtcttccttttgtctaaaag-----gacttatcagctct--ggttctaggagattgatcactctatac--taactttgtctcgtgca------cagTGTTTGTTGAAACATTGGACAGATGCTTCAAGAATGTATGCGAGCTTGACATCGTATTTAACTTCAACAAG
                                                   |  ||| ||  | | ||    ||    |  |   |||||      |  ||| |  | |   |  | |      |  ||| ||| | |    |  |  |||  || |      |||||||||| || ||||||||| |||| ||||||||||| || |||||||| || || |  ||||||  ||||
gtatgttttctgaagagagattctaattctaccttaccttgttatcctactagtactaaatgcat-ttgaagctaggatcagaggaaaagctattaatctatgatttttttagcccaaatctgcttgtcaatcttttcagcgaagtgttcttctggaactttgcagTGTTTGTAGAGACATTGGACCGATGTTTCAAGAATGTCTGTGAGCTTGATATAGTTTACAACTTCGGCAAG

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|211467101|gb|FK972980.1|FK972980
EST:     -G------ATAGCTCTGAGAACGAGCTTGCCATGCTCGACCTCGTACAAG                         TGTTTGTTGAAACATTGGACAGA
genomic: TGTCTTTGATAGCTCTGAGAACGAGCTTGCCATGCTCGACCTCGTACAAGgtaacccaat ... tcgtgcacagTGTTTGTTGAAACATTGGACAGA
EST: gi|71447059|gb|DR828109.1|DR828109
EST:     TGTCTTTGATAGCTCTGAGAACGAGCTTGCCATGCTCGACCTCGTACAAG                         TGTTTGTTGAAACATTGGACAGATGCTTCAAGAATGTATGCGAGCTTGACA
genomic: TGTCTTTGATAGCTCTGAGAACGAGCTTGCCATGCTCGACCTCGTACAAGgtaacccaat ... tcgtgcacagTGTTTGTTGAAACATTGGACAGATGCTTCAAGAATGTATGCGAGCTTGACA
EST: gi|149090359|gb|EE179665.2|EE179665
EST:     TGTCTTTGATAGCTCTGAGAACGAGCTTGCCATGCTCGACCTCGTACAAG                         TGTTTGTTGAAACATTGGACAGATGNCTTCA-GAATGTATGCGAGCTTGAC
genomic: TGTCTTTGATAGCTCTGAGAACGAGCTTGCCATGCTCGACCTCGTACAAGgtaacccaat ... tcgtgcacagTGTTTGTTGAAACATTGGACAGATG-CTTCAAGAATGTATGCGAGCTTGAC
EST: gi|149073163|gb|EE161440.2|EE161440
EST:     TGTCTTTGATAGCTCTGAGAACGAGCTTGCCATGCTCGACCTCGTACAAG                         TGTTTGTTGAAACATTGGACAGATGCTTCAAGAATGTATGCGAGCTTGACA
genomic: TGTCTTTGATAGCTCTGAGAACGAGCTTGCCATGCTCGACCTCGTACAAGgtaacccaat ... tcgtgcacagTGTTTGTTGAAACATTGGACAGATGCTTCAAGAATGTATGCGAGCTTGACA
EST: gi|211467090|gb|FK972969.1|FK972969
EST:     GTCTTTGATAGCTCTGAAGAACGAGCTTGCCATGCTCGACCTCGTACAAG                         TGTTTGTTGAAACATTGGACAGATGCTTCAAGAATGTATGCGAGCTTGACA
genomic: GTCTTTGATAGCTCTGA-GAACGAGCTTGCCATGCTCGACCTCGTACAAGgtaacccaat ... tcgtgcacagTGTTTGTTGAAACATTGGACAGATGCTTCAAGAATGTATGCGAGCTTGACA
EST: gi|5499044|gb|AI854911.1|AI854911
EST:     TGTCTTTGATAGCTCTGAGAACGAGCTTGCCATGCTCGACCTCGTACAAG                         TGTTTGTTGAAACATTGGACAGATGCTTCAAGAATGTATGCGAGCTTGACA
genomic: TGTCTTTGATAGCTCTGAGAACGAGCTTGCCATGCTCGACCTCGTACAAGgtaacccaat ... tcgtgcacagTGTTTGTTGAAACATTGGACAGATGCTTCAAGAATGTATGCGAGCTTGACA
EST: gi|211472147|gb|FK972996.1|FK972996
EST:     TGTCTTTGATAGCTCTGAGAACGAGCTTGCCATGCTCGACCTCGTACAAG                         TGTTTGTTGAAACATTGGACAGATGCTT
genomic: TGTCTTTGATAGCTCTGAGAACGAGCTTGCCATGCTCGACCTCGTACAAGgtaacccaat ... tcgtgcacagTGTTTGTTGAAACATTGGACAGATGCTT
EST: gi|211467100|gb|FK972979.1|FK972979
EST:     TGTCTTTGATAGCTCTGAGAACGAGCTTGCCATGCTCGACCTCGTACAAG                         TGTTTGTTGAAACATTGGACAGATGCTTCAAGAATGTATGCGAGCTTGACA
genomic: TGTCTTTGATAGCTCTGAGAACGAGCTTGCCATGCTCGACCTCGTACAAGgtaacccaat ... tcgtgcacagTGTTTGTTGAAACATTGGACAGATGCTTCAAGAATGTATGCGAGCTTGACA
EST: gi|211467088|gb|FK972967.1|FK972967
EST:     TGTCTTTGATAGCTCTGAGAACGAGCTTGCCATGCTCGACCTCGTACAAG                         TGTTTTGT-GAAAACAT-GGACAGATGCTTTCA-GAATGTATGCGAGCTTG
genomic: TGTCTTTGATAGCTCTGAGAACGAGCTTGCCATGCTCGACCTCGTACAAGgtaacccaat ... tcgtgcacagTGTTT-GTTGAAA-CATTGGACAGATGCTT-CAAGAATGTATGCGAGCTTG
EST: gi|211469626|gb|FK972993.1|FK972993
EST:     TGTCTTTGATAGCTCTGAGAACGAGCTTGCCATGCTCGACCTCGTACAAG                         TGTTTGTTGAAACATTGGACAGATGCT
genomic: TGTCTTTGATAGCTCTGAGAACGAGCTTGCCATGCTCGACCTCGTACAAGgtaacccaat ... tcgtgcacagTGTTTGTTGAAACATTGGACAGATGCT

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: 45 (upstream exon), 49 (downstream exon)
Score: 145

GGAACAAAAATGGTCTACAAGCATTTGGCCACACTATACTTTGTTTTTGTCTTTGATAGCTCTGAGAACGAGCTTGCCATGCTCGACCTCGTACAAGgtaacccaat ... tcgtgcacagTGTTTGTTGAAACATTGGACAGATGCTTCAAGAATGTATGCGAGCTTGACATCGTATTTAACTTCAACAAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 175

GGAACAAAAATGGTCTACAAGCATTTGGCCACACTATACTTTGTTTTTGTCTTTGATAGCTCTGAGAACGAGCTTGCCATGCTCGACCTCGTACAAGgtaacccaat ... tcgtgcacagTGTTTGTTGAAACATTGGACAGATGCTTCAAGAATGTATGCGAGCTTGACATCGTATTTAACTTCAACAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 182

GGAACAAAAATGGTCTACAAGCATTTGGCCACACTATACTTTGTTTTTGTCTTTGATAGCTCTGAGAACGAGCTTGCCATGCTCGACCTCGTACAAGgtaacccaat ... tcgtgcacagTGTTTGTTGAAACATTGGACAGATGCTTCAAGAATGTATGCGAGCTTGACATCGTATTTAACTTCAACAAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 158

GGAACAAAAATGGTCTACAAGCATTTGGCCACACTATACTTTGTTTTTGTCTTTGATAGCTCTGAGAACGAGCTTGCCATGCTCGACCTCGTACAAGgtaacccaat ... tcgtgcacagTGTTTGTTGAAACATTGGACAGATGCTTCAAGAATGTATGCGAGCTTGACATCGTATTTAACTTCAACAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcagctctggttctaggagattgatcactctatactaactttgtctcgtgcacagTGTTTGTTGAAACATTGGACAGATGCTTCAAGAATGTATGCGAGCTTGACATCGTATTTAACTTCAACAAG
                                tactaac  putative branch site (score: 158)
                                      ctttgtctc  CT-rich tract
                              tatactaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ataactgaagacttattttgtcttccttttgtctaaaaggacttatcagctctggttctaggagattgatcactctatactaactttgtctcgtgcacagTGTTTGTTGAAACATTGGACAGATGCTTCAAGAATGTATGCGAGCTTGACATCGTATTTAACTTCAACAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT