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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ataactgaagacttattttgtcttccttttgtctaaaaggacttatcagctctggttctaggagattgatcactctatactaactttgtctcgtgcacagTGTTTGTTGAAACATTGGACAGATGCTTCAAGAATGTATGCGAGCTTGACATCGTATTTAACTTCAACAAGGTACCATATGTCCATATGATCCTACTTTT

Basic information

species Zea mays
transcript GRMZM2G177914_T05
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G177914_T05 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os03g12710.1 (Oryza sativa), 3'ss of exon 5
ataactgaagacttattttgtcttccttttgtctaaaaggacttatcagctctggttctaggagattgatcactctatactaa-ctttgtctcgtgcacagTGTTTGTTGAAACATTGGACAGATGCTTCAAGAATGTATGCGAGCTTGACATCGTATTTAACTTCAACAAGGTACCATATGTCCATATGATCCTACTTTT
|   ||    |||| | ||   |||  |||  ||    |   ||||||||  || ||  || ||||  || | ||| ||  || |||| ||| ||||||||| ||||||||||||||||||||||||||||||||||| || ||||||||||||||||||||||||||||||                             
agctcttttcacttctgttaagttcactttaactccccgt-tttatcagccatgattgcagcagatcaattaatctgtagaaaactttatcttgtgcacagTTTTTGTTGAAACATTGGACAGATGCTTCAAGAATGTGTGTGAGCTTGACATCGTATTTAACTTCAACAAG-----------------------------

upper sequence: GRMZM2G177914_T05 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os01g25110.1 (Oryza sativa), 3'ss of exon 4
--ataactgaagacttattttgtcttccttttgtctaaaaggacttatcagctctggttctaggagattgatcactctatactaactttgtctcgtgcacagTGTTTGTTGAAACATTGGACAGATGCTTCAAGAATGTATGCGAGCTTGACATCGTATTTAACTTCAACAAGGTACCATATGTCCATATGATCCTACTTTT
  | | |   |     | |     | |  ||        |    ||||||||  || ||   | ||||  || | ||| ||  |||||| ||| ||||||||| ||||||||||||||||||||||||||||||||||| || |||||| |||| ||||||||||||||||||                             
gcacagcctcaaggacagtaaaaatgctcttaactctccat--tttatcagccatgattgcggcagatcaattaatctgtagaaactttatcttgtgcacagTTTTTGTTGAAACATTGGACAGATGCTTCAAGAATGTGTGTGAGCTTCACATTGTATTTAACTTCAACAAG-----------------------------

upper sequence: GRMZM2G177914_T05 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA16G25400.1 (Glycine max), 3'ss of exon 5
-ataactgaagacttattttgtcttccttttgtctaaaaggacttat-cagctctggttctaggagattgatcactctatactaactttgtctcgtgcacagTGTTTGTTGAAACATTGGACAGATGCTTCAAGAATGTATGCGAGCTTGACATCGTATTTAACTTCAACAAGGTACCATATGTCCATATGATCCTACTTTT
      ||   |  | |  |  |     ||| | |  |    ||||    | | |   | |    |||||||     ||   |     | ||| |    |||||||||||||||||||||||| ||||||||  |||||||| |||||||| ||||| || ||||  |  |||                             
ggcttttgtgtagatgtgctaacagttgtttat-tgcagcctcttacattgttgttaattttatggattgatttgcttactttgttcctttct-gccttcagTGTTTGTTGAAACATTGGACAAATGCTTCAGAAATGTATGTGAGCTTGATATCGTGTTCAACTATAGTAAG-----------------------------

upper sequence: GRMZM2G177914_T05 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA02G06350.2 (Glycine max), 3'ss of exon 5
-ataactgaagacttattttgtcttccttttgtctaaaaggacttat-cagctctggttctaggagattgatcactctatactaactttgtctcgtgcacagTGTTTGTTGAAACATTGGACAGATGCTTCAAGAATGTATGCGAGCTTGACATCGTATTTAACTTCAACAAGGTACCATATGTCCATATGATCCTACTTTT
    | ||   |  | |  |  |     ||| | ||      ||||    | | |   | | |  | |||||     ||   |  |  | ||| |    ||||| |||| ||||||||||||| ||||||||  |||||||| |||||||| ||||| || ||||  |  |||                             
ggctattgtgcaaatgtgctaacagttgtttat-tactgcctcttacattgttgttaattttgtggtttgatttgcttactttgtccctttct-gccttcagTGCTTGTGGAAACATTGGACAAATGCTTCAGAAATGTATGTGAGCTTGATATCGTGTTCAACTATAGTAAG-----------------------------

upper sequence: GRMZM2G177914_T05 (Zea mays), 3'ss of exon 4
lower sequence: Vv04s0023g01770.t01 (Vitis vinifera), 3'ss of exon 4
ataactgaagacttattttgtcttc-cttttgtctaaaaggacttatcagctctggttctaggagattgatcactctatactaactttgtctcgtgcacagTGTTTGTTGAAACATTGGACAGATGCTTCAAGAATGTATGCGAGCTTGACATCGTATTTAACTTCAACAAGGTACCATATGTCCATATGATCCTACTTTT
|  |    |   | || |    |   ||    |  || ||  ||| | |  | || |  | |     | ||   | ||  ||    |  ||| |    ||||  | || |||||||||||||  |||||||| |||||||||||||||||||| || || || |  | ||||                             
agcatatcatcttcatatcaaataagctaaaatacaacagtgcttttgatatttgttaatggtcatatcatttgtttactcttgactcttct-gccttcagTTCTGGTGGAAACATTGGACAAGTGCTTCAAAAATGTATGCGAGCTTGACATAGTGTTCAATTATAGCAAG-----------------------------

upper sequence: GRMZM2G177914_T05 (Zea mays), 3'ss of exon 4
lower sequence: PP1S128_112V6.1 (Physcomitrella patens), 3'ss of exon 4
---------------------------------------------------ataactgaagacttattttgtcttccttttgtctaaaag-----gacttatcagctct--ggttctaggagattgatcactctatac--taactttgtctcgtgca------cagTGTTTGTTGAAACATTGGACAGATGCTTCAAGAATGTATGCGAGCTTGACATCGTATTTAACTTCAACAAGGTACCATATGTCCATATGATCCTACTTTT
                                                   |  ||| ||  | | ||    ||    |  |   |||||      |  ||| |  | |   |  | |      |  ||| ||| | |    |  |  |||  || |      |||||||||| || ||||||||| |||| ||||||||||| || |||||||| || || |  ||||||  ||||                             
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|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


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcagctctggttctaggagattgatcactctatactaactttgtctcgtgcacagTGTTTGTTGAAACATTGGACAGATGCTTCAAGAATGTATGCGAGCTTGACATCGTATTTAACTTCAACAAGGTACCATATGTCCATATGATCCTACTTTT
                                tactaac  putative branch site (score: 0)
                                      ctttgtctc  CT-rich tract
                              tatactaa  TA-rich tract