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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agcatatcatcttcatatcaaataagctaaaatacaacagtgcttttgatatttgttaatggtcatatcatttgtttactcttgactcttctgccttcagTTCTGGTGGAAACATTGGACAAGTGCTTCAAAAATGTATGCGAGCTTGACATAGTGTTCAATTATAGCAAG

Basic information

species Vitis vinifera
transcript Vv04s0023g01770.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


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

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

upper sequence: Vv04s0023g01770.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA02G06350.2 (Glycine max), 3'ss of exon 5
agcatatcatcttcatatcaaataagctaaaatacaacagtgcttttgatatttgttaat--ggtcatatcatttgtttactcttgactcttctgccttcagTTCTGGTGGAAACATTGGACAAGTGCTTCAAAAATGTATGCGAGCTTGACATAGTGTTCAATTATAGCAAG
 |  |||  |    || |   |  || |    ||  || |    ||  ||  ||||||||   ||  | | ||||| ||||| |   |  ||||||||||||| || ||||||||||||||||| ||||||| ||||||||| |||||||| || |||||||| ||||| |||
-ggctattgtgcaaatgtgctaacagttgtt-tattactgcctcttacattgttgttaattttgtggtttgatttgcttactttgtccctttctgccttcagTGCTTGTGGAAACATTGGACAAATGCTTCAGAAATGTATGTGAGCTTGATATCGTGTTCAACTATAGTAAG

upper sequence: Vv04s0023g01770.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA16G25400.1 (Glycine max), 3'ss of exon 5
agcatatcatcttcatatcaaataagctaaaatacaacagtgcttttgatatttgttaat--ggtcatatcatttgtttactcttgactcttctgccttcagTTCTGGTGGAAACATTGGACAAGTGCTTCAAAAATGTATGCGAGCTTGACATAGTGTTCAATTATAGCAAG
 |  | |  | |  || |   |  || |    ||   |||    ||  ||  ||||||||    |    | ||||| ||||| |   |  |||||||||||||  | || |||||||||||||| ||||||| ||||||||| |||||||| || |||||||| ||||| |||
-ggcttttgtgtagatgtgctaacagttgtt-tattgcagcctcttacattgttgttaattttatggattgatttgcttactttgttcctttctgccttcagTGTTTGTTGAAACATTGGACAAATGCTTCAGAAATGTATGTGAGCTTGATATCGTGTTCAACTATAGTAAG

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|294966870|gb|GW839745.1|GW839745
EST:     TGTATTTGATAGTTCTGAAAATGAGTTAGCCATGCTTGATTTGATACAAG                         TTCTGGTGGAAACATTGGACAAGTGCTTCAAAAATGTATGCGAGCTTGACA
genomic: TGTATTTGATAGTTCTGAAAATGAGTTAGCCATGCTTGATTTGATACAAGgtatgtgcta ... ctgccttcagTTCTGGTGGAAACATTGGACAAGTGCTTCAAAAATGTATGCGAGCTTGACA
EST: gi|161719015|gb|FC067635.1|FC067635
EST:     TGTATTTGATAGTTCTGAAAATGAGTTAGCCATGCTTGATTTGATACAAG                         TTCTGGTGGAAACATTGGACAAGTGCTTCAAAAATGTATGCGAGCTTGACA
genomic: TGTATTTGATAGTTCTGAAAATGAGTTAGCCATGCTTGATTTGATACAAGgtatgtgcta ... ctgccttcagTTCTGGTGGAAACATTGGACAAGTGCTTCAAAAATGTATGCGAGCTTGACA
EST: gi|161718282|gb|FC066033.1|FC066033
EST:     TGTATTTGATAGTTCTGAAAATGAGTTAGCCATGCTTGATTTGATACAAG                         TTCTGGTGGAAACATTGGACAAGTGCTTCAAAAATGTATGCGAGCTTGACA
genomic: TGTATTTGATAGTTCTGAAAATGAGTTAGCCATGCTTGATTTGATACAAGgtatgtgcta ... ctgccttcagTTCTGGTGGAAACATTGGACAAGTGCTTCAAAAATGTATGCGAGCTTGACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgatatttgttaatggtcatatcatttgtttactcttgactcttctgccttcagTTCTGGTGGAAACATTGGACAAGTGCTTCAAAAATGTATGCGAGCTTGACATAGTGTTCAATTATAGCAAG
                                  tcttgac  putative branch site (score: 3)
                                        ctcttctgccttc  CT-rich tract
                   atatcatttgttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agcatatcatcttcatatcaaataagctaaaatacaacagtgcttttgatatttgttaatggtcatatcatttgtttactcttgactcttctgccttcagTTCTGGTGGAAACATTGGACAAGTGCTTCAAAAATGTATGCGAGCTTGACATAGTGTTCAATTATAGCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - -catcttc
- - - - - - - - - caaataa
- - - - - - - - - - - - - - aaaatac