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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttccttgtattccagttatctgcaaaatctataatatgaatttgtcaatcttttggtttttgtgttcaaagatttctaatcaccagataatgacttgcagGGAAGACTGTTATTACCAGCGATCATGCGCTCAAACTGGAGTCTGTTCCTGATTGGATAGCCATTGTAGGAAGTGGTTATATTGGTCTTGAATTCAGTGA

Basic information

species Vitis vinifera
transcript Vv05s0077g01210.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0077g01210.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os05g06460.1 (Oryza sativa), 3'ss of exon 4
---ttccttgtattccagttatctgcaaaatctataatatgaatttgtcaatcttttggtttttgtgttcaaagatttctaatcaccagataatgacttgcagGGAAGACTGTTATTACCAGCGATCATGCGCTCAAACTGGAGTCTGTTCCTGATTGGATAGCCATTGTAGGAAGTGGTTATATTGGTCTTGAATTCAGTGA
    |      | |   |||  | |    |  | |  |    |    |   | || |   | ||||  | | |||   ||  |   ||  |  ||   ||||||||| |||||| ||||||| |||||||| || ||||| |||||||| || || |||||||| || || |||||||| || ||||| ||||||||||||||
aagattagcacaattgggtttgcagacccaaatgtgttgcctaccatttcttgttatacctattgttcttacagaagcctgctgggcaacttttg---tgcagGGAAAACTGTTTTTACCAGTGATCATGCACTAAAACTTGAGTCTGTCCCGGACTGGATAGCAATCGTTGGAAGTGGATACATTGGGCTTGAATTCAGTGA

upper sequence: Vv05s0077g01210.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os01g23610.1 (Oryza sativa), 3'ss of exon 4
--ttccttgta-ttccagttatctgcaaaatctataatatgaatttgtcaatcttttggtttttgtgttcaaagatttctaatcaccagataatgacttgcagGGAAGACTGTTATTACCAGCGATCATGCGCTCAAACTGGAGTCTGTTCCTGATTGGATAGCCATTGTAGGAAGTGGTTATATTGGTCTTGAATTCAGTGA
  | | || || | ||| |||  |  |  ||  |  | |  |  |  |  || |     ||     ||||  | |   ||   | |   ||  |    |||||| || || ||  |||| || |||||||| || ||||| ||||| |||||||| ||||| || || || ||||| ||||| ||||| || |||||||||||
gctcctttctaataccatttacatatattattcaggaaaatatgtgttgcatatgcacattcactagttcttacagagct---cgctgaatggttttatgcagGTAAAACCGTATTTACTAGTGATCATGCACTAAAACTTGAGTCAGTTCCTGACTGGATTGCTATCGTGGGAAGCGGTTACATTGGACTGGAATTCAGTGA

upper sequence: Vv05s0077g01210.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G073774_T01 (Zea mays), 3'ss of exon 4
---ttccttgtattccagttatctgcaaaatctataatatgaatt-tgtcaatcttttggtttttgtgttcaaagatttctaatcaccagataatgacttgcagGGAAGACTGTTATTACCAGCGATCATGCGCTCAAACTGGAGTCTGTTCCTGATTGGATAGCCATTGTAGGAAGTGGTTATATTGGTCTTGAATTCAGTGA
    | | | | ||   || |  ||   | |   | | ||   || |||   |   ||| | | |||  ||| | | |||||    |  ||| || |  ||||||||| |||||  |||| || |||||||| || ||||| ||||| ||||| || |||||||| ||||| ||||||||||| ||||| ||||| ||||||||
tgggtgcattttttattgtgacatgtgtattagttgacattttttgtgtactttccttgttgtatgttctcacaaaattcta----ctggatgattatatgcagGGAAAACTGTATTTACTAGTGATCATGCACTGAAACTTGAGTCAGTTCCAGACTGGATAGCTATTGTTGGAAGTGGTTACATTGGACTTGAGTTCAGTGA

upper sequence: Vv05s0077g01210.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G145595_T02 (Zea mays), 3'ss of exon 3
ttccttgtattcca-gttatctgcaaaatctataatatgaatttgtcaatcttttggtttttgtgttcaaagatttctaatcaccagataatgactt---gcagGGAAGACTGTTATTACCAGCGATCATGCGCTCAAACTGGAGTCTGTTCCTGATTGGATAGCCATTGTAGGAAGTGGTTATATTGGTCTTGAATTCAGTGA
  |||| |  |  | |||   | | | | || ||| ||| ||||||     ||    |||   | |   |    ||  ||       |  |||  ||   ||||| || |||||  |||| || |||||||| || ||||| ||||| || ||||| ||||| || ||||| ||||||||||| ||||| ||||||||||||||
--ccttatcatatatgttgcatactacagct-taa-atgcatttgttgccattcctatttcattctagcatccctttaaaagcttgcaccatggttttatgcagGTAAAACTGTATTTACTAGTGATCATGCACTAAAACTTGAGTCAGTCCCTGAATGGATTGCTATTGTTGGAAGTGGTTACATTGGACTTGAATTCAGTGA

upper sequence: Vv05s0077g01210.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: PP1S112_186V6.1 (Physcomitrella patens), 3'ss of exon 4
ttccttgtattccagttatctgcaaaatctataatatgaatttgtcaatcttttggtttttgtgttcaaa-gatt-tctaatcaccagataatgact-tgcagGGAAGACTGTTATTACCAGCGATCATGCGCTCAAACTGGAGTCTGTTCCTGATTGGATAGCCATTGTAGGAAGTGGTTATATTGGTCTTGAATTCAGTGA
      | | ||  | |   ||    ||   ||| |||  |||     |  |   | |    |||  ||| |||| |||  | | || |    |  | | |||| ||||| ||  | ||||||||||||||||| || |||||||   | || || ||||| |||||||| ||||||||||| ||||||||||| ||||| ||
--gtaagaagtcatggtcgttggtggat---taaaatgcttttaaagtttatgctggtcgattgtaaaaatgattatctcttgatcaaactgcgtgtatccagGAAAGACGGTGTTCACCAGCGATCATGCGCTGAAGCTGGAGTGGATCCCAGACTGGATTGCCATTGTTGGAAGTGGTTACATTGGTCTTGAGTTCAGCGA

upper sequence: Vv05s0077g01210.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: PP1S35_94V6.1 (Physcomitrella patens), 3'ss of exon 4
ttccttgtattccagttatctgcaaaatctataatatgaat-ttgtcaatcttttggtttttgtgttcaaag--atttctaatcaccagataatgacttgcagGGAAGACTGTTATTACCAGCGATCATGCGCTCAAACTGGAGTCTGTTCCTGATTGGATAGCCATTGTAGGAAGTGGTTATATTGGTCTTGAATTCAGTGA
             ||  |    ||   |  ||| | |  ||  | ||||   ||   ||   | | | | |   |  ||| ||    |   |  ||    |||| ||||| ||  | || || || |||||| | || |||||||   |||| || |||||  | ||||| ||||||||||| ||||||||||| ||||||||
----------gtaagaaactatcatcgttgatactttagatgctttcaaatcttgtattgccgcgataagaacaaaatctgattcatatggag-gatgctcagGAAAGACGGTGTTCACGAGTGACCATGCGTTGAAGCTGGAGTGGATTCCCGACTGGATCACTATTGTCGGAAGTGGTTACATTGGTCTTGAGTTCAGTGA

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|349826900|gb|FQ418991.1|FQ418991
EST:     CATTGCTACTGGTTCTGTTCCTTTTGTCCCAAAAGGGATTGAAGTTGATG                         GGAAGACTGTTATTACCAGCGATCATGCGCTCAAACTGGAGTCTGTTCCTG
genomic: CATTGCTACTGGTTCTGTTCCTTTTGTCCCAAAAGGGATTGAAGTTGATGgtaagcatcc ... tgacttgcagGGAAGACTGTTATTACCAGCGATCATGCGCTCAAACTGGAGTCTGTTCCTG
EST: gi|351031178|gb|FQ445005.1|FQ445005
EST:     CATTGCTACTGGTTCTGTTCCTTTTGTCCCAAAAGGGATTGAAGTTGATG                         GGAAGACTGTTATTACCAGCGATCATGCGCTCAAACTGGAGTCTGTTCCTG
genomic: CATTGCTACTGGTTCTGTTCCTTTTGTCCCAAAAGGGATTGAAGTTGATGgtaagcatcc ... tgacttgcagGGAAGACTGTTATTACCAGCGATCATGCGCTCAAACTGGAGTCTGTTCCTG
EST: gi|71877655|gb|DT026710.1|DT026710
EST:     CATTGCTACTGGTTCTGTTCCTTTTGTCCCAAAAGGGATTGAAGTTGATG                         GGAAGACTGTTATTACCAGCGATCATGCGCTCAAACTGGAGTCTGTTCCTG
genomic: CATTGCTACTGGTTCTGTTCCTTTTGTCCCAAAAGGGATTGAAGTTGATGgtaagcatcc ... tgacttgcagGGAAGACTGTTATTACCAGCGATCATGCGCTCAAACTGGAGTCTGTTCCTG
EST: gi|71877913|gb|DT026968.1|DT026968
EST:     CATTGCTACTGGTTCTGTTCCTTTTGTCCCAAAAGGGATTGAAGTTGATG                         GGAAGACTGTTATTACCAGCGATCATGCGCTCAAACTGGAGTCTGTTCCTG
genomic: CATTGCTACTGGTTCTGTTCCTTTTGTCCCAAAAGGGATTGAAGTTGATGgtaagcatcc ... tgacttgcagGGAAGACTGTTATTACCAGCGATCATGCGCTCAAACTGGAGTCTGTTCCTG
EST: gi|351022014|gb|FQ437801.1|FQ437801
EST:     CATTGCTACTGGTTCTGTTCCTTTTGTCCCAAAGGGGATTGAAGTTGATG                         GGAAGACTGTTATTACCAGCGATCAAGCGC
genomic: CATTGCTACTGGTTCTGTTCCTTTTGTCCCAAAAGGGATTGAAGTTGATGgtaagcatcc ... tgacttgcagGGAAGACTGTTATTACCAGCGATCATGCGC
EST: gi|351014262|gb|FQ434851.1|FQ434851
EST:     CATTGCTACTGGTTCTGTTCCTTTTGTCCCAAAAGGGATTGAAGTTGATG                         GGAAGACTGTTATTACCAGCGATCATGCGCTCAAACTGGAGTCTGTTCCTG
genomic: CATTGCTACTGGTTCTGTTCCTTTTGTCCCAAAAGGGATTGAAGTTGATGgtaagcatcc ... tgacttgcagGGAAGACTGTTATTACCAGCGATCATGCGCTCAAACTGGAGTCTGTTCCTG
EST: gi|351023248|gb|FQ432631.1|FQ432631
EST:     CATTGCTACTGGTTCTGTTCCTTTTGTCCCAAAAGGGATTGAAGTTGATG                         GGAAGACTGTTATTACCAGCGATCATGCGCTCAAACTGGAGTCTGTTCCTG
genomic: CATTGCTACTGGTTCTGTTCCTTTTGTCCCAAAAGGGATTGAAGTTGATGgtaagcatcc ... tgacttgcagGGAAGACTGTTATTACCAGCGATCATGCGCTCAAACTGGAGTCTGTTCCTG
EST: gi|71878131|gb|DT027186.1|DT027186
EST:     CATTGCTACTGGTTCTGTTCCTTTTGTCCCAAAAGGGATTGAAGTTGATG                         GGAAGACTGTTATTACCAGCGATCATGCGCTCAAACTGGAGTCTGTTCCTG
genomic: CATTGCTACTGGTTCTGTTCCTTTTGTCCCAAAAGGGATTGAAGTTGATGgtaagcatcc ... tgacttgcagGGAAGACTGTTATTACCAGCGATCATGCGCTCAAACTGGAGTCTGTTCCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caatcttttggtttttgtgttcaaagatttctaatcaccagataatgacttgcagGGAAGACTGTTATTACCAGCGATCATGCGCTCAAACTGGAGTCTGTTCCTGATTGGATAGCCATTGTAGGAAGTGGTTATATTGGTCTTGAATTCAGTGA
                            ttctaat  putative branch site (score: 2)
                          atttctaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttccttgtattccagttatctgcaaaatctataatatgaatttgtcaatcttttggtttttgtgttcaaagatttctaatcaccagataatgacttgcagGGAAGACTGTTATTACCAGCGATCATGCGCTCAAACTGGAGTCTGTTCCTGATTGGATAGCCATTGTAGGAAGTGGTTATATTGGTCTTGAATTCAGTGA

ttccttg
- - - - - - - - - - - caaaatc
- - - - - - - - - - - - - - - - aatatgaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgtgttc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - atcacca