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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatatatctactctttttctaaattttttttctgggtagttgctgataataccatgaagagctgtggaataacaagaaatacccgtgttgaagtttctaactgataatctaccttatacattttgacagGTTCTTGGAAAATGTCAGCTTCAGGAGGCTGTCCAGGAAAAGGAAGAGGGTCTAGGCTCCATTG

Basic information

species Vitis vinifera
transcript Vv16s0050g02480.t01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv16s0050g02480.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: AC234203.1_FGT004 (Zea mays), 3'ss of exon 8
gtaatatatctactctttttctaaattttttttctgggtagttgctgataataccatgaagagctgtggaataacaagaaatacccgtgttgaagtttctaactgataatctaccttatacattttgacagGTTCTTGGAAAATGTCAGCTTCAGGAGGCTGTCCAGGAAAAGGAAGAGGGTCTAGGCTCCATTG
||    | |||       | |  || | ||  |    || ||| |||    |    |    |   ||  |  | |   || | |       | | |  || |  | ||   ||| || |    ||   ||||||||||  |||||||||||||  || ||||||||||| |||||| ||||  | | |||  |||
gtgcggtgtcttacaacatacacaactattcat----gttgtttctggccctgttgt----actagtttaccagctcaaacttcaaa----gcaatcacttaaagtta--ttactttctgttcttgtgcagGTTCTTGACAAATGTCAGCTTCTTGAAGCTGTCCAGGAGAAGGAACAGGGATTGGACTCACTTG
















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|32270844|gb|CD720003.1|CD720003
EST:     GATACAATTTGGATCCCTTGTCCCAACACACTGACCATGAAATATGGGAG                         GTTCTTGGAAAATGTCAGCTTCGGGAGGCTGTCCAGGAAAAG
genomic: GATACAATTTGGATCCCTTGTCCCAACACACTGACCATGAAATATGGGAGgtaatatatc ... attttgacagGTTCTTGGAAAATGTCAGCTTCAGGAGGCTGTCCAGGAAAAG
EST: gi|110699494|gb|EE076542.1|EE076542
EST:     GATACAATTTGGATCCCTTGTCCCAACACACTGACCATGAAATATGGGAG                         GTTCTTGGAAAATGTCAGCTTCAGGAGGCTGTCCAGGAAAAGGAAGAGGGT
genomic: GATACAATTTGGATCCCTTGTCCCAACACACTGACCATGAAATATGGGAGgtaatatatc ... attttgacagGTTCTTGGAAAATGTCAGCTTCAGGAGGCTGTCCAGGAAAAGGAAGAGGGT
EST: gi|110713613|gb|EE089685.1|EE089685
EST:     GATACAATTTGGATCCCTTGTCCCAACACACTGACCATGAAATATGGGAG                         GTTCTTGGAAAATGTCAGCTTCAGGAAGCTGTCCAGGAAAAAGAAGAGGGT
genomic: GATACAATTTGGATCCCTTGTCCCAACACACTGACCATGAAATATGGGAGgtaatatatc ... attttgacagGTTCTTGGAAAATGTCAGCTTCAGGAGGCTGTCCAGGAAAAGGAAGAGGGT
EST: gi|32268391|gb|CD717550.1|CD717550
EST:     GATACAATTTGGATCCCTTGTCCCAACACACTGACCATGAAATATGNGAG                         GTTCTTGNAAAATGTCAGCTTCGGGAGGCTGTCCAGGAAAAG
genomic: GATACAATTTGGATCCCTTGTCCCAACACACTGACCATGAAATATGGGAGgtaatatatc ... attttgacagGTTCTTGGAAAATGTCAGCTTCAGGAGGCTGTCCAGGAAAAG
EST: gi|30323099|gb|CD006361.1|CD006361
EST:     GATACAATTTGGATCCCTTGTCCCAACACACTGACCATGAAATATGGGAG                         GTTCTTGGAAAATGTCAGCTTCGGGAGGCTGTCCA
genomic: GATACAATTTGGATCCCTTGTCCCAACACACTGACCATGAAATATGGGAGgtaatatatc ... attttgacagGTTCTTGGAAAATGTCAGCTTCAGGAGGCTGTCCA
EST: gi|34362924|gb|CF404509.1|CF404509
EST:     GATACAATTTGGATCCCTTGTCCCAACACCCTGACCATGAAATATGGGAG                         GTTCTTGGAAAATGTCAGCTTCAGGAGGCTGTCCAGGAAAAGGAAGAGGGT
genomic: GATACAATTTGGATCCCTTGTCCCAACACACTGACCATGAAATATGGGAGgtaatatatc ... attttgacagGTTCTTGGAAAATGTCAGCTTCAGGAGGCTGTCCAGGAAAAGGAAGAGGGT
EST: gi|30300431|gb|CB977225.1|CB977225
EST:     GATACAATTTGGATCCCTTGTCCCAACCCCCTGACCATGAAATATGGGAG                         GTTCTTGGAAAATGTCAGCTTCAGGAGGCTGTCCAGGAAAAGGAAGAGGGT
genomic: GATACAATTTGGATCCCTTGTCCCAACACACTGACCATGAAATATGGGAGgtaatatatc ... attttgacagGTTCTTGGAAAATGTCAGCTTCAGGAGGCTGTCCAGGAAAAGGAAGAGGGT
EST: gi|110695979|gb|EE074612.1|EE074612
EST:     TGAAATATGGGAG                         GTTCTTGGAAAATGTCAGCTTCAGGAGGCTGTCCAGGAAAAGGAAGAGGGT
genomic: TGAAATATGGGAGgtaatatatc ... attttgacagGTTCTTGGAAAATGTCAGCTTCAGGAGGCTGTCCAGGAAAAGGAAGAGGGT
EST: gi|32249769|gb|CD715588.1|CD715588
EST:     GATACAATTTGGATCCCTTGTCCCAACACACTGACCATGAAATATGGGAG                         GTTCTTGGAAAATGTCAGCTTCGGGAGGCTGTCCAGGAAAAGGAAGAGGGT
genomic: GATACAATTTGGATCCCTTGTCCCAACACACTGACCATGAAATATGGGAGgtaatatatc ... attttgacagGTTCTTGGAAAATGTCAGCTTCAGGAGGCTGTCCAGGAAAAGGAAGAGGGT
EST: gi|34542733|gb|CF510965.1|CF510965
EST:     GATACAATTTGGATCCCTTGTCCCAACACACTGACCATGAAATATGGGAG                         GTTCTTGGAAAATGTCAGCTTCAGGAGGCTGTCCAGGAAAAGGAAGAGGGT
genomic: GATACAATTTGGATCCCTTGTCCCAACACACTGACCATGAAATATGGGAGgtaatatatc ... attttgacagGTTCTTGGAAAATGTCAGCTTCAGGAGGCTGTCCAGGAAAAGGAAGAGGGT
EST: gi|34549752|gb|CF517984.1|CF517984
EST:     GATACAATTTGGATCCCTTGTCCCAACACACTGACCATGAAATATGGGAG                         GTTCTTGGAAAATGTCAGCTTCGGGAGGCTGTCCAGGAAAAGTTAGAGGGT
genomic: GATACAATTTGGATCCCTTGTCCCAACACACTGACCATGAAATATGGGAGgtaatatatc ... attttgacagGTTCTTGGAAAATGTCAGCTTCAGGAGGCTGTCCAGGAAAAGGAAGAGGGT
EST: gi|34542820|gb|CF511052.1|CF511052
EST:     GATACAATTTGGATCCCTTGTCCCAACACACTGACCATGAAATATGGGAG                         GTTCTTGGAAAATGTCAGCTTCAGGAGGCTGTCCAGGAAAAGGAAGAGGGT
genomic: GATACAATTTGGATCCCTTGTCCCAACACACTGACCATGAAATATGGGAGgtaatatatc ... attttgacagGTTCTTGGAAAATGTCAGCTTCAGGAGGCTGTCCAGGAAAAGGAAGAGGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agaaatacccgtgttgaagtttctaactgataatctaccttatacattttgacagGTTCTTGGAAAATGTCAGCTTCAGGAGGCTGTCCAGGAAAAGGAAGAGGGTCTAGGCTCCATTG
                                       ttatacatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatatatctactctttttctaaattttttttctgggtagttgctgataataccatgaagagctgtggaataacaagaaatacccgtgttgaagtttctaactgataatctaccttatacattttgacagGTTCTTGGAAAATGTCAGCTTCAGGAGGCTGTCCAGGAAAAGGAAGAGGGTCTAGGCTCCATTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG