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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttcttaaacactcaaatattccaatgttttgatacactgtcatcatttatttctctttttcccccttttttgattttaatttctcttaagggtagATGTATCCACAAGGAAGGATGTCCCATCATTTTCGGGAGATGTGTGAAGGTGATTACCTGGCTGTGAAGGGACCTAAG

Basic information

species Vitis vinifera
transcript Vv06s0009g01710.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0009g01710.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G133213_T01 (Zea mays), 3'ss of exon 3
gttcttaaacactcaaata---ttccaatgttttgatacactgtcatcatttatttctctttttcccccttttttgattttaatttctcttaa--gggtagATGTATCCACAAGGAAGGATGTCCCATCATTTTCGGGAGATGTGTGAAGGTGATTACCTGGCTGTGAAGGGACCTAAG
     |||| | | | ||    || |  ||||  |||||  | | ||  |||    ||| | |     |      | | || | | || || |      |||||||||| ||||| || |||||||||||||| || ||||||   |  ||||||||  || |||||||||||||||||
----gtaaatatttagatcgattttccttgttcggatacttt-ttatgctttgca-ctcatatgttgacacaccagttctttaatccttttgatcacacagATGTATCCCCAAGGGAGAATGTCCCATCATTTCCGCGAGATGAAAGTTGGTGATTATTTGTCTGTGAAGGGACCTAAG

upper sequence: Vv06s0009g01710.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G157263_T01 (Zea mays), 3'ss of exon 3
-----------------------------------------gttcttaaacactcaaatat---tccaatgttttgatacactgtca-tcatttatttctctttttcccc-cttttttgatt-----------ttaatttctcttaa--gggtagATGTATCCACAAGGAAGGATGTCCCATCATTTTCGGGAGATGTGTGAAGGTGATTACCTGGCTGTGAAGGGACCTAAG
                                          ||| ||  || |  | | |   |||| |  | | || ||   ||  ||||  ||    || |||   | || || |||||           ||  || ||  |    | | |||||||||| |||||||| ||||| |||||||| || ||||||   |  ||||||||  || |||||||||||||||||
gtaagttttcaatgagatgccccccccccccttttttttcttttcctagtcatttcattgtatctccagttgtgttatgcatcttcggtcatcgatgcaactatttgtgcactgttgtgattcaccacatgttttctttccttctcgtcgtgaagATGTATCCCCAAGGAAGAATGTCTCATCATTTCCGTGAGATGAAAGTTGGTGATTATATGTCTGTGAAGGGACCTAAG

upper sequence: Vv06s0009g01710.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA20G05640.1 (Glycine max), 3'ss of exon 3
---------------gttcttaaacactcaaatattccaatgtt-ttgatacactgtcatcatttatttctctttttcccccttttttgattttaatttctcttaagggtagATGTATCCACAAGGAAGGATGTCCCATCATTTTCGGGAGATGTGTGAAGGTGATTACCTGGCTGTGAAGGGACCTAAG
                || ||         | | ||  | | || |  ||  | | |  | |  |||   | ||         |   ||  ||   ||| | | |    |||||||||||||||||| ||||||| ||||| ||| |||||||  |||||||||||||| |||||||||||||||| |||
gttatttgccactatttttttttttttctcagtgtttgattattgtcaatttattatttttaactatagatattgacttttgctacctgtatt--gtttgtataataattagATGTATCCACAAGGACGGATGTCTCATCACTTTAGGGAGATACGTGAAGGTGATTACATGGCTGTGAAGGGACCAAAG

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|110720681|gb|EE096826.1|EE096826
EST:     CTCCAACCACTTTAGATTCAGATCTTGGATACTTTGAACTCGTTATAAAG                         ATGTATCCACAAGGAAGGATGTCCCATCATTTTCGGGAGATGTGTGAAGGT
genomic: CTCCAACCACTTTAGATTCAGATCTTGGATACTTTGAACTCGTTATAAAGgttcttaaac ... ttaagggtagATGTATCCACAAGGAAGGATGTCCCATCATTTTCGGGAGATGTGTGAAGGT
EST: gi|33406066|gb|CF211693.1|CF211693
EST:     CTCCAACCACTTTAGATTCAGATCTTGGATACTTTGAACTCGTTATAAAG                         ATGTATCCACAAGGAAGGATGTCCCATCATTTTCGGGAGATGTGTGAAGGT
genomic: CTCCAACCACTTTAGATTCAGATCTTGGATACTTTGAACTCGTTATAAAGgttcttaaac ... ttaagggtagATGTATCCACAAGGAAGGATGTCCCATCATTTTCGGGAGATGTGTGAAGGT
EST: gi|33405978|gb|CF211605.1|CF211605
EST:     CTCCAACCACTTTAGATTCAGATCTTGGATACTTTGAACTCGTTATAAAG                         ATGTATCCACAAGGAAGGATGTCCCATCATTTTCGGGAGATGTGTGAAGGT
genomic: CTCCAACCACTTTAGATTCAGATCTTGGATACTTTGAACTCGTTATAAAGgttcttaaac ... ttaagggtagATGTATCCACAAGGAAGGATGTCCCATCATTTTCGGGAGATGTGTGAAGGT
EST: gi|71864812|gb|DT013867.1|DT013867
EST:     CTCCAACCACTTTAGATTCAGATCTTGGATACTTTGAACTCGTTATAAAG                         ATGTATCCACAAGGAAGGATGTCCCATCATTTTCGGGAGATGTGTGAAGGT
genomic: CTCCAACCACTTTAGATTCAGATCTTGGATACTTTGAACTCGTTATAAAGgttcttaaac ... ttaagggtagATGTATCCACAAGGAAGGATGTCCCATCATTTTCGGGAGATGTGTGAAGGT
EST: gi|110688836|gb|EE067844.1|EE067844
EST:     CTCCAACCACTTTAGATTCAGATCTTGGATACTTTGAACTCGTTATAAAG                         ATGTATCCACAAGGAAGGATGTCCCATCATTTTCGGGAGATGTGTGAAGGT
genomic: CTCCAACCACTTTAGATTCAGATCTTGGATACTTTGAACTCGTTATAAAGgttcttaaac ... ttaagggtagATGTATCCACAAGGAAGGATGTCCCATCATTTTCGGGAGATGTGTGAAGGT
EST: gi|110718332|gb|EE095045.1|EE095045
EST:     CTCCAACCACTTTAGATTCAGATCTTGGATACTTTGAACTCGTTATAAAG                         ATGTATCCACAAGGAAGGATGTCCCATCATTTTCGGGAGATGTGTGAAGGT
genomic: CTCCAACCACTTTAGATTCAGATCTTGGATACTTTGAACTCGTTATAAAGgttcttaaac ... ttaagggtagATGTATCCACAAGGAAGGATGTCCCATCATTTTCGGGAGATGTGTGAAGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catcatttatttctctttttcccccttttttgattttaatttctcttaagggtagATGTATCCACAAGGAAGGATGTCCCATCATTTTCGGGAGATGTGTGAAGGTGATTACCTGGCTGTGAAGGGACCTAAG
                                 ttttaat  putative branch site (score: 3)
         tttctctttttccccc  CT-rich tract
                         ttttttgattttaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttcttaaacactcaaatattccaatgttttgatacactgtcatcatttatttctctttttcccccttttttgattttaatttctcttaagggtagATGTATCCACAAGGAAGGATGTCCCATCATTTTCGGGAGATGTGTGAAGGTGATTACCTGGCTGTGAAGGGACCTAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG