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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attaatttgtttacttctacctttaatcctttgggtttttgataccgactcattatggtcctattcctctaatggtttattttaatacatgttgctgcagTTCCCAGTTGGCCGCATCCACCGACTTCTGAAGTCAAGGGTCACAGCAAATGGAAGAGTTGGAGCAACAGCAGCTGTGTACTCAGCAGCCATCTTAGAGT

Basic information

species Vitis vinifera
transcript Vv04s0008g04700.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0008g04700.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA06G07510.1 (Glycine max), 3'ss of exon 1
----attaatttgtttacttctacctttaatcctttgggtttttgataccgactcattatggtcctattcctctaatggtttattttaatacatgttgctgcagTTCCCAGTTGGCCGCATCCACCGACTTCTGAAGTCAAGGGTCACAGCAAATGGAAGAGTTGGAGCAACAGCAGCTGTGTACTCAGCAGCCATCTTAGAGT
      | ||   |||     |   |  | || ||| | || ||  ||   | | ||  |   | ||||  |   |||   | || ||  |  | ||| | ||||| || ||||| || || ||||| ||| ||||||||||||| |  || |||||||||||||| || ||||| |||||||| || || || ||  | ||||
aaatcatgatgaatttcagcgtgtttgaagtctttttgtttgttagtat--aataatcgtaa-catattttttgtatgtcatcttgta-catgttttgatacagTTTCCTGTTGGACGAATTCACCGTCTTTTGAAGTCAAGGGTGAGTGCCAATGGAAGAGTTGGGGCCACAGCTGCTGTGTATTCTGCTGCTATACTGGAGT

upper sequence: Vv04s0008g04700.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: PP1S46_245V6.1 (Physcomitrella patens), 3'ss of exon 1
attaatttgtttacttctacctttaatcct-ttgggtttttgatacc--gactcattatggtcctattcctctaatggtttattttaatacatgttgctgcagTTCCCAGTTGGCCGCATCCACCGACTTCTGAAGTCAAGGGTCACAGCAAATGGAAGAGTTGGAGCAACAGCAGCTGTGTACTCAGCAGCCATCTTAGAGT
     |    |||   |     ||| |  | ||  | |||   ||||  || ||     |      ||||  |||  | |||  |   |     ||    ||||| ||||| || || || ||||| || || |||||||||||  | |||||||||||||| || ||||| || ||||| ||||||||||||||| |||| |
---ggtcctcttaaacccgggcttagttttgttaagctttgactacctggaatctcagggagatccttccgataagtgcttacatgtgttgtgtttagaacagTTTCCAGTCGGACGTATTCACCGGCTGCTTAAGTCAAGGGTGGCCGCAAATGGAAGAGTGGGTGCAACTGCCGCTGTTTACTCAGCAGCCATCCTAGAAT

upper sequence: Vv04s0008g04700.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: PP1S219_44V6.1 (Physcomitrella patens), 3'ss of exon 1
attaatttgtttacttctacctttaatcctttgggtttttgataccgactcattatggtcctattcctctaatggtt--tattttaatacatgttgctg-cagTTCCCAGTTGGCCGCATCCACCGACTTCTGAAGTCAAGGGTCACAGCAAATGGAAGAGTTGGAGCAACAGCAGCTGTGTACTCAGCAGCCATCTTAGAGT
  |  ||| || |       | |   |   |    |  | |   |||       | ||    || |   | ||| ||  ||  ||  |   || |   | |||||||| || || || || ||| |  | || |||||||||||  | || ||||||||||| || || ||||| || |||||||||||||||||||||||||
--tgctttcttcagcgagggcatagttttgtcaaatgctcgccgccg-taggacacggggacatgctattgatgattgctaacttgtttggtggtttggacagTTCCCCGTAGGACGTATTCACAGGTTGCTTAAGTCAAGGGTGGCCGCGAATGGAAGAGTGGGTGCTACAGCCGCAGTGTACTCAGCAGCCATCTTAGAGT

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|22013805|gb|BQ798839.1|BQ798839
EST:     ACAAGGACAAGAAGAAGCCTGTTTCTCGTTCCTCTCGTGCTGGTCTCCAG                         TTCCCAGTTGGCCGCATCCACCGACTTCTGAAGTCAAGGGTCACAGCAAAT
genomic: ACAAGGACAAGAAGAAGCCCGTTTCTCGTTCCTCTCGTGCTGGTCTCCAGgtcttttttc ... gttgctgcagTTCCCAGTTGGCCGCATCCACCGACTTCTGAAGTCAAGGGTCACAGCAAAT
EST: gi|26265617|gb|CA816680.1|CA816680
EST:     ACAAGGACAAGAAGAAGCCCGTTTCTCGTTCCTCTCGTGCTGGTCTCCAG                         TTCCCAGTTGGCCGCATCCACCGACTTCTGAAGTCAAGGGTCACAGCAAAT
genomic: ACAAGGACAAGAAGAAGCCCGTTTCTCGTTCCTCTCGTGCTGGTCTCCAGgtcttttttc ... gttgctgcagTTCCCAGTTGGCCGCATCCACCGACTTCTGAAGTCAAGGGTCACAGCAAAT
EST: gi|110359473|gb|EC921008.1|EC921008
EST:     ACAAGGACAAGAAGAAGCCCGTTTCTCGTTCCTCTCGTGCTGGTCTCCAG                         TTCCCAGTTGGCCGCATCCACCGACTTCTGAAGTCAAGGGTCACAGCAAAT
genomic: ACAAGGACAAGAAGAAGCCCGTTTCTCGTTCCTCTCGTGCTGGTCTCCAGgtcttttttc ... gttgctgcagTTCCCAGTTGGCCGCATCCACCGACTTCTGAAGTCAAGGGTCACAGCAAAT
EST: gi|27583572|gb|CB006267.1|CB006267
EST:     ACAAGGACAAGAAGAAGCCCGTTTCTCGTTCCTCTCGTGCTGGTCTCCAG                         TTCCCAGTTGGCCGCATCCACCGACTTCTGAAGTCAAGGGTCACAGCAAAT
genomic: ACAAGGACAAGAAGAAGCCCGTTTCTCGTTCCTCTCGTGCTGGTCTCCAGgtcttttttc ... gttgctgcagTTCCCAGTTGGCCGCATCCACCGACTTCTGAAGTCAAGGGTCACAGCAAAT
EST: gi|110366310|gb|EC930143.1|EC930143
EST:     ACAAGGACAAGAAGAAGCCCGTTTCTCGTTCCTCTCGTGCTGGTCTCCAG                         TTCCCAGTTGGCCGCATCCACCGACTTCTGAAGTCAAGGGTCACAGCAAAT
genomic: ACAAGGACAAGAAGAAGCCCGTTTCTCGTTCCTCTCGTGCTGGTCTCCAGgtcttttttc ... gttgctgcagTTCCCAGTTGGCCGCATCCACCGACTTCTGAAGTCAAGGGTCACAGCAAAT
EST: gi|34550173|gb|CF518391.1|CF518391
EST:     ACAAGGACAAGAAGAAGCCCGTTTCTCGTTCCTCTCGTGCTGGTCTCCAG                         TTCCAAGTTGGCCGCATCCACCGACTTCTGAAGTCAAGGGTCACAGCAAAT
genomic: ACAAGGACAAGAAGAAGCCCGTTTCTCGTTCCTCTCGTGCTGGTCTCCAGgtcttttttc ... gttgctgcagTTCCCAGTTGGCCGCATCCACCGACTTCTGAAGTCAAGGGTCACAGCAAAT
EST: gi|30134659|gb|CB919997.1|CB919997
EST:     ACAAGGACAAGAAGAAGCCCGTTTCTCGTTCCTCTCGTGCTGGTCTCCAG                         TTCCCAGTTGGCCGCATCCACCGACTTCTGAAGTCAAGGGTCACAGCAAAT
genomic: ACAAGGACAAGAAGAAGCCCGTTTCTCGTTCCTCTCGTGCTGGTCTCCAGgtcttttttc ... gttgctgcagTTCCCAGTTGGCCGCATCCACCGACTTCTGAAGTCAAGGGTCACAGCAAAT
EST: gi|110714991|gb|EE092528.1|EE092528
EST:     ACAAGGACAAGAAGAAGCCCGTTTCTCGTTCCTCTCGTGCTGGTCTCCAG                         TTCCCAGTTGGCCGCATCCACCGACTTCTGAAGTCAAGGGTCACAGCAAAT
genomic: ACAAGGACAAGAAGAAGCCCGTTTCTCGTTCCTCTCGTGCTGGTCTCCAGgtcttttttc ... gttgctgcagTTCCCAGTTGGCCGCATCCACCGACTTCTGAAGTCAAGGGTCACAGCAAAT
EST: gi|30329431|gb|CD012693.1|CD012693
EST:     ACAAGGACAAGAAGAAGCCCGTTTCTCGTTCCTCTCGTGCTGGTCTCCAG                         TTCCCAGTTGGCCGCATCCACCGACTTCTGAAGTCAAGGGTCACAGCAAAT
genomic: ACAAGGACAAGAAGAAGCCCGTTTCTCGTTCCTCTCGTGCTGGTCTCCAGgtcttttttc ... gttgctgcagTTCCCAGTTGGCCGCATCCACCGACTTCTGAAGTCAAGGGTCACAGCAAAT
EST: gi|34550730|gb|CF518948.1|CF518948
EST:     ACAAGGACAAGAAGAAGCCCGTTTCTCGTTCCTCTCGTGCTGGTCTCCAG                         TTCCCAGTTGGCCGCATCCACCGACTTCTGAAGTCAAGGGTCACAGCAAAT
genomic: ACAAGGACAAGAAGAAGCCCGTTTCTCGTTCCTCTCGTGCTGGTCTCCAGgtcttttttc ... gttgctgcagTTCCCAGTTGGCCGCATCCACCGACTTCTGAAGTCAAGGGTCACAGCAAAT
EST: gi|51989943|gb|CV179398.1|CV179398
EST:     ACAAGGACAAGAAGAAGCCCGTTTCTCGTTCCTCTCGTGCTGGTCTCCAG                         TTCCCAGTTGGCCGCATCCACCGACTTCTGAAGTCAAGGGTCACAGCAAAT
genomic: ACAAGGACAAGAAGAAGCCCGTTTCTCGTTCCTCTCGTGCTGGTCTCCAGgtcttttttc ... gttgctgcagTTCCCAGTTGGCCGCATCCACCGACTTCTGAAGTCAAGGGTCACAGCAAAT
EST: gi|110392374|gb|EC957750.1|EC957750
EST:     ACAAGGACAAGAAGAAGCCCGTTTCTCGTTCCTCTCGTGCTGGTCTCCAG                         TTCCCAGTTGGCCGCATCCACCGACTTCTGAAGTCAAGGGTCACAGCAAAT
genomic: ACAAGGACAAGAAGAAGCCCGTTTCTCGTTCCTCTCGTGCTGGTCTCCAGgtcttttttc ... gttgctgcagTTCCCAGTTGGCCGCATCCACCGACTTCTGAAGTCAAGGGTCACAGCAAAT
EST: gi|110386429|gb|EC951023.1|EC951023
EST:     ACAAGGACAAGAAGAAGCCCGTTTCTCGTTCCTCTCGTGCTGGTCTCCAG                         TTCCCAGTTGGCCGCATCCACCGACTTCTGAAGTCAAGGGTCACAGCAAAT
genomic: ACAAGGACAAGAAGAAGCCCGTTTCTCGTTCCTCTCGTGCTGGTCTCCAGgtcttttttc ... gttgctgcagTTCCCAGTTGGCCGCATCCACCGACTTCTGAAGTCAAGGGTCACAGCAAAT
EST: gi|110408000|gb|EC973620.1|EC973620
EST:     ACAAGGACAAGAAGAAGCCCGTTTCTCGTTCCTCTCGTGCTGGTCTCCAG                         TTCCCAGTTGGCCGCATCCACCGACTTCTGAAGTCAAGGGTCACAGCAAAT
genomic: ACAAGGACAAGAAGAAGCCCGTTTCTCGTTCCTCTCGTGCTGGTCTCCAGgtcttttttc ... gttgctgcagTTCCCAGTTGGCCGCATCCACCGACTTCTGAAGTCAAGGGTCACAGCAAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgactcattatggtcctattcctctaatggtttattttaatacatgttgctgcagTTCCCAGTTGGCCGCATCCACCGACTTCTGAAGTCAAGGGTCACAGCAAATGGAAGAGTTGGAGCAACAGCAGCTGTGTACTCAGCAGCCATCTTAGAGT
                                  ttttaat  putative branch site (score: 3)
                        taatggtttattttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attaatttgtttacttctacctttaatcctttgggtttttgataccgactcattatggtcctattcctctaatggtttattttaatacatgttgctgcagTTCCCAGTTGGCCGCATCCACCGACTTCTGAAGTCAAGGGTCACAGCAAATGGAAGAGTTGGAGCAACAGCAGCTGTGTACTCAGCAGCCATCTTAGAGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - ttctacc
- - - - - - - - - - - - - - - - - - - - - - ccgactc