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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCTGCTTCAGAGACACTCCCTCGAAATGAGGTTCTTGGAGGGTACATCTTTGTGTGTAACAATGATACCATGCAGGAAGATTTGAAGCGACAACTATTTGgtaatagtgattttcttgctttatattctcctcatttaacttatgtactttgctgggaacagttcaggcattttacactcattaactcatataatatgtg...

Basic information

species Vitis vinifera
transcript Vv14s0068g02040.t01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0068g02040.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GRMZM2G011923_T01 (Zea mays), 5'ss of exon 2
CCTGCTTCAGAGACACTCCCTCGAAATGAGGTTCTTGGAGGGTACATCTTTGTGTGTAACAATGATACCATGCAGGAAGATTTGAAGCGACAACTATTTGgtaatagtgattttcttgctttatattctcctcatttaacttatgtactttgctgggaacagttcaggcattttacactca---ttaactcatataata-tgtg-----------------------------------
||  |    ||||  || ||    || || || ||||| |||||||||||||| || ||||| |||||||||||||| ||  | ||| | || || |||||||    ||  ||| ||  |||  ||  | | ||| |  |||  | | |    ||| ||| |||| || |  | |   |      || |  ||||| || | ||                                   
CCGACGAGCGAGATGCTGCCGAAGAACGAAGTCCTTGGTGGGTACATCTTTGTCTGCAACAACGATACCATGCAGGAGGACCTCAAGAGGCAGCTTTTTGgta----tgtctttttt--tttggatcttgc-catatcccttgaggaatcaaatggtaactgttctggaaaatcagttttgatcctagcgtatatactaatttggtaatggtgccttaagatctgttgctcttctgcag

upper sequence: Vv14s0068g02040.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GRMZM2G033117_T01 (Zea mays), 5'ss of exon 2
CCTGCTTCAGAGACACTCCCTCGAAATGAGGTTCTTGGAGGGTACATCTTTGTGTGTAACAATGATACCATGCAGGAAGATTTGAAGCGACAACTATTTGgtaatagtgattttcttgctttatattctcctcatttaacttatgtactttgctgggaacagttcaggca-ttttacactcattaactcatataatatgtg----------------------------
||  |    ||||  || ||  | ||||| || ||||| || ||||||||||| || ||||| |||||||||||||| ||| | ||| | || || |||||||          ||    ||   | ||   | ||     || || | |||  |   || |    |   | ||||     || |   | ||   |||   |                            
CCGACGAGTGAGATGCTACCGAGGAATGAAGTCCTTGGTGGATACATCTTTGTCTGCAACAACGATACCATGCAGGAGGATCTCAAGAGGCAGCTTTTTGgtatgttatcccgtcccttttagaaatcaaatgataactgttctggattttttttaaaaaaaaatatatagttttgatgccagtgtgtaattcgataatggtatctcaagatctattgctcttctgcag

upper sequence: Vv14s0068g02040.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GLYMA16G06100.1 (Glycine max), 5'ss of exon 2
CCTGCTTCAGAGACACTCCCTCGAAATGAGGTTCTTGGAGGGTACATCTTTGTGTGTAACAATGATACCATGCAGGAAGATTTGAAGCGACAACTATTTGgtaatagtgattttcttgctttatattctcctcatttaacttatgtactttgctgggaacagttcaggcattttacactcattaactcatataatatgtg-------
|||||| | ||||||||||| || |||||||| |||||||| ||||||||||| ||||||||||| || ||||||||||| ||||| || || |||||||||    ||| || |      ||| ||      ||| ||  || | ||  |||   |  |    |||   | || |   | | | |||| |  ||| | |        
CCTGCTGCGGAGACACTCCCGCGCAATGAGGTGCTTGGAGGATACATCTTTGTCTGTAACAATGACACAATGCAGGAAGACTTGAAACGTCAGCTATTTGgtgt--gtgcttattagttattaaatga----catctatttt-tctatcttgaatgttattaatcaaatacttcatgatgactgactctttcaatgttttttgatag

upper sequence: Vv14s0068g02040.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GLYMA19G25870.1 (Glycine max), 5'ss of exon 2
CCTGCTTCAGAGACACTCCCTCGAAATGAGGTTCTTGGAGGGTACATCTTTGTGTGTAACAATGATACCATGCAGGAAGATTTGAAGCGACAACTATTTGgt-aatagtgatt--ttcttgctttatattctcctcatttaacttatgtactttgctgggaacagttca-ggcattttacactcattaactcatataatatgtg
|||||| | ||||||||||| || |||||||| |||||||| ||||||||||| ||||||||||| || ||||||||||| ||||| || || ||||||||| | || | |||  || ||   | | || ||  |  | || |||    | | |      || | |||| |     | |  ||   ||  |  | | |||    
CCTGCTGCGGAGACACTCCCCCGCAATGAGGTGCTTGGAGGATACATCTTTGTCTGTAACAATGACACAATGCAGGAAGACTTGAAACGTCAGCTATTTGgtgagtacttattagttattaaatgacat-ctatttttctatcttgaagattattaatcaaatacttcatgatgactgattctttctatgttttttgatag---

upper sequence: Vv14s0068g02040.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: AT3G27090.1 (Arabidopsis thaliana), 5'ss of exon 2
CCTGCTTCAGAGACACTCCCTCGAAATGAGGTTCTTGGAGGGTACATCTTTGTGTGTAACAATGATACCATGCAGGAAGATTTGAAGCGACAACTATTTGgtaatagtgattttcttgctttatattctcctcatttaacttatgtactttgctgggaacagttcaggcattttacactcattaactcatataatatgtg
|||||||| ||||| || ||  | ||||| |||||||| || ||||||||||| || ||||||||||| |||||||| ||| |||| || || || |||||||||       |||    |     ||       ||| ||| || | |    |||  |  |  | |    ||| ||  |||| |  |  |  |       
CCTGCTTCGGAGACTCTTCCGAGGAATGAAGTTCTTGGTGGTTACATCTTTGTTTGCAACAATGATACTATGCAGGAGGATATGAAACGTCACCTCTTTGgtaat-------ttcccaatacccttttctagtgttttactgatattcaa-actgcaagtaaat-aactttttgactttcatca--ttgttcag------

upper sequence: Vv14s0068g02040.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: EFJ24245 (Selaginella moellendorffii), 5'ss of exon 1
CCTGCTTCAGAGACACTCCCTCGAAATGAGGTTCTTGGAGGGTACATCTTTGTGTGTAACAATGATACCATGCAGGAAGATTTGAAGCGACAACTATTTGgtaatagtgattttc--ttg--------ctttatattctcctcatttaacttatgtactttgctgggaacagttcaggcattttacactcattaactcatataatatgtg----------------------------------------
||| | || ||||| || || || |  ||||| || || ||||| ||||| ||||| ||||| ||||||||||| |||||| | ||||| ||||| || |||||   | |  | |  |||        ||  |   |||||   |||  ||  ||  ||  ||    ||  | ||     || |    || ||  ||  | |  ||| |                                         
CCTCCATCCGAGACGCTTCCCCGGAGCGAGGTCCTCGGTGGGTATATCTTCGTGTGCAACAACGATACCATGCAAGAAGATCTCAAGCGCCAACTCTTCGgtaaaccttacatcccgttgaaacaaaactccaccatctccatttttt-ctcttgctctcggccataaaacgctcgtaagttcttttttc-ttctcttgttttttatttttttctttcctttatctcgtttctcacctagaacttcgcag

upper sequence: Vv14s0068g02040.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: EFJ35508 (Selaginella moellendorffii), 5'ss of exon 1
CCTGCTTCAGAGACACTCCCTCGAAATGAGGTTCTTGGAGGGTACATCTTTGTGTGTAACAATGATACCATGCAGGAAGATTTGAAGCGACAACTATTTGgtaatagtgattttc--ttg--------ctttatattctcctcatttaacttatgtactttgctgggaacagttc---aggcattttacactcattaactcatataatatgtg-----------------------------------------
||| | || ||||| || || || |  ||||| || || ||||| ||||| ||||| ||||| ||||||||||| |||||| | ||||| ||||| || |||||   | |  | |  |||        ||  |   |||||   |||  ||  ||  ||  ||    ||  | ||   ||   ||||    ||  |   |  | |||| | |                                          
CCTCCATCCGAGACGCTTCCCCGGAGCGAGGTCCTCGGTGGGTATATCTTCGTGTGCAACAACGATACCATGCAAGAAGATCTCAAGCGCCAACTCTTCGgtaaaccttacatcccgttgaaacaaaactccaccatctccatttttt-ctcttgctctcggccataaaacgctcgtaagtttttttttcttctcttgtttttttaatttttttctttcctttatctcgtttctcacctagaagaacttcgcag

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|161715634|gb|FC066792.1|FC066792
EST:     TGTGTGTAACAATGATACCATGCAGGAAGATTTGAAGCGACAACTATTTG                         GTCTACCTCCCAGATATAGAGACTCTGTTCGGGCTATAACACCAGGCTTAC
genomic: TGTGTGTAACAATGATACCATGCAGGAAGATTTGAAGCGACAACTATTTGgtaatagtga ... catttgttagGTCTACCTCCAAGATATAGAGACTCTGTTCGGGCTATAACACCAGGCTTAC
EST: gi|352795214|gb|FQ477324.1|FQ477324
EST:     TGTGTGTAACAATGATACCATGCAGGAAGATTTGAAGCGACAACTATTTG                         GTCTACCTCCAAGATATAGAGACTCTGTTCGGGCTATAACACCAGGCTTAC
genomic: TGTGTGTAACAATGATACCATGCAGGAAGATTTGAAGCGACAACTATTTGgtaatagtga ... catttgttagGTCTACCTCCAAGATATAGAGACTCTGTTCGGGCTATAACACCAGGCTTAC
EST: gi|110702016|gb|EE080244.1|EE080244
EST:     TGTGTGTAACAATGATACCATGCAAGAAGATTTGAAGCGACAACTATTTG                         GTCTACCTCCAAGATATAGAGACTCTGTTCGGGCTATAACAC-AGGCTTAC
genomic: TGTGTGTAACAATGATACCATGCAGGAAGATTTGAAGCGACAACTATTTGgtaatagtga ... catttgttagGTCTACCTCCAAGATATAGAGACTCTGTTCGGGCTATAACACCAGGCTTAC
EST: gi|110689556|gb|EE065885.1|EE065885
EST:     TGTGTGTAACAATGATACCATGCAGGAAGATTTGAAGCGACAACTATTTG                         GTCTACCTCCAAGATATAGAGACTCTGTTCGGGCTATAACACCAGGCTTAC
genomic: TGTGTGTAACAATGATACCATGCAGGAAGATTTGAAGCGACAACTATTTGgtaatagtga ... catttgttagGTCTACCTCCAAGATATAGAGACTCTGTTCGGGCTATAACACCAGGCTTAC
EST: gi|110689555|gb|EE065884.1|EE065884
EST:     TGTGTGTAACAATGATACCATGCANGAAGATTTGAAGCGACAACTATTTG                         GTCTACCTCCAAGATATANAGACTCTGTTCGGGCTATAACACCANGCTTAC
genomic: TGTGTGTAACAATGATACCATGCAGGAAGATTTGAAGCGACAACTATTTGgtaatagtga ... catttgttagGTCTACCTCCAAGATATAGAGACTCTGTTCGGGCTATAACACCAGGCTTAC
EST: gi|161719902|gb|FC066124.1|FC066124
EST:     TGTGTGTAACAATGATACCATGCAGGAAGATTTGAAGCGACAACTATTTG                         GTCTACCTCCAAGATATAGAGACTCTGTTCGGGCTATAACACCAGGCTTAC
genomic: TGTGTGTAACAATGATACCATGCAGGAAGATTTGAAGCGACAACTATTTGgtaatagtga ... catttgttagGTCTACCTCCAAGATATAGAGACTCTGTTCGGGCTATAACACCAGGCTTAC
EST: gi|30251482|gb|CB969215.1|CB969215
EST:     TGTGTGTAACAATGATACCATGCAGGAAGATTTGAAGCGACAACTATTTG                         GTCTACCTCCAAGATATAGAGACTCTGTTCGGGCTATAACACCAGGCTTAC
genomic: TGTGTGTAACAATGATACCATGCAGGAAGATTTGAAGCGACAACTATTTGgtaatagtga ... catttgttagGTCTACCTCCAAGATATAGAGACTCTGTTCGGGCTATAACACCAGGCTTAC
EST: gi|33405079|gb|CF210706.1|CF210706
EST:     TGTGTGTAACAATGATACCATGCAGGAAGATTTGAAGCGACAACTATTTG                         GTCTACCTCCAAGATATAGAGACTCTGTTCGGGCTATAACACCAGGCTTAC
genomic: TGTGTGTAACAATGATACCATGCAGGAAGATTTGAAGCGACAACTATTTGgtaatagtga ... catttgttagGTCTACCTCCAAGATATAGAGACTCTGTTCGGGCTATAACACCAGGCTTAC
EST: gi|110396191|gb|EC961872.1|EC961872
EST:     TGTGTGTAACAATGATACCATGCAGGAAGATTTGAAGCGACAACTATTTG                         GTCTACCTCCAAGATATAGAGACTCTGTTCGGGCTATAACACCAGGCTTAC
genomic: TGTGTGTAACAATGATACCATGCAGGAAGATTTGAAGCGACAACTATTTGgtaatagtga ... catttgttagGTCTACCTCCAAGATATAGAGACTCTGTTCGGGCTATAACACCAGGCTTAC
EST: gi|110709022|gb|EE084118.1|EE084118
EST:     TGTGTGTAACAATGATACCATGCAGGAAGATTTGAAGCGACAACTATTTG                         GTCTACCTCCAAGATATAGAGACTCTGTTCGGGCTATAACACCAGGCTTTA
genomic: TGTGTGTAACAATGATACCATGCAGGAAGATTTGAAGCGACAACTATTTGgtaatagtga ... catttgttagGTCTACCTCCAAGATATAGAGACTCTGTTCGGGCTATAACACCAGGCTT-A
EST: gi|351029823|gb|FQ427663.1|FQ427663
EST:     TGTGTGTAACAATGATACCATGCAGGAAGATTTGAAGCGACAACTATTTG                         GTCTACCTCCAAGATATAGAGACTCTGTTCGGGCTATAACACCAGGCTTAC
genomic: TGTGTGTAACAATGATACCATGCAGGAAGATTTGAAGCGACAACTATTTGgtaatagtga ... catttgttagGTCTACCTCCAAGATATAGAGACTCTGTTCGGGCTATAACACCAGGCTTAC
EST: gi|110384179|gb|EC948598.1|EC948598
EST:     TGTGTGTAACAATGATACCATGCAGGAAGATTTGAAGCGACAACTATTTG                         GTCTACCTCCAAGATATAGAGACTCTGTTCGGGCTATAACACCAGGCTTAC
genomic: TGTGTGTAACAATGATACCATGCAGGAAGATTTGAAGCGACAACTATTTGgtaatagtga ... catttgttagGTCTACCTCCAAGATATAGAGACTCTGTTCGGGCTATAACACCAGGCTTAC
EST: gi|110687785|gb|EE065593.1|EE065593
EST:     TGTGTGTAACAATGATACCATGCAGGAAGATTTGAAGCGACAACTATTTG                         GTCTACCTCCAAGATATAGAGACTCTGTTCGGGCTATAACACCAGGCTTAC
genomic: TGTGTGTAACAATGATACCATGCAGGAAGATTTGAAGCGACAACTATTTGgtaatagtga ... catttgttagGTCTACCTCCAAGATATAGAGACTCTGTTCGGGCTATAACACCAGGCTTAC
EST: gi|110687073|gb|EE064163.1|EE064163
EST:     TGTGTGTAACAATGATACCATGCAGGAAGATTTGAAGCGACAACTATTTG                         GTCTACCTCCAAGATATAGAGACTCTGTTCGGGCTATAACACCAGGCTTAC
genomic: TGTGTGTAACAATGATACCATGCAGGAAGATTTGAAGCGACAACTATTTGgtaatagtga ... catttgttagGTCTACCTCCAAGATATAGAGACTCTGTTCGGGCTATAACACCAGGCTTAC
EST: gi|110728646|gb|EE104397.1|EE104397
EST:     TGTGTGTAACCATGATACCATGCAAGAAGATTTGAAGCGACAACTATTTG                         GTCTACCTCCAAGATATAAAGACTCTGTTCGGGGCTATA-CACCCGGGCTT
genomic: TGTGTGTAACAATGATACCATGCAGGAAGATTTGAAGCGACAACTATTTGgtaatagtga ... catttgttagGTCTACCTCCAAGATATAGAGACTCTGTTCGGG-CTATAACACCAGG-CTT
EST: gi|110687425|gb|EE064823.1|EE064823
EST:     TGTGTGTAACAATGATACCATGCAGGAAGATTTGAAGCGACAACTATTTG                         GTCTACCTCCAAGATATAGAGACTCTGTTCGGGCTATAACACCAGGCTTAC
genomic: TGTGTGTAACAATGATACCATGCAGGAAGATTTGAAGCGACAACTATTTGgtaatagtga ... catttgttagGTCTACCTCCAAGATATAGAGACTCTGTTCGGGCTATAACACCAGGCTTAC
EST: gi|30296133|gb|CB972927.1|CB972927
EST:     TGTGTGTAACAATGATACCATGCAGGAAGATTTGAAGCGACAACTATTTG                         GTCTACCTCCAAGATATAGAGACTCTGTTCGGGCTATAACACCAGGCTTAC
genomic: TGTGTGTAACAATGATACCATGCAGGAAGATTTGAAGCGACAACTATTTGgtaatagtga ... catttgttagGTCTACCTCCAAGATATAGAGACTCTGTTCGGGCTATAACACCAGGCTTAC
EST: gi|161721523|gb|FC069739.1|FC069739
EST:     TGTGTGTAACAATGATACCATGCAGGAAGATTTGAAGCGACAACTATTTG                         GTCTACCTCCAAGATATAGAGACTCTGTTCGGGCTATAACACCAGGCTTAC
genomic: TGTGTGTAACAATGATACCATGCAGGAAGATTTGAAGCGACAACTATTTGgtaatagtga ... catttgttagGTCTACCTCCAAGATATAGAGACTCTGTTCGGGCTATAACACCAGGCTTAC
EST: gi|26257057|gb|CA808120.1|CA808120
EST:     TGTGTGTAACAATGATACCATGCAGGAAGATTTGAAGCGACAACTATTTG                         GTCTACCTCCAAGATATAGAGACTCTGTTCGGGCTATAACACCAGGCTTAC
genomic: TGTGTGTAACAATGATACCATGCAGGAAGATTTGAAGCGACAACTATTTGgtaatagtga ... catttgttagGTCTACCTCCAAGATATAGAGACTCTGTTCGGGCTATAACACCAGGCTTAC
EST: gi|110723367|gb|EE100597.1|EE100597
EST:     TGTGTGTAACAATGATACCATGCAGGAAGATTTGAAGCGACAACTATTTG                         GTCTACCTCCAAGATATAGAGACTCTGTTCGGGCTATAACAC-AGGCTTAC
genomic: TGTGTGTAACAATGATACCATGCAGGAAGATTTGAAGCGACAACTATTTGgtaatagtga ... catttgttagGTCTACCTCCAAGATATAGAGACTCTGTTCGGGCTATAACACCAGGCTTAC
EST: gi|351019333|gb|FQ429493.1|FQ429493
EST:     TGTGTGTAACAATGATACCATGCAGGAAGATTTGAAGCGACAACTATTTG                         GTCTACCTCCAAGATATAGAGACTCTGTTCGGGCTATAACACCAGGCTTAC
genomic: TGTGTGTAACAATGATACCATGCAGGAAGATTTGAAGCGACAACTATTTGgtaatagtga ... catttgttagGTCTACCTCCAAGATATAGAGACTCTGTTCGGGCTATAACACCAGGCTTAC
EST: gi|110688436|gb|EE066988.1|EE066988
EST:     TGTGTGTAACAATGATACCATGCAGGAAGATTTGAAGCGACAACTATTTG                         GTCTACCTCCAAGATATAGAGACTCTGTTCGGGCTATAACACCAGGCTTAA
genomic: TGTGTGTAACAATGATACCATGCAGGAAGATTTGAAGCGACAACTATTTGgtaatagtga ... catttgttagGTCTACCTCCAAGATATAGAGACTCTGTTCGGGCTATAACACCAGGCTTAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCTGCTTCAGAGACACTCCCTCGAAATGAGGTTCTTGGAGGGTACATCTTTGTGTGTAACAATGATACCATGCAGGAAGATTTGAAGCGACAACTATTTGgtaatagtgattttcttgctttatattctcctcatttaacttatgtactttgctgggaacagttcaggcattttacactcattaactcatataatatgtg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gggaaca