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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttgatattaaatcttgaaaatttcttgttttagctaatgctttggtccatggatttcaataaatagaactccttttttgtttgatttcaccagATGTCTGATCCATTGACCGCTCTGATGCATGCTGTTCAAGTGATGAACTTGCTAAAGACCCTGATCACAAAAACACTAAGGGAACGGGAAGAAAGCCCGG

Basic information

species Vitis vinifera
transcript Vv07s0104g01120.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv07s0104g01120.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os07g22580.1 (Oryza sativa), 3'ss of exon 4
gttgatattaa-atcttgaaaatttcttgttttagctaatgctttggtccatggatttcaataaatagaactccttttttgtttgatttcaccagATGTCTGATCCATTGACCGCTCTGATGCATGCTGTTCAAGTGATGAACTTGCTAAAGACCCTGATCACAAAAACACTAAGGGAACGGGAAGAAAGCCCGG
||   | ||   | | | | ||||| ||    |    |||  | || |      | | |  |||   ||  |  ||      |||  ||||   |||||| |||||  | || |||||||||||||||||||||||||||||  | || |||||  ||||    || || || || ||||| ||  |        
gtaatttttcttaccataagaatttttttacgtgatcaattgtatgctgatgcaagtgcgctaagatgagatagttc---acttgcattca---gATGTCAGATCCTCTTACTGCTCTGATGCATGCTGTTCAAGTGATGAATCTTCTCAAGACATTGATTCTCAAGACGCTTAGAGAACGTGAGCATGATGAAA

upper sequence: Vv07s0104g01120.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os12g34840.1 (Oryza sativa), 3'ss of exon 4
------------------------gttgatattaaatcttgaaaatttcttgttttagctaatgctttggtccatggatttcaataaatagaactccttttttgtttgatttca--ccagATGTCTGATCCATTGACCGCTCTGATGCATGCTGTTCAAGTGATGAACTTGCTAAAGACCCTGATCACAAAAACACTAAGGGAACGGGAAGAAAGCCCGG
                           |  || |  |  |    |  |  |  || || || |          | | |  | | | |      ||| ||| || || | ||  |  | ||||||| ||||| ||||| || || ||||||||||| ||||| |||||||| || |||||  |||||   |  |||||  | || || || ||     |  
gtaatctccatttctgtaattttgcaggggatcaggtgatacgtaggtgattcttcag-tactttccctacaaaagaacctgactgaggtttgctcttttgtttttgggttctatgctagATGTCAGATCCTTTGACAGCCCTAATGCATGCTGTCCAAGTCATGAACTTCCTCAAGACATTGATCTTGAGGACACTTCGAGAGCGTGACGATGCAGCTA

upper sequence: Vv07s0104g01120.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G143253_T01 (Zea mays), 3'ss of exon 4
gttgatattaaatcttga-aaatttcttgttttagctaatgctttggtccatg-gatttcaataaatagaactccttttttgtttgatttcac-cagATGTCTGATCCATTGACCGCTCTGATGCATGCTGTTCAAGTGATGAACTTGCTAAAGACCCTGATCACAAAAACACTAAGGGAACGGGAAGAAAGCCCGG
   |   ||   |||||  || |    |     | |     | ||| |   || ||      |    | ||   | |     |||   | ||  |||||||| |||||  |||| || |||||||||||||||||||||||||||||||| || ||| | ||    ||||||||  ||||||| || ||       |
---gtatttccttcttgccaagtcctctaacacatcgtcgaccttgtttgctgtgacacttgtgctaacaagaacatcgaaattttcctccatacagATGTCCGATCCTCTGACAGCACTGATGCATGCTGTTCAAGTGATGAACTTGCTCAAAACCTTAATTCTCAAAACACTTCGGGAACGCGAGGATGATGATG

upper sequence: Vv07s0104g01120.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA03G36630.1 (Glycine max), 3'ss of exon 3
----------------------------------------------------------------gttgatattaa--atcttgaaaatttcttgttttagctaatgctttg-gtccatggatttcaataaatagaactc-----cttttttgtttgatttcaccagATGTCTGATCCATTGACCGCTCTGATGCATGCTGTTCAAGTGATGAACTTGCTAAAGACCCTGATCACAAAAACACTAAGGGAACGGGAAGAAAGCCCGG
                                                                |||| || |    | | | |  || | ||  | |    |   || ||    |  | | |  | ||  |   | ||      ||| || ||   ||  | ||||||||||||||| | || |||||||||||||| || ||||||||||| || ||||||||||| ||    || ||||| || ||||| |||||||   | |
gtatgttacatgtatgcttaatgagctcatattttaattatacatgtaacatctttactatgacgttgttacttgttaccattagcatgtattcatatgatgataactatgcaaactggaaatctagtattttttattcacatattttatttttctcttgaaacagATGTCTGATCCACTAACTGCTCTGATGCATGCGGTCCAAGTGATGAATTTACTAAAGACCCTAATATTGAAGACACTTAGAGAACGCGAAGAAACAGCTG

upper sequence: Vv07s0104g01120.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA02G17070.1 (Glycine max), 3'ss of exon 3
--------gttgatattaaatcttgaaaatttcttgttttagctaatgctttggtccatggatttcaataaataga-actccttttttgtttgatttcaccagATGTCTGATCCATTGACCGCTCTGATGCATGCTGTTCAAGTGATGAACTTGCTAAAGACCCTGATCACAAAAACACTAAGGGAACGGGAAGAAAGCCCGG
        | | | | ||     ||  |   |||| ||      |   ||  |     ||||      |   |    | | | | ||||  |   |  | ||||||||||||||  | || || ||||||||||| ||||||||||||||||| || ||||| || ||||  || ||||| || ||||| |||||||   |  
catgttttgcttacactaggctatgcta--ctcttattcacatgagaactacgaatgctggaaaatggtctgtttctaattcatctttgcctc-ctggaacagATGTCTGATCCTCTAACTGCCCTGATGCATGCGGTTCAAGTGATGAACTTACTCAAGACACTTATCATGAAGACACTTAGAGAACGCGAAGAAACAGCAA

upper sequence: Vv07s0104g01120.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA10G02720.1 (Glycine max), 3'ss of exon 3
----------gttgatattaaatcttgaaaatttcttgttttagctaatgctttg-gtccatggatttcaataaatagaactccttttttgtttgatttcaccagATGTCTGATCCATTGACCGCTCTGATGCATGCTGTTCAAGTGATGAACTTGCTAAAGACCCTGATCACAAAAACACTAAGGGAACGGGAAGAAAGCCCGG
          | | | | ||     |  |    |||| |       ||  || ||  |   || |  |     | |   | | | | | ||| |   |  | ||||||||||||||  | || || ||||||||||| ||||||||||||||||| || ||||| || ||||  || ||||| || ||||  ||| |||   |  
gccatattttgcttacagtaggctataga----tcttatgcacatgaaaactatgtatagttgaaaatggtctattgctaattcatctgtgtctc-ctggaacagATGTCTGATCCTCTAACAGCCCTGATGCATGCGGTTCAAGTGATGAACTTACTCAAGACACTCATCATGAAGACACTTAGAGAACACGAACAAACAGCAA

upper sequence: Vv07s0104g01120.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT4G03100.1 (Arabidopsis thaliana), 3'ss of exon 3
gttgatattaaatcttgaaaatttcttgttttagctaatgctttggtccatggatttcaataaatagaactccttttttgtttgatttcacc--agATGTCTGATCCATTGACCGCTCTGATGCATGCTGTTCAAGTGATGAACTTGCTAAAGACCCTGATCACAAAAACACTAAGGGAACGGGAAGAAAGCCCGG
       | ||| |      |    |||||  |   |||     |   ||  || |  | | | ||  | |   || |||  |  | | ||   ||||| | |||||||| || ||||| ||||||||||||||||||||||||||||| ||||| || |||||||| ||||||   |||||||||||||   |  
------gtaaaaacaaagttaacctttgttc-aatgaataa---gaatcactgagt--agttactaacatttgattcttgcattctctaactgtagATGACAGATCCATTAACGGCTCTTATGCATGCTGTTCAAGTGATGAACTTGCTTAAGACTCTTATCACAAAGACACTAGCTGAACGGGAAGAAAATGCTA

upper sequence: Vv07s0104g01120.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: PP1S13_243V6.1 (Physcomitrella patens), 3'ss of exon 4
-----------------------gttgatattaaatcttgaaaatttcttg----ttttagctaatgctttggtccat----ggatttcaat--aaatagaactccttttttg--tttgatttcaccagATGTCTGATCCATTGACCGCTCTGATGCATGCTGTTCAAGTGATGAACTTGCTAAAGACCCTGATCACAAAAACACTAAGGGAACGGGAAGAAAGCCCGG-
                        | |||  |    |||||| |    ||     ||||   | |  |||     |||    | |    ||   ||    ||| ||| ||| |   |  || ||  |||||| | || || ||||| ||||| ||||| || |||||||||||||||||||| |||||  ||||   |  |||  | |  || | |  || | ||     
gtaagtcatcttcgacctcccccttggatgctggcacttgaataccatttacgatttttttttcactcttcacctcattttggaacgctaactgaagcctaacacctgtttcgacctctatatctgcagATGGCCGACCCTTTGACTGCTCTTATGCACGCAGTTCAAGTGATGAACTTGCTGAAGACGTTGATACTACGAACCTTGAAAGA-CAGAGAGGAGGCGATAT

upper sequence: Vv07s0104g01120.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: PP1S256_73V6.1 (Physcomitrella patens), 3'ss of exon 6
-----------------------------------------gttgatattaaat-cttgaaaatttcttgttttagctaatgctttggtccatggatttcaat---aaataga--actccttttttgtttgatttcac------cagATGTCTGATCCATTGACCGCTCTGATGCATGCTGTTCAAGTGATGAACTTGCTAAAGACCCTGATCACAAAAACACTAAGGGAACGGGAAGAAAGCCCGG
                                          |  | || |  | |   ||||  || |  ||   || ||  || |   ||   ||| || |   | ||     | |  ||| || |  ||  |         |||||| | || || ||||| ||||| ||||| || ||||| ||||||||||| |||||||| |||||   || |||  | |  |   |||||||        
gtacgtcattctgaacccctcctcagatgctgggctttattctgaacataatctgcccaaaaaaatcgtccttcgcctcat--ttcgaaacaaaaattccagttcgacattatttatttatttcttctccgacctttgtatttgcagATGGCCGACCCTTTGACTGCTCTAATGCACGCAGTTCAGGTGATGAACTTCCTAAAGACGCTGATTCTAAGAACTTTGAAAGGTAGGGAAGAGGCGATAC

upper sequence: Vv07s0104g01120.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: PP1S107_15V6.1 (Physcomitrella patens), 3'ss of exon 5
--------------------------------------------------------------------------------------------gttg-atatta----aatcttgaaaatttcttgtt-ttagctaatgct---ttggtccatggatttcaataaatagaactccttttttgtttgatttcaccagATGTCTGATCCATTGACCGCTCTGATGCATGCTGTTCAAGTGATGAACTTGCTAAAGACCCTGATCACAAAAACACTAAGGGAACGGGAAGAAAGCCCGG
                                                                                             ||| | ||||    |  || |||  |   ||||| |||| |  || |   |  ||  | | |  |||     | ||     |   ||  |||    |  ||||||  ||||||  | || |||||||||||||| |||||||||||||||||| | || ||  ||||   |   ||| | | ||| ||| | |  |    | 
gtatagagcacctcttcggtggtctctttcttttgaaactagtttagagctaaaactgtgtagcgtgttgtctcccgtgttttctcatgatctttgcacattatttcagcctcgaaggtcgtttgttgttagttggtgttcgatctgttgacgaaggtcatctctttgataatttgagtttcttg--ccctgcagATGGTTGATCCGCTAACGGCTCTGATGCATGCCGTTCAAGTGATGAACTTGTTGAAAACTTTGATTCTACGCACATTGAAGGACCGGAAGGCTACTTTGC

upper sequence: Vv07s0104g01120.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: PP1S159_36V6.1 (Physcomitrella patens), 3'ss of exon 5
------------------------------------------------------------------------------gttgatattaaatctt--ga--aaatttct---tgttttagctaatgctttggtccatggatttca-ataaatagaactccttttttgtt-tgatt--tcac---cagATGTCTGATCCATTGACCGCTCTGATGCATGCTGTTCAAGTGATGAACTTGCTAAAGACCCTGATCACAAAAACACTAAGGGAACGGGAAGAAAGCCCGG
                                                                              || | ||  | |   |  ||  | ||||||   || | ||   ||   ||||    | |  | | | || ||  |||   | | ||   | |||||  | ||   |||||| |||| |||||||| || |||||||||||||||||||| ||||| ||||| || || |||||       || || | ||| ||| | |     | | 
gtatgtgatgtcgctgcaattgtgcgcctccccaaacttgtgacacttttcttaccagacttgtagagattcggtcctgtagttagcagactctccgactagatttctacgtgatctaaggaagtatttgtgttaagcttgttatatgaagtgaataacatattaactatgattcattacttgcagATGGCTGACCCATTGACAGCACTGATGCATGCTGTTCAAGTTATGAATTTGCTCAAAACTCTGATTCTCCGCACTCTCAAGGACCGGAAGGCCTCGCTGC

upper sequence: Vv07s0104g01120.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: PP1S60_256V6.1 (Physcomitrella patens), 3'ss of exon 4
-------------------------------------------------------------------------------------------------------gttgatattaaatcttgaaaatttcttgttttagctaatgctttggtccatggatttcaataaatagaactcctt--ttttgtttgatt--tcaccagATGTCTGATCCATTGACCGCTCTGATGCATGCTGTTCAAGTGATGAACTTGCTAAAGACCCTGATCACAAAAACACTAAGGGAACGGGAAGAAAGCCCGG
                                                                                                       | |||  || || | |    ||| | |||||    |  || ||   |   || |    |||   ||  | |  ||    ||| || |||   |  |||||| |||||||| |||| ||||||||||||||||||||||| ||||||||||| || || |||||       ||||| | ||| ||  | |  |    | 
gtatagtgttgtttctacgcttttcacccagagaagctgatgaccattacaagatcagactcgtagagatttcactacagatgctgtcttcgacgtttcatgtgctgaatttgaa-cgtaggtattccgtgttta---tggtgtttcaattgttgta---gaatgtgtaacatttattgacattgcttcattatccttcagATGGCTGATCCACTGACAGCTCTGATGCATGCTGTTCAAGTCATGAACTTGCTCAAAACTCTGATTCTTCGCACACTGAAGGACCGAAAGGCCACTTTGC

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|32248627|gb|CD714446.1|CD714446
EST:     AAATGAATGCGAGAAATATTGCAATGGTTTTTGCTCCAAATATGACTCAG                         ATGTCTGATCCATTGACCGCTCTGATGCATGCTGTTCAAGTGATGAACTTG
genomic: AAATGAATGCGAGAAATATTGCAATGGTTTTTGCTCCAAATATGACTCAGgttgatatta ... atttcaccagATGTCTGATCCATTGACCGCTCTGATGCATGCTGTTCAAGTGATGAACTTG
EST: gi|32272070|gb|CD721229.1|CD721229
EST:     AAATGAATGCGAGAAATATTGCAATGGTTTTTGCTCCAAATATGACTCAG                         ATGTCTGATCCATTGACCGCTCTGATGCATGCTGTTCAAGTGATGAACTTG
genomic: AAATGAATGCGAGAAATATTGCAATGGTTTTTGCTCCAAATATGACTCAGgttgatatta ... atttcaccagATGTCTGATCCATTGACCGCTCTGATGCATGCTGTTCAAGTGATGAACTTG
EST: gi|32268340|gb|CD717499.1|CD717499
EST:     AAATGAATGCGAGAAATATTGCAATGGTTTTTGCTCCAAATATGACTCAG                         ATGTCTGATCCATTGACCGCTCTGATGCATGCTGTTCAAGTGATGAACTTG
genomic: AAATGAATGCGAGAAATATTGCAATGGTTTTTGCTCCAAATATGACTCAGgttgatatta ... atttcaccagATGTCTGATCCATTGACCGCTCTGATGCATGCTGTTCAAGTGATGAACTTG
EST: gi|32248076|gb|CD713895.1|CD713895
EST:     AAATGAATGCGAGAAATATTGCAATGGTTTTTGCTCCAAATATGACTCAG                         ATGTCTGATCCATTGACCGCTCTGATGCATGCTGTTCAAGTGATGAACTTG
genomic: AAATGAATGCGAGAAATATTGCAATGGTTTTTGCTCCAAATATGACTCAGgttgatatta ... atttcaccagATGTCTGATCCATTGACCGCTCTGATGCATGCTGTTCAAGTGATGAACTTG
EST: gi|32247815|gb|CD713634.1|CD713634
EST:     AAATGAATGCGAGAAATATTGCAATGGTTTTTGCTCCAAATATGACTCAG                         ATGTCTGATCCATTGACCGCTCTGATGCATGCTGTTCAAGTGATGAACTTG
genomic: AAATGAATGCGAGAAATATTGCAATGGTTTTTGCTCCAAATATGACTCAGgttgatatta ... atttcaccagATGTCTGATCCATTGACCGCTCTGATGCATGCTGTTCAAGTGATGAACTTG
EST: gi|110700193|gb|EE077949.1|EE077949
EST:     AAATGAATGCGAGAAATATTGCAATGGTTTTTGCTCCAAATATGACTCAG                         ATGTCTGATCCATTGACCGCTCTGATGCATGCTGTTCAAGTGATGAACTTG
genomic: AAATGAATGCGAGAAATATTGCAATGGTTTTTGCTCCAAATATGACTCAGgttgatatta ... atttcaccagATGTCTGATCCATTGACCGCTCTGATGCATGCTGTTCAAGTGATGAACTTG
EST: gi|32271575|gb|CD720734.1|CD720734
EST:     AAATGAATGCGAGAAATATTGCAATGGTTTTTGCTCCAAATATGACTCAG                         ATGTCTGATCCATTGACCGCTCTGATGCATGCTGTTCAAGTGATGAACTTG
genomic: AAATGAATGCGAGAAATATTGCAATGGTTTTTGCTCCAAATATGACTCAGgttgatatta ... atttcaccagATGTCTGATCCATTGACCGCTCTGATGCATGCTGTTCAAGTGATGAACTTG
EST: gi|32270904|gb|CD720063.1|CD720063
EST:     AAATGAATGCGAGAAATATTGCAATGGTTTTTGCTCCAAATATGACTCAG                         ATGTCTGATCCATTGACCGCTCTGATGCATGCTGTTCAAGTGATGAACTTG
genomic: AAATGAATGCGAGAAATATTGCAATGGTTTTTGCTCCAAATATGACTCAGgttgatatta ... atttcaccagATGTCTGATCCATTGACCGCTCTGATGCATGCTGTTCAAGTGATGAACTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gctttggtccatggatttcaataaatagaactccttttttgtttgatttcaccagATGTCTGATCCATTGACCGCTCTGATGCATGCTGTTCAAGTGATGAACTTGCTAAAGACCCTGATCACAAAAACACTAAGGGAACGGGAAGAAAGCCCGG
                                        gtttgat  putative branch site (score: 5)
                                              tttcacc  CT-rich tract
              atttcaataaatagaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttgatattaaatcttgaaaatttcttgttttagctaatgctttggtccatggatttcaataaatagaactccttttttgtttgatttcaccagATGTCTGATCCATTGACCGCTCTGATGCATGCTGTTCAAGTGATGAACTTGCTAAAGACCCTGATCACAAAAACACTAAGGGAACGGGAAGAAAGCCCGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA