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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtgggcttgttttcatttctgttaaatcaattcttgtgtcgaatatggttgtttgttgttatgttaatgaattggattttgcagTCTCTTGTTGCAAACGAGGAATTTCAGCACATTCTTCGTGTGCTCAACACCAACGTCGATGGGAAGCAGAAGATCATGTTTGCCCTCACTTCCATCAAGG

Basic information

species Vitis vinifera
transcript Vv05s0020g03450.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0020g03450.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os03g58050.1 (Oryza sativa), 3'ss of exon 1
-------------gtgagtgggcttgttttcatttctgtt---aaatcaa-ttcttgtgtcgaatatggttgtttgttgttatgttaatgaattggattttgcagTCTCTTGTTGCAAACGAGGAATTTCAGCACATTCTTCGTGTGCTCAACACCAACGTCGATGGGAAGCAGAAGATCATGTTTGCCCTCACTTCCATCAAGG
               |  |   ||    | |||| | ||     | ||   |||| ||| ||  |    |   |   | |   |||   |  |  |     |||||| ||  | ||    ||||| || |||||||| || ||| |||| ||||||||||||||||||||||||||||||||||| || ||||| ||||||||||
gtaaccttctcgctcgcttctcctctcctccattcccgtctccgattcgccttctcgtgacgcctcctctgactgactctc--gttggcgcttctgtccccgcagTCGCTGATCGCCGGGGAGGACTTCCAGCACATCCTGCGTCTGCTGAACACCAACGTCGATGGGAAGCAGAAGATCATGTTCGCGCTCACCTCCATCAAGG

upper sequence: Vv05s0020g03450.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os07g07709.1 (Oryza sativa), 3'ss of exon 1
gtgagtgggcttgttttc------atttctgttaaatcaattcttgtgt-cgaatatggttgtttgttgttatgttaatgaattggattttgcagTCTCTTGTTGCAAACGAGGAATTTCAGCACATTCTTCGTGTGCTCAACACCAACGTCGATGGGAAGCAGAAGATCATGTTTGCCCTCACTTCCATCAAGG
|| ||     ||  | ||       |  |  ||  |    |   | ||  |   |      |   |   |   ||   ||  |||  |||||||||| ||  | ||    ||||| || |||||||| || ||| |||| ||||| ||||| ||||||||||||||||||||||| || ||||| ||||||||||
gtaagctccgttcctctcccgcatctcccctttgcagtggtctctttgcgcaggtgctaaggggaggaatcgcgtgtgtgt-ttgatttttgcagTCGCTGATCGCGGGGGAGGATTTCCAGCACATCCTGCGTCTGCTGAACACGAACGTGGATGGGAAGCAGAAGATCATGTTCGCGCTCACCTCCATCAAGG

upper sequence: Vv05s0020g03450.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G062911_T01 (Zea mays), 3'ss of exon 1
gtgagtgggcttgttttcatttctgttaaatcaattcttgtgtcgaatatggttgtttgttgttatgttaatgaattggattttgcagTCTCTTGTTGCAAACGAGGAATTTCAGCACATTCTTCGTGTGCTCAACACCAACGTCGATGGGAAGCAGAAGATCATGTTTGCCCTCACTTCCATCAAGG
  |   | |||  |    |   |  ||   |||  ||  | ||||     | ||  |   ||  | |    ||   | |  ||||||||| ||  ||||    ||||| ||||||||||| || ||| |||| ||||||||||| ||||| |||||||||||||||||||||||||| ||||||||||
--gtaagagctcctccctacccc-attttgtca--tcacgggtcgg---cgattagtc--tgacacgcggttggcattggctttgcagTCGCTGATTGCGGGGGAGGACTTTCAGCACATCCTGCGTTTGCTTAACACCAACGTGGATGGCAAGCAGAAGATCATGTTTGCCCTCACCTCCATCAAGG

upper sequence: Vv05s0020g03450.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G178341_T02 (Zea mays), 3'ss of exon 1
gtgagtgggcttgttttcatttctgttaaatcaattcttgtgtcgaatatggttgtttgt--tgttatgttaatgaattggatttt---gcagTCTCTTGTTGCAAACGAGGAATTTCAGCACATTCTTCGTGTGCTCAACACCAACGTCGATGGGAAGCAGAAGATCATGTTTGCCCTCACTTCCATCAAGG
|| |     | |    | ||| ||       | | ||| ||   | | ||| || | | |  |||| || |   |    |  | ||   |||||| ||  | ||   |||||| || || || ||||| ||| |||| ||||||||||| ||||||||||||||||||||||| ||| | || ||||| ||||
gtaacct--cctacacttattcctccccg-ccgactctcgttgtgcagatgtttttgtatcgtgttctgattccgtgacgactgttgccgcagTCGCTGATCGCCGGCGAGGACTTCCAACATATTCTGCGTCTGCTGAACACCAACGTGGATGGGAAGCAGAAGATCATGTTCGCCATGACCTCCATAAAGG

upper sequence: Vv05s0020g03450.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G130544_T02 (Zea mays), 3'ss of exon 1
gtgagtgggcttgttt--tcatttctgttaaatcaattcttgtgt-cgaatatggttgtttgttgttatgttaatga-attggattttgcagTCTCTTGTTGCAAACGAGGAATTTCAGCACATTCTTCGTGTGCTCAACACCAACGTCGATGGGAAGCAGAAGATCATGTTTGCCCTCACTTCCATCAAGG
    ||   ||| |    ||| ||||    | |   |    |||| |  ||||  || |   ||  |   |   |||  |  |     |||||| ||  | ||    ||||| || ||||| || || ||| |||| ||||||||||| ||||||||||||||||||||||| ||| | || || |||||||
----gtaaccttctccactcacttctccccattgcttctcggtgtgcagatatttttatagtttcctgactccgtgacgtctgtggccgcagTCGCTGATCGCCGGGGAGGACTTCCAGCATATCCTGCGTTTGCTGAACACCAACGTGGATGGGAAGCAGAAGATCATGTTCGCCATGACCTCAATCAAGG

upper sequence: Vv05s0020g03450.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: PP1S242_94V6.1 (Physcomitrella patens), 3'ss of exon 1
-----------------------------------------------------gtgag-tgggcttgttttcatttctgttaaatcaattcttgtgtcgaatatggttgtttgttgttatgttaatgaattggattttg-cagTCTCTTGTTGCAAACGAGGAATTTCAGCACATTCTTCGTGTGCTCAACACCAACGTCGATGGGAAGCAGAAGATCATGTTTGCCCTCACTTCCATCAAGG
                                                     ||  | || | ||||| |  ||| | ||    ||| | ||||         || |   ||    | ||      |  ||| | |   ||||| ||  ||||   |||||||||||||||||||||||||||||| ||||| |||||||||||    |||||||||||||||||||| ||||| || ||||
gtgcgtgttcatcgcttcctccccatgcagctttcgtcgactcgtttctttgcgtacgatgagattgttat--ttttttttcttccaaatgttgtacacttctagggttcgtgcatctgtgactgaaagctggttgtgaacagTCGCTCATTGCGGGCGAGGAATTTCAGCACATTCTTCGTGTGCTGAACACTAACGTCGATGGACGTCAGAAGATCATGTTTGCCCTGACTTCGATTAAGG

upper sequence: Vv05s0020g03450.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: PP1S14_433V6.1 (Physcomitrella patens), 3'ss of exon 1
------------------------------------------------------------------------------gtgagtgggcttgttttcatttctgttaaatcaattcttgtgtcgaatatggtt-------gtttgttgttatgttaatgaa-ttgg-----attttg--cagTCTCTTGTTGCAAACGAGGAATTTCAGCACATTCTTCGTGTGCTCAACACCAACGTCGATGGGAAGCAGAAGATCATGTTTGCCCTCACTTCCATCAAGG
                                                                               |   |    || ||||  ||| || |   |||||| ||  ||  |  || |||       |||  |||   ||| | |||  ||||      || ||  ||||| ||  | ||    ||||| ||||||||||||||||||||| | ||||| |||||||||||    || ||||| ||||||||| | || ||||| ||||
gtttgtgctcctctgctgttgcgtatatctgtggtgtcgttttttgtttggtactgagttctgggtgtgtttttttttttttttttttttttttttttttttggtttttcaatttttaggttaatgatcgtttgctagggttaattgggctgtgactgaggttggtggcggttgtggccagTCGCTGATCGCGGGTGAGGAGTTTCAGCACATTCTTCGTGTGTTGAACACTAACGTCGATGGACGTCAAAAGATTATGTTTGCCTTGACCTCCATTAAGG

upper sequence: Vv05s0020g03450.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: PP1S215_71V6.1 (Physcomitrella patens), 3'ss of exon 1
-------------------------------------------------gtgagtgggcttgttttcatttctgttaaatc--aattcttgtgtcgaa-----tatggttgtttgttgttatgttaatgaattggattttg-cagTCTCTTGTTGCAAACGAGGAATTTCAGCACATTCTTCGTGTGCTCAACACCAACGTCGATGGGAAGCAGAAGATCATGTTTGCCCTCACTTCCATCAAGG
                                                  |     |   | | ||| | |  || ||||   |  | | | ||  |      | ||  ||   |||| | |||   ||  |  ||| ||| ||||| ||  ||||   |||||| || ||||||||||||||||| || || |||||||||||||||   |||||||| ||||||||||| || ||||||||||
gtgtgtctgatctgcctcgtccttgtcattgtgctgctcttcttggctcttattcagtgctatcttcgtgttcgtgaaattttatgtttagggtttacgtctttgtgactgaaagttggt-tgtgtgtgtttccgatgttggcagTCGCTCATTGCGGGCGAGGAGTTCCAGCACATTCTTCGTGTTCTGAATACCAACGTCGATGGGCGTCAGAAGATTATGTTTGCCCTAACCTCCATCAAGG

upper sequence: Vv05s0020g03450.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: PP1S14_438V6.1 (Physcomitrella patens), 3'ss of exon 1
----------------------------------------------gtgagtgggct-tgttttcatttctgttaaatcaattcttgtgt-cgaatatggttgtttgttgttatgttaatgaattggattttgc-agTCTCTTGTTGCAAACGAGGAATTTCAGCACATTCTTCGTGTGCTCAACACCAACGTCGATGGGAAGCAGAAGATCATGTTTGCCCTCACTTCCATCAAGG
                                                |  |  | | |||||  | |  | ||   || | | | | ||  | |  |   || |     ||   | |      ||| | |  | |||| ||  | ||    || || ||||| || |||||||||||||| || || |||||||||||   ||||||||||||||| ||||| || ||||| || |
gtgggtagtttctcccacctgtgctacacgtaaaaatttcagtttttcggttccgttctgtttggagtgttttttgctcgactttagggtgtgcaggttcatgatctaaattggttcagaatggtgggtgtgactagTCGCTCATCGCGGGTGAAGAGTTTCAACATATTCTTCGTGTGCTGAATACAAACGTCGATGGACGGCAGAAGATCATGTTCGCCCTGACCTCCATTAAAG

upper sequence: Vv05s0020g03450.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: PP1S215_81V6.1 (Physcomitrella patens), 3'ss of exon 1
---------------gtgagtgggcttgttttcatttctgttaaatcaattcttgtgtcgaata-tggttgtttgttgttatgttaatgaattggattttgcagTCTCTTGTTGCAAACGAGGAATTTCAGCACATTCTTCGTGTGCTCAACACCAACGTCGATGGGAAGCAGAAGATCATGTTTGCCCTCACTTCCATCAAGG
                     |   |||||    | |  | |  ||      | ||| |  ||| | ||||| |||   | |||   ||  | |  |||| ||||| ||  | ||    |||||||||||||||||||||||||| || ||||| |||||||||||    |||||||||||||||||| | || ||||| ||||
tcctctcgctctctctccgacgacattgttgatgtctagggtttat--gccgtcgtgactgatactagttgtgtgtgtgtgtgt-ggtgg-tggtttttttcagTCGCTCATCGCGGGTGAGGAATTTCAGCACATTCTTCGTGTCCTTAACACGAACGTCGATGGACGCCAGAAGATCATGTTTGCCTTGACCTCCATTAAGG

upper sequence: Vv05s0020g03450.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: PP1S72_222V6.2 (Physcomitrella patens), 3'ss of exon 1
-------------------------------------------------------------------gtgagtgggcttgttttcatttctgttaaatca-attcttgtgtcgaatatggttgtttgttgttatgt-----taatgaattggattttg----------cagTCTCTTGTTGCAAACGAGGAATTTCAGCACATTCTTCGTGTGCTCAACACCAACGTCGATGGGAAGCAGAAGATCATGTTTGCCCTCACTTCCATCAAGG
                                                                    |   |    |  ||||| ||   |||   |      | ||| |   || |    |||||  | |||||     |  |   || | |||||          ||||| || |||||    ||||| || || || |||||||||||||||||||| |||||||||||    |||||||||||||||||||| || |||       
gtgtgtagtttcccctccctctgctgtgtgcacaagctggatttttttcttttcattttctcggttctttctttctgtcattttcgttatggtttggttgtgcacatgtttgagattttagggtttgaaggtatgtgaccctggttggtttggttttgttgaagCGGCCAGTCGCTCGTTGCGGGTGAGGAGTTCCAACATATTCTTCGTGTGCTCAACACGAACGTCGATGGACGTCAGAAGATCATGTTTGCCCTGACCTCC-------

upper sequence: Vv05s0020g03450.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: PP1S72_222V6.1 (Physcomitrella patens), 3'ss of exon 1
-------------------------------------------------------------------gtgagtgggcttgttttcatttctgttaaatca-attcttgtgtcgaatatggttgtttgttgttatgt-----taatgaattggattttg----------cagTCTCTTGTTGCAAACGAGGAATTTCAGCACATTCTTCGTGTGCTCAACACCAACGTCGATGGGAAGCAGAAGATCATGTTTGCCCTCACTTCCATCAAGG
                                                                    |   |    |  ||||| ||   |||   |      | ||| |   || |    |||||  | |||||     |  |   || | |||||          ||||| || |||||    ||||| || || || |||||||||||||||||||| |||||||||||    |||||||||||||||||||| || ||||| ||||
gtgtgtagtttcccctccctctgctgtgtgcacaagctggatttttttcttttcattttctcggttctttctttctgtcattttcgttatggtttggttgtgcacatgtttgagattttagggtttgaaggtatgtgaccctggttggtttggttttgttgaagcggccagTCGCTCGTTGCGGGTGAGGAGTTCCAACATATTCTTCGTGTGCTCAACACGAACGTCGATGGACGTCAGAAGATCATGTTTGCCCTGACCTCCATTAAGG

upper sequence: Vv05s0020g03450.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: EFJ22352 (Selaginella moellendorffii), 3'ss of exon 1
gtgagtgggcttgttttcatttctgttaaatcaattcttgtgtcgaatatggttgtttgttgttatgttaatgaattggattttgcagTCTCTTGTTGCAAACGAGGAATTTCAGCACATTCTTCGTGTGCTCAACACCAACGTCGATGGGAAGCAGAAGATCATGTTTGCCCTCACTTCCATCAAGG
                                 |||||||||| |  | | |        |  |        |  |  | ||| ||||||||| ||    || ||||| || |||||||||||||||||||||||||| || || || |||  ||||||||| ||||| || || |||||||||||||
----------------------------gtatgattcttgtgttgggtgttga-----aataatcctccggcgcctctgttttggcagTCTCTGGTGAGCAATGAGGAGTTCCAGCACATTCTTCGTGTGCTCAACACGAATGTGGACGGGCGGCAGAAGATTATGTTCGCGCTGACTTCCATCAAGG

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|294964772|gb|GW838575.1|GW838575
EST:     CTTTGAGCGCTAATCCTAACCCTAGCCATG                         TCTCTTGTTGCAAACGAGGAATTTCAGCGCATTCTTCGTGTGCTCAACACC
genomic: CTTTGAGCCCTAATCCTAACCCTAGCCATGgtgagtgggc ... gattttgcagTCTCTTGTTGCAAACGAGGAATTTCAGCACATTCTTCGTGTGCTCAACACC
EST: gi|30136491|gb|CB921829.1|CB921829
EST:     TTGAGCTCTAATCCTAACCCTAGCCATG                         TCTCTTGTTGCAAACGAGGAATTTCAGCACATTCTTCGTGTGCTCAACACC
genomic: TTGAGCCCTAATCCTAACCCTAGCCATGgtgagtgggc ... gattttgcagTCTCTTGTTGCAAACGAGGAATTTCAGCACATTCTTCGTGTGCTCAACACC
EST: gi|110688699|gb|EE067547.1|EE067547
EST:     CTTTGAGCCCTAATCCTAACCCTAGCCATG                         TCTCTTGTTGCAAACGAGGAATTTCAGCACATTCTTCGTGTGCTCAACACC
genomic: CTTTGAGCCCTAATCCTAACCCTAGCCATGgtgagtgggc ... gattttgcagTCTCTTGTTGCAAACGAGGAATTTCAGCACATTCTTCGTGTGCTCAACACC
EST: gi|110716629|gb|EE091780.1|EE091780
EST:     CCTAACCCTAGCCATG                         TCTCTTGTTGCAAACGAGGAATTTCAGCACATTCTTCGTGTGCTCAACACC
genomic: CCTAACCCTAGCCATGgtgagtgggc ... gattttgcagTCTCTTGTTGCAAACGAGGAATTTCAGCACATTCTTCGTGTGCTCAACACC
EST: gi|32248682|gb|CD714501.1|CD714501
EST:     CTTTGAGCCCTAATCCTAACCCTAGCCATG                         TCTCTTGTTGCAAACGAGGAATTTCAGCACATTCTTCGTGTGCTCAACACC
genomic: CTTTGAGCCCTAATCCTAACCCTAGCCATGgtgagtgggc ... gattttgcagTCTCTTGTTGCAAACGAGGAATTTCAGCACATTCTTCGTGTGCTCAACACC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attcttgtgtcgaatatggttgtttgttgttatgttaatgaattggattttgcagTCTCTTGTTGCAAACGAGGAATTTCAGCACATTCTTCGTGTGCTCAACACCAACGTCGATGGGAAGCAGAAGATCATGTTTGCCCTCACTTCCATCAAGG
                                tgttaat  putative branch site (score: 3)
                             ttatgttaatgaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtgggcttgttttcatttctgttaaatcaattcttgtgtcgaatatggttgtttgttgttatgttaatgaattggattttgcagTCTCTTGTTGCAAACGAGGAATTTCAGCACATTCTTCGTGTGCTCAACACCAACGTCGATGGGAAGCAGAAGATCATGTTTGCCCTCACTTCCATCAAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA