Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttttacgctttttacccaattgtccatgcatttgtccaagaaattcataaaatccttaggagggctgagggtaaaattggaatgtttgcatgtatggcagGGCTACGGGATGACAGAGGCGGGACCCGTGTTGGCAATGTGCTTGGCCTTTGCCAAAGAGCCATTCGAGATCAAGTCTGGGTCTTGTGGCACAGTGGTCA

Basic information

species Vitis vinifera
transcript Vv11s0052g01090.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv11s0052g01090.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os02g08100.1 (Oryza sativa), 3'ss of exon 2
--------------ttttacgctttttacccaattgtccatgcatttgtccaagaaattcataaaatccttaggagggctga-gggtaaaattggaatgtttgcatgtatggcagGGCTACGGGATGACAGAGGCGGGACCCGTGTTGGCAATGTGCTTGGCCTTTGCCAAAGAGCCATTCGAGATCAAGTCTGGGTCTTGTGGCACAGTGGTCA
                ||||  |  || | |    |   |   | |   |        || |    |  || |     ||||   || |    |  || |   | | |     |||| ||||| ||||| ||||| || || ||| ||||||||||| |||| |||||||| ||||| ||| || | ||||| ||||| || || ||||||||  
gtaaattgatgccacattacaatcattgcgcggacgaaaacaaaatctcctctctctctcttt---ttttttgagtcactgacaagttagtccgtcatatcc-cttcttctttagGGTTACGGTATGACTGAGGCTGGGCCAGTGCTGGCAATGTGCCTGGCGTTTGCCAAGGAGCCCTTCAAGGTTAAGTCCGGGTCGTGCGGTACAGTGGTGC

upper sequence: Vv11s0052g01090.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os06g44620.2 (Oryza sativa), 3'ss of exon 2
---ttttacgctttttacccaattgtccatgcatttgtccaagaaattcataaaatccttaggagggctgagggtaaaattggaatgtttgcatgtatggcagGGCTACGGGATGACAGAGGCGGGACCCGTGTTGGCAATGTGCTTGGCCTTTGCCAAAGAGCCATTCGAGATCAAGTCTGGGTCTTGTGGCACAGTGGTCA
    |    |    | || |   |||  |    | ||  |   || |   | ||   || || |   |   |  |    ||    | |||   | | || ||||| || |||||||| ||||| ||||| ||| |||| |||||  ||||||| || || |||||||||||| ||||||| || || || || ||||| ||||
accgtgggtgacactgacactgatgtgaa-atttctgatccttaagtgactgaatcgctgagaaattcactgcatttcgtttt--tttttctttttctgacagGGGTATGGGATGACTGAGGCTGGACCTGTGCTGGCCATGTGTCTGGCCTTCGCAAAGGAGCCATTCGAGGTCAAGTCCGGCTCGTGCGGGACAGTCGTCA

upper sequence: Vv11s0052g01090.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G055320_T02 (Zea mays), 3'ss of exon 2
ttttacgctttttacccaattgtccatgcatttgtccaaga-aattcataaaatcctt------aggagggctgagggtaaaattggaatgtttgcatgtatggcagGGCTACGGGATGACAGAGGCGGGACCCGTGTTGGCAATGTGCTTGGCCTTTGCCAAAGAGCCATTCGAGATCAAGTCTGGGTCTTGTGGCACAGTGGTCA
            |||    |||| | || |   | || |||  ||   |    ||  |       |||  |    |  ||  | |    | | | | | |    ||||| ||||||||||| |||||||| |||||| |||| |||||| ||||||| ||||| ||||| |||||| ||||||| || || |||||||| || ||||
-------gcacctacatcgttgtacttgtacaagaccgagacgataggttttgtctgttgaaacgggaatgtgatgtttacgaataacctctgttcgtttccaccagGGGTACGGGATGACCGAGGCGGGGCCCGTGCTGGCCATGTGCCTGGCCTTCGCCAAGGAGCCGTTCGAGGTCAAGTCCGGCTCCTGTGGCACCGTCGTCA

upper sequence: Vv11s0052g01090.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G075333_T01 (Zea mays), 3'ss of exon 2
ttttacgctttttacccaattgtccatgcatttgtccaagaaattcataaaatccttaggagggctgagggtaaaattggaatgtttgcatg---tatggcagGGCTACGGGATGACAGAGGCGGGACCCGTGTTGGCAATGTGCTTGGCCTTTGCCAAAGAGCCATTCGAGATCAAGTCTGGGTCTTGTGGCACAGTGGTCA
   ||||    |   |   | ||||     ||| ||   |   ||| | |   |    |      |  |     | |  ||    |   |||   |    ||||| ||||||||||| ||||| || |||||| |||| |||||| ||||||| ||||| ||||| | |  | ||||||| ||||| || ||||| |||||  
--gtacgtccgtcgtc--gtcgtccgaagctttttc---ggttttcctgatgacacgcgttccattccgttcccattccgaccaatgcaatgcaatgcaacagGGGTACGGGATGACGGAGGCAGGCCCCGTGCTGGCGATGTGCCTGGCCTTCGCCAAGGAGCCGTACCCGGTCAAGTCCGGGTCGTGCGGCACCGTGGTGC

upper sequence: Vv11s0052g01090.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: PP1S185_66V6.1 (Physcomitrella patens), 3'ss of exon 2
---------------------ttttacgctttttacc-caattgtccatgcatttgtccaagaaattcataaaatccttaggagggctgagggtaaaattggaatgtttg---catgtatggcagGGCTACGGGATGACAGAGGCGGGACCCGTGTTGGCAATGTGCTTGGCCTTTGCCAAAGAGCCATTCGAGATCAAGTCTGGGTCTTGTGGCACAGTGGTCA
                     | || ||    |  |  | | |||| |    ||  || ||  | |   |    | | |   |  |   |  |   | |  || ||||||   | ||  |  |||||||| || |||||||| || || || |||||||||||||||||||| || || ||    ||||||  | | ||| | ||||| || |||||||| ||| 
gtaactaaaccattcaccaattcttgcggccatggcgacgagtgtcta-attttcttcaaaatactgggtttttttccttaaaaagagaattgacgagt--gattgtttggttcgtgattcacagGGCTATGGAATGACAGAAGCTGGTCCAGTGTTGGCAATGTGCTTGGCATTCGCGAAGACTCCATTCTCGGTGAAGCCAGGGTCATGCGGCACAGTAGTCC

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|30321211|gb|CD004473.1|CD004473
EST:     AGCTTGAAGACACTGTCAGAGCCAAGCTCCCCAACGCCAAGCTTGGACAG                         GGCTACGGGATGACAGAGGCGGGACCCGTGTTGGCAATGTGCTTGGCCTTT
genomic: AGCTTGAAGACACTGTCAGAGCCAAGCTCCCTAACGCCAAGCTTGGACAGgtaattttca ... tgtatggcagGGCTACGGGATGACAGAGGCGGGACCCGTGTTGGCAATGTGCTTGGCCTTT
EST: gi|33402238|gb|CF207865.1|CF207865
EST:     AGCTTGAAGACACTGTCAGAGCCAAGCTCCCTAACGCCAAGCTTGGACAG                         GGCTACGGGATGACAGAGGCGGGACCCGTGTTGGCAATGTGCTTGGCCTTT
genomic: AGCTTGAAGACACTGTCAGAGCCAAGCTCCCTAACGCCAAGCTTGGACAGgtaattttca ... tgtatggcagGGCTACGGGATGACAGAGGCGGGACCCGTGTTGGCAATGTGCTTGGCCTTT
EST: gi|37185997|gb|CF605350.1|CF605350
EST:     AGCTTGAAGACACTGTCAGAGCCAAGCTCCCCAACGCCAAGCTTGGACAG                         GGCTACGGGATGACAGAGGCGGGACCCGTGTTGGCAATGTGCTTGGCCTTT
genomic: AGCTTGAAGACACTGTCAGAGCCAAGCTCCCTAACGCCAAGCTTGGACAGgtaattttca ... tgtatggcagGGCTACGGGATGACAGAGGCGGGACCCGTGTTGGCAATGTGCTTGGCCTTT
EST: gi|161714158|gb|FC062903.1|FC062903
EST:     AGCTTGAAGACACTGTCAGAGCCAAGCTCCCTAACGCCAAGCTTGGACAG                         GGCTACGGGATGACAGAGGCGGGACCCGTGTTGGCAATGTGCTTGGCCTTT
genomic: AGCTTGAAGACACTGTCAGAGCCAAGCTCCCTAACGCCAAGCTTGGACAGgtaattttca ... tgtatggcagGGCTACGGGATGACAGAGGCGGGACCCGTGTTGGCAATGTGCTTGGCCTTT
EST: gi|33403621|gb|CF209248.1|CF209248
EST:     GAGCCAAGCTCCCCAACGCCAAGCTTGGACAG                         GGCTACGGGATGACAGAGGCGGGACCCGTGTTGGCAATGTGCTTGGCCTTT
genomic: GAGCCAAGCTCCCTAACGCCAAGCTTGGACAGgtaattttca ... tgtatggcagGGCTACGGGATGACAGAGGCGGGACCCGTGTTGGCAATGTGCTTGGCCTTT
EST: gi|110690401|gb|EE067466.1|EE067466
EST:     AGCTTGAAGACACTGTCAGAGCCAAGCTCCCCAACGCCAAGCTTGGACAG                         GGCTACGGGATGACAGAGGCGGGACCCGTGTTGGCAATGTGCTTGGCCTTT
genomic: AGCTTGAAGACACTGTCAGAGCCAAGCTCCCTAACGCCAAGCTTGGACAGgtaattttca ... tgtatggcagGGCTACGGGATGACAGAGGCGGGACCCGTGTTGGCAATGTGCTTGGCCTTT
EST: gi|33402316|gb|CF207943.1|CF207943
EST:     AGCTTGAAGACACTGTCAGAGCCAAGCTCCCTAACGCCAAGCTTGGACAG                         GNCTACGGGATGACAGAGGCGGGACCCGTGTTGGCAATGTGCTTGGCCTTT
genomic: AGCTTGAAGACACTGTCAGAGCCAAGCTCCCTAACGCCAAGCTTGGACAGgtaattttca ... tgtatggcagGGCTACGGGATGACAGAGGCGGGACCCGTGTTGGCAATGTGCTTGGCCTTT
EST: gi|161712219|gb|FC061593.1|FC061593
EST:     AGCTTGAAGACACTGTCAGAGCCAAGCTCCCTAACGCCAAGCTTGGACAG                         GGCTACGGGATGACAGAGGCGGGACCCGTGTTGGCAATGTGCTTGGCCTTT
genomic: AGCTTGAAGACACTGTCAGAGCCAAGCTCCCTAACGCCAAGCTTGGACAGgtaattttca ... tgtatggcagGGCTACGGGATGACAGAGGCGGGACCCGTGTTGGCAATGTGCTTGGCCTTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cataaaatccttaggagggctgagggtaaaattggaatgtttgcatgtatggcagGGCTACGGGATGACAGAGGCGGGACCCGTGTTGGCAATGTGCTTGGCCTTTGCCAAAGAGCCATTCGAGATCAAGTCTGGGTCTTGTGGCACAGTGGTCA
                          taaaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttttacgctttttacccaattgtccatgcatttgtccaagaaattcataaaatccttaggagggctgagggtaaaattggaatgtttgcatgtatggcagGGCTACGGGATGACAGAGGCGGGACCCGTGTTGGCAATGTGCTTGGCCTTTGCCAAAGAGCCATTCGAGATCAAGTCTGGGTCTTGTGGCACAGTGGTCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA
- - - - - - tacccaa
- - - - - - - - - - - -ccatgca
- - - - - - - - - - - - - - - - - -ccaagaa
- - - - - - - - - - - - - - - - - - - - - - -cataaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gggctga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggtaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgtttgc