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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACCCGGAGATCCAAGAACTCGTTGACGGACCCACGCTTCCGACTCGGGGATCTGACGAATTCCGGCCGTTCGTGCGCCGCCTCCCGGAGTTCAAGTTCTGgtgcgtcaactattatattactcgcattgtttgaccatttctagggttcccctttttcgtcttaatttggcctgatttatacatattatcacattgaacg...

Basic information

species Vitis vinifera
transcript Vv07s0031g00030.t01
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv07s0031g00030.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: LOC_Os08g21760.1 (Oryza sativa), 5'ss of exon 1
ACCCGGAGATCCAAGAACTCGTTGACGG---ACCCACGCTTCCGACTCGGGGATCTGACGAATTCCGGCCGTTCGTGCGCCGCCTCCCGGAGTTCAAGTTCTGgtgcgtc---aactattatattactcg-cattgtttgaccatttctagggttcccctttttcgtcttaatttggcctgatttatacatattatcacattgaacg
    ||    | | |  ||||  || ||     || |||| || || || | ||||||||| ||||| || ||||| || ||||| ||||||||||| ||||||| ||     | |      | | |||  | |||||  |      || |  ||      |  | ||||  ||||       |  ||   |    | | | ||   
---AGGTCGCCGAGGTGCTCGGCGAGGGGGGGGCCGCGCTCCCCACCCGCGCATCTGACGAGTTCCGCCCTTTCGTCCGTCGCCTTCCGGAGTTCAAATTCTGgttcgatccgatccgacgcaatcctcttccttgttgcaatccagctcgaattgtgggatccc-tctttttttgtgtgctatcgtatggacgtgctcgtcga---

upper sequence: Vv07s0031g00030.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: GLYMA05G20940.1 (Glycine max), 5'ss of exon 1
---ACCCGGAGATCCAAGAACTCGTTGACGGACCCACGCTTCCGACTCGGGGATCTGACGAATTCCGGCCGTTCGTGCGCCGCCTCCCGGAGTTCAAGTTCTGgtgcgtcaactattatat-tactcgcattgtttgaccatttctagggttcccctttttcgtcttaatttggc-ctgatttatacatattatcacattgaacg
   |  | | ||| |  ||   ||  ||||  ||||| || ||  |    |  || |||||||| || || ||||| ||||||||||| |||||||||||||||| |||    | || |   || |  ||   | | |    |  |    |   |  |   ||    |   ||   | |||  ||    || ||| |   |||| 
CCGAGACCGTGATTCTCGA---CGCCGACGTCCCCACCCTCCCCTCCACCGCTTCCGACGAATTTCGTCCCTTCGTTCGCCGCCTCCCCGAGTTCAAGTTCTGgttcgtgccttcttctccctattttcagattctaatttataattacttcatcggtccccgaacaacggtgattccgatgaatcacaatcatctcg--gaacc

upper sequence: Vv07s0031g00030.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: GLYMA01G39640.1 (Glycine max), 5'ss of exon 1
ACCCGGA--GATCCAAGAACTCGTTGACGGACCCACGCTTCCGACTCGGGGATCTGACGAATTCCGGCCGTTCGTGCGCCGCCTCCCGGAGTTCAAGTTCTGgtgcgtcaactattatattactcgcattgtttgaccatttctagggttcccct-ttttcgtcttaatttggcctgatttatacatattatcac--attgaacg
 | | |   |||||    | | |  ||||| ||||| || || || || ||||| ||||| ||||| || ||||| || |||||||| |||||||||||||||| ||   | | |    || |     |       | | |||||||||| |    |   |  | || |||      |||      || | |     ||||   |
-CTCAGGTCGATCCCGAGATTAGC-GACGGCCCCACCCTCCCCACCCGAGGATCCGACGAGTTCCGCCCTTTCGTTCGACGCCTCCCCGAGTTCAAGTTCTGgtacg---aatttccctttccctaattcccccttctacttctagggtttcgtaatccaccacgtagttttattatattatattttactgttttctattgtgag

upper sequence: Vv07s0031g00030.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: GLYMA17G18430.2 (Glycine max), 5'ss of exon 1
ACCCGGAGATCCAAGAACTC---GTTGACGGACCCACGCTTCCGACTCGGGGATCTGACGAATTCCGGCCGTTCGTGCGCCGCCTCCCGGAGTTCAAGTTCTGgtgcgtcaact-attatattact-cgcattgtttgaccatttctagggttcccctttt-tcgtcttaatttggcctgatttatacatattatcacattgaacg
   | |||| |      |||   |  ||||  || |  || || |     |  || ||||| || || || ||||| ||||||||||| ||||||||||||||||  |  |  |   ||  ||  |   | | ||||      |||| || ||    |    | |    ||||  |    ||  ||    ||||    |||     
---CCGAGACCGCGATTCTCAACGCCGACGACCCTATACTCCCCATCGCCGCCTCCGACGAGTTTCGCCCCTTCGTTCGCCGCCTCCCCGAGTTCAAGTTCTGgtatgctattttgctaccttcttatacctagttttttttcttctcggattttattagagttgctccaattcag---aatccattttgattaatttatttttta

upper sequence: Vv07s0031g00030.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: EDP03103 (Chlamydomonas reinhardtii), 5'ss of exon 2
ACCCGGAGATCCAAGAACTCGTT-GACGGACCCACGCTTCCGACTCGGGGATCTGACGAATTCCGGCCGTTCGTGCGCCGCCTCCCGGAGTTCAAGTTCTGgtgcgt-------------caactattatattactcgcattgtttgac-catttctagggttcccctttttcgtcttaat--ttggcctgatttatacatattatcaca-ttgaacg-----------------------------------------------------------------------------------
 |||    || | |   |  ||  || || ||   ||| |||||   ||    ||| || |||||||| |||||||| || || ||||||||||| |||||||||||             ||      |    || |||   |  |||| |||     | |  | |||     |  |   |   | ||     | |    |   |||||| ||| ||                                                                                    
-CCCCCCAATTCGACCCCGAGTCCGAGGGGCCAGAGCTGCCGACAAAGGCGGATGAGGAGTTCCGGCCATTCGTGCGGCGGCTGCCGGAGTTCAAATTCTGgtgcgtgtgaggacaggggcagggggcaggacacgcgcggcgcctgacacatgaaacgtggacgcctagcaggcatcggtagctagctcacatcacggctgc-atcacacttgcaccacatgctttgtcgcactcgttttcctacgcggttgccgaaacccggccgcaccctccgctgttcaccgttctcgcttgcgcag

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|110687065|gb|EE064148.1|EE064148
EST:     TCTGACGAATTCCGGCCGTTCGTGCGCCGCCTCCCGGAGTTCAAGTTCTG                         GTACTCTATCACAAAAGCCTTCTGCATTGCTTTTGTAATGACATTCTTCAG
genomic: TCTGACGAATTCCGGCCGTTCGTGCGCCGCCTCCCGGAGTTCAAGTTCTGgtgcgtcaac ... tccctggaagGTACTCTATCACAAAAGCCTTCTGCATTGCTTTTGTAATGACATTCTTCAG
EST: gi|37190408|gb|CF609757.1|CF609757
EST:     TCTGACGAATTCCGGCCGTTCGTGCGCCGCCTCCCGGAGTTCAAGTTCTG                         GTACTCTATCACAAAAGCCTTCTGCATTGCTTTTGTAAT
genomic: TCTGACGAATTCCGGCCGTTCGTGCGCCGCCTCCCGGAGTTCAAGTTCTGgtgcgtcaac ... tccctggaagGTACTCTATCACAAAAGCCTTCTGCATTGCTTTTGTAAT
EST: gi|352785943|gb|FQ475946.1|FQ475946
EST:     TCTGACGAATTCCGGCCGTTCGTGCGCCGCCTCCCGGAGTTCAAGTTCTG                         GTACTCTATCAGCAAA-GCCTTCTGCATTGGTTTTGTAATGACATTCTTCA
genomic: TCTGACGAATTCCGGCCGTTCGTGCGCCGCCTCCCGGAGTTCAAGTTCTGgtgcgtcaac ... tccctggaagGTACTCTATCA-CAAAAGCCTTCTGCATTGCTTTTGTAATGACATTCTTCA
EST: gi|110684805|gb|EE062504.1|EE062504
EST:     TCTGACGAATTCCGGCCGTTCGTGCGCCGCCTCCCGGAGTTCAAGTTCTG                         GTACTCTATCACAAAAGCCTTCTGCATTGCTTTTGTAATGACATTCTTCAG
genomic: TCTGACGAATTCCGGCCGTTCGTGCGCCGCCTCCCGGAGTTCAAGTTCTGgtgcgtcaac ... tccctggaagGTACTCTATCACAAAAGCCTTCTGCATTGCTTTTGTAATGACATTCTTCAG
EST: gi|37187330|gb|CF606683.1|CF606683
EST:     TCTGACGAATTCCGGCCGTTCGTGCGCCGCCTCCCGGAGTTCAAGTTCTG                         GTACTCTATCACAAAAGCCTTCTGCATTGCTTTTGTAATGAC
genomic: TCTGACGAATTCCGGCCGTTCGTGCGCCGCCTCCCGGAGTTCAAGTTCTGgtgcgtcaac ... tccctggaagGTACTCTATCACAAAAGCCTTCTGCATTGCTTTTGTAATGAC
EST: gi|27583432|gb|CB006127.1|CB006127
EST:     TCTGACGAATTCCGGCCGTTCGTGCGCCGCCTCCCGGAGTTCAAGTTCTG                         GTACTCTATCACAAAAGCCTTCTGCATTGCTTTTGTAATGACATTCTTCAG
genomic: TCTGACGAATTCCGGCCGTTCGTGCGCCGCCTCCCGGAGTTCAAGTTCTGgtgcgtcaac ... tccctggaagGTACTCTATCACAAAAGCCTTCTGCATTGCTTTTGTAATGACATTCTTCAG
EST: gi|30304103|gb|CB980897.1|CB980897
EST:     TCTGACGAATTCCGGCCGTTCGCGCGCTGCCTCCCGGAGTTCAAGTTCTG                         GTACTCTATCACAAAAGCCTTCTGCATTGCTTTTGTAATGACATTCTTCAG
genomic: TCTGACGAATTCCGGCCGTTCGTGCGCCGCCTCCCGGAGTTCAAGTTCTGgtgcgtcaac ... tccctggaagGTACTCTATCACAAAAGCCTTCTGCATTGCTTTTGTAATGACATTCTTCAG
EST: gi|110374573|gb|EC939425.1|EC939425
EST:     TCTGACGAATTCCGGCCGTTCGTGCGCCGCCTCCCGGAGTTCAAGTTCTG                         GTACTCTATCACAAAAGCCTTCTGCATTGCTTTTGTAATGACATTCTTCAG
genomic: TCTGACGAATTCCGGCCGTTCGTGCGCCGCCTCCCGGAGTTCAAGTTCTGgtgcgtcaac ... tccctggaagGTACTCTATCACAAAAGCCTTCTGCATTGCTTTTGTAATGACATTCTTCAG
EST: gi|110726472|gb|EE102283.1|EE102283
EST:     TCTGACGAATTCCGGCCGTTCGTGCGCCGCCTCCCGGAGTTCAAGTTCTG                         GTACTCTATCACAAAAGCCTTCTGCATTGCTTTTGTAATGACATTCTTCAG
genomic: TCTGACGAATTCCGGCCGTTCGTGCGCCGCCTCCCGGAGTTCAAGTTCTGgtgcgtcaac ... tccctggaagGTACTCTATCACAAAAGCCTTCTGCATTGCTTTTGTAATGACATTCTTCAG
EST: gi|71858749|gb|DT007804.1|DT007804
EST:     TCTGACGAATTCCGGCCGTTCGTGCGCCGCCTCCCGGAGTTCAAGTTCTG                         GTACTCTATCACAAAAGCCTTCTGCATTGCTTTTGTAATGACATTCTTCAG
genomic: TCTGACGAATTCCGGCCGTTCGTGCGCCGCCTCCCGGAGTTCAAGTTCTGgtgcgtcaac ... tccctggaagGTACTCTATCACAAAAGCCTTCTGCATTGCTTTTGTAATGACATTCTTCAG
EST: gi|294964241|gb|GW838044.1|GW838044
EST:     TCTGACGAATTCCGGCCGTTCGTGCGCCGCCTCCCGGAGTTCAAGTTCTG                         GTACTCTATCACAAAAGCCTTCTGCATTGCTTTTGTAATGACATTCTTCAG
genomic: TCTGACGAATTCCGGCCGTTCGTGCGCCGCCTCCCGGAGTTCAAGTTCTGgtgcgtcaac ... tccctggaagGTACTCTATCACAAAAGCCTTCTGCATTGCTTTTGTAATGACATTCTTCAG
EST: gi|161705805|gb|FC056676.1|FC056676
EST:     TCTGACGAATTCCGGCCGTTCGTGCGCCGCCTCCCGGAGTTCAAGTTCTG                         GTACTCTATCACAAAAGCCTTCT
genomic: TCTGACGAATTCCGGCCGTTCGTGCGCCGCCTCCCGGAGTTCAAGTTCTGgtgcgtcaac ... tccctggaagGTACTCTATCACAAAAGCCTTCT
EST: gi|37184551|gb|CF603905.1|CF603905
EST:     TCTGACGAATTCCGGCCGTTCGTGCGCCGCCTCCCGGAGTTCAAGTTCTG                         GTACTCTATCACAAAAGCCTTCTGCATTGCTTTTGTAATGACATTCTTCAG
genomic: TCTGACGAATTCCGGCCGTTCGTGCGCCGCCTCCCGGAGTTCAAGTTCTGgtgcgtcaac ... tccctggaagGTACTCTATCACAAAAGCCTTCTGCATTGCTTTTGTAATGACATTCTTCAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACCCGGAGATCCAAGAACTCGTTGACGGACCCACGCTTCCGACTCGGGGATCTGACGAATTCCGGCCGTTCGTGCGCCGCCTCCCGGAGTTCAAGTTCTGgtgcgtcaactattatattactcgcattgtttgaccatttctagggttcccctttttcgtcttaatttggcctgatttatacatattatcacattgaacg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttcccct