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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattgtctatctctttattgtggatgtgatatccttttgcttttgttttcatgtgttatttgataaccatgttggatgactgcattgatgttcaaatcagactgatcttattgctggggaatactgttggatattgagtaattctcacgagtacttctcatgcaatgcagGATCCTGGGTGACGTTTTCATGGGTCAGTACCACACGGTATTTGATTACGGAAATATGAAAGTTGGATTCGCGGAAGCTGCATAACTCAATCTTATCTTT

Basic information

species Vitis vinifera
transcript Vv19s0090g00830.t01
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv19s0090g00830.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: LOC_Os05g49200.2 (Oryza sativa), 3'ss of exon 12
gtattgtctatctctttattgtggatgtgatatccttttgcttttgttttcatgtgttatttgataaccatgttggatgactgcattgatgttcaaatcagactgatcttattgctggggaatactgttggatattgagtaattctcacgagtacttctcatgcaatgcagGATCCTGGGTGACGTTTTCATGGGTCAGTACCACACGGTATTTGATTACGGAAATATGAAAGTTGGATTCGCGGAAGCTGCATAA-CTCAATCTTATCTTT
                                                              |  ||| |||       |   | ||||  ||   |    | | || | | | || |     | | |||    |||| | || | | | |  | ||          |||||||||||||||||||||||||||||   ||||| || || || || ||||| || ||||  ||||| |||||| |  | || ||| |    | || ||   
--------------------------------------------------------------gtaaactatgcatttccaaacccttga-attagcagtgaaataatttcacttcttgt---catttttgatctttgactgatgcaccctacaattt----------gcagGATCCTGGGTGACGTTTTCATGGGTGCCTACCATACCGTGTTCGACTACGGCAAGATGAGGGTTGGCTTCGCGAAGTCGGCCTAAACGTGTTGTTGTCAC-
















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|352789999|gb|FQ479609.1|FQ479609
EST:     ATTAGTGGATTTACAGCTTTGGATGTGCCACCTCCTCATGGACCTCTCTG                         GATCCTGGGTGACGTTTTCATGGGTCAGTACCACACGGTATTTGATTACGG
genomic: ATTAGTGGATTTACAGCTTTGGATGTGCCACCTCCTCATGGACCTCTCTGgtattgtcta ... tgcaatgcagGATCCTGGGTGACGTTTTCATGGGTCAGTACCACACGGTATTTGATTACGG
EST: gi|349814602|gb|FQ399242.1|FQ399242
EST:     ATTAGTGGATTTACAGCTTTGGATGTGCCACCTCCTCATGGACCTCTCTG                         GATCCTGGGTGACTTTTTCATGGGTCAGTACCACACGGTATTTGATTAC
genomic: ATTAGTGGATTTACAGCTTTGGATGTGCCACCTCCTCATGGACCTCTCTGgtattgtcta ... tgcaatgcagGATCCTGGGTGACGTTTTCATGGGTCAGTACCACACGGTATTTGATTAC
EST: gi|349817267|gb|FQ405271.1|FQ405271
EST:     ATTAGTGGATTTACAGCTTTGGATGTGCCACCTCCTCATGGACCTCTCTG                         GATCCGGGGTGACGTTTTCATGGGTCAATACCACACGGTATTTGAT
genomic: ATTAGTGGATTTACAGCTTTGGATGTGCCACCTCCTCATGGACCTCTCTGgtattgtcta ... tgcaatgcagGATCCTGGGTGACGTTTTCATGGGTCAGTACCACACGGTATTTGAT
EST: gi|349811177|gb|FQ406165.1|FQ406165
EST:     ATTAGTGGATTTACAGCTTTGGATGTGCCACCTCCTCATGGACCTCTCTG                         GATCCTGGGTGACGTTTTCATGGGTCAGTAACACACGGTATTTTATTAC
genomic: ATTAGTGGATTTACAGCTTTGGATGTGCCACCTCCTCATGGACCTCTCTGgtattgtcta ... tgcaatgcagGATCCTGGGTGACGTTTTCATGGGTCAGTACCACACGGTATTTGATTAC
EST: gi|352763582|gb|FQ473285.1|FQ473285
EST:     ATTAGTGGATTTACAGCTTTGGATGTGCCACCTCCTCATGGACCTCTCTG                         GATCCTGGGTGACGTTTTCATGGGTCAGTACCACACGGTATTTGATTACGG
genomic: ATTAGTGGATTTACAGCTTTGGATGTGCCACCTCCTCATGGACCTCTCTGgtattgtcta ... tgcaatgcagGATCCTGGGTGACGTTTTCATGGGTCAGTACCACACGGTATTTGATTACGG
EST: gi|110362682|gb|EC926231.1|EC926231
EST:     ATTAGTGGATTTACAGCTTTGGATGTGCCACCTCCTCATGGACCTCTCTG                         GATCCTGGGTGACGTTTTCATGGGTCAGTACCACACGGTATTTGATTACGG
genomic: ATTAGTGGATTTACAGCTTTGGATGTGCCACCTCCTCATGGACCTCTCTGgtattgtcta ... tgcaatgcagGATCCTGGGTGACGTTTTCATGGGTCAGTACCACACGGTATTTGATTACGG
EST: gi|349807900|gb|FQ402291.1|FQ402291
EST:     ATTAGTGGATTTACAGCTTTGGATGTGCCACCTCCTCATGGACCTCTCTG                         GATCCTGGGTGACGTTTTCATGGGTCAGTACCACACGGTATTTGATTACGG
genomic: ATTAGTGGATTTACAGCTTTGGATGTGCCACCTCCTCATGGACCTCTCTGgtattgtcta ... tgcaatgcagGATCCTGGGTGACGTTTTCATGGGTCAGTACCACACGGTATTTGATTACGG
EST: gi|352798701|gb|FQ480726.1|FQ480726
EST:     ATTAGTGGATTTACAGCTTTGGATGTGCCACCTCCTCATGGACCTCTCTG                         GATCCTGGGTGACGTTTTCATGGGTCAGTACCACACGGTATTTG
genomic: ATTAGTGGATTTACAGCTTTGGATGTGCCACCTCCTCATGGACCTCTCTGgtattgtcta ... tgcaatgcagGATCCTGGGTGACGTTTTCATGGGTCAGTACCACACGGTATTTG
EST: gi|110418441|gb|EC984598.1|EC984598
EST:     ATTAGTGGATTTACAGCTTTGGATGTGCCACCTCCTCATGGACCTCTCTG                         GATCCTGGGTGACGTTTTCATGGGTCAGTACCACACGGTATTTGATTACGG
genomic: ATTAGTGGATTTACAGCTTTGGATGTGCCACCTCCTCATGGACCTCTCTGgtattgtcta ... tgcaatgcagGATCCTGGGTGACGTTTTCATGGGTCAGTACCACACGGTATTTGATTACGG
EST: gi|351036374|gb|FQ458749.1|FQ458749
EST:     ATTAGTGGATTTACAGCTTTGGATGTGCCACCTCCTCATGGACCTCTCTG                         GATCCTGGGTGACGTTTTCATGGGTCAGTACCACACGGTATTTGATTACGG
genomic: ATTAGTGGATTTACAGCTTTGGATGTGCCACCTCCTCATGGACCTCTCTGgtattgtcta ... tgcaatgcagGATCCTGGGTGACGTTTTCATGGGTCAGTACCACACGGTATTTGATTACGG
EST: gi|349816754|gb|FQ399622.1|FQ399622
EST:     ATTAGTGGATTTACAGCTTTGGATGTGCCACCTCCTCATGGACCTCTCTG                         GATCCTGGGTGACGTTTTCATGGGTCAATACCCCACGGTATTTGA
genomic: ATTAGTGGATTTACAGCTTTGGATGTGCCACCTCCTCATGGACCTCTCTGgtattgtcta ... tgcaatgcagGATCCTGGGTGACGTTTTCATGGGTCAGTACCACACGGTATTTGA
EST: gi|351051626|gb|FQ450178.1|FQ450178
EST:     ATTAGTGGATTTACAGCTTTGGATGTGCCACCTCCTCATGGACCTCTCTG                         GATCCTGGGTGACGTTTTCATGGGTCAGTACCACATGGTATTTGATTAC
genomic: ATTAGTGGATTTACAGCTTTGGATGTGCCACCTCCTCATGGACCTCTCTGgtattgtcta ... tgcaatgcagGATCCTGGGTGACGTTTTCATGGGTCAGTACCACACGGTATTTGATTAC
EST: gi|349814554|gb|FQ399194.1|FQ399194
EST:     ATTAGTGGATTTACAGCTTTGGATGTGCCACCTCCTCATGGACCTCTCTG                         GATCCTGGGTGACGTTTTTC-TGGGTCAGTACCACACGGTATTTGATTACG
genomic: ATTAGTGGATTTACAGCTTTGGATGTGCCACCTCCTCATGGACCTCTCTGgtattgtcta ... tgcaatgcagGATCCTGGGTGACGTTTT-CATGGGTCAGTACCACACGGTATTTGATTACG
EST: gi|351037515|gb|FQ460714.1|FQ460714
EST:     ATTAGTGGATTTACAGCTTTGGATGTGCCACCTCCTCATGGACCTCTCTG                         GATCCTGGGTGACGTTTTCATGGGTCAGTACCACACGGTATTTGATTACCG
genomic: ATTAGTGGATTTACAGCTTTGGATGTGCCACCTCCTCATGGACCTCTCTGgtattgtcta ... tgcaatgcagGATCCTGGGTGACGTTTTCATGGGTCAGTACCACACGGTATTTGATTACGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggggaatactgttggatattgagtaattctcacgagtacttctcatgcaatgcagGATCCTGGGTGACGTTTTCATGGGTCAGTACCACACGGTATTTGATTACGGAAATATGAAAGTTGGATTCGCGGAAGCTGCATAACTCAATCTTATCTTT
                          ttctcac  putative branch site (score: 2)
                                      cttctcat  putative PPT
               atattga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattgtctatctctttattgtggatgtgatatccttttgcttttgttttcatgtgttatttgataaccatgttggatgactgcattgatgttcaaatcagactgatcttattgctggggaatactgttggatattgagtaattctcacgagtacttctcatgcaatgcagGATCCTGGGTGACGTTTTCATGGGTCAGTACCACACGGTATTTGATTACGGAAATATGAAAGTTGGATTCGCGGAAGCTGCATAACTCAATCTTATCTTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC