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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTCCTTGCTGCTGTCCCCTGGTATGTTGGGTTCTTCCTTCTACTTTGTGCCAGAGTAGACTACAGAGAGAAACCAGGCTACATTGCCTGCACAATTGCTgtgagtaaactttattgctcatttgattttaactttatggaagatgtttagtgcttacttttccacctgtgtcttctcgttcacctttaagttttgtaat...

Basic information

species Vitis vinifera
transcript Vv19s0135g00070.t01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv19s0135g00070.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: LOC_Os05g49020.1 (Oryza sativa), 5'ss of exon 3
CTTCCTTGCTGCTGTCCCCTGGTATGTTGGGTTCTTCCTTCTACTTTGTGCCAGAGTA---GACTACAGAGAGAAACCAGGCTACATTGCCTGCACAATTGCTgtgagtaaactttattgctcatttgattttaactttatggaagatgtttagtgcttacttttccacctgtgtct---tctcgttcacctttaagttttgtaat---
   |||||||||  |||| ||||||||||||   ||| | ||| | |||| | |||||   |||||||||||||||||||| ||  ||||||||||  ||||||| |||| | ||   | || ||  |  |  ||    || |    | | |  | | | | |  | |  |||  ||   ||| | | |   |   | |  | |||   
---CCTTGCTGCCATCCCATGGTATGTTGGGGCTTTCATACTAATATGTGTCCGAGTACATGACTACAGAGAGAAACCAGGATATGTTGCCTGCACTGTTGCTgtaagtatatttc--tactgatgcg-ctgcaatcacattgt---tatattctccctccgtcacaaaatgtagctatttctggctaagaatctggatcagaaatagc

upper sequence: Vv19s0135g00070.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GRMZM2G022453_T01 (Zea mays), 5'ss of exon 3
CTTCCTTGCTGCTGTCCCCTGGTATGTTGGGTTCTTCCTTCTACTTTGTGCCAGAGTA---GACTACAGAGAGAAACCAGGCTACATTGCCTGCACAATTGCTgtgagtaaactttattgctcatttgattttaactttatgga-agatgtttagtgcttacttttccacctgtgtcttctcgttcacctttaagttttgtaat--
   | | |||||  | || ||||   ||||    ||| ||||  | ||||   | |||   ||| |  ||||||||||||| ||| |||| |||||||||||||| |||   | ||  |  | ||   ||   | | |  ||   |  ||||||    |    |||     || |     | |  |   |  |||     |  |  
---CTTGGCTGCCATTCCATGGTTCATTGGAGCTTTCGTTCTTATATGTGTGCGGGTACATGACCAACGAGAGAAACCAGGATACGTTGCTTGCACAATTGCTgtaagtt--cctttctattaatacaatgcaaccctgctgctcatttgtttacctttggaatttgagattgagctgcatggaac-tgtggaagcaaactgtttg

upper sequence: Vv19s0135g00070.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: AT1G17080.1 (Arabidopsis thaliana), 5'ss of exon 3
CTTCCTTGCTGCTGTCCCCTGGTATGTTGGGTTCTTCCTTCTACTTTGTGCCAG---AGTAGACTACAGAGAGAAACCAGGCTACATTGCCTGCACAATTGCTgtgagtaaactttattgctcatttgattttaactt-tatggaagatgtttagtgcttacttttccacctgtgtctt--------ctcgttcacctttaagttttgtaat
   |||||  ||  |||| |||||||| || || ||| |  |  | | ||  ||   | | || ||||| ||||||||||| |||||||||||||| || ||||| |   |  | |  | ||| | ||   ||| ||| | | |    |  |||   |  | |   |  ||      ||         |  ||||  | |||   ||| |  
---CCTTGGAGCAATCCCTTGGTATGTCGGATTGTTCATCATGATGTTTGGAAGGAGAATCGATTACAGGGAGAAACCAGGATACATTGCCTGCACTATCGCTgtaat--atttcttctactc-tctgtccttatcttctctcgtttttccttatatcccattggactcccgacaaattaaattaaattgattcatgtctaaacgttgcag-

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|30329790|gb|CD013052.1|CD013052
EST:     CCAGAGTAGACTACAGAGAGAAACCAGGCTACATTGCCTGCACAATTGCT                         GCTATTCTCGCCACAATTGCTATTATTTTTGGAGTAACAAAGGGAACAGGT
genomic: CCAGAGTAGACTACAGAGAGAAACCAGGCTACATTGCCTGCACAATTGCTgtgagtaaac ... tattgtgcagGCTATTCTCGCCACAATTGCTATTATTTTTGGAGTAACAAAGGGAACAGGT
EST: gi|110727603|gb|EE104554.1|EE104554
EST:     CCAGAGTAGACTACAGAGAGAAACCAGGCTACATTGCCTGCACAATTGCT                         GCTATTCTCGCCACAATTGCTATTATTTTTGGAGTAACAAAGGGAACAGGT
genomic: CCAGAGTAGACTACAGAGAGAAACCAGGCTACATTGCCTGCACAATTGCTgtgagtaaac ... tattgtgcagGCTATTCTCGCCACAATTGCTATTATTTTTGGAGTAACAAAGGGAACAGGT
EST: gi|110711423|gb|EE087888.1|EE087888
EST:     CCAGAGTAGACTACAGAGAGAAACCAGGCTACATTGCCTGCACAATTGCT                         GCTATTCTCGCCACAATTGCTATTATTTTTGGAGTAACAAAGGGAACAGGT
genomic: CCAGAGTAGACTACAGAGAGAAACCAGGCTACATTGCCTGCACAATTGCTgtgagtaaac ... tattgtgcagGCTATTCTCGCCACAATTGCTATTATTTTTGGAGTAACAAAGGGAACAGGT
EST: gi|352789936|gb|FQ479546.1|FQ479546
EST:     CCAGAGTAGACTACAGAGAGAAACCAGGCTACATTGCCTGCACAATTGCT                         GCTATTCTCGCCACAATTGCTATTATTTTTGGAGTAACAAAGGGAACAGGT
genomic: CCAGAGTAGACTACAGAGAGAAACCAGGCTACATTGCCTGCACAATTGCTgtgagtaaac ... tattgtgcagGCTATTCTCGCCACAATTGCTATTATTTTTGGAGTAACAAAGGGAACAGGT
EST: gi|110377734|gb|EC942817.1|EC942817
EST:     CCAGAGTAGACTACAGAGAGAAACCAGGCTACATTGCCTGCACAATTGCT                         GCTATTCTCGCCACAATTGCTATTATTTTTGGAGTAACAAAGGGAACAGGT
genomic: CCAGAGTAGACTACAGAGAGAAACCAGGCTACATTGCCTGCACAATTGCTgtgagtaaac ... tattgtgcagGCTATTCTCGCCACAATTGCTATTATTTTTGGAGTAACAAAGGGAACAGGT
EST: gi|46918820|gb|CN548149.1|CN548149
EST:     CCAGAGTAGACTACAGAGAGAAACCAGGCTACATTGCCTGCACAATTGCT                         GCTATTCTTGCCACAATTGCTATTATTTTTGGTGTAACAAAGGGAACAGGT
genomic: CCAGAGTAGACTACAGAGAGAAACCAGGCTACATTGCCTGCACAATTGCTgtgagtaaac ... tattgtgcagGCTATTCTCGCCACAATTGCTATTATTTTTGGAGTAACAAAGGGAACAGGT
EST: gi|110695589|gb|EE073782.1|EE073782
EST:     CCAGAGTAGACTACAGAGAGAAACCAGGCTACATTGCCTGCACAATTGCT                         GCTATTCTTGCCACAATTGCTATTATTTTTGGTGTAACAAAGGGAACAGGT
genomic: CCAGAGTAGACTACAGAGAGAAACCAGGCTACATTGCCTGCACAATTGCTgtgagtaaac ... tattgtgcagGCTATTCTCGCCACAATTGCTATTATTTTTGGAGTAACAAAGGGAACAGGT
EST: gi|30128877|gb|CB914216.1|CB914216
EST:     CCAGAGTAGACTACAGAGAGAAACCAGGCTACATTGCCTGCACAATTGCT                         GCTATTCTCGCCACAATTGCTATTATTTTTGGAGTAACAAAGGGAACAGGT
genomic: CCAGAGTAGACTACAGAGAGAAACCAGGCTACATTGCCTGCACAATTGCTgtgagtaaac ... tattgtgcagGCTATTCTCGCCACAATTGCTATTATTTTTGGAGTAACAAAGGGAACAGGT
EST: gi|110714619|gb|EE091732.1|EE091732
EST:     CCAGAGTAGACTACAGAGAGAAACCAGGCTACATTGCCTGCACAATTGCT                         GCTATTCTCGCCACAATTGCTATTATTTTTGGAGTAACAAAGGGAACAGGT
genomic: CCAGAGTAGACTACAGAGAGAAACCAGGCTACATTGCCTGCACAATTGCTgtgagtaaac ... tattgtgcagGCTATTCTCGCCACAATTGCTATTATTTTTGGAGTAACAAAGGGAACAGGT
EST: gi|110410701|gb|EC976393.1|EC976393
EST:     CCAGAGTAGACTACAGAGAGAAACCAGGCTACATTGCCTGCACAATTGCT                         GCTATTCTTGCCACAATTGCTATTATTTTTGGTGTTACAAAGGGAACAGGT
genomic: CCAGAGTAGACTACAGAGAGAAACCAGGCTACATTGCCTGCACAATTGCTgtgagtaaac ... tattgtgcagGCTATTCTCGCCACAATTGCTATTATTTTTGGAGTAACAAAGGGAACAGGT
EST: gi|46911261|gb|CN546636.1|CN546636
EST:     CCAGAGTAGACTACAGAGAGAAACCAGGCTACATTGCCTGCACAATTGCT                         GCCATTCTCGCCACAATTGCTATTATTTTTGGAGTAACAAAGGGAACAGGT
genomic: CCAGAGTAGACTACAGAGAGAAACCAGGCTACATTGCCTGCACAATTGCTgtgagtaaac ... tattgtgcagGCTATTCTCGCCACAATTGCTATTATTTTTGGAGTAACAAAGGGAACAGGT
EST: gi|110724789|gb|EE100922.1|EE100922
EST:     CCAGAGTAGACTACAGAGAGAAACCAGGCTACATTGCCTGCACAATTGCT                         GCTATTCTCGCCACAATTGCTATTATTTTTGGAGTAACAAAGGGAACAGGT
genomic: CCAGAGTAGACTACAGAGAGAAACCAGGCTACATTGCCTGCACAATTGCTgtgagtaaac ... tattgtgcagGCTATTCTCGCCACAATTGCTATTATTTTTGGAGTAACAAAGGGAACAGGT
EST: gi|34544140|gb|CF512372.1|CF512372
EST:     CCAGAGTAGACTACAGAGAGAAACCAGGCTACATTGCCTGCACAATTGCT                         GCTATTCTCGCCACAATTGCTATTATTTTTGGAGTAACAAAGGGAACAGGT
genomic: CCAGAGTAGACTACAGAGAGAAACCAGGCTACATTGCCTGCACAATTGCTgtgagtaaac ... tattgtgcagGCTATTCTCGCCACAATTGCTATTATTTTTGGAGTAACAAAGGGAACAGGT
EST: gi|110706196|gb|EE081509.1|EE081509
EST:     CCAGAGTAGACTACAGAGAGAAACCAGGCTACATTGCCTGCACAATTGCT                         GCTATTCTTGCCACAATTGCTATTATTTTTGGTGTAACAAAGGGAACAGGT
genomic: CCAGAGTAGACTACAGAGAGAAACCAGGCTACATTGCCTGCACAATTGCTgtgagtaaac ... tattgtgcagGCTATTCTCGCCACAATTGCTATTATTTTTGGAGTAACAAAGGGAACAGGT
EST: gi|32459782|gb|CD800956.1|CD800956
EST:     TGCTGCTATTCTCGCCACAATTGCTATTATTTTTGGAGTAACAAAGGGAACAGGTGAGTAGTAGCCTCATGGCCGCAGTTGT-GAGAAGATTTCTGGGTGT
genomic: TGCTGCTATTCTCGCCACAATTGCTATTATTTTTGGAGTAACAAAGGGAACAGGTGAGTAGTAGCCTCATGGCCGCAGTTGTGGAGAAGATTTCTGGGTGT
EST: gi|71866828|gb|DT015883.1|DT015883
EST:     CCAGAGTAGACTACAGAGAGAAACCAGGCTACATTGCCTGCACAATTGCT                         GCTATTCTTGCCACAATTGCTATTATTTTTGGAGTAACAAAGGGAACAGGT
genomic: CCAGAGTAGACTACAGAGAGAAACCAGGCTACATTGCCTGCACAATTGCTgtgagtaaac ... tattgtgcagGCTATTCTCGCCACAATTGCTATTATTTTTGGAGTAACAAAGGGAACAGGT
EST: gi|110405476|gb|EC971017.1|EC971017
EST:     CCAGAGTAGACTACAGAGAGAAACCAGGCTACATTGCCTGCACAATTGCT                         GCTATTCTCGCCACAATTGCTATTATTTTTGGAGTAACAAAGGGAACAGGT
genomic: CCAGAGTAGACTACAGAGAGAAACCAGGCTACATTGCCTGCACAATTGCTgtgagtaaac ... tattgtgcagGCTATTCTCGCCACAATTGCTATTATTTTTGGAGTAACAAAGGGAACAGGT
EST: gi|110407221|gb|EC972818.1|EC972818
EST:     CCAGAGTAGACTACAGAGAGAAACCAGGCTACATTGCCTGCACAATTGCT                         GCTATTCTTGCCACAATTGCTATTATTTTTGGTGTTACAAAGGGAACAGGT
genomic: CCAGAGTAGACTACAGAGAGAAACCAGGCTACATTGCCTGCACAATTGCTgtgagtaaac ... tattgtgcagGCTATTCTCGCCACAATTGCTATTATTTTTGGAGTAACAAAGGGAACAGGT
EST: gi|351023972|gb|FQ423395.1|FQ423395
EST:     CCAGAGTAGACTACAGAGAGAAACCAGGCTACATTGCCTGCACAATTGCT                         GCTATTCTCGCCACAATTGCTATTATTTTTGGAGTAACAAAGGGAACAGGT
genomic: CCAGAGTAGACTACAGAGAGAAACCAGGCTACATTGCCTGCACAATTGCTgtgagtaaac ... tattgtgcagGCTATTCTCGCCACAATTGCTATTATTTTTGGAGTAACAAAGGGAACAGGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTTCCTTGCTGCTGTCCCCTGGTATGTTGGGTTCTTCCTTCTACTTTGTGCCAGAGTAGACTACAGAGAGAAACCAGGCTACATTGCCTGCACAATTGCTgtgagtaaactttattgctcatttgattttaactttatggaagatgtttagtgcttacttttccacctgtgtcttctcgttcacctttaagttttgtaat

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tggaagat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tttccacc