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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGAAACAGAAGATAATGTTTGCCCTCACGTCAATCAAGGGTATTGGGAGGCGATTCGCTAATATTGTTTGCAAGAAGGCCGATGTTGACATGAACAAAAGgtctctgccttttcttttattctaagccctctgtttgatttcacggaaaatatgggaaaggaaggatttggaattttagttaatgcacttcttaatgcta...

Basic information

species Vitis vinifera
transcript Vv18s0072g00060.t01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0072g00060.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA20G30730.1 (Glycine max), 5'ss of exon 2
GGAAACAGAAGATAATGTTTGCCCTCACGTCAATCAAGGGTATTGGGAGGCGATTCGCTAATATTGTTTGCAAGAAGGCCGATGTTGACATGAACAAAAGgt---ctctgccttttcttttattctaagccctctgtttgatttcacggaaaatatg------ggaaaggaaggatttggaattttagtt--aatgcacttcttaatgcta---------------------------------------------------------
|||| |||||||||||||| || || || |||||||| ||||||||||||||||| |||| ||| ||||||||||| |||||||||||||||||||||| || | | || | ||| | | | ||| | || || || | ||| | | | || | || ||| || || ||||
GGAAGCAGAAGATAATGTTCGCTCTTACCTCAATCAAAGGTATTGGGAGGCGATTTTCTAACATTTGCTGCAAGAAGGCTGATGTTGACATGAACAAAAGgtttgctttactttcattgccattattgttgttttcattgttagttaataatatttgtttattgttgcataagagtgttgtggttcaattggaatttgctgctgcttgctgtggatttggtttttcatgttttgtattgaaatgggctttggttatttttgttggcag

upper sequence: Vv18s0072g00060.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA20G30970.1 (Glycine max), 5'ss of exon 2
GGAAACAGAAGATAATGTTTGCCCTCACGTCAATCAAGGGTATTGGGAGGCGATTCGCTAATATTGTTTGCAAGAAGGCCGATGTTGACATGAACAAAAGgtctctgccttttcttttattctaagccct-ctgt---ttgatttcacggaaaatatgggaaaggaaggatttgga-attttagttaatgcacttcttaatgcta
|||| |||||||||||||| || | || || |||||||||||||| ||| ||||||| || || | ||||||||||||||||||||||||||||||||||| | | | | | | || | || |||||| | | ||| | | | | |||| |||| ||| | || | |
GGAAGCAGAAGATAATGTTCGCTATGACCTCCATCAAGGGTATTGGAAGGAGATTCGCCAACATCGCTTGCAAGAAGGCCGATGTTGACATGAACAAAAGgtgtttttttaaaaaaatttgttgagttcaattgcacgttgattcgcatgtttttgtggttattgttgaaattgggtgtttttgtttgtttgtttgtcag-----

upper sequence: Vv18s0072g00060.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA10G36610.3 (Glycine max), 5'ss of exon 2
GGAAACAGAAGATAATGTTTGCCCTCACGTCAATCAAGGGTATTGGGAGGCGATTCGCTAATATTGTTTGCAAGAAGGCCGATGTTGACATGAACAAAAGgt-ctctgccttttcttttattctaagccctctgtttgatttcacggaaaatatgggaaaggaaggatttggaattttagttaatgcacttcttaatgcta
|||| |||||||||||||| || | || || |||||||||||||| ||| ||||||| || || | |||||||||||| |||||||||||||||||||||| || | || | || | | ||| | ||| | ||| | | | | |||| ||||| ||| |
GGAAGCAGAAGATAATGTTCGCAATGACCTCCATCAAGGGTATTGGAAGGAGATTCGCCAACATCGCTTGCAAGAAGGCTGATGTTGACATGAACAAAAGgtgcttttttttattggttgagttcaattgctcgttaattcgcacatttt-tgtggttattgttgaaattgggatttttgtttgtcag-------------

upper sequence: Vv18s0072g00060.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA02G08690.1 (Glycine max), 5'ss of exon 2
GGAAACAGAAGATAATGTTTGCCCTCACGTCAATCAAGGGTATTGGGAGGCGATTCGCTAATATTGTTTGCAAGAAGGCCGATGTTGACATGAACAAAAGgtctctgcctttt----cttttattctaagccctctgtttgatttcacgga---aaatatgggaaaggaaggatttggaattttagttaatgcacttcttaatgcta
|||| |||||||||||||| || ||||| || ||||| |||||||| |||||||||||||| ||| ||||| || || ||||| ||||||||||| |||| || | | | | ||| || | | ||| | || | || | | | | || | || | ||||||| | | ||||||
GGAAGCAGAAGATAATGTTCGCTCTCACCTCTATCAAAGGTATTGGCAGGCGATTCGCTAACATTTGCTGCAAAAAAGCTGATGTCGACATGAACAAGAGgt-tcggtttcatgaaacctttgtttttgttttattctttattgtcggatagttaagtctttgccatgagg--ttgtgtcatttagttttttctattcttaca----

upper sequence: Vv18s0072g00060.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA07G24710.1 (Glycine max), 5'ss of exon 1
GGAAACAGAAGATAATGTTTGCCCTCACGTCAATCAAGGGTATTGGGAGGCGATTCGCTAATATTGTTTGCAAGAAGGCCGATGTTGACATGAACAAAAGgtctctgcctttt---cttttattctaagccctctgtttgatttcacggaaaatatgggaaaggaaggatttggaattttagttaatgcacttcttaatgcta---
||||||||||||||||| ||||| || ||||| |||||||| |||| |||| |||| ||| |||| | || |||||||||||||||| |||| | | | ||| || | | ||| | | | | || | || | | | || | ||| | || || | |
-----CAGAAGATAATGTTTGCTCTCACCTCTATCAAAGGTATTGGCAGGCAATTCACTAACATTTGCAGCAAAATAGCTAATGTTGACATGAACAAGAGGTTTGgtttcatgaaacctttgtttttgttacagggttgggggtggtacacattagtgcgcagtcatgtcattatgttcaaaataa-accttttttgacagtgtag

upper sequence: Vv18s0072g00060.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: AT4G09800.1 (Arabidopsis thaliana), 5'ss of exon 2
GGAAACAGAAGATAATGTTTGCCCTCACGTCAATCAAGGGTATTGGGAGGCGATTCGCTAATATTGTTTGCAAGAAGGCCGATGTTGACATGAACAAAAGgtctctgccttttcttttattctaagccctctgtttgatttcacggaaaatatggg--aaaggaaggatttggaattt-tagttaatgcacttcttaatgcta
| || |||||||| ||||||||||| || || ||||| |||||||| |||||||| ||||| ||||| ||||||||||| ||||| |||||||||||||||| | || ||| | | ||||| | | ||| | || | | || | || | ||||| || | | | | | || | ||
GTAAGCAGAAGATTATGTTTGCCCTTACCTCTATCAAAGGTATTGGTAGGCGATTGGCTAACATTGTCTGCAAGAAGGCTGATGTCGACATGAACAAAAGgtttgagcttttgttgctcttctacg---tttgtctttctttagtgtgaacttaaatcaattgtgacatttgagatatattgaagagtaatagttttgagata

upper sequence: Vv18s0072g00060.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: AT1G22780.1 (Arabidopsis thaliana), 5'ss of exon 2
GGAAACAGAAGATAATGTTTGCCCTCACGTCAATCAAGGGTATTGGGAGGCGATTCGCTAATATTGTTTGCAAGAAGGCCGATGTTGACATGAACAAAAGgtctctgccttttcttttattctaagccctctgtttgatttcacggaaaatatgggaaaggaaggatttggaatttta-gttaatgcacttcttaatgcta-----
|||| || || || |||||||| | || ||||||||||||||||| |||||||| ||||| ||||| ||||||||||| ||||||||||||||||| |||| | | ||| ||| |||| | || || || | | || | | | | ||||||| |||| || | | | ||| | |
GGAAGCAAAAAATTATGTTTGCTTTGACCTCAATCAAGGGTATTGGAAGGCGATTGGCTAACATTGTGTGCAAGAAGGCTGATGTTGACATGAACAAGAGgtttgtttcttagcttg-gttcttaatact---ttcagttacttaggaattctatggat--aaggattatgaatcttgcgaggttttggatgttagtagaaaatgt

upper sequence: Vv18s0072g00060.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: AT1G34030.1 (Arabidopsis thaliana), 5'ss of exon 2
GGAAACAGAAGATAATGTTTGCCCTCACGTCAATCAAGGGTATTGGGAGGCGATTCGCTAATATTGTTTGCAAGAAGGCCGATGTTGACATGAACAAAAGgtctctgccttttcttttattctaagccctctgtttgatttcacggaaaatatgggaaaggaaggatttggaattttagtta-atgcacttcttaatgcta-
| || || ||||| ||||||||||| || || ||||| |||||||| ||| |||| || || ||||| |||||||| |||||||| ||||||||||| |||| | ||| | | | | || | | | | | |||| || | | |||| | || | | || | ||
GTAAGCAAAAGATTATGTTTGCCCTTACCTCTATCAAAGGTATTGGAAGGAGATTGGCCAACATTGTCTGCAAGAAAGCCGATGTCGACATGAACAAGAGgtattga--tttcaatcaaacttcaacctttggaaagttagaattgaaattagcagtctctgtttgcatttgatttgatttgtgtatgtgttttgagtcttg

upper sequence: Vv18s0072g00060.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: PP1S14_433V6.1 (Physcomitrella patens), 5'ss of exon 2
GGAAACAGAAGATAATGTTTGCCCTCACGTCAATCAAGGGTATTGGGAGGCGATTCGCTAATATTGTTTGCAAGAAGGCCGATGTTGACATGAACAAAAGgtctctgccttttcttttattctaagccctctgtttgatttcacggaaaatatgggaaaggaaggatttggaattttagttaatgcacttc-ttaatgcta---
| || ||||| ||||||||| | || || || ||||| |||| | || || || ||| | || ||||||||||||||||||||||||| ||| |||| || | || | || | | || | ||| || | | | | || | || | | | |||| | || ||
GACGTCAAAAGATTATGTTTGCCTTGACCTCCATTAAGGGAGTTGGACGTCGTTTTGCGAATTTGGTCTGCAAGAAGGCCGATGTTGACATGAGCAAGAGgt----gcgtattatattcctgaagtttcttactatgagttgattcggagtttttacaaatattttttgtatcacgcaatgcttatccttcatcgatagtacat

upper sequence: Vv18s0072g00060.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: PP1S72_222V6.2 (Physcomitrella patens), 5'ss of exon 2
GGAAACAGAAGATAATGTTTGCCCTCACGTCAATCAAGGGTATTGGGAGGCGATTCGCTAATATTGTTTGCAAGAAGGCCGATGTTGACATGAACAAAAGgtctctgccttttcttttattctaagccctctgtttgatttcacggaaaatatgggaaaggaaggatttggaattttagttaatgcacttcttaatgcta-
| |||||||| ||||||||||| || || || ||||| ||||| | || || || || | |||||||||||||||||||| ||||||| ||| |||| | || | || ||| ||| | | | | | ||| | |||| || || | | | |
GACGTCAGAAGATCATGTTTGCCCTGACCTCCATTAAGGGGGTTGGGCGTCGTTTTGCCAACTTGGTTTGCAAGAAGGCCGATGTCGACATGAGCAAGAGgtatgtga-tcttgtttgatttttgtattttataccggtatttttatttttatttttatttttatatttttttcttgccttcgtctctgcccacacgtccc

upper sequence: Vv18s0072g00060.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: EFJ25542 (Selaginella moellendorffii), 5'ss of exon 2
GGAAACAGAAGATAATGTTTGCCCTCACGTCAATCAAGGGTATTGGGAGGCGATTCGCTAATATTGTTTGCAAGAAGGCCGATGTTGACATGAACAAAAGgtctc---tgccttttcttttattctaagccctctgtttgatttcacggaaaatatgggaaaggaaggatttggaatttt-agttaatgcacttcttaatgcta
|| |||||||| ||||| || || || || |||||||| |||||| | |||||||| || || || ||||||||||| ||||| ||||||||||| |||| | |||| |||||||| ||| | ||| | || | | || | | | | | | || ||| | | || | | |||
GGCGGCAGAAGATTATGTTCGCGCTGACTTCCATCAAGGGAATTGGGCGCCGATTCGCCAACATCGTCTGCAAGAAGGCGGATGTGGACATGAACAAGAGgtattgtttgccctttcttttcctcttgctctgctggt-gagctgaaagatcttgttttctcgtcattttcttgatctttcgggttgggcttctatggatg---

upper sequence: Vv18s0072g00060.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: EFJ22352 (Selaginella moellendorffii), 5'ss of exon 2
GGAAACAGAAGATAATGTTTGCCCTCACGTCAATCAAGGGTATTGGGAGGCGATTCGCTAATATTGTTTGCAAGAAGGCCGATGTTGACATGAACAAAAGgtct--ctgccttttcttttattctaagccctctgtttgatttcacggaaaatatgggaaaggaaggatttggaattttagttaa-tgcacttcttaatgcta-----------------------------------------------------------------------------------------
|| |||||||| ||||| || || || || |||||||| |||||| | |||||||| || || || ||||||||||| ||||| ||||||||||| |||| | |||| |||||||| ||| | ||| | | | || || | | |||| | | | | | | | ||| || |
GGCGGCAGAAGATTATGTTCGCGCTGACTTCCATCAAGGGAATTGGGCGCCGATTCGCCAACATCGTCTGCAAGAAGGCGGATGTGGACATGAACAAGAGgtatgtttgccctttcttttcctcttgctctgctggtgagct----gaaagatcttgttttctcgtcattttcttctatggatgactatcttccttgatctttcggattgattgattgagcttcttcattgatttgaaaaaaaaaatctgtgcttatcatttttctttgtttctttctcttccatcgaacag

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|110700267|gb|EE078111.1|EE078111
EST:     CGATTCGCTAATATTGTTTGCAAGAAGGCCGATGTTGACATGAACAAAAG                         GGCTGGTGAATTATCTGCTGCTGAGCTGGAGAACCTCATGGTTATTGTTGC
genomic: CGATTCGCTAATATTGTTTGCAAGAAGGCCGATGTTGACATGAACAAAAGgtctctgcct ... atgctctcagGGCTGGTGAATTATCTGCTGCTGAGCTGGAGAACCTCATGGTTATTGTTGC
EST: gi|110732426|gb|EE107700.1|EE107700
EST:     CGATTCGCTAATATTGTTTGCAAGAAGGCCGATGTTGACATGAACAAAAG                         GGCTGGTGAATTATCTGCTGCTGAGCTGGAGAACCTCATGGTTATTGTTGC
genomic: CGATTCGCTAATATTGTTTGCAAGAAGGCCGATGTTGACATGAACAAAAGgtctctgcct ... atgctctcagGGCTGGTGAATTATCTGCTGCTGAGCTGGAGAACCTCATGGTTATTGTTGC
EST: gi|110387218|gb|EC951868.1|EC951868
EST:     CGATTCGCTAATATTGTTTGCAAGAAGGCCGATGTTGACATGAACAAAAG                         GGCTGGTGAATTATCTGCTGCTGAGCTGGAGAACCTCATGGTTATTGTTGC
genomic: CGATTCGCTAATATTGTTTGCAAGAAGGCCGATGTTGACATGAACAAAAGgtctctgcct ... atgctctcagGGCTGGTGAATTATCTGCTGCTGAGCTGGAGAACCTCATGGTTATTGTTGC
EST: gi|110371313|gb|EC935234.1|EC935234
EST:     CGATTCGCTAATATTGTTTGCAAGAAGGCCGATGTTGACATGAACAAAAG                         GGCTGGTGAATTATCTGCTGCTGAGCTGGAGAACCTCATGGTTATTGTTGC
genomic: CGATTCGCTAATATTGTTTGCAAGAAGGCCGATGTTGACATGAACAAAAGgtctctgcct ... atgctctcagGGCTGGTGAATTATCTGCTGCTGAGCTGGAGAACCTCATGGTTATTGTTGC
EST: gi|110730467|gb|EE107583.1|EE107583
EST:     CGATTCGCTAATATTGTTTGCAAGAAGGCCGATGTTGACATGAACAAAAG                         GGCTGGTGAATTATCTGCTGCTGAGCTGGAGAACCTCATGGTTATTGTTGC
genomic: CGATTCGCTAATATTGTTTGCAAGAAGGCCGATGTTGACATGAACAAAAGgtctctgcct ... atgctctcagGGCTGGTGAATTATCTGCTGCTGAGCTGGAGAACCTCATGGTTATTGTTGC
EST: gi|110391677|gb|EC956670.1|EC956670
EST:     CGATTCGCTAATATTGTTTGCAAGAAGGCCGATGTTGACATGAACAAAAG                         GGCTGGTGAATTATCTGCTGCTGAGCTGGAGAACCTCATGGTTATTGTTGC
genomic: CGATTCGCTAATATTGTTTGCAAGAAGGCCGATGTTGACATGAACAAAAGgtctctgcct ... atgctctcagGGCTGGTGAATTATCTGCTGCTGAGCTGGAGAACCTCATGGTTATTGTTGC
EST: gi|351016436|gb|FQ423863.1|FQ423863
EST:     CGATTCGCTAATATTGTTTGCAAGAAGGCCGATGTTGACATGAACAAAAG                         GGCTGGTGAATTATCTGCTGCTGAGCTGGAGAACCTCATGGTTATTGTTGC
genomic: CGATTCGCTAATATTGTTTGCAAGAAGGCCGATGTTGACATGAACAAAAGgtctctgcct ... atgctctcagGGCTGGTGAATTATCTGCTGCTGAGCTGGAGAACCTCATGGTTATTGTTGC
EST: gi|77579580|gb|DV218639.1|DV218639
EST:     CGATTCGCTAATATTGTTTGCAAGAAGGCCGATGTTGACATGAACAAAAG                         GGCTGGTGAATTATCTGCTGCTGAGCTGGAGAACCTCATGGTTATTGTTGC
genomic: CGATTCGCTAATATTGTTTGCAAGAAGGCCGATGTTGACATGAACAAAAGgtctctgcct ... atgctctcagGGCTGGTGAATTATCTGCTGCTGAGCTGGAGAACCTCATGGTTATTGTTGC
EST: gi|71872730|gb|DT021785.1|DT021785
EST:     CGATTCGCTAATATTGTTTGCAAGAAGGCCGATGTTGACATGAACAAAAG                         GGCTGGTGAATTATCTGCTGCTGAGCTGGAGAACCTCATGGTTATTGTTGC
genomic: CGATTCGCTAATATTGTTTGCAAGAAGGCCGATGTTGACATGAACAAAAGgtctctgcct ... atgctctcagGGCTGGTGAATTATCTGCTGCTGAGCTGGAGAACCTCATGGTTATTGTTGC
EST: gi|110419379|gb|EC985599.1|EC985599
EST:     CGATTCGCTAATATTGTTTGCAAGAAGGCCGATGTTGACATGAACAAAAG                         GGCTGGTGAATTATCTGCTGCTGAGCTGGAGAACCTCATGGTTATTGTTGC
genomic: CGATTCGCTAATATTGTTTGCAAGAAGGCCGATGTTGACATGAACAAAAGgtctctgcct ... atgctctcagGGCTGGTGAATTATCTGCTGCTGAGCTGGAGAACCTCATGGTTATTGTTGC
EST: gi|110689883|gb|EE066499.1|EE066499
EST:     CGATTCGCTAATATTGTTTGCAAGAAGGCCGATGTTGACATGAACAAAAG                         GGCTGGTGAATTATCTGCTGCTGAGCTGGAGAACCTCATGGTTATTGTTGC
genomic: CGATTCGCTAATATTGTTTGCAAGAAGGCCGATGTTGACATGAACAAAAGgtctctgcct ... atgctctcagGGCTGGTGAATTATCTGCTGCTGAGCTGGAGAACCTCATGGTTATTGTTGC
EST: gi|110700974|gb|EE078100.1|EE078100
EST:     CGATTCGCTAATATTGTTTGCAAGAAGGCCGATGTTGACATGAACAAAAG                         GGCTGGTGAATTATCTGCTGCTGAGCTGGAGAACCTCATGGTTATTGTTGC
genomic: CGATTCGCTAATATTGTTTGCAAGAAGGCCGATGTTGACATGAACAAAAGgtctctgcct ... atgctctcagGGCTGGTGAATTATCTGCTGCTGAGCTGGAGAACCTCATGGTTATTGTTGC
EST: gi|110420043|gb|EC986304.1|EC986304
EST:     CGATTCGCTAATATTGTTTGCAAGAAGGCCGATGTTGACATGAACAAAAG                         GGCTGGTGAATTATCTGCTGCTGAGCTGGAGAACCTCATGGTTATTGTTGC
genomic: CGATTCGCTAATATTGTTTGCAAGAAGGCCGATGTTGACATGAACAAAAGgtctctgcct ... atgctctcagGGCTGGTGAATTATCTGCTGCTGAGCTGGAGAACCTCATGGTTATTGTTGC
EST: gi|110360370|gb|EC923419.1|EC923419
EST:     CGATTCGCTAATATTGTTTGCAAGAAGGCCGATGTTGACATGAACAAAAG                         GGCTGGTGAATTATCTGCTGCTGAGCTGGAGAACCTCATGGTTATTGTTGC
genomic: CGATTCGCTAATATTGTTTGCAAGAAGGCCGATGTTGACATGAACAAAAGgtctctgcct ... atgctctcagGGCTGGTGAATTATCTGCTGCTGAGCTGGAGAACCTCATGGTTATTGTTGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGAAACAGAAGATAATGTTTGCCCTCACGTCAATCAAGGGTATTGGGAGGCGATTCGCTAATATTGTTTGCAAGAAGGCCGATGTTGACATGAACAAAAGgtctctgccttttcttttattctaagccctctgtttgatttcacggaaaatatgggaaaggaaggatttggaattttagttaatgcacttcttaatgcta

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccctctgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaaaata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaggaag