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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGAAGTACAGTGTGGAGAAGGATATAGCTGAGAATATAAAGAAGGAGTTTGACAAGAAACATGGTGCTACTTGGCATTGCATTGTTGGTCGCAACTTTGgttagttccctcctctccttcgcttaatttctccttaaggtggcatttttcgatgaaaagttctcagttagggaatagtgatttcttagtaagtatatct...

Basic information

species Arabidopsis thaliana
transcript AT4G15930.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G15930.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GRMZM2G472231_T01 (Zea mays), 5'ss of exon 2
GAGAAGTACAGTGTGGAGAAGGATATAGCTGAGAATATAAAGAAGGAGTTTGACAAGAAACATGGTGCTACTTGGCATTGCATTGTTGGTCGCAACTTTGgttagttccctcctctccttcgctta----atttctccttaaggtggcatttttcgat-gaaaagttctcagttagggaatagtgatttcttagtaagtatatct
|||||| ||||| |||||||||| || || ||| | |||||||||||||| |||||||| || ||  | || ||||| ||||| || || |||||||| ||| | | | || ||| |   | ||||    |   ||||||||  | | | |    ||| |   |  |    ||| | |  ||||    | |   |  || | |  
GAGAAGCACAGTATGGAGAAGGACATCGCGGAGTACATAAAGAAGGAGTTCGACAAGAACCACGGCCCCACCTGGCACTGCATCGTCGGCCGCAACTTCGgt-aatgctcttctcccaaccccttatgggaaccctccttaat-tagtactgaatgattgcgcaagttgtggttggtgtctagtctgatatgcttgcgt-tgt--

upper sequence: AT4G15930.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GRMZM2G146012_T01 (Zea mays), 5'ss of exon 2
GAGAAGTACAGTGTGGAGAAGGATATAGCTGAGAATATAAAGAAGGAGTTTGACAAGAAACATGGTGCTACTTGGCATTGCATTGTTGGTCGCAACTTTGgt-tagttccctcctctccttcgctt--aatttctccttaaggtggcatttttcgatgaaaagttctcagttagggaatagtgatttcttagtaagtatatct
|| ||| ||||  |||||||||| || |||||| | |||||||||||||| |||||||| || ||  | || ||||| ||||| || || |||||||| ||| | | ||  |      |  |  ||   |   ||||||||  | | | |    |||         |  | | |||    |   | |||       |||   |
GATAAGCACAGCATGGAGAAGGACATCGCTGAGTACATAAAGAAGGAGTTCGACAAGAACCACGGCCCAACCTGGCACTGCATCGTCGGCCGCAACTTCGgtattgctctttttcaaaccccttttgggaaccctccttaat-tagtactgaatgatttcgccagttgtggtcggggtcgg--gtgtctagtctgatatgctt

upper sequence: AT4G15930.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA15G16050.1 (Glycine max), 5'ss of exon 2
GAGAAGTACAGTGTGGAGAAGGATATAGCTGAGAATATAAAGAAGGAGTTTGACAAGAAACATGGTGCTACTTGGCATTGCATTGTTGGTCGCAACTTTGgttagttccctcctctccttcgcttaatttctccttaaggtggcattt--ttcgatgaaaagttctcagttagggaatagtgatttcttagtaagtatatct
|||||||||| ||||||||| ||| | || ||| | |||||||||||||| || ||||  |||||  | |||||||||||||| |||||||| || |||||| |||  |    | |  ||   ||| ||     | |   ||| | ||   |  |  |  | ||     ||| |  || ||  |||  ||| || |   |  
GAGAAGTACAATGTGGAGAAAGATGTTGCGGAGCAGATAAAGAAGGAGTTCGATAAGAGGCATGGCCCCACTTGGCATTGCATCGTTGGTCGTAATTTTGgtaagtctctcttttttttttaattacttgtcaatcattttggtacttgggttcactaggatttggggtttatgtgattgttctttagtagaaattgagt--

upper sequence: AT4G15930.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA09G04830.1 (Glycine max), 5'ss of exon 2
GAGAAGTACAGTGTGGAGAAGGATATAGCTGAGAATATAAAGAAGGAGTTTGACAAGAAACATGGTGCTACTTGGCATTGCATTGTTGGTCGCAACTTTGgttagttccctcctctccttcgcttaatttctccttaaggtggcatttt--tcgatgaaaagttctcagttagggaatagtgatttcttagtaagtatatct---
|||||||||| ||||||||| ||  | || ||| | |||||||||||||| || ||||  |||||  | |||||||||||||| |||||||| || |||||| || |      | |  ||   ||| ||     | |   ||| | ||   |  |   | | || |   |||    || ||  |||  ||| || |   |     
GAGAAGTACAATGTGGAGAAAGACGTTGCGGAGCAGATAAAGAAGGAGTTCGATAAGAGGCATGGACCCACTTGGCATTGCATCGTTGGTCGTAATTTTGgtaagctt-----ttttttttaattacttgtcaatgattttggtacttgggtttactcagatttgtggtttatatgattgttctttagtagaaattgagtagatg

upper sequence: AT4G15930.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA15G16060.1 (Glycine max), 5'ss of exon 2
GAGAAGTACAGTGTGGAGAAGGATATAGCTGAGAATATAAAGAAGGAGTTTGACAAGAAACATGGTGCTACTTGGCATTGCATTGTTGGTCGCAACTTTGgttagttccctcctctccttcgcttaatttctccttaaggtggcatttttcgatgaaaagttctcagttagggaatagtg-atttcttagtaagtatatct-
|||| ||||| ||||||||| ||  | || ||  | |||||||||||||| || ||||  |||||  | |||||||||||||| |||||||| || |||||| | | || |  | |  ||   ||  || |   |     ||   ||  |   ||   |    |   || | |  | |||   |||||    |||| |  | 
GAGAGGTACAATGTGGAGAAAGACGTCGCGGAACAGATAAAGAAGGAGTTCGATAAGAGGCATGGCCCCACTTGGCATTGCATCGTTGGTCGTAATTTTGgtaactccctttttgtttttt--ttccttgcatttgtcaatgattttggtatttgggtatacttggatttgtggtttgtgtgcttcttttatagtagaaatt

upper sequence: AT4G15930.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: Vv05s0077g02110.t01 (Vitis vinifera), 5'ss of exon 2
GAGAAGTACAGTGTGGAGAAGGATATAGCTGAGAATATAAAGAAGGAGTTTGACAAGAAACATGGTGCTACTTGGCATTGCATTGTTGGTCGCAACTTTGgttagttccctcctctc-cttcgcttaatttctccttaaggtggcatttttcgatgaaaagttctcagttagggaatagtgatttcttagtaagtatatct
|||||  |||||||||||||  | || || ||| |||| ||||||||||| || ||||| |||||  |||| |||||||||||||| |||||||| || ||| | | || |    ||  ||  ||||   | |   |||  |    || | |     | | |  |   | |   |   ||| | |  | ||   || || |
GAGAATCACAGTGTGGAGAAAAACATTGCGGAGTATATCAAGAAGGAGTTCGATAAGAAGCATGGACCTACCTGGCATTGCATTGTCGGTCGCAATTTCGgtaattcccgtttaatcatttttcttataatatatgtaatatcaatttctactggatagattaattgatgaatcagcggtggtgttct-gttgttacatat

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|86074680|gb|DR370437.1|DR370437
EST:     TGACAAGAAACATGGTGCTACTTGGCATTGCATTGTTGGTCGCAACTTTG                         GTTCTTATGTAACGCACGAGACAAACCATTTCGTTTACTTCTACCTCGACC
genomic: TGACAAGAAACATGGTGCTACTTGGCATTGCATTGTTGGTCGCAACTTTGgttagttccc ... tttcttgcagGTTCTTATGTAACGCATGAGACAAACCATTTCGTTTACTTCTACCTCGACC
EST: gi|125318722|gb|EL332807.1|EL332807
EST:     CTTGGCATTGCATTGTTGGTCGCAACTTTG                         GTTCTTATGTAACGCATGAGACAAACCATTTCGTTTACTTCTACCTCGACC
genomic: CTTGGCATTGCATTGTTGGTCGCAACTTTGgttagttccc ... tttcttgcagGTTCTTATGTAACGCATGAGACAAACCATTTCGTTTACTTCTACCTCGACC
EST: gi|86081177|gb|DR376934.1|DR376934
EST:     TGACAAGAAACATGGTGCTACTTGGCATTGCATTGTTGGTCGCAACTTTG                         GTTCTTATGTAACGCATGAGACAAACCATTTCGTTTACTTCTACCTCGACC
genomic: TGACAAGAAACATGGTGCTACTTGGCATTGCATTGTTGGTCGCAACTTTGgttagttccc ... tttcttgcagGTTCTTATGTAACGCATGAGACAAACCATTTCGTTTACTTCTACCTCGACC
EST: gi|19741173|gb|AU226526.1|AU226526
EST:     TGACAAGAAACATGGTGCTACTTGGCATTGCATTGTTGGTCGCAACTTTG                         GTTCTTATGTAACGCATGAGACAAACCATTTCCTTTACTTCTACCTCGACC
genomic: TGACAAGAAACATGGTGCTACTTGGCATTGCATTGTTGGTCGCAACTTTGgttagttccc ... tttcttgcagGTTCTTATGTAACGCATGAGACAAACCATTTCGTTTACTTCTACCTCGACC
EST: gi|124714688|gb|EH806090.1|EH806090
EST:     ACTTGGCATTGCATTGTTGGTCGCAACTTTG                         GTTCTTATGTAACGCATGAGACAAACCATTTCGTTTACTTCTACCTCGACC
genomic: ACTTGGCATTGCATTGTTGGTCGCAACTTTGgttagttccc ... tttcttgcagGTTCTTATGTAACGCATGAGACAAACCATTTCGTTTACTTCTACCTCGACC
EST: gi|164001931|gb|ES108959.1|ES108959
EST:     TTGTTGGTCGCAACTTTG                         GTTCTTATGTAACGCACGAGACAAACCATTTCGTTTACTTCTACCTCGACC
genomic: TTGTTGGTCGCAACTTTGgttagttccc ... tttcttgcagGTTCTTATGTAACGCATGAGACAAACCATTTCGTTTACTTCTACCTCGACC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAGAAGTACAGTGTGGAGAAGGATATAGCTGAGAATATAAAGAAGGAGTTTGACAAGAAACATGGTGCTACTTGGCATTGCATTGTTGGTCGCAACTTTGgttagttccctcctctccttcgcttaatttctccttaaggtggcatttttcgatgaaaagttctcagttagggaatagtgatttcttagtaagtatatct

- - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctcctctc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gatgaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -agggaata