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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttcttgaatcttcctctcttctttagttttctgctcctcttgtctccactttgatgcttaattgaacgcatttgtaaatcaatgtaatcttgcatagtcattattattcaacacactgcgaggtaaatttctttgatttgcttgtccagGTATTTGAGGGAACATCTGGAATCGACAACAAGTACACAACTGTGCAATTTACAGGAGAG

Basic information

species Arabidopsis thaliana
transcript AT4G38510.4
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G38510.4 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA20G24070.1 (Glycine max), 3'ss of exon 5
gtttcttgaatcttcctctcttctttagttttctgctcctcttgtctccactttgatgcttaattgaacgcatttgtaaatcaatgtaatcttgcatagtcattattattcaacacactgcgaggtaaatttctttgatttgcttgtccagGTATTTGAGGGAACATCTGGAATCGACAACAAGTACACAACTGTGCAATTTACAGGAGAG
                                                  |  |      ||| |     || |  | |||  |  || |||   |    |||||| | |      |     |   |  ||| ||| |  |  ||| |||||||||||| || |||||||| |||||||| ||||  ||||||||||||||||| ||||||
-------------------------------------------------tcaatagcaaataactttgt-cactgtttaatttagctattctgctagtaccattatcaatggtttaaagtttattcaccttttttttaact-tttgaccagGTATTTGAAGGCACATCTGGGATCGACAATAAGTTTACAACTGTGCAATTTACTGGAGAG

upper sequence: AT4G38510.4 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA10G42940.3 (Glycine max), 3'ss of exon 4
gtttcttgaatcttcctctcttctttagttttctgctcctcttgtctccactttgatgcttaattgaacgcatttgtaaatcaatgtaatcttgcatagtcattattattcaacacactgcgaggtaaatttctttgatttgcttgtccagGTATTTGAGGGAACATCTGGAATCGACAACAAGTACACAACTGTGCAATTTACAGGAGAG
                                           |  | || |        |||||     || |  ||  |  | |  ||  ||| |||| |  ||||| |||   |     |   |  ||| ||| | |   ||| |||||||||||| || ||||||||||||||||| || |  || |||||||||||||| ||||||
------------------------------------------aggattcaat--agcaaataattttgt-cactgttaggttta-gctattctgc-tagt-accattat-caatggaagtttattcacctttttttaacta--ttgaccagGTATTTGAAGGTACATCTGGAATCGACAATAAATTTACGACTGTGCAATTTACTGGAGAG

upper sequence: AT4G38510.4 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA09G38110.2 (Glycine max), 3'ss of exon 4
gtttcttgaatcttcctctcttctttagttttctgctcctcttgtctccactttgatgcttaattgaacgcatttgtaaatca-atgtaatcttgcatagtcattattattcaacacactgcga--ggtaaatttctttgatttgc--ttgtccagGTATTTGAGGGAACATCTGGAATCGACAACAAGTACACAACTGTGCAATTTACAGGAGAG
                                                        | |   |   || |  |||||   ||   |   |||||     ||   |||||||  | ||| || |   | | | || |  |  | | |  ||  |||||| |||||||| |||||||| || ||||| || |  ||||||||||||||||| ||||||
--------------------------------------------------------ttcaatagcaaatggttttgtctgtcttgttctatcttctgctgttgctattattgcaaacagtgggcttgtttatttaccatattgtaccattcaccagGTCTTTGAGGGTACATCTGGGATTGACAATAAATTTACAACTGTGCAATTTACCGGAGAG

upper sequence: AT4G38510.4 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA18G48280.1 (Glycine max), 3'ss of exon 4
gtttcttgaatcttcctctcttctttagttttctgctcctcttgtctccactttgatgcttaattgaacgcatttgtaaatca-atgtaatcttgcatagtcattattattcaa-cacactgcgaggtaaatttctttgatttgc--ttgtccagGTATTTGAGGGAACATCTGGAATCGACAACAAGTACACAACTGTGCAATTTACAGGAGAG-
                                                        | |   |   || |  |||||  |||   | | |||||     |    ||||||| || ||    ||  | | | || |  |  | |    ||  |||||| |||||||| |||||||| || ||||| || |  ||||||||||||||||| |||||| 
--------------------------------------------------------ttcaatagcaaatggttttgtctatcttgttttatcttctgctgctgctattattaaaacagtgggcttgtttatttaccattgtgtatcattcaccaggTCTTTGAGGGTACATCTGGGATTGACAATAAATTTACAACTGTGCAATTTACTGGAGAGG

upper sequence: AT4G38510.4 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv03s0038g02760.t01 (Vitis vinifera), 3'ss of exon 4
gtttcttgaatcttcctctcttctttagttttctgctcctcttgtctccactttgatgcttaattgaacgcatt-tgtaaatcaatgtaatcttgcatagtcattattattcaacacactgcgaggtaaatttctttgatttgcttgtccagGTATTTGAGGGAACATCTGGAATCGACAACAAGTACACAACTGTGCAATTTACAGGAGAG
                                                   ||||  ||||| |    |   |  | |   |  ||   || ||   || |  || || |||||   | | |    ||     |||   ||   ||| |||||| ||||| ||||| |||||||| |||||||| ||||||||||| ||||||||||| |||
-----------------------------------------------gtgttttg--gcttagtccttcttgtcatattgttatataggatttt-tttattttttgtttttcaattaaatact--ttactcagcttatgttgttttggccagGTTTTTGAAGGAACTTCTGGAATTGACAACAAATACACAACTGTTCAATTTACAGGGGAG

upper sequence: AT4G38510.4 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: PP1S425_12V6.1 (Physcomitrella patens), 3'ss of exon 3
gtttcttgaatcttcctctcttctttagttttctgctcctcttgtctccactttgatgcttaattgaacgcatttgtaaatcaatgtaatcttgcatagtcattattattcaacacactgcgaggtaaatttct-ttgatttgcttgtccagGTATTTGAGGGAACATCTGGAATCGACAACAAGTACACAACTGTGCAATTTACAGGAGAG
|||| |      ||| |    ||   | || |   |  | |    ||  |  |       |   |         ||  |    ||   ||  || | | |  ||||| |   |         ||    | |  | ||   |||| | ||||||| ||||||||||| ||||||||||| |||||| |||| ||  |  |||| || ||||||
gtttgtatcggtttcttagtctcgaaaattgtagccatcgcaaaactttagctctccctctgtctaggtcagactgctatctgattagattgtg-acaatgtttattttcgtatgagtgtttagactgactcatatttgattgcct-tccagGTCTTTGAGGGAACTTCTGGAATCGATAACAAGCACACCACCATTGAATTCACTGGAGAG

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|86066803|gb|DR362560.1|DR362560
EST:     CCCGACGTGGTCAAGTTCTCGAAGTTGATGGAGAGAAAGCTGTTGTTCAG                         GTATTTGAGGGAACATCTGGAATCGACAACAAGTACACAACTGNGNAATTT
genomic: CCCGACGTGGTCAAGTTCTCGAAGTTGATGGAGAGAAAGCTGTTGTTCAGgtttcttgaa ... gcttgtccagGTATTTGAGGGAACATCTGGAATCGACAACAAGTACACAACTGTGCAATTT
EST: gi|125015941|gb|EL088210.1|EL088210
EST:     TTGATGGAGAGAAAGCTGTTGTTCAG                         GTATTTGAGGGAACATCTGGAATCGACAACAAGTACACAACTGTGCAATTT
genomic: TTGATGGAGAGAAAGCTGTTGTTCAGgtttcttgaa ... gcttgtccagGTATTTGAGGGAACATCTGGAATCGACAACAAGTACACAACTGTGCAATTT
EST: gi|86066806|gb|DR362563.1|DR362563
EST:     CCCGACGTGGTCAAGTTCTCGAAGTTGATGGAGAGAAAGCTGTTGTTCAG                         GTATTTGAGGGAACATCTGGAATCGACAACAAGTACACAACTGNGCAATTT
genomic: CCCGACGTGGTCAAGTTCTCGAAGTTGATGGAGAGAAAGCTGTTGTTCAGgtttcttgaa ... gcttgtccagGTATTTGAGGGAACATCTGGAATCGACAACAAGTACACAACTGTGCAATTT
EST: gi|125018910|gb|EL091179.1|EL091179
EST:     CAAGTTCTCGAAGTTGATGGAGAGAAAGCTGTTGTTCAG                         GTATTTGAGGGAACATCTGGAATCGACAACAAGTACACAACTGTGCAATTT
genomic: CAAGTTCTCGAAGTTGATGGAGAGAAAGCTGTTGTTCAGgtttcttgaa ... gcttgtccagGTATTTGAGGGAACATCTGGAATCGACAACAAGTACACAACTGTGCAATTT
EST: gi|86066801|gb|DR362558.1|DR362558
EST:     CCCGACGTGGTCAAGTTCTCGAAGTTGATGGAGAGAAAGCTGTTGTTCAG                         GTATTTGAGGGAACATCTGGAATCGACAACAAGTACACAACTGTGCAATTT
genomic: CCCGACGTGGTCAAGTTCTCGAAGTTGATGGAGAGAAAGCTGTTGTTCAGgtttcttgaa ... gcttgtccagGTATTTGAGGGAACATCTGGAATCGACAACAAGTACACAACTGTGCAATTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagtcattattattcaacacactgcgaggtaaatttctttgatttgcttgtccagGTATTTGAGGGAACATCTGGAATCGACAACAAGTACACAACTGTGCAATTTACAGGAGAG
                                    ctttgat  putative branch site (score: 5)
                                          tttgctt  CT-rich tract
                             taaatttctttgattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttcttgaatcttcctctcttctttagttttctgctcctcttgtctccactttgatgcttaattgaacgcatttgtaaatcaatgtaatcttgcatagtcattattattcaacacactgcgaggtaaatttctttgatttgcttgtccagGTATTTGAGGGAACATCTGGAATCGACAACAAGTACACAACTGTGCAATTTACAGGAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA