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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCATGAGAGATTTCAAGAGGCTGCAACAAGACCCGCCTGCAGGAATCAGCGGGGCACCTCAGGATAACAACATAATGCTGTGGAACGCTGTCATATTTGGgtgagttgaattgaaattggataaagagaaactattctgcttacttgaataatatagtcatactgctattattttattttttcccacactttgtgtaagtatggatggataagcaatttctgctttcttgtctgctttggattgcag

Basic information

species Glycine max
transcript GLYMA05G01270.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA05G01270.1 (Glycine max), 5'ss of exon 2
lower sequence: GRMZM2G110983_T02 (Zea mays), 5'ss of exon 2
TCATGAGAGATTTCAAGAGGCTGCAACAAGACCCGCCTGCAGGAATCAGCGGGGCACCTCAGGATAACAACATAATGCTGTGGAACGCTGTCATATTTGGgtgagttgaattgaaattggataaagagaaactattctgcttacttgaataatatagtcatactgctattattttattttttcccacactttgtgtaagtatggatggataagcaatttctgctttcttgtctgctttggattgcag
| ||||| ||||||||| || ||   || ||||| || || || || || || || || |||||||||||||||||||||||||| ||||||||||||||||  | || |        | ||         |  || | |  ||||      |  | |  || |  | | |  |  | |||    |  |||  |     ||  |                                           
TGATGAGGGATTTCAAGCGGTTGATGCAGGACCCTCCGGCCGGCATAAGTGGCGCCCCGCAGGATAACAACATAATGCTGTGGAATGCTGTCATATTTGGgtatgatgca--------gaatccccccgcccccttttccccacttcttagtttgaattgtaatatt-tgacatcgtctttggatatgcttatttcttttacag-------------------------------------------

upper sequence: GLYMA05G01270.1 (Glycine max), 5'ss of exon 2
lower sequence: Vv17s0000g05820.t01 (Vitis vinifera), 5'ss of exon 2
TCATGAGAGATTTCAAGAGGCTGCAACAAGACCCGCCTGCAGGAATCAGCGGGGCACCTCAGGATAACAACATAATGCTGTGGAACGCTGTCATATTTGGgtgagttgaattgaaattggataaagagaaactattctgcttacttgaataatatagtcatactgctattattttattttttcccacactttgtgtaagtatggatggataagcaatttctgctttcttgtctgctttggattgcag
| ||||||||||| |||||| ||||||| ||||| ||||| || ||||| || || || || || ||||| |||||||| ||||| ||||| |||||||||| |   | |   |||||  || || |     |||| || || |||   | || |  | ||  |  |    ||||| ||| ||    | | ||| ||||||||| ||||||||| ||||||| |||||| |||| ||||||||||||
TGATGAGAGATTTTAAGAGGTTGCAACAGGACCCCCCTGCCGGCATCAGTGGAGCTCCCCAAGACAACAATATAATGCTTTGGAATGCTGTTATATTTGGgtaatgggcaacaaaattc-atgaaaactg-ttattgtgtttgcttatgttatgtgtttat-ttatttgccttttactttctc----agtatgtttaagtatggttggataagccatttctggtttcttttctgatttggattgcag

upper sequence: GLYMA05G01270.1 (Glycine max), 5'ss of exon 2
lower sequence: Vv17s0000g05820.t01 (Vitis vinifera), 5'ss of exon 2
TCATGAGAGATTTCAAGAGGCTGCAACAAGACCCGCCTGCAGGAATCAGCGGGGCACCTCAGGATAACAACATAATGCTGTGGAACGCTGTCATATTTGGgtgagttgaattgaaattggataaagagaaactattctgcttacttgaataatatagtcatactgctattattttattttttcccacactttgtgtaagtatggatggataagcaatttctgctttcttgtctgctttggattgcag
| ||||||||||| |||||| ||||||| ||||| ||||| || ||||| || || || || || ||||| |||||||| ||||| ||||| |||||||||| |   | |   |||||  || || |     |||| || || |||   | || |  | ||  |  |    ||||| ||| ||    | | ||| ||||||||| ||||||||| ||||||| |||||| |||| ||||||||||||
TGATGAGAGATTTTAAGAGGTTGCAACAGGACCCCCCTGCCGGCATCAGTGGAGCTCCCCAAGACAACAATATAATGCTTTGGAATGCTGTTATATTTGGgtaatgggcaacaaaattc-atgaaaactg-ttattgtgtttgcttatgttatgtgtttat-ttatttgccttttactttctc----agtatgtttaagtatggttggataagccatttctggtttcttttctgatttggattgcag

upper sequence: GLYMA05G01270.1 (Glycine max), 5'ss of exon 2
lower sequence: PP1S91_87V6.1 (Physcomitrella patens), 5'ss of exon 1
TCATGAGAGATTTCAAGAGGCTGCAACAAGACCCGCCTGCAGGAATCAGCGGGGCACCTCAGGATAACAACATAATGCTGTGGAACGCTGTCATATTTGGgtgagttgaattgaaattggataaagagaaactattctgcttacttgaataatatagtcatactgctattattttattttttcccacactttgtgtaagtatggatggataagcaatttctgctttcttgtctgctttggattgcag
| ||| | || |||||| | ||||| || || || || || || |||||||| || || ||||| |||||||| ||| ||||||| ||||||||||| |||| |    || |       |||            |||||| | ||  | |      ||   | ||| |  | ||  |      |     ||||  |     ||   |  |                                     
TGATGCGCGACTTCAAGCGCCTGCAGCATGATCCTCCGGCCGGCATCAGCGGCGCCCCGCAGGACAACAACATCATGTTGTGGAATGCTGTCATATTCGGgt-acccaaactcctccccgatt-------ttcgttctgcatgctcaattgtgtcggtatgaatgcga--aattcgtggggcgcggagatttgcatggcggtgtcggttt-------------------------------------

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|151408894|gb|EV278702.1|EV278702
EST:     GGGGCACCTCAGGATAGCAACATAATGCTGTGGAACGCTGTCAAATTTGG                         TCCTGATGATACTCCATGGGATGGAG
genomic: GGGGCACCTCAGGATAACAACATAATGCTGTGGAACGCTGTCATATTTGGgtgagttgaa ... tggattgcagTCCTGATGATACTCCATGGGATGGAG
EST: gi|120530431|gb|EH258564.1|EH258564
EST:     GGGGCACCTCAGGATAACAACATAATGCTGTGGAACGCTGTCATATTTGG                         TCCTGATGATACTCCATGGGATGGAG
genomic: GGGGCACCTCAGGATAACAACATAATGCTGTGGAACGCTGTCATATTTGGgtgagttgaa ... tggattgcagTCCTGATGATACTCCATGGGATGGAG
EST: gi|21887693|gb|BQ740906.1|BQ740906
EST:     CGCTGTCATATTTGG                         TCCTGATGATACTCCATGGGATGGAG
genomic: CGCTGTCATATTTGGgtgagttgaa ... tggattgcagTCCTGATGATACTCCATGGGATGGAG
EST: gi|151398226|gb|EV268104.1|EV268104
EST:     GGGGCACCTCAGGATAACAACATAATGCTGTGGAACGCTGTCATATTTGG                         TCCTGATGATACTCCATGGGATGGAG
genomic: GGGGCACCTCAGGATAACAACATAATGCTGTGGAACGCTGTCATATTTGGgtgagttgaa ... tggattgcagTCCTGATGATACTCCATGGGATGGAG
EST: gi|208204410|gb|GE007817.1|GE007817
EST:     ATAACAACATAATGCTGTGGAACGCTGTCATATTTGG                         TCCTGATGATACTCCATGGGATGGAG
genomic: ATAACAACATAATGCTGTGGAACGCTGTCATATTTGGgtgagttgaa ... tggattgcagTCCTGATGATACTCCATGGGATGGAG
EST: gi|26047615|gb|CA784343.1|CA784343
EST:     GGGGCACCTCAGGATAACAACATAATGCTGTGGAACGCTGTCATATTTGG                         TCCTGATGATACTCCATGGGATGGAG
genomic: GGGGCACCTCAGGATAACAACATAATGCTGTGGAACGCTGTCATATTTGGgtgagttgaa ... tggattgcagTCCTGATGATACTCCATGGGATGGAG
EST: gi|31460020|gb|CD402048.1|CD402048
EST:     GGGGCACCTCAGGATAACAACATAATGCTGTGGAACGCTGTCATATTTGG                         TCCTGATGATACTCCATGGGATGGAG
genomic: GGGGCACCTCAGGATAACAACATAATGCTGTGGAACGCTGTCATATTTGGgtgagttgaa ... tggattgcagTCCTGATGATACTCCATGGGATGGAG
EST: gi|192299657|gb|FG990010.1|FG990010
EST:     GGGGCACCTCAGGATAACAACATAATGCTGTGGAACGCTGTCATATTTGG                         TCCTGATGATACTCCATGGGATGGAG
genomic: GGGGCACCTCAGGATAACAACATAATGCTGTGGAACGCTGTCATATTTGGgtgagttgaa ... tggattgcagTCCTGATGATACTCCATGGGATGGAG
EST: gi|27427583|gb|CA939103.1|CA939103
EST:     GGGGCACCTCAGGATAACAACATAATGCTGTGGAACGCTGTCATATTTGG                         TCCTGATGATACTCCATGGGATGGAG
genomic: GGGGCACCTCAGGATAACAACATAATGCTGTGGAACGCTGTCATATTTGGgtgagttgaa ... tggattgcagTCCTGATGATACTCCATGGGATGGAG
EST: gi|254349242|gb|GR860040.1|GR860040
EST:     GGGGCACCTCAGGATAACAACATAATGCTGTGGAACGCTGTCATATTTGG                         TCCTGATGATACTCCATGGGATGGAG
genomic: GGGGCACCTCAGGATAACAACATAATGCTGTGGAACGCTGTCATATTTGGgtgagttgaa ... tggattgcagTCCTGATGATACTCCATGGGATGGAG
EST: gi|4397477|gb|AI496474.1|AI496474
EST:     GGTGCACCTTAGGATAACAACATAATGCTGTGGAACGCTGTCATATTTGG                         TCCTGATGATACTCCATGGGATGGAG
genomic: GGGGCACCTCAGGATAACAACATAATGCTGTGGAACGCTGTCATATTTGGgtgagttgaa ... tggattgcagTCCTGATGATACTCCATGGGATGGAG
EST: gi|151396142|gb|EV266019.1|EV266019
EST:     GGGGCACCTCAGGATAACAACATAATGCTGTGGAACGCTGTCATATTTGG                         TCCTGATGATACTCCATGGGATGGAG
genomic: GGGGCACCTCAGGATAACAACATAATGCTGTGGAACGCTGTCATATTTGGgtgagttgaa ... tggattgcagTCCTGATGATACTCCATGGGATGGAG
EST: gi|7691194|gb|AW759326.1|AW759326
EST:     GTCATATTTGG                         TCCTGATGATACTCCATGGGATGGAG
genomic: GTCATATTTGGgtgagttgaa ... tggattgcagTCCTGATGATACTCCATGGGATGGAG
EST: gi|19054147|gb|BM732814.1|BM732814
EST:     GGGGCACCTCAGGATAACAACATAATGCTGTGGAACGCTGTCATATTTGG                         TCCTGATGATACTCCATGGGATGGAG
genomic: GGGGCACCTCAGGATAACAACATAATGCTGTGGAACGCTGTCATATTTGGgtgagttgaa ... tggattgcagTCCTGATGATACTCCATGGGATGGAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCATGAGAGATTTCAAGAGGCTGCAACAAGACCCGCCTGCAGGAATCAGCGGGGCACCTCAGGATAACAACATAATGCTGTGGAACGCTGTCATATTTGGgtgagttgaattgaaattggataaagagaaactattctgcttacttgaataatatagtcatactgctattattttattttttcccacactttgtgtaagtatggatggataagcaatttctgctttcttgtctgctttggattgcag

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