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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcttgcatgtttttgtttatgaaattattctcgtttagattggatacctgttttccttttcctggaatgtaataattgtattcctatgttttgtcctcagGTTGGAGGTTGCGCTTTTGTTGATAGTATATCTTGCTTATGGCTATAATGAAGGTGGTGCACTCTCATATATTCTTTTGAGTATAAGCAGTTGGTTTATG

Basic information

species Glycine max
transcript GLYMA20G38860.1
intron # 47
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G38860.1 (Glycine max), 3'ss of exon 47
lower sequence: Vv06s0004g01200.t01 (Vitis vinifera), 3'ss of exon 42
-----------------------------------tcttgcatgtttttgtttatgaaattattctcgttta--gattggatacct---gttttccttttcctggaatgtaataattgtattc-ctatgtt--ttgtcctcagGTTGGAGGTTGCGCTTTTGTTGATAGTATATCTTGCTTATGGCTATAATGAAGGTGGTGCACTCTCATATATTCTTTTGAGTATAAGCAGTTGGTTTATG---
                                      |   ||| | || |   ||  |||||  | ||||  | ||   || ||   | ||| |||   || |     | || || ||||   ||  ||  || || |||| || ||||||| |||||||||||||||||| ||||| ||||| ||||| ||||| |   |||| || || |||||| | || || ||||||||||| |||   
gtactctctctctctctctctctctctaaccacccgtctatttgtctgtggtgcggatgttatttgcatttattggtttattatcttcagatttgcttaaactaggg-acattatttatatttattactttggttatcttcagATTAGAGGTTGTGCTTTTGTTGATAGTATACCTTGCATATGGGTATAACGAAGGCG---CACTATCGTACATTCTTCTTAGCATTAGCAGTTGGTTCATGGCT
















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|193380795|gb|FK346078.1|FK346078
EST:     AAATTTTCAGAGAACTACAGACTCTACTCTCGTAGTCATTTTGTTAAAGG                         GTTGGAGGTTGCGCTTTTGTTGATAGTATATCTTGCTTATGGCTATAATGA
genomic: AAATTTTCAGAGAACTACAGACTCTACTCTCGTAGTCATTTTGTTAAAGGgtgagacgtg ... ttgtcctcagGTTGGAGGTTGCGCTTTTGTTGATAGTATATCTTGCTTATGGCTATAATGA
EST: gi|208140913|gb|GD935255.1|GD935255
EST:     AAATTTTCAGAGAACTACAGACTCTACTCTCGTAGTCATTTTGTTAAAGG                         GTTGGAGGTTGCGCTTTTGTTGATAGTATATCTTGCTTATGGCTATAATGA
genomic: AAATTTTCAGAGAACTACAGACTCTACTCTCGTAGTCATTTTGTTAAAGGgtgagacgtg ... ttgtcctcagGTTGGAGGTTGCGCTTTTGTTGATAGTATATCTTGCTTATGGCTATAATGA
EST: gi|193376576|gb|FK343165.1|FK343165
EST:     ACTCTACTCTCGTAGTCATTTTGTTAAAGG                         GTTGGAGGTTGCGCTTTTGTTGATAGTATATCTTGCTTATGGCTATAATGA
genomic: ACTCTACTCTCGTAGTCATTTTGTTAAAGGgtgagacgtg ... ttgtcctcagGTTGGAGGTTGCGCTTTTGTTGATAGTATATCTTGCTTATGGCTATAATGA
EST: gi|207758289|gb|GD730183.1|GD730183
EST:     AAATTTTCAGAGAACTACAGACTCTACTCTCGTAGTCATTTTGTTAAAGG                         GTTGGAGGTTGCGCTTTTGTTGATAGTATATCTTGCTTATGGCTATAATGA
genomic: AAATTTTCAGAGAACTACAGACTCTACTCTCGTAGTCATTTTGTTAAAGGgtgagacgtg ... ttgtcctcagGTTGGAGGTTGCGCTTTTGTTGATAGTATATCTTGCTTATGGCTATAATGA
EST: gi|208043450|gb|GD839608.1|GD839608
EST:     AAATTTTCAGAGAACTACAGACTCTACTCTCGTAGTCATTTTGTTAAAGG                         GTTGGAGGTTGCGCTTTTGTTGATAGTATATCTTGCTTATGGCTATAATGA
genomic: AAATTTTCAGAGAACTACAGACTCTACTCTCGTAGTCATTTTGTTAAAGGgtgagacgtg ... ttgtcctcagGTTGGAGGTTGCGCTTTTGTTGATAGTATATCTTGCTTATGGCTATAATGA
EST: gi|193439831|gb|FK408078.1|FK408078
EST:     AAATTTTCAGAGAACTACAGACTCTACTCTCGTAGTCATTTTGTTAAAGG                         GTTGGAGGTTGCGCTTTTGTTGATAGTATATCTTGCTT
genomic: AAATTTTCAGAGAACTACAGACTCTACTCTCGTAGTCATTTTGTTAAAGGgtgagacgtg ... ttgtcctcagGTTGGAGGTTGCGCTTTTGTTGATAGTATATCTTGCTT
EST: gi|193435451|gb|FK401939.1|FK401939
EST:     AAATTTTCAGAGAACTACAGACTCTACTCTCGTAGTCATTTTGTTAAAGG                         GTTAGGAGGTTGCGCTTTTGTTGATAGTATATCTTGCTTATGGCTATAATG
genomic: AAATTTTCAGAGAACTACAGACTCTACTCTCGTAGTCATTTTGTTAAAGGgtgagacgtg ... ttgtcctcagGTT-GGAGGTTGCGCTTTTGTTGATAGTATATCTTGCTTATGGCTATAATG
EST: gi|254331761|gb|GR843611.1|GR843611
EST:     AAATTTTCAGAGAACTACAGACTCTACTCTCGTAGTCATTTTGTTAAAGG                         GTTGGAGGTTGCACTTCTGTTGATAGTATATCTTGCTTATGGCTCTAATGA
genomic: AAATTTTCAGAGAACTACAGACTCTACTCTCGTAGTCATTTTGTTAAAGGgtgagacgtg ... ttgtcctcagGTTGGAGGTTGCGCTTTTGTTGATAGTATATCTTGCTTATGGCTATAATGA
EST: gi|208128813|gb|GD927553.1|GD927553
EST:     GAATTTTCAGAGAACTACAGACTCTACTCTCGTAGTCATTTTGTTAAAGG                         GTTGGAGGTTGCGCTTTTGTTGATAGTATATCTTGCTTATGGCTATAATGA
genomic: AAATTTTCAGAGAACTACAGACTCTACTCTCGTAGTCATTTTGTTAAAGGgtgagacgtg ... ttgtcctcagGTTGGAGGTTGCGCTTTTGTTGATAGTATATCTTGCTTATGGCTATAATGA
EST: gi|208066301|gb|GD865960.1|GD865960
EST:     AAATTTTCAGAGAACTACAGACTCTACTCTCGTAGTCATTTTGTTAAAGG                         GTTGGAGGTTGCGCTTTTGTTGATAGTATATCTTGCTTATGGCTATAATGA
genomic: AAATTTTCAGAGAACTACAGACTCTACTCTCGTAGTCATTTTGTTAAAGGgtgagacgtg ... ttgtcctcagGTTGGAGGTTGCGCTTTTGTTGATAGTATATCTTGCTTATGGCTATAATGA
EST: gi|298188356|gb|HO035049.1|HO035049
EST:     AAATTTTCAGAGAACTACAGACTCTACTCTCGTAGTCATTTTGTTAAAGG                         GTTGGAGGTTGCACTTCTGTTGATAGTATATCTTGCTTATGGCTCTAATGA
genomic: AAATTTTCAGAGAACTACAGACTCTACTCTCGTAGTCATTTTGTTAAAGGgtgagacgtg ... ttgtcctcagGTTGGAGGTTGCGCTTTTGTTGATAGTATATCTTGCTTATGGCTATAATGA
EST: gi|208089199|gb|GD888252.1|GD888252
EST:     AAATTTTCAGAGAACTACAGACTCTACTCTCGTAGTCATTTTGTTAAAGG                         GTTGGAGGTTGCGCTTTTGTTGATAGTATATCTTGCTTATGGCTATAATGA
genomic: AAATTTTCAGAGAACTACAGACTCTACTCTCGTAGTCATTTTGTTAAAGGgtgagacgtg ... ttgtcctcagGTTGGAGGTTGCGCTTTTGTTGATAGTATATCTTGCTTATGGCTATAATGA
EST: gi|193524673|gb|FK482292.1|FK482292
EST:     AAATTTTCAGAGAACTACAGACTCTACTCTCGTAGTCATTTTGTTAAAGG                         GTTGGAGGTTGCGCTTTTGTTGATAGTATATCTTGCTTATGGCTATAATGA
genomic: AAATTTTCAGAGAACTACAGACTCTACTCTCGTAGTCATTTTGTTAAAGGgtgagacgtg ... ttgtcctcagGTTGGAGGTTGCGCTTTTGTTGATAGTATATCTTGCTTATGGCTATAATGA
EST: gi|208037175|gb|GD836126.1|GD836126
EST:     AAATTTTCAGAGAACTACAGACTCTACTCTCGTAGTCATTTTGTTAAAGG                         GTTGGAGGTTGCGCTTTTGTTGATAGTATATCTTGCTTATGGCTATAATGA
genomic: AAATTTTCAGAGAACTACAGACTCTACTCTCGTAGTCATTTTGTTAAAGGgtgagacgtg ... ttgtcctcagGTTGGAGGTTGCGCTTTTGTTGATAGTATATCTTGCTTATGGCTATAATGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acctgttttccttttcctggaatgtaataattgtattcctatgttttgtcctcagGTTGGAGGTTGCGCTTTTGTTGATAGTATATCTTGCTTATGGCTATAATGAAGGTGGTGCACTCTCATATATTCTTTTGAGTATAAGCAGTTGGTTTATG
                                           ttttgtcctc  CT-rich tract
                    aatgtaataattgtat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcttgcatgtttttgtttatgaaattattctcgtttagattggatacctgttttccttttcctggaatgtaataattgtattcctatgttttgtcctcagGTTGGAGGTTGCGCTTTTGTTGATAGTATATCTTGCTTATGGCTATAATGAAGGTGGTGCACTCTCATATATTCTTTTGAGTATAAGCAGTTGGTTTATG

- - gcatgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaatgta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cctatgt