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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATACCCATCTCCTCTCGGCTATGGTAGTTTTCCTAAGAGTGTCTGCACATCTGTAAATGAATGCATTTGCCATGGAATACCAGATTCCCGTGCCCTTGAGgttcttctatacaagttcttttgaagttaaacatcctgtgtgaaaaaaaatttgttgacacattctttatttgcag

Basic information

species Glycine max
transcript GLYMA01G39200.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA01G39200.1 (Glycine max), 5'ss of exon 4
lower sequence: LOC_Os02g52420.1 (Oryza sativa), 5'ss of exon 4
ATACCCATCTCCTCTCGGCTATGGTAGTTTTCCTAAGAGTGTCTGCACATCTGTAAATGAATGCATTTGCCATGGAATACCAGATTCCCGTGCCCTTGAGgttcttctatacaagttcttttgaagttaaacatcctgtgtg---aaaaaaaatttgttgacacat-tctttatttgcag
|||||| || || || || ||| |  ||||||| |||||||||||||| || || ||||| ||||| || ||||| ||||| ||||| ||| | ||||| ||    |     || ||      ||   | |||| |||  |    | || ||| ||    |   |  || ||  || |||
ATACCCTTCGCCACTTGGTTATTGCGGTTTTCCAAAGAGTGTCTGCACCTCAGTGAATGAGTGCATCTGTCATGGTATACCTGATTCTCGTCCTCTTGAAgtaagccatccaaaattggagataacacacacatactgcatacatataagaaagttacaaattgacctcctttgttacag

upper sequence: GLYMA01G39200.1 (Glycine max), 5'ss of exon 4
lower sequence: GRMZM2G101438_T02 (Zea mays), 5'ss of exon 4
ATACCCATCTCCTCTCGGCTATGGTAGTTTTCCTAAGAGTGTCTGCACATCTGTAAATGAATGCATTTGCCATGGAATACCAGATTCCCGTGCCCTTGAGgttcttctatacaagttcttttgaagttaaacatcctgtgtgaaaaaaaatttgttgacacattctttatttgcag
||| || || ||||| || ||| || | |  || |||||||||||||| || || ||||||||||| || ||||| || || ||||| ||| ||||||||||    | || |||  ||      || |||  |   ||  | || || ||    |  |   | | || ||  ||||
ATATCCTTCACCTCTTGGTTATTGTGGATACCCAAAGAGTGTCTGCACTTCAGTGAATGAATGCATCTGTCATGGGATTCCGGATTCTCGTCCCCTTGAGgtaagcc-atccaaaatcc---agagataacaactttgaataaataagaaaacttacaattaattttcatg-gcag

upper sequence: GLYMA01G39200.1 (Glycine max), 5'ss of exon 4
lower sequence: AT4G37040.1 (Arabidopsis thaliana), 5'ss of exon 4
ATACCCATCTCCTCTCGGCTATGGTAGTTTTCCTAAGAGTGTCTGCACATCTGTAAATGAATGCATTTGCCATGGAATACCAGATTCCCGTGCCCTTGAGgttc--ttctatacaagttctttt--gaagttaaaca---------tcctgtgtgaaaaaaaatttgttgacacattctttattt--gcag
 || || || ||||| || |||||  |||| || || ||||| ||||||||||| |||||||||||||||||||| |||||||||||  |  | |||||||| |  || | || ||| | |||   |  | ||||||           ||||     |  ||  ||  | |   ||| |||  ||  ||||
TTATCCTTCGCCTCTTGGTTATGGAGGTTTCCCGAAAAGTGTTTGCACATCTGTGAATGAATGCATTTGCCATGGTATACCAGATTCAAGACCACTTGAGgtgcgcttttttaaaaggtgtttgtaggggctaaacagatttttatctctgtcccttatgaatcttaataatgtattgtttcctttggcag

upper sequence: GLYMA01G39200.1 (Glycine max), 5'ss of exon 4
lower sequence: Vv07s0031g00820.t01 (Vitis vinifera), 5'ss of exon 4
ATACCCATCTCCTCTCGGCTATGGTAGTTTTCCTAAGAGTGTCTGCACATCTGTAAATGAATGCATTTGCCATGGAATACCAGATTCCCGTGCCCTTGAGgttc-ttctatacaagttctt-------ttgaa--------gttaaa-catcctgtgtgaaaaaa---aatttgttgacacat--tctttatttgcag
 ||||| || || || ||||||||| | ||||| ||||| ||||||||||| || |||||||||||||||||||||||||||||||||||| | ||||||||   || ||   |||  |||       ||||         |||||  |||  ||| |  ||  |   || |   | | |||   |  | ||||||||
GTACCCTTCCCCCCTAGGCTATGGTGGATTTCCAAAGAGCGTCTGCACATCAGTGAATGAATGCATTTGCCATGGAATACCAGATTCCCGTCCACTTGAGgtctattttacttaaggacttagatttcttgagccagtgtggttaagtcattgtgtttttaagtagtcaaatcacttatacaaaattgtcatttgcag

upper sequence: GLYMA01G39200.1 (Glycine max), 5'ss of exon 4
lower sequence: PP1S392_8V6.2 (Physcomitrella patens), 5'ss of exon 4
ATACCCATCTCCTCTCGGCTATGGTAGTTTTCCTAAGAGTGTCTGCACATCTGTAAATGAATGCATTTGCCATGGAATACCAGATTCCCGTGCCCTTGAGgtt--cttctatacaagttctt------ttgaagttaaacatcctgtgtgaaaaaaaatttgttgacacattctttatttgcag-------------------------------------------------------------------------------------------
 || || |||||||| ||||||||  | ||||| |||||||| || || |||||||| || |||||||||||||| || || || || ||| | |||||||||  | | | |   | ||  |      ||| |||      | |||| ||||||   || ||  |   ||    | | |||                                                                                              
GTATCCCTCTCCTCTTGGCTATGGAGGCTTTCCGAAGAGTGTTTGTACTTCTGTAAACGAGTGCATTTGCCATGGCATTCCCGACTCTCGTCCTCTTGAGgttagcgtttgtggtattttataatcacttgcagtcgtg-gttctgtttgaaaactcatctgaagtggcaccaatcacttgggttagcagcatgtactaataattttaagatcgaaagctgtcactgcatatggtgtacccaactattgatgaaagtgacgttaattgcatgcag

upper sequence: GLYMA01G39200.1 (Glycine max), 5'ss of exon 4
lower sequence: PP1S90_139V6.2 (Physcomitrella patens), 5'ss of exon 4
ATACCCATCTCCTCTCGGCTATGGTAGTTTTCCTAAGAGTGTCTGCACATCTGTAAATGAATGCATTTGCCATGGAATACCAGATTCCCGTGCCCTTGAGgttcttct----atacaa------gttcttttgaagttaaacatcctgtgtga----aaaaaaatttgttgacac-----attctttatttgcag-----
 || || |||||||| || ||||| |||||||| ||||| || || || ||||||||||| ||||| || ||||| || || || |||||| | |||||||||  | |    ||||||      | ||| |||     |||  |  ||         |   |   | | ||| |      | ||||  ||||| |     
TTATCCTTCTCCTCTTGGTTATGGAAGTTTTCCAAAGAGCGTTTGTACCTCTGTAAATGAGTGCATCTGTCATGGCATTCCTGACTCCCGTCCACTTGAGgttggtttggaaatacaatctagtgctctcttgggtcgaaaacttatgaaccgctctagcgaccctgggtgatagtgcgaagtcttagtttgctggtcac

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|209704050|gb|BW673650.1|BW673650
EST:     CTGTAAATGAATGCATTTGCCATGGAATACCAGATTCCCGTGCCCTTGAG                         GATGGTGATATAATCAACATTGATNGT-ACTGTTTATCTAAATGGCTATC
genomic: CTGTAAATGAATGCATTTGCCATGGAATACCAGATTCCCGTGCCCTTGAGgttcttctat ... ttatttgcagGATGGTGATATAATCAACATTGAT-GTTACTGTTTATCTAAATGGCTATC
EST: gi|12691283|gb|BG157619.1|BG157619
EST:     GTAA-TGAATGCATTTGCCATGGAATACCAAGAT-CCCGTGCTCCTTGAA                         GATGGTGATATTATCAAC
genomic: GTAAATGAATGCATTTGCCATGGAATACCA-GATTCCCGTGC-CCTTGAGgttcttctat ... ttatttgcagGATGGTGATATAATCAAC
EST: gi|151401050|gb|EV270864.1|EV270864
EST:     CTGTAAATGAATGCATTTGCCATGGAATACCACATTCCCGTGCCCTTGAG                         -ATGGTGATATAATCAACATTGATGT
genomic: CTGTAAATGAATGCATTTGCCATGGAATACCAGATTCCCGTGCCCTTGAGgttcttctat ... ttatttgcagGATGGTGATATAATCAACATTGATGT
EST: gi|192305235|gb|FG993973.1|FG993973
EST:     CTGTAAATGAATGCATTTGCCATGGAATACCAGATTCCCGTGCCCTTGAG                         GATGGTGATATAATCAACATTGATGTTACTGTTTATCTAAAT
genomic: CTGTAAATGAATGCATTTGCCATGGAATACCAGATTCCCGTGCCCTTGAGgttcttctat ... ttatttgcagGATGGTGATATAATCAACATTGATGTTACTGTTTATCTAAAT
EST: gi|192300116|gb|FG991892.1|FG991892
EST:     CTGTAAATGAATGCATTTGCCATGGAATACCAGATTCCCGTGCCCTTGAG                         GATGGTGATATAATCAACATTGATGTTACTGTTTATCTAAAT
genomic: CTGTAAATGAATGCATTTGCCATGGAATACCAGATTCCCGTGCCCTTGAGgttcttctat ... ttatttgcagGATGGTGATATAATCAACATTGATGTTACTGTTTATCTAAAT
EST: gi|51335002|gb|CO978868.1|CO978868
EST:     CTGTAAATGAATGCATTTGCCATGGAATACCAGATTCCCGTGCCCTTGAG                         GATGGTGATATAATCAACATTGATGTTACTGTTTATCTAAAT
genomic: CTGTAAATGAATGCATTTGCCATGGAATACCAGATTCCCGTGCCCTTGAGgttcttctat ... ttatttgcagGATGGTGATATAATCAACATTGATGTTACTGTTTATCTAAAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATACCCATCTCCTCTCGGCTATGGTAGTTTTCCTAAGAGTGTCTGCACATCTGTAAATGAATGCATTTGCCATGGAATACCAGATTCCCGTGCCCTTGAGgttcttctatacaagttcttttgaagttaaacatcctgtgtgaaaaaaaatttgttgacacattctttatttgcag

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