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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTTATGAGACGGTAGAAGAAGGATCTTACATAAAAATGATTGACATGGCCAGTGGACATGGAGGGCAAATACAAgtaaggtttacatttaattatgtcattttatgaggcaaactgaacaattttacataaatcattgtctggtttgctggtatttcaagtttgataattgata...

Basic information

species Glycine max
transcript GLYMA02G39390.1
intron # 14
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G39390.1 (Glycine max), 5'ss of exon 14
lower sequence: GRMZM5G824405_T02 (Zea mays), 5'ss of exon 12
GTTTATGAGACGGTAGAAGAAGGATCTTACATAAAAATGATTGACATGGCCAGTGGACATGGAGGGCAAATACAAgtaag-gtttacatttaattatgtcattttatgaggcaaactgaacaatttta---cataaatcattgtctggtttgctggtattt-caagtttgataattgata
|| |||||  |||| |||||||| |||||||||||||||||||||||||  |||||  | || || ||| || | ||| |  |  ||| | || |    ||| | |  | | ||  | || | || ||   | |     |||| ||  |||     | ||| |  ||   ||  |  |  
GTCTATGAACCGGTGGAAGAAGGTTCTTACATAAAAATGATTGACATGGTTAGTGGGAAGGGGGGCCAACTAAAGgtatgtatgaacagtcaagtgacacatgtaa--aagtaatatcaaaagttctattccctgtgctattg-ctactttatatatgtttacttgtgcaatcttaaa--

upper sequence: GLYMA02G39390.1 (Glycine max), 5'ss of exon 14
lower sequence: AT1G07110.1 (Arabidopsis thaliana), 5'ss of exon 14
GTTTATGAGACGGTAGAAGAAGGATCTTACATAAAAATGATTGACATGGCCAGTGGACATGGAGGGCAAATACAAgtaaggtttacatttaattatgtcattttat----gaggcaaactgaacaattttacata-----aatcattgtctggtttgctggtatttcaagt-ttgataattgata-----------------
||||||||| | ||||||||||| || ||||| ||||||||||| |||| ||||||  | || || || ||||||||| | | |   | |  || ||| |  |||     | |    ||    | |||| |  ||     |||||   | ||||          ||| | | || || | || ||                 
GTTTATGAGCCTGTAGAAGAAGGTTCGTACATCAAAATGATTGATATGGTCAGTGGGAACGGTGGACAGATACAAgtacg-tctctgtctgtttctgtaaaattaaattggcgtttcacatggctatttcatctagtcttaatcacgatatggtacttgatcggttcgactgttcatgactgttattctacttttgttgcag

upper sequence: GLYMA02G39390.1 (Glycine max), 5'ss of exon 14
lower sequence: Vv06s0004g06920.t01 (Vitis vinifera), 5'ss of exon 14
GTTTATGAGACGGTAGAAGAAGGATCTTACATAAAAATGATTGACATGGCCAGTGGACATGGAGGGCAAATACAAgtaaggtttacatttaattatgtcattttatgaggcaaactgaacaattt-tacataaa--tcattgtctg---gtttgctggtatttcaagtttgataattgata
||||||||| | || |||||||| |||||||| ||||||||||| ||||   |||| || |  || || ||||| ||||| || || |    |||  | |||    ||| ||  ||    | | | ||| |||   | | |   ||   |||||     |||||   |||  |  ||    
GTTTATGAGCCAGTGGAAGAAGGCTCTTACATCAAAATGATTGATATGGTTGGTGGCCAAGATGGACAGATACAGgtaagtttcacctc---ttaaatgattaacagagacatgcttttaattatgtacttaaggtttactaagtgcatgtttggatacatttcctattttttggttt---

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|7283901|gb|AW596502.1|AW596502
EST:     CTTACATAAAAATGATTGACATGGCCAGTGGACATGGAGGGCAAATACAA                         GTGAAAAATATCAGTGGCTACCTACCTGGGCGGATAGTATGTTTCTTG
genomic: CTTACATAAAAATGATTGACATGGCCAGTGGACATGGAGGGCAAATACAAgtaaggttta ... tttggtttagGTGAAAAATATCAGTGGCTACCTACCTGGGCGGATAGTATGTTTCTTG
EST: gi|23728948|gb|BU762545.1|BU762545
EST:     CTTACATAAAAATGATTGACATGGCCAGTGGACATGGAGGGCAAATACAA                         GTGAAAAATATCAGTGGCTACCTACCTGGGCGGATAGTATGTTTCTTG
genomic: CTTACATAAAAATGATTGACATGGCCAGTGGACATGGAGGGCAAATACAAgtaaggttta ... tttggtttagGTGAAAAATATCAGTGGCTACCTACCTGGGCGGATAGTATGTTTCTTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTTATGAGACGGTAGAAGAAGGATCTTACATAAAAATGATTGACATGGCCAGTGGACATGGAGGGCAAATACAAgtaaggtttacatttaattatgtcattttatgaggcaaactgaacaattttacataaatcattgtctggtttgctggtatttcaagtttgataattgata

- - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG