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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacattgttaaaaacctagaattatgagctattgagattttgtttcctgtttaattaaactgacaagctaagtttcagttcagtaccatcatgattgttaatatttgatgaggaattcaatggtgatatcagGTGGCCAATTGGTTCATCAATGCAAGGGTGCGTCTCTGGAAGCCAATGGTTGAGGAAATGTACAAAGAGGAGTTTGGAGACTCCGAGATGAACTGCAACC

Basic information

species Glycine max
transcript GLYMA06G03200.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G03200.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os03g06930.1 (Oryza sativa), 3'ss of exon 5
gtacattgttaaaaacctagaattatgagctattgagattttgtttcctgtttaattaaactgacaagctaagtttcagttcagtaccatcatgattgttaatatttgatgaggaattcaatggtgatatcagGTGGCCAATTGGTTCATCAATGCAAGGGTGCGTCTCTGGAAGCCAATGGTTGAGGAAATGTACAAAGAGGAGTTTGGAGACTCCGAGATGAACTGCAACC---
                 |   |||  |  | || ||  |      ||   |  ||   | ||||     | |  |  ||   || |    |||| || ||    |||         |||  |  | |  | ||||  | || ||||||||||| ||  | ||||| || |||||||||||| | ||||| |||||||| |||||||| || |   | |||||| ||| ||||    
----------------gtgagattgagctccat-gaactcgacgctctcatgcaa---agctgatggattcaaatcaagaagagaatt-ccatggttttt----ttt---------ttctttttttacgt-agGTATCGAACTGGTTCATCAACGCGCGCGTGCGGCTGTGGAAGCCAATGATCGAGGAGATGTACAAGGAGGAGTTCGGCG---CGGAGATGGACTCCAACTCGT

upper sequence: GLYMA06G03200.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv18s0001g13150.t01 (Vitis vinifera), 3'ss of exon 4
gtacattgttaaaaacctagaattatgagctattgagattttgtttcctgtttaattaaactgacaagctaagtttcagttcagtaccatcatgattgttaatatttgatgaggaattcaatg--gtgatatcagGTGGCCAATTGGTTCATCAATGCAAGGGTGCGTCTCTGGAAGCCAATGGTTGAGGAAATGTACAAAGAGGAGTTTGGAGACTCCGAGATGAACTGCAACC
                                   |   |||   |    || ||  ||| | ||||| ||   ||        |  | |  |  || ||  ||| ||||  |   |  |||    || | |||||| || || ||||| || |||||| |||||||||| |||||||| ||||||||||| || || ||||| ||| |||| || || ||||  || |  ||  
---------------------------------caatgctttcaatttccttaaaacaaaatcacaag-tacaattggccctcttttcttgttctttatttttatgtgatatgatctctaatctcatggt-tcagGTTGCAAACTGGTTTATAAATGCACGGGTGCGTCTTTGGAAGCCCATGGTTGAGGAGATTTATAAAGAAGAGATTGGTGATTCAGAGACAAAGTCTAAAT

upper sequence: GLYMA06G03200.1 (Glycine max), 3'ss of exon 4
lower sequence: PP1S220_67V6.1 (Physcomitrella patens), 3'ss of exon 4
gtacattgttaaaaacctagaattatgagctattgagattttgtttcctgtttaattaaac--tgacaagctaagtttcagttcagtaccatcatgattgtt--aatatttgatgaggaattcaatgg--tgatatcagGTGGCCAATTGGTTCATCAATGCAAGGGTGCGTCTCTGGAAGCCAATGGTTGAGGAAATGTACAAAGAGGAGTTTGGAGACTCCGAGATGAACTGCAACC
                                        |    ||| |     || |||  ||| ||| | |||        || |  |  |||| | |   ||| |  ||||     || | | |  ||  | |||||  | |||||||||||||| ||| | || || || |||||||||||||| ||||| ||||||  ||||||      ||| | |       |    |   
--------------------------------------cctccactccagaacgcttgaacagtgagaagatcagtcatcaggtagcagaaa-atgaatatctgaatctacgatgttttgttgacttgcatgcgagcagGTTTCTAATTGGTTCATCAACGCACGAGTACGGCTGTGGAAGCCAATGGTAGAGGAGATGTACGTAGAGGAACAAAAAGAGTACCCTGGAGATCATACTG

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|193329735|gb|FK294033.1|FK294033
EST:     ATTCTGAGAAAATTATGCTGGCTAGGCAAACAGGCTTGACCAGAAACCAG                         GTGGCAAATTGGTTCATCAATGCAAGGGTGCGTCTCTGGAAGCCAATGGTT
genomic: ATTCTGAGAAAATTATGCTGGCTAGGCAAACAGGCTTGACCAGAAACCAGgtacattgtt ... gtgatatcagGTGGCCAATTGGTTCATCAATGCAAGGGTGCGTCTCTGGAAGCCAATGGTT
EST: gi|193512503|gb|FK469071.1|FK469071
EST:     TTCTGAGAAAATTATGCTGGCTAGGCAAACAGGCTTGACCAGAAACCAG                         GTGGCCAATTGGTTCATCAATGCAAGGGTGCGTCTCTGGAAGCCAATGGTT
genomic: TTCTGAGAAAATTATGCTGGCTAGGCAAACAGGCTTGACCAGAAACCAGgtacattgtt ... gtgatatcagGTGGCCAATTGGTTCATCAATGCAAGGGTGCGTCTCTGGAAGCCAATGGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttcagtaccatcatgattgttaatatttgatgaggaattcaatggtgatatcagGTGGCCAATTGGTTCATCAATGCAAGGGTGCGTCTCTGGAAGCCAATGGTTGAGGAAATGTACAAAGAGGAGTTTGGAGACTCCGAGATGAACTGCAACC
             atgattgttaatattt  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
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacattgttaaaaacctagaattatgagctattgagattttgtttcctgtttaattaaactgacaagctaagtttcagttcagtaccatcatgattgttaatatttgatgaggaattcaatggtgatatcagGTGGCCAATTGGTTCATCAATGCAAGGGTGCGTCTCTGGAAGCCAATGGTTGAGGAAATGTACAAAGAGGAGTTTGGAGACTCCGAGATGAACTGCAACC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG