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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTCTTTGCTTGGTTGCTATGGAAAAACCAGTTTCTCTCAGGCCTGAGCACATTCGGGATGAGAAAGTGAAGgtgtgcctctttccattcaattttcattggaattattactctcttctttcattttattctgcctacttttttctgacacaaactaatcaatatcagtacc...

Basic information

species Glycine max
transcript GLYMA19G24250.3
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G24250.1 (Glycine max), 5'ss of exon 10
lower sequence: LOC_Os04g40874.1 (Oryza sativa), 5'ss of exon 9
----------------------------GTTCTTTGCTTGGTTGCTATGGAAAAACCAGTTTCTCTCAGGCCTGAGCACATTCGGGATGAGAAAGTGAAGgtg---tgcctctttccattcaattttcattggaattattactctcttctttcattttattctgcc-----tacttttttctgacacaa---------actaatcaatatcagtacc-------------
                            ||| | || |||||||| |||||||| || || ||||| | ||||||||||||| | ||||||||||| |||||    | ||| | || ||||  |     |    | |||    |   |     ||  |||  | |      || | | || |    |           |||||  || | |||| ||             
ATTTAATGAACTGTTGCTTCTTCTGCAGGTTTTCTGTTTGGTTGCAATGGAAAAGCCTGTCTCTCTTAAGCCTGAGCACATTAGAGATGAGAAAGTCAAGgtactttacctttctctattctctacatgtcaatactatattgcagcttgccaatactataatactaagagtattatgttttagtccgtttctttagtactaaataaaaccagttccctgttaatgccag

upper sequence: GLYMA19G24250.1 (Glycine max), 5'ss of exon 10
lower sequence: AT5G40760.1 (Arabidopsis thaliana), 5'ss of exon 10
GTTCTTTGCTTGGTTGCTATGGAAAAACCAGTTTCTCTCAGGCCTGAGCACATTCGGGATGAGAAAGTGAAGgtgtgcc--tctttccattcaattttcattggaattattactctcttctttcattttattctgcctacttttttctgacacaaactaatcaatatcagtacc
||||||||| | ||||| ||||| |||||| | ||||| |  |||||||| || |||||||||||||||||||||  |   |  ||   || |    |  |||  ||| |  ||   ||   |    |  || |  ||   ||  | |||   | |    ||| | |  |  | 
GTTCTTTGCCTTGTTGCCATGGAGAAACCAATATCTCTTAAACCTGAGCATATCCGGGATGAGAAAGTGAAGgtgaacaaatacttttcttgaccactttttgccattctatctggttttcgttgcctc-ttttatctgaattcatatgattgagaacc-tcactgtttgatct

upper sequence: GLYMA19G24250.1 (Glycine max), 5'ss of exon 10
lower sequence: AT3G27300.2 (Arabidopsis thaliana), 5'ss of exon 11
GTTCTTTGCTTGGTTGCTATGGAAAAACCAGTTTCTCTCAGGCCTGAGCACATTCGGGATGAGAAAGTGAAGgtg-----------------tgcctctttccattcaattttcattggaattat-tactctcttctttcattttattctgcctacttttttctgacacaaactaatcaatatcagtacc---------
||||||||| | || || ||||| |||||| | ||||| |  || |||||||| |||||||||||||||||||||                   | |||||   |||||  ||   | |||| |  |  | ||||| ||    || ||| ||| | ||  |  | | |  |||| |   || ||   |           
GTTCTTTGCCTTGTCGCCATGGAGAAACCAATCTCTCTTAAACCCGAGCACATCCGGGATGAGAAAGTGAAGgtgattacagttttcttgatcacatctttagtttcaaacttttgtagaatcaagtgatatcttcatttgcatt-ttcagcc-aattaatattaataacaactgactgatttcttaaatgaacttcag

upper sequence: GLYMA19G24250.1 (Glycine max), 5'ss of exon 10
lower sequence: Vv14s0171g00490.t01 (Vitis vinifera), 5'ss of exon 10
GTTCTTTGCTTGGTTGCTATGGAAAAACCAGTTTCTCTCAGGCCTGAGCACATTCGGGATGAGAAAGTGAAGgtgtgcctctttccattcaattttcattggaattattactctcttctttcattttattctgcct---acttttttctgacacaaactaatcaatatcagtacc
|| |||||| ||||||| ||||| || || || |||||||  ||||||||||| || ||||||||||||||||||      ||   | ||  | |    |  || |  ||  |   | ||| |||||||| |       |  ||||  |||||    ||||| |||   | ||  
GTCCTTTGCCTGGTTGCCATGGAGAAGCCCGTCTCTCTCAAACCTGAGCACATCCGAGATGAGAAAGTGAAGgtgcatactttgatactc--tctcacataaaactcataggcaactgttttattttattatttactaaaaattttgttgacatcttctaat-aatcaaaataaa

upper sequence: GLYMA19G24250.1 (Glycine max), 5'ss of exon 10
lower sequence: PP1S222_130V6.3 (Physcomitrella patens), 5'ss of exon 10
GTTCTTTGCTTGGTTGCTATGGAAAAACCAGTTTCTCTCAGGCCTGAGCACATTCGGGATGAGAAAGTGAAGgtgtgcctctttccattcaattttcattggaattattactctcttctttcattttattctgcctacttttttctgacacaaactaatcaatatcagtacc
||||| ||  |||| || ||||| ||||| ||||||||||| ||||||||  |||||||||| ||||| |||||  ||    |    ||  |||| || |  ||||        || ||| ||| |     |    | || |   |   | |   |  |||    |||    
GTTCTGTGTCTGGTAGCCATGGAGAAACCTGTTTCTCTCAGCCCTGAGCATGTTCGGGATGAAAAAGTCAAGgtacgctgaatctttttgcatttgcaatacaatt-----cacctgcttgcatgtgtggttcatcaattctgattattatacgtt--tcacggacag----

upper sequence: GLYMA19G24250.1 (Glycine max), 5'ss of exon 10
lower sequence: PP1S192_39V6.4 (Physcomitrella patens), 5'ss of exon 10
GTTCTTTGCTTGGTTGCTATGGAAAAACCAGTTTCTCTCAGGCCTGAGCACATTCGGGATGAGAAAGTGAAGgtgtg-----cctctttccatt-----caattttcattggaattattactc-----------tcttctttcatt------------ttattctgcct---acttttttctgacacaaactaatcaatatcagtacc-----------------------------------------
 |||| ||  |  | || |||||||||||| |||| ||||| |||||||| ||||||||||||||||| |||||  |      || | |  |||     ||||  |  ||| |   | | ||            | || | | |||            ||  | ||| |   |||  |||| || || || ||| |   | || |||                                          
ATTCTGTGTCTTTTGGCCATGGAAAAACCAATTTCCCTCAGTCCTGAGCATATTCGGGATGAGAAAGTCAAGgtaaggataatctttctggatttgcagcaatacttgttgtaccaaatgcttcatacatttcatgttttcttattgtagttgtgtgattggtttgcatgaaactgctttccgatactaattaagcttcaccattacactttttaatttgtttcaggttgtgatgtttttggtggtcag

upper sequence: GLYMA19G24250.1 (Glycine max), 5'ss of exon 10
lower sequence: PP1S73_244V6.1 (Physcomitrella patens), 5'ss of exon 8
GTTCTTTGCTTGGTTGCTATGGAAAAACCAGTTTCTCTCAGGCCTGAGCACATTCGGGATGAGAAAGTGAAGgtgtgcctct--ttccattcaattttcattggaattattactctct--------tctttcattttattctgcctacttttttctgacacaaact--aatcaatatca-gtacc-------------------------------------------------------------------------------
|| || |||||||| || ||||| ||||||||||| || || || ||||||||||||||||||||||| |||||| |  |    | ||  | ||| |  |||  ||||     |||||           |  |     ||  || | |    || |   |  || |  || |   |||| |||                                                                                 
GTGCTGTGCTTGGTGGCCATGGAGAAACCAGTTTCACTAAGTCCGGAGCACATTCGGGATGAGAAAGTCAAGgtgcggttacagtccctgtgaatatggatttcaatttaccttctctagcaagtgctatatacacctttaggcttgccaaattgttgtatgaaatgaaaaccgcatcaagtataggttacaactagagcttttctaatctatataagaaagattatcctgacctgtcttcctgttctgttctataatgagcag

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|151404199|gb|EV274009.1|EV274009
EST:     TTTCTCTCAGGCCTGAGCACATTCGGGAGGAGAAAGTGAAG                         GTTCTTGAATCAGTGCTCCCTATTAGAGATGATGAGGTTGTTCTTGGACAA
genomic: TTTCTCTCAGGCCTGAGCACATTCGGGATGAGAAAGTGAAGgtgtgcctct ... aaaaatgcagGTTCTTGAATCAGTGCTCCCTATTAGAGATGATGAGGTTGTTCTTGGACAA
EST: gi|254338293|gb|GR849818.1|GR849818
EST:     AAAAACCAGTTTCTCTCAGGCCTGAGCACATTCGGGATGAGAAAGTGAAG                         GTTCTTGAATCAGTGCTCCCTATTAGAGATGATGAGGTTGTTCTTGGACAA
genomic: AAAAACCAGTTTCTCTCAGGCCTGAGCACATTCGGGATGAGAAAGTGAAGgtgtgcctct ... aaaaatgcagGTTCTTGAATCAGTGCTCCCTATTAGAGATGATGAGGTTGTTCTTGGACAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTCTTTGCTTGGTTGCTATGGAAAAACCAGTTTCTCTCAGGCCTGAGCACATTCGGGATGAGAAAGTGAAGgtgtgcctctttccattcaattttcattggaattattactctcttctttcattttattctgcctacttttttctgacacaaactaatcaatatcagtacc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctctttcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctctcttc