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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GACTGGATTATGGAGCAGTGGGAGAAAAATTACTATATCAGTTCAATAGCTGGCGCAGTTAATGGAAGTTCCTTGGTTGTCATGTCCAAAGgtatataatatctataattttatgacctactcctccttcacatactattgattaatttatttttgaaatgcctttgcaaaatctccttgctattttactt...

Basic information

species Glycine max
transcript GLYMA16G04580.1
intron # 14
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G04580.1 (Glycine max), 5'ss of exon 14
lower sequence: LOC_Os01g56580.1 (Oryza sativa), 5'ss of exon 14
GACTGGATTATGGAGCAGTGGGAGAAAAATTACTATATCAGTTCAATAGCTGGCGCAGTTAATGGAAGTTCCTTGGTTGTCATGTCCAAAGgtatataatatctataattttatgacctactcctccttcacatactattgattaatttatttttgaaatgcctttgcaaaatctccttgctattttactt
|| |||||||||||||| |||||||| |||||||| |||||| | ||||| || |||   ||||||||||||||||| |||||||| |||||| | |   | || |  |||| |         ||| |     ||| |||| |    ||  |   | |    || ||   |    | | ||   |||   |
GATTGGATTATGGAGCAATGGGAGAATAATTACTACATCAGTGCCATAGCGGGTGCAACAAATGGAAGTTCCTTGGTGGTCATGTCAAAAGgtttgtctcagctgttcttttgttggaggtctctcatgttactaccattgttattcttcataaaggaccatctatgtttagaaacttggcctgtttctct

upper sequence: GLYMA16G04580.1 (Glycine max), 5'ss of exon 14
lower sequence: LOC_Os03g57940.1 (Oryza sativa), 5'ss of exon 14
GACTGGATTATGGAGCAGTGGGAGAAAAATTACTATATCAGTTCAATAGCTGGCGCAGTTAATGGAAGTTCCTTGGTTGTCATGTCCAAAGgt--atataatatctataattttatgacctactcctccttcacatactattgattaatttatttttgaaatgcctttgc-aaaatctccttgctattttactt
|| ||||||||||||||||||||||| ||||| || || |   ||||||| || |||   |||||||| || |||||||| ||||||||||||   || |||| || |  | |  || |  |||  |  | |  |   |    |||  ||     ||||||   |   |   |    |      || || |   
GATTGGATTATGGAGCAGTGGGAGAAGAATTATTACATAACGGCAATAGCAGGAGCAACCAATGGAAGCTCATTGGTTGTAATGTCCAAAGgttggtaaaataccttttctctgctggcaaactaattttac-taccttggctatttcttagaacttgaaacaaccccgttgatgaatatgaaatagttgaa--

upper sequence: GLYMA16G04580.1 (Glycine max), 5'ss of exon 14
lower sequence: LOC_Os07g07560.2 (Oryza sativa), 5'ss of exon 14
GACTGGATTATGGAGCAGTGGGAGAAAAATTACTATATCAGTTCAATAGCTGGCGCAGTTAATGGAAGTTCCTTGGTTGTCATGTCCAAAGgtatataat---------atctataattttatgacctactcctccttcacatactattgattaatt-tatttttgaaatgcctttgcaaaatctccttgctattttactt-------------------------------------------------------
|||||||| ||||| ||||||||||| |||| ||| || |   ||||||||||  ||| ||| |||||||| || ||||| |||||||||||| |   ||         ||   | |||||||  ||    | | ||||    || ||  ||||    ||| ||| | |||   ||    ||||   ||| |  |   | |                                                       
GACTGGATAATGGATCAGTGGGAGAAGAATTTCTACATAACAGCAATAGCTGGATCAGCTAACGGAAGTTCTTTAGTTGTGATGTCCAAAGgtctgggatgtgtttcttattagtcattttatatcccgaccattcttctttgacgatgaattatccatatgtttcatatggactt----aatcattttgttgctccccatgagttaacctggcttagttgtgatcacctatagtttgatatgtccattattgcag

upper sequence: GLYMA16G04580.1 (Glycine max), 5'ss of exon 14
lower sequence: GRMZM2G116086_T01 (Zea mays), 5'ss of exon 14
GACTGGATTATGGAGCAGTGGGAGAAAAATTACTATATCAGTTCAATAGCTGGCGCAGTTAATGGAAGTTCCTTGGTTGTCATGTCCAAAGgtatataatatct-ataattttatgacctactcctccttcacatactattgatta-atttatttttgaaatgcctttgcaaaatctccttgctattttactt
|| |||||||||||||||||||| || || ||||| |||||| | |||||||| ||| | ||||| ||||||||||| |||||||| |||||| |    ||  | ||   | |||     |  |||| |  |  || || | |||| ||| || |   |||    |  |     ||| | |  |    | || 
GATTGGATTATGGAGCAGTGGGAAAATAACTACTACATCAGTGCCATAGCTGGTGCAATGAATGGGAGTTCCTTGGTGGTCATGTCAAAAGgtctgccctaattgatggctgtat--ttgaggcctcttatatttattagttattacattcatatgaaaaaaaattgagtggtgtctacatagttaaatgctc

upper sequence: GLYMA16G04580.1 (Glycine max), 5'ss of exon 14
lower sequence: GRMZM2G164265_T02 (Zea mays), 5'ss of exon 14
GACTGGATTATGGAGCAGTGGGAGAAAAATTACTATATCAGTTCAATAGCTGGCGCAGTTAATGGAAGTTCCTTGGTTGTCATGTCCAAAGgtat--ataatatctataattttatgacctactcctcc---ttcacatactattgattaatttatttttgaaatgcctttgcaaaatctccttgctattttactt
|||||||| ||||||||||||||||||| |||||| || |   |||| |||||  ||   ||||| ||||| ||||||||||||||||||||| |  ||  ||  | |  | ||||  |  || | | |   || ||   | |||   | |   |||||   | |  |  | |||||||    || |  | |    
GACTGGATAATGGAGCAGTGGGAGAAAAGTTACTACATAACAGCAATTGCTGGATCAACCAATGGGAGTTCATTGGTTGTCATGTCCAAAGgtctgaattttacttttcttattattgctcacacgtgcatattgaccctccattttctcacc-attttcccagtagcagtacaaaatcctaatgtttctct----

upper sequence: GLYMA16G04580.1 (Glycine max), 5'ss of exon 14
lower sequence: AT3G03940.1 (Arabidopsis thaliana), 5'ss of exon 14
GACTGGATTATGGAGCAGTGGGAGAAAAATTACTATATCAGTTCAATAGCTGGCGCAGTTAATGGAAGTTCCTTGGTTGTCATGTCCAAAGgtatataatatctataattttatgacctactcctccttcacatactattgattaatttatttttgaaatgcctttgcaaaatctccttgctattttactt---
|||||||| ||||| || ||||| || || |||||||||||||| |||||||| |||  ||||||||| || |||||||| ||| | ||||||   || |  |     | | ||||   |||   ||     |   |||||||| ||  |   |  ||     ||| |  | ||  |||  | |  | |     
GACTGGATCATGGAACAATGGGAAAAGAACTACTATATCAGTTCCATAGCTGGTGCAAATAATGGAAGCTCGTTGGTTGTTATGGCTAAAGgtcggtagtcac----gtctcatgata-actttgccaatgaac-ttattgattcataaagcatgaaagccgttttacttattccacttcatgtaatgcgatag

upper sequence: GLYMA16G04580.1 (Glycine max), 5'ss of exon 14
lower sequence: AT5G18190.1 (Arabidopsis thaliana), 5'ss of exon 14
GACTGGATTATGGAGCAGTGGGAGAAAAATTACTATATCAGTTCAATAGCTGGCGCAGTTAATGGAAGTTCCTTGGTTGTCATGTCCAAAGgtatataatatctataattttatg-acctactcctccttcacatactattgattaa---------tttatttttgaaatgcctttgcaaaat------ctccttgctattttactt------------------
|||||||||||||| || ||||| || || |||||||||||||| ||||||||  ||| ||| || |  || || ||||| ||||| ||||||   |  ||    || |  | || |  |  |  |    |||| ||  |||| ||            || |||    ||  |  |  || ||       || || ||| |||  |                   
GACTGGATTATGGAACAATGGGAAAAGAACTACTATATCAGTTCCATAGCTGGTTCAGATAACGGGAACTCATTAGTTGTTATGTCAAAAGgttggtgttaatggtagtaatctgcaaatttttatgtcacacaaacacttgactatagaaaatgtcgtactttcattataaccatataacatggagtcttctttactaattttgtgcttgttgtaaattggtag

upper sequence: GLYMA16G04580.1 (Glycine max), 5'ss of exon 14
lower sequence: Vv08s0007g07420.t01 (Vitis vinifera), 5'ss of exon 14
GACTGGATTATGGAGCAGTGGGAGAAAAATTACTATATCAGTTCAATAGCTGGCGCAGTTAATGGAAGTTCCTTGGTTGTCATGTCCAAAGgt---atataatatctataattttatgacctactcctccttcacatactattgattaatttatttttgaaatgcctttgcaaaatctccttgctattttactt---
|| ||||||||||| |||||||| || |||||||| ||||| |||||||| || || | |||||| ||||| |||||||||||||| ||||||   ||   ||  | |||  ||  | |   | |  | ||     |     ||  |  ||  |||||    ||| | | ||   | ||  ||| |||| ||||   
GATTGGATTATGGAACAGTGGGAAAAGAATTACTACATCAGCTCAATAGCAGGGGCTGCTAATGGGAGTTCTTTGGTTGTCATGTCTAAAGgttggatcacattcccatagattgttaaggcatttattctctgtgtttgtctgtctgtttccttttt----tgcttct-cattttttctctgc-atttaactttct

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|58016025|gb|CX702767.1|CX702767
EST:     TTCAATAGCTGGCGCAGTTAATGGAAGTTCCTTGGTTGTCATGTCCAAAG                         GAACTCCTTACACGCAGCAGTCCTACAAAGTGAGTGAATCATTTCCTTTCA
genomic: TTCAATAGCTGGCGCAGTTAATGGAAGTTCCTTGGTTGTCATGTCCAAAGgtatataata ... tactttatagGAACTCCTTACACGCAGCAGTCCTACAAAGTGAGTGAATCATTTCCTTTCA
EST: gi|254328402|gb|GR835367.1|GR835367
EST:     AATAGCTGGCGCAGTTAATGGAAGTTCCTTGGTTGTCATGTCCAAAG                         GAACTCCTTACACGCAGCAGTCCTACAAAGTGAGTGAATCATTTCCTTTCA
genomic: AATAGCTGGCGCAGTTAATGGAAGTTCCTTGGTTGTCATGTCCAAAGgtatataata ... tactttatagGAACTCCTTACACGCAGCAGTCCTACAAAGTGAGTGAATCATTTCCTTTCA
EST: gi|15664402|gb|BI701773.1|BI701773
EST:     TTCAATAGCTGGCGCAGTTAATGGAAGTTCCTTGGTTGTCATGTCCAAAG                         GAACTCCTTAC
genomic: TTCAATAGCTGGCGCAGTTAATGGAAGTTCCTTGGTTGTCATGTCCAAAGgtatataata ... tactttatagGAACTCCTTAC
EST: gi|58019124|gb|CX705866.1|CX705866
EST:     TTCAATAGCTGGCGCAGTTAATGGAAGTTCCTTGGTTGTCATGTCCAAAG                         GAACTCCTTACACGCAGCAGTCCTACAAAGTGAGTGAATCATTTCCTTTCA
genomic: TTCAATAGCTGGCGCAGTTAATGGAAGTTCCTTGGTTGTCATGTCCAAAGgtatataata ... tactttatagGAACTCCTTACACGCAGCAGTCCTACAAAGTGAGTGAATCATTTCCTTTCA
EST: gi|207841925|gb|GD815881.1|GD815881
EST:     TTCAATAGCTGGCGCAGTTAATGGAAGTTCCTTGGTTGTCATGTCCAAAG                         GAACTCCTTACACGCA
genomic: TTCAATAGCTGGCGCAGTTAATGGAAGTTCCTTGGTTGTCATGTCCAAAGgtatataata ... tactttatagGAACTCCTTACACGCA
EST: gi|24135575|gb|BU926085.1|BU926085
EST:     TTCAATAGCTGGCGCAGTTAATGGAAGTTCCTTGGTTGTCATGTCCAAAG                         GAACTCCTTACACGCAGCAGTCCTACAAAGTGAGTGAATCATTTCCTTTCA
genomic: TTCAATAGCTGGCGCAGTTAATGGAAGTTCCTTGGTTGTCATGTCCAAAGgtatataata ... tactttatagGAACTCCTTACACGCAGCAGTCCTACAAAGTGAGTGAATCATTTCCTTTCA
EST: gi|193461096|gb|FK427193.1|FK427193
EST:     TTGTCATGTCCAAAG                         GAACTCCTTACACGCAGCAGTCCTACAAAGTGAGTGAATCATTTCCTTTCA
genomic: TTGTCATGTCCAAAGgtatataata ... tactttatagGAACTCCTTACACGCAGCAGTCCTACAAAGTGAGTGAATCATTTCCTTTCA
EST: gi|57574923|gb|CX547898.1|CX547898
EST:     TTCAATAGCTGGCGCAGTTAATGGAAGTTCCTTGGTTGTCATGTCCAAAG                         GAACTCCTTACACGCAGCAGTCCTACAAAGTGAGTGAATCATTTCCTTTCA
genomic: TTCAATAGCTGGCGCAGTTAATGGAAGTTCCTTGGTTGTCATGTCCAAAGgtatataata ... tactttatagGAACTCCTTACACGCAGCAGTCCTACAAAGTGAGTGAATCATTTCCTTTCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GACTGGATTATGGAGCAGTGGGAGAAAAATTACTATATCAGTTCAATAGCTGGCGCAGTTAATGGAAGTTCCTTGGTTGTCATGTCCAAAGgtatataatatctataattttatgacctactcctccttcacatactattgattaatttatttttgaaatgcctttgcaaaatctccttgctattttactt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctcctcc