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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTCATTCGATCCGTGAGGCAGCTGCTAACAATTTGAAGCGCCTAGCTGAAGAATTTGGTCCTGAGTGGGCTATGCAACACATAATTCCACAGgttcatgtcttggcttaagaattattatttcagtattatacactatgcctatatgaatgtgtttgtgttggtatgtttctgtatcttctacttgaatttc...

Basic information

species Glycine max
transcript GLYMA02G10790.1
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G10790.2 (Glycine max), 5'ss of exon 10
lower sequence: LOC_Os09g07510.1 (Oryza sativa), 5'ss of exon 10
GTTCATTCGATCCGTGAGGCAGCTGCTAACAATTTGAAGCGCCTAGCTGAAGAATTTGGTCCTGAGTGGGCTATGCAACACATAATTCCACAGgttcatgtcttggcttaagaattattatttcagtatt---atacactatgcctatatg-aatgtgtttgtgttggtatgtttctgtatcttctacttgaatttc
||    || ||| | || || ||||| ||||| ||||||||||||||||| || |||||||| || ||||| ||||| || ||||| || ||||||  |         |  |||   |  |  |||||||   ||     |   |  || | ||  ||  | | |||  ||||  || ||         || |    
GTCTTCTCAATCAGAGATGCTGCTGCAAACAACTTGAAGCGCCTAGCTGAGGAGTTTGGTCCAGAATGGGCGATGCAGCATATAATCCCTCAGgttatttataaaatatttgaaccctagt--cagtatttgcatttgtgaaatccttaagcaagctgacttttttgtaatgtagctctactggaagtctggaac--

upper sequence: GLYMA02G10790.2 (Glycine max), 5'ss of exon 10
lower sequence: GRMZM2G164352_T03 (Zea mays), 5'ss of exon 10
GTTCATTCGATCCGTGAGGCAGCTGCTAACAATTTGAAGCGCCTAGCTGAAGAATTTGGTCCTGAGTGGGCTATGCAACACATAATTCCACAGgtt---catgtcttggcttaagaattattatttcagtattatacactatgcctatatgaatgtgtttgtgttggtatgtttctgtatcttctacttgaatttc
||   ||| ||| | || || || |||||||| ||||||||||| || ||||| |||||||| |||||||| ||||| || ||||| || ||||||    || |  |  || || |  |  ||||||       |   || ||| || ||  |    ||  || |  | | ||| |  | |     ||  ||  | 
GTCTTTTCAATCAGAGATGCTGCCGCTAACAACTTGAAGCGCCTTGCAGAAGAGTTTGGTCCAGAGTGGGCAATGCAGCATATAATCCCTCAGgttatttatatactatctcaataccttatatttcctacaactgtgctgtgcata-atataatccttgatgctaatttatttat-caacagtagctacaacat-

upper sequence: GLYMA02G10790.2 (Glycine max), 5'ss of exon 10
lower sequence: GRMZM2G102858_T01 (Zea mays), 5'ss of exon 10
GTTCATTCGATCCGTGAGGCAGCTGCTAACAATTTGAAGCGCCTAGCTGAAGAATTTGGTCCTGAGTGGGCTATGCAACACATAATTCCACAGgttcatgtcttggct-taagaattattatttcagtattatacactatgcctatatgaatgtgtttgtgttggtatgttt--ctgtatcttctacttgaatttc
|||   |||||| | || || | ||| || ||||| |||||  |  | || |||||||| ||||||||||| |||||||| |||||||| ||||||    |     || | | || | | ||  || |  | | |  ||    | |     |||  ||  | |   |   ||  ||  | |   ||| ||| |   
GTTTTCTCGATCAGAGATGCTGGTGCCAATAATTTAAAGCGTTTGACAGAGGAATTTGGCCCTGAGTGGGCGATGCAACATATAATTCCTCAGgttagctttagtactgtgaaaaatgtaatagcatttat-tgcgataaatttcttattttgttcttaagctttaaaccttgacttgagcaaatacatgagtc--

upper sequence: GLYMA02G10790.2 (Glycine max), 5'ss of exon 10
lower sequence: GRMZM2G122135_T02 (Zea mays), 5'ss of exon 10
GTTCATTCGATCCGTGAGGCAGCTGCTAACAATTTGAAGCGCCTAGCTGAAGAATTTGGTCCTGAGTGGGCTATGCAACACATAATTCCACAGgttcatgtcttggcttaagaattattatttcagtattatacactatgccta-tatgaatgtgtttgtgttggtatgtttctgtatcttctacttgaatttc
||    || ||| | || || || || ||||| ||||||||||| || ||||| || ||||| |||||||| ||||| || |||||||| |||||| || | |   ||     | ||   | |   |  || | ||| ||| || ||| |   |  |  |    | |   |  | | | |||            
GTCTTCTCAATCAGAGATGCTGCCGCCAACAACTTGAAGCGCCTTGCGGAAGAGTTCGGTCCAGAGTGGGCAATGCAGCATATAATTCCTCAGgtt-atttatctactatgtcaataccttgtatttcctaca-actgtgcataatataatccttctatttcctgcaacctgttctgttttcccag--------

upper sequence: GLYMA02G10790.2 (Glycine max), 5'ss of exon 10
lower sequence: AT1G13320.1 (Arabidopsis thaliana), 5'ss of exon 10
GTTCATTCGATCCGTGAGGCAGCTGCTAACAATTTGAAGCGCCTAGCTGAAGAATTTGGTCCTGAGTGGGCTATGCAACACATAATTCCACAGgttcatgtcttgg-cttaagaat-tattatttcagtattatacactatgcctatatgaatgtgtttgtgttggtatgtttctgtatcttctacttgaatttc
||||| || |||||||| || ||||| |||||| ||||||| || |||||||| ||||||||||| ||||| ||||| || ||| |||| ||||||  |||      |||||| || || ||| |    | |  | |    || | |  |    || || |    |||| |||   | |                
GTTCACTCAATCCGTGAAGCTGCTGCAAACAATCTGAAGCGTCTTGCTGAAGAGTTTGGTCCTGAATGGGCAATGCAGCATATAGTTCCTCAGgtttgtgtagaaatcttaagcatatagtatgttttcaattcaaatcgagcattttagctattggttattggagtatatttacttgttcag------------

upper sequence: GLYMA02G10790.2 (Glycine max), 5'ss of exon 10
lower sequence: AT3G25800.1 (Arabidopsis thaliana), 5'ss of exon 9
GTTCATTCGATCCGTGAGGCAGCTGCTAACAATTTGAAGCGCCTAGCTGAAGAATTTGGTCCTGAGTGGGCTATGCAACACATAATTCCACAGgttcatgtcttggcttaagaattattatttcagtattatacactatgcctatatgaatgtgtttgtgttggtatgtttctgtatcttctacttgaatttc
||||| || ||||| || || |||||||||||| | ||||| || ||||| |||||||||||||| ||||| |||||||| ||| |||| ||||||  |||||       |||||| |||   |  ||  | |  |  || |||| |     |||| |||||  |  ||  || | || |  |   | |    
GTTCACTCAATCCGCGATGCTGCTGCTAACAATCTCAAGCGGCTTGCTGAGGAATTTGGTCCTGAATGGGCAATGCAACATATAGTTCCTCAGgtt--tgtct-------agaatttttacaactttagaaaagtcagtgtctatct-----tgttagtgttaattagtcgctat-tcattaatccgcag---

upper sequence: GLYMA02G10790.2 (Glycine max), 5'ss of exon 10
lower sequence: Vv01s0011g03280.t01 (Vitis vinifera), 5'ss of exon 9
GTTCATTCGATCCGTGAGGCAGCTGCTAACAATTTGAAGCGCCTAGCTGAAGAATTTGGTCCTGAGTGGGCTATGCAACACATAATTCCACAGgttcatgtcttggct-taagaattattatttcagtattatacactatgcctatatgaatgtgtttgtgttggtatgtttctgtatcttctacttgaatttc----
||| | || || ||||| || ||||||||||| || |||||||| || ||||||||||||||||| ||||| ||||| ||| ||||||||||||||  | |  ||| | | | |||||  ||| |  |||||    || ||   |    | ||  | || |||   |  | ||    | ||  | ||   |||     
GTTTACTCCATTCGTGATGCTGCTGCTAACAACTTAAAGCGCCTTGCAGAAGAATTTGGTCCTGACTGGGCAATGCAGCACTTAATTCCACAGgtttgtctagtggttgtgacaatta--attgc--tattagtggct-tgtaaaggatagtggatatgagtttcaaattctcatcttatttcattttggtttgtctc

upper sequence: GLYMA02G10790.2 (Glycine max), 5'ss of exon 10
lower sequence: PP1S214_34V6.1 (Physcomitrella patens), 5'ss of exon 9
GTTCATTCGATCCGTGAGGCAGCTGCTAACAATTTGAAGCGCCTAGCTGAAGAATTTGGTCCTGAGTGGGCTATGCAACACATAATTCCACAGgttcatgtctt----ggct-taagaattattatttcagtattatacactatgcctatatgaatgtgttt---gtgttggtatgtttctgtatcttctac-ttgaatttc-----------------------------------------------------------
||  | || ||||| ||||||||||| |||||| | ||||| || || ||||| |||||||||||||||||  |||| ||||| ||||||||||| |  |  ||    |  | ||   |  | ||| |  |||        ||      |  |  | |   |   |    ||  ||| | | | ||   | | || ||  |                                                            
GTGTACTCTATCCGAGAGGCAGCTGCCAACAATCTCAAGCGTCTTGCCGAAGAGTTTGGTCCTGAGTGGGCATTGCAGCACATCATTCCACAGgtactcgctttataagattgtagtgaggactatcttggtaacgagtg-tagaatcgtgggcttttacatacagcacaggcttgtctatctgtcagatccgttaaacatgagataactttcattcaattcctacgttattgttttctgatgaattggtgggacttgcag

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|15202124|gb|BI425235.1|BI425235
EST:     TAGCTGAAGAATTTGGTCCTGAGTGGGCTATGCAACACATAATTCCACAG                         GTTTTGGAGATGATTAGCAATCCTCACTATTTGTATCGAATGACCATACTC
genomic: TAGCTGAAGAATTTGGTCCTGAGTGGGCTATGCAACACATAATTCCACAGgttcatgtct ... catgaaacagGTTTTGGAGATGATTAGCAATCCTCACTATTTGTATCGAATGACCATACTC
EST: gi|58015550|gb|CX702292.1|CX702292
EST:     TAGCTGAAGAATTTGGTCNTGAGTGGGCTATGCAACACATAATTCCACAG                         GTTTTGGAGATGATTAGCAATCCTCACTATTTGTATCGAATGACCATACTC
genomic: TAGCTGAAGAATTTGGTCCTGAGTGGGCTATGCAACACATAATTCCACAGgttcatgtct ... catgaaacagGTTTTGGAGATGATTAGCAATCCTCACTATTTGTATCGAATGACCATACTC
EST: gi|6666156|gb|AW277615.1|AW277615
EST:     TAGCTGAAGAATTTGGTCCTGAGTGGGCTATGCAACACATAATTCCACAG                         GTTTTGGAGATGATTAGCAATCCTCACTATTTGTATCGAATGACCATACTC
genomic: TAGCTGAAGAATTTGGTCCTGAGTGGGCTATGCAACACATAATTCCACAGgttcatgtct ... catgaaacagGTTTTGGAGATGATTAGCAATCCTCACTATTTGTATCGAATGACCATACTC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTCATTCGATCCGTGAGGCAGCTGCTAACAATTTGAAGCGCCTAGCTGAAGAATTTGGTCCTGAGTGGGCTATGCAACACATAATTCCACAGgttcatgtcttggcttaagaattattatttcagtattatacactatgcctatatgaatgtgtttgtgttggtatgtttctgtatcttctacttgaatttc

- - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - -  TGAAGA