Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   		14  
 5'  3'   		15  
 5'  3'   		16  
 5'  3'   		17  
 5'  3'   		18  
 5'  3'   		19  
 5'  3'   		20  
 5'  3'   
21  
 5'  3'   		22  
 5'  3'   		23  
 5'  3'   		24  
 5'  3'   		25  
 5'  3'   		26  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGGTCTGCGTACAAAAGATAAAGAGCGTGTACTTGTTCTTGCTGCTACAAACAGGCCTTTTGATCTTGATGAGGCTGTTATTAGGAGGCTTCCTCGACGgtgagcatgttatgtttaatgttaacttgtattttcatgttttacagatgacatctattctaatgcatggtctgacttcattttttttttgtag

Basic information

species Glycine max
transcript GLYMA10G02400.1
intron # 23
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G02400.1 (Glycine max), 5'ss of exon 23
lower sequence: LOC_Os03g22420.1 (Oryza sativa), 5'ss of exon 24
ATGGTCTGCGTACAAAAGATAAAGAGCGTGTACTTGTTCTTGCTGCTACAAACAGGCCTTTTGATCTTGATGAGGCTGTTATTAGGAGGCTTCCTCGACGgtgagcatgttatgtttaatgttaacttgtattttca--tgttttacagatgacatctattcta-atgcatggtctgacttcattttttttttgtag--------------
|||||||  | ||||||||||||||||||||| | || |||||||| || || ||||| ||||| ||||||||||||||| |||||||||||||| | ||||||| ||  ||| ||| || | |  ||    ||| |  |||  | |  ||   ||   || || ||   ||   |||||     | | |||||                 
ATGGTCTAAGAACAAAAGATAAAGAGCGTGTATTAGTACTTGCTGCAACTAATAGGCCATTTGACCTTGATGAGGCTGTTGTTAGGAGGCTTCCTAGGCGgtgagtatcatatttttcat-tcattttaagatttgaactgtggtgctaattttatgatttttagataattgacttgactatgcatgtgttttggtatatgtattgcttag

upper sequence: GLYMA10G02400.1 (Glycine max), 5'ss of exon 23
lower sequence: LOC_Os11g43970.1 (Oryza sativa), 5'ss of exon 24
ATGGTCTGCGTACAAAAGATAAAGAGCGTGTACTTGTTCTTGCTGCTACAAACAGGCCTTTTGATCTTGATGAGGCTGTTATTAGGAGGCTTCCTCGACGgtgagcatgttatgtttaatgttaacttgtattttcatgttttacagatgacatctattc-taatgcatggtctgacttcattttttttttgtag
||||  | || || ||||||||||| |||||||| ||||||| ||| ||||| |||||||| || || ||||||||||| ||||||||| | || ||  |||||      ||   ||  ||||     |  ||   ||  |  | |  ||   | | ||  |     |   | ||        ||  |  |||||
ATGGATTACGCACTAAAGATAAAGAACGTGTACTGGTTCTTGGTGCCACAAATAGGCCTTTCGACCTGGATGAGGCTGTCATTAGGAGGTTCCCGCGCAGgtgacagctataaccttg-tgttg----gggttgggataatgaaaaattgctgtttgttgatttctaaccatttggtcgttaattactactgtag

upper sequence: GLYMA10G02400.1 (Glycine max), 5'ss of exon 23
lower sequence: LOC_Os07g47530.1 (Oryza sativa), 5'ss of exon 24
ATGGTCTGCGTACAAAAGATAAAGAGCGTGTACTTGTTCTTGCTGCTACAAACAGGCCTTTTGATCTTGATGAGGCTGTTATTAGGAGGCTTCCTCGACGgtgagcatgttatgtttaatgttaacttgtattttcatgttttacagatgacatctattctaatgcatggtctgacttcattttttttttgtag
|||||||| | |||||||||||||| || ||| | || |||||||| || || || || |||||||||||||| |||||| |||||||||| ||  |  ||| |   | ||   |  |  | |    | |   ||    ||||||| |||| ||         ||| ||  ||||   ||| |   ||| |   
ATGGTCTGAGAACAAAAGATAAAGAACGCGTATTAGTACTTGCTGCCACCAATAGACCATTTGATCTTGATGAAGCTGTTGTTAGGAGGCTCCCCAGGAGgtaactttttt---tacatcgctgtggtattccttttatttttaca-atgaaatgctaatggttgcttg-cctgatcacatatcaatttag---

upper sequence: GLYMA10G02400.1 (Glycine max), 5'ss of exon 23
lower sequence: GRMZM2G042074_T02 (Zea mays), 5'ss of exon 19
ATGGTCTGCGTACAAAAGATAAAGAGCGTGTACTTGTTCTTGCTGCTACAAACAGGCCTTTTGATCTTGATGAGGCTGTTATTAGGAGGCTTCCTCGACGgtgagcatgttatgtttaatgttaacttgtattttcatgttttacagatgacatctattctaatgcatggtctgacttcattttttttttgtag
|||||||| | ||||| || ||||| |||||| | || |||||||| || |||||||| ||||||||||||||||||||||||||| |||||||  |  |||||          |||| ||||   || ||   | ||     |||  || ||  || | || ||            |  | | | || | |||
ATGGTCTGAGAACAAAGGAGAAAGAACGTGTATTAGTACTTGCTGCAACTAACAGGCCATTTGATCTTGATGAGGCTGTTATTAGGCGGCTTCCAAGGAGgtga----------tttattgtttgtttatagcctaatacg--acatctgtcaa-tagtttattg---acctcagtcttgtgtgtgttctctag

upper sequence: GLYMA10G02400.1 (Glycine max), 5'ss of exon 23
lower sequence: GRMZM2G126453_T02 (Zea mays), 5'ss of exon 9
ATGGTCTGCGTACAAAAGATAAAGAGCGTGTACTTGTTCTTGCTGCTACAAACAGGCCTTTTGATCTTGATGAGGCTGTTATTAGGAGGCTTCCTCGACGgtgagcat-gttatgtttaatgttaacttgtattttcatgttttacagatgacatctattctaatg---catggtc-tgacttcattttttttttgtag----------------------------------------------
||||  |||| || |||||||| |||||||| |||||||||| ||||||||| ||||||||||| || || |||||||| ||||||||| | || ||  ||| |   | |||   || | ||  |   || |||  |  ||| || |  ||   | |  |    ||   |||| |  |    || ||  ||||  ||||                                              
ATGGGTTGCGCACTAAAGATAAGGAGCGTGTGCTTGTTCTTGGTGCTACAAATAGGCCTTTTGACCTCGACGAGGCTGTGATTAGGAGGTTCCCCCGCAGgtaaatgttgtttcattcagtggga--ctggattacccagttgtataactgtagttttgttcggtgggccatgattatctaatcgttgcttttgggtagcaatagtttggttccatattcatcaccatcttactcattgtttcag

upper sequence: GLYMA10G02400.1 (Glycine max), 5'ss of exon 23
lower sequence: GRMZM2G370521_T01 (Zea mays), 5'ss of exon 2
ATGGTCTGCGTACAAAAGATAAAGAGCGTGTACTTGTTCTTGCTGCTACAAACAGGCCTTTTGATCTTGATGAGGCTGTTATTAGGAGGCTTCCTCGACGgtgagcatgttatgtttaatgttaacttgtattttcatgttttacagatgacatctattctaatgcatggtctgacttcattttttttttgtag
|||||||| | ||||  || ||||| |||||| | || |||||||| || |||||||| ||||||||||||||||||||| ||||| |||||||  |  |||||   | |   ||||  |  || | |       ||| | | |  | |    |    ||      ||||    |  | |||| |||       
ATGGTCTGAGAACAAGGGAGAAAGAACGTGTATTAGTACTTGCTGCAACTAACAGGCCATTTGATCTTGATGAGGCTGTTGTTAGGCGGCTTCCAAGGAGgtga---tttatcgtttgtttatagcctaatacagcatctgtcaatggttttttgacctcagtcttatggggcaa--taatttctttag-----

upper sequence: GLYMA10G02400.1 (Glycine max), 5'ss of exon 23
lower sequence: GRMZM2G168228_T01 (Zea mays), 5'ss of exon 3
ATGGTCTGCGTACAAAAGATAAAGAGCGTGTACTTGTTCTTGCTGCTACAAACAGGCCTTTTGATCTTGATGAGGCTGTTATTAGGAGGCTTCCTCGACGgtgagcatgttatgtttaatgttaacttgtattttcatgttttacagatgacatctattctaatgcatggtctgacttcattttttttttgtag
|||||||| | ||||  || ||||| |||||| | || |||||||| || |||||||| ||||||||||||||||||||| ||||| |||||||  |  |||||   | |   ||||  |  || | |       ||| | | |  | |    |    ||      ||||    |  | |||| |||       
ATGGTCTGAGAACAAGGGAGAAAGAACGTGTATTAGTACTTGCTGCAACTAACAGGCCATTTGATCTTGATGAGGCTGTTGTTAGGCGGCTTCCAAGGAGgtga---tttatcgtttgtttatagcctaatacaacatctgtcaatggttttttgacctcagtcttatggggcaa--tgatttctttag-----

upper sequence: GLYMA10G02400.1 (Glycine max), 5'ss of exon 23
lower sequence: GRMZM2G409190_T01 (Zea mays), 5'ss of exon 2
ATGGTCTGCGTACAAAAGATAAAGAGCGTGTACTTGTTCTTGCTGCTACAAACAGGCCTTTTGATCTTGATGAGGCTGTTATTAGGAGGCTTCCTCGACGgtgagcatgttatgtttaatgttaacttgtattttcatgttttacagatgacatctattctaatgcatggtctgacttcattttttttttgtag
|||||||| | ||||  || ||||| |||||| | || |||||||| || || ||||| ||||||||||||||||||||| ||||| |||||||  |  |||||   | |   ||||  |  || | |  | |   |  | |  ||   |   | |   || | |  |  |  | |   | ||| |||      
ATGGTCTGAGAACAAGGGAGAAAGAACGTGTATTAGTACTTGCTGCAACTAATAGGCCATTTGATCTTGATGAGGCTGTTGTTAGGCGGCTTCCAAGGAGgtga---tttatcgtttgtttatagcct--aatacaacatctgtcaatggttttttgacctca-gtcttatggggcaataatttctttag----

upper sequence: GLYMA10G02400.1 (Glycine max), 5'ss of exon 23
lower sequence: GRMZM2G417650_T01 (Zea mays), 5'ss of exon 2
ATGGTCTGCGTACAAAAGATAAAGAGCGTGTACTTGTTCTTGCTGCTACAAACAGGCCTTTTGATCTTGATGAGGCTGTTATTAGGAGGCTTCCTCGACGgtgagcatgttatgtttaatgttaacttgtattttcatgttttacagatgacatctattctaatgcatggtctgacttcattttttttttgtag
|||||||  | ||||  || ||||| |||||| | || |||||||| || |||| ||| ||||||||||||||||||||| ||||| |||||||  |  |||||   | |   ||||  |  || | |       ||| | | |  | |    |    ||      ||||    |  | |||| |||       
ATGGTCTAAGAACAAGGGAGAAAGAACGTGTATTAGTACTTGCTGCAACTAACAAGCCATTTGATCTTGATGAGGCTGTTGTTAGGCGGCTTCCAAGGAGgtga---tttatcgtttgtttatagcctaatacagcatctgtcaatggttttttgacctcagtcttatggggcaa--taatttctttag-----

upper sequence: GLYMA10G02400.1 (Glycine max), 5'ss of exon 23
lower sequence: GRMZM2G157621_T03 (Zea mays), 5'ss of exon 24
ATGGTCTGCGTACAAAAGATAAAGAGCGTGTACTTGTTCTTGCTGCTACAAACAGGCCTTTTGATCTTGATGAGGCTGTTATTAGGAGGCTTCCTCGACGgtgagcatgttatgtttaatgttaacttgtattttcatgttttacagatgacatctattctaatgcatggtctgacttcattttttttttgtag
|||||||  | |||||||| ||||| ||||| || || |||||||| || || ||||| ||||||||||| ||||||||| | |||||||| ||  |  ||| |     ||    |   | || |      |||||   ||  |    ||||||   || |||   ||   | | |  ||  || | ||     
ATGGTCTTAGGACAAAAGACAAAGAACGTGTTCTGGTACTTGCTGCCACTAATAGGCCATTTGATCTTGACGAGGCTGTTGTCAGGAGGCTCCCCAGGAGgtaaa----ttgcactccgtatttatgctacttttc---ttccaactgtgacatg-gttataa---ataacccggccacaacttctcttcag--

upper sequence: GLYMA10G02400.1 (Glycine max), 5'ss of exon 23
lower sequence: GRMZM2G482077_T01 (Zea mays), 5'ss of exon 2
ATGGTCTGCGTACAAAAGATAAAGAGCGTGTACTTGTTCTTGCTGCTACAAACAGGCCTTTTGATCTTGATGAGGCTGTTATTAGGAGGCTTCCTCGACGgtgagcatgttatgtttaatgttaacttgtattttcatgttttacagatgacatctattctaatgcatggtctgacttcattttttttttgtag
||| |||| | ||||  || |||||  ||||| | || |||||||| || |||||||| |||||||||||||| | |||| ||||| |||||    |  |||||   | |   ||||  |  || | |  | |   |  | |  ||   |   | |   || | |  |  |  | |   | ||| |||      
ATGATCTGAGAACAAGGGAGAAAGAATGTGTATTAGTACTTGCTGCAACTAACAGGCCATTTGATCTTGATGATGTTGTTGTTAGGCGGCTTAGAAGGAGgtga---tttatcgtttgtttatagcct--aatacaacatctgtcaatggttttttgacctca-gtcttatggggcaataatttctttag----

upper sequence: GLYMA10G02400.1 (Glycine max), 5'ss of exon 23
lower sequence: Vv07s0005g00200.t01 (Vitis vinifera), 5'ss of exon 23
ATGGTCTGCGTACAAAAGATAAAGAGCGTGTACTTGTTCTTGCTGCTACAAACAGGCCTTTTGATCTTGATGAGGCTGTTATTAGGAGGCTTCCTCGACGgtgagcatgttatgtttaatgttaacttgtattttcatgttttacagatgacatctattctaatgcatggtctgacttcattttttttttgtag-----------
|||| || |||||||| |||||||| |||||| | || ||||| || || || ||||||||||| |||||||||||||||||||||||||| ||  |  ||| | |||  |||| ||| |  |  ||||  || |  ||   ||    |   |   |  | |    |     | | | | |  | | | |||             
ATGGCCTACGTACAAAGGATAAAGAACGTGTATTGGTACTTGCCGCCACCAATAGGCCTTTTGACCTTGATGAGGCTGTTATTAGGAGGCTACCCAGGAGgtaaacatcatatgatta-taatcccttgatttgttgtg---tatgagtattagtcaacccag-aaaaaccttaattccctactatgtatgttaactgccaacac

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|16279552|gb|BI943495.1|BI943495
EST:     AACAGGCCTTTTGATCTTGATGAGGCTGTTATTAGGAGGCTTCCTCGACG                         ATTGATGGTTAATTTGCCAGATGCTCCAAACAGAGAAAAAATTTTCAGAGT
genomic: AACAGGCCTTTTGATCTTGATGAGGCTGTTATTAGGAGGCTTCCTCGACGgtgagcatgt ... ttttttgtagATTGATGGTTAATTTGCCAGATGCTCCAAACAGAGAAAAAATTCTCAGAGT
EST: gi|24135420|gb|BU925930.1|BU925930
EST:     AACAGGCCTTTTGATCTTGATGAGGCTGTTATTAGGAGGCTTCCTCGACG                         ATTGATGGTTAATTTGCCAGATGCTCCAAACAGAGAAAAAATTCTCAGAGT
genomic: AACAGGCCTTTTGATCTTGATGAGGCTGTTATTAGGAGGCTTCCTCGACGgtgagcatgt ... ttttttgtagATTGATGGTTAATTTGCCAGATGCTCCAAACAGAGAAAAAATTCTCAGAGT
EST: gi|19347186|gb|BM892066.1|BM892066
EST:     AACAGGCCTTTTGATCTTGATGAGGCTGTTATTAGGAGGCTTCCTCGACG                         ATTGATGGTTAATTTGCCAGATGCTCCAAA
genomic: AACAGGCCTTTTGATCTTGATGAGGCTGTTATTAGGAGGCTTCCTCGACGgtgagcatgt ... ttttttgtagATTGATGGTTAATTTGCCAGATGCTCCAAA
EST: gi|58019392|gb|CX706134.1|CX706134
EST:     TGTTATTAGGAGGCTTCCTCGACG                         ATTGATGGTTAATTTGCCAGATGCTCCAAACAGAGAAAAAATTCTCAGAGT
genomic: TGTTATTAGGAGGCTTCCTCGACGgtgagcatgt ... ttttttgtagATTGATGGTTAATTTGCCAGATGCTCCAAACAGAGAAAAAATTCTCAGAGT
EST: gi|37994806|gb|CF806395.1|CF806395
EST:     AACAGGCCTTTTGATCTTGATGAGGCTGTTATTAGGAGGCTTCCTCGACG                         ATTGATGGTTAATTTGCCAGATGCTCCAAACAGAGAAAAAATTCTCAGAGT
genomic: AACAGGCCTTTTGATCTTGATGAGGCTGTTATTAGGAGGCTTCCTCGACGgtgagcatgt ... ttttttgtagATTGATGGTTAATTTGCCAGATGCTCCAAACAGAGAAAAAATTCTCAGAGT
EST: gi|15814532|gb|BI786807.1|BI786807
EST:     GCTTCCTCGACG                         ATTGATGGTTAATTTGCCAGATGCTCCAAACAGAGAAAAAATTCTCAGAGT
genomic: GCTTCCTCGACGgtgagcatgt ... ttttttgtagATTGATGGTTAATTTGCCAGATGCTCCAAACAGAGAAAAAATTCTCAGAGT
EST: gi|26057754|gb|CA800668.1|CA800668
EST:     AACAGGCCTTTTGATCTTGATGAGGCTGTTATTAGGAGGCTTCCTCGACG                         ATTGATGGTTAATTTGCCAGATGCTCCAAACAGAGAAAAAATTCTCAGAGT
genomic: AACAGGCCTTTTGATCTTGATGAGGCTGTTATTAGGAGGCTTCCTCGACGgtgagcatgt ... ttttttgtagATTGATGGTTAATTTGCCAGATGCTCCAAACAGAGAAAAAATTCTCAGAGT
EST: gi|192316471|gb|FK009296.1|FK009296
EST:     AACAGGCCTTTTGATCTTGATGAGGCTGTTATTAGGAGGCTTCCTCGACG                         ATTGATGGTTAATTTGCCAGATGCTCCAAACAGAGAAAAAATTCTCAGAGT
genomic: AACAGGCCTTTTGATCTTGATGAGGCTGTTATTAGGAGGCTTCCTCGACGgtgagcatgt ... ttttttgtagATTGATGGTTAATTTGCCAGATGCTCCAAACAGAGAAAAAATTCTCAGAGT
EST: gi|192312529|gb|FK005001.1|FK005001
EST:     AACAGGCCTTTTGATCTTGATGAGGCTGTTATTAGGAGGCTTCCTCGACG                         ATTGATGGTTAATTTGCCAGATGCTCCAAACAGAGAAAAAATTCTCAGAGT
genomic: AACAGGCCTTTTGATCTTGATGAGGCTGTTATTAGGAGGCTTCCTCGACGgtgagcatgt ... ttttttgtagATTGATGGTTAATTTGCCAGATGCTCCAAACAGAGAAAAAATTCTCAGAGT
EST: gi|20811998|gb|BQ296476.1|BQ296476
EST:     AACAGGCCTTTTGATCTTGATGAGGCTGTTATTAGGAGGCTTCCTCGACG                         ATT-ATGGTTAATTTGCCAGATGCTCCAAACAGAGAAAAAATTCTCAGAGT
genomic: AACAGGCCTTTTGATCTTGATGAGGCTGTTATTAGGAGGCTTCCTCGACGgtgagcatgt ... ttttttgtagATTGATGGTTAATTTGCCAGATGCTCCAAACAGAGAAAAAATTCTCAGAGT
EST: gi|192312514|gb|FK005000.1|FK005000
EST:     AACAGGCCTTTTGATCTTGATGAGGCTGTTATTAGGAGGCTTCCTCGACG                         ATTGATGGTTAATTTGCCAGATGCTCCAAACAGAGAAAAAATTCTCAGAGT
genomic: AACAGGCCTTTTGATCTTGATGAGGCTGTTATTAGGAGGCTTCCTCGACGgtgagcatgt ... ttttttgtagATTGATGGTTAATTTGCCAGATGCTCCAAACAGAGAAAAAATTCTCAGAGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATGGTCTGCGTACAAAAGATAAAGAGCGTGTACTTGTTCTTGCTGCTACAAACAGGCCTTTTGATCTTGATGAGGCTGTTATTAGGAGGCTTCCTCGACGgtgagcatgttatgtttaatgttaacttgtattttcatgttttacagatgacatctattctaatgcatggtctgacttcattttttttttgtag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT