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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACATTCAAGCGCAGGAATGGAGGTCGCAACAAACACGGCCGCGGCCATGTCAAATTCATCCGATGCTCCAACTGCGGAAAATGCTGCCCCAAGgttgtttttattattatttatttcactttcttccaccttcaaattttttgtgcgaagcatttcaattaattgaaaaaaataaaataataacag

Basic information

species Glycine max
transcript GLYMA14G38950.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA14G38950.1 (Glycine max), 5'ss of exon 2
lower sequence: LOC_Os05g39960.1 (Oryza sativa), 5'ss of exon 2
ACATTCAAGCGCAGGAATGGAGGTCGCAACAAACACGGCCGCGGCCATGTCAAATTCATCCGATGCTCCAACTGCGGAAAATGCTGCCCCAAGgtt-----gtttttattattattta----tttcactttcttccaccttcaaatt--ttttgtgcgaagcatttcaattaattgaaaaaaataaaataataacag-------------------
|| |||||||||||||| || || |||||||| || |||||||||||||| || | |||||| |||||||||||||  || |||||||||||||||      ||   ||| |  |  |    | | | | || | || | |   |||  | ||  |||||   |     ||           ||    |  |    |                   
ACCTTCAAGCGCAGGAACGGCGGCCGCAACAAGCATGGCCGCGGCCATGTGAAGTACATCCGCTGCTCCAACTGCGCCAAGTGCTGCCCCAAGgttcgcggattcagattctcttgcagatttgttattatcattcagcgtgttattactgttacgcgaaatctgcggtttcggcttggctgattcgttggttcttgggtcgtcgccttgtcgcag

upper sequence: GLYMA14G38950.1 (Glycine max), 5'ss of exon 2
lower sequence: LOC_Os05g39960.2 (Oryza sativa), 5'ss of exon 2
ACATTCAAGCGCAGGAATGGAGGTCGCAACAAACACGGCCGCGGCCATGTCAAATTCATCCGATGCTCCAACTGCGGAAAATGCTGCCCCAAGgtt-----gtttttattattattta----tttcactttcttccaccttcaaatt--ttttgtgcgaagcatttcaattaattgaaaaaaataaaataataacag-------------------------
|| |||||||||||||| || || |||||||| || |||||||||||||| || | |||||| |||||||||||||  || |||||||||||||||      ||   ||| |  |  |    | | | | || | || | |   |||  | ||  |||||   |     ||           ||    |  |    |                         
ACCTTCAAGCGCAGGAACGGCGGCCGCAACAAGCATGGCCGCGGCCATGTGAAGTACATCCGCTGCTCCAACTGCGCCAAGTGCTGCCCCAAGgttcgcggattcagattctcttgcagatttgttattatcattcagcgtgttattactgttacgcgaaatctgcggtttcggcttggctgattcgttggttcttgggtcgtcgccttgtcgcaggacaag

upper sequence: GLYMA14G38950.1 (Glycine max), 5'ss of exon 2
lower sequence: LOC_Os01g60790.1 (Oryza sativa), 5'ss of exon 2
ACATTCAAGCGCAGGAATGGAGGTCGCAACAAACACGGCCGCGGCCATGTCAAATTCATCCGATGCTCCAACTGCGGAAAATGCTGCCCCAAGgttgtttttattattatttatttcactttcttccacc-ttcaaattttttgtgcgaagcatttcaattaattgaaaaaaataaaataataacag-------
|| ||||||||| | ||||| || |||||||| ||||| |||||||| ||||| | |||||| |||||||||||||  || ||||||||||||||       |          |||  |  |||  |      |            |      | |   || |||    ||  |    |               
ACCTTCAAGCGCCGCAATGGCGGCCGCAACAAGCACGGTCGCGGCCACGTCAAGTACATCCGCTGCTCCAACTGCGCCAAGTGCTGCCCCAAGgtaaggcgaagcgaatccccttttgccctctctcgttgcgcgcgaggcacccactggatctctgtgttgatttgggaatctttgctttgggtgcgggacag

upper sequence: GLYMA14G38950.1 (Glycine max), 5'ss of exon 2
lower sequence: GRMZM5G899149_T01 (Zea mays), 5'ss of exon 2
ACATTCAAGCGCAGGAATGGAGGTCGCAACAAACACGGCCGCGGCCATGTCAAATTCATCCGATGCTCCAACTGCGGAAAATGCTGCCCCAAGgttgtttttattattatttatttcactttcttccaccttcaaattttttgtgcgaagcatttcaattaattgaaaaaaataaaataataacag---------------
|| |||||||| |||||||| || |||||||| ||||| |||||||| ||||| | |||||| |||||||||||||  || ||||||||||||||     ||    |    ||   | |  |  |      |  |     |    ||   | ||    |||  || |   ||     || |  |                 
ACGTTCAAGCGGAGGAATGGCGGACGCAACAAGCACGGGCGCGGCCACGTCAAGTACATCCGCTGCTCCAACTGCGCCAAGTGCTGCCCCAAGgtaacacttcccttcccatagagcgcggttgtttgtgatgga-----tgaatcgggccgtt---gttagctgcagggaaagtggtattctcgagtctagacctctcgt

upper sequence: GLYMA14G38950.1 (Glycine max), 5'ss of exon 2
lower sequence: GRMZM2G129015_T02 (Zea mays), 5'ss of exon 2
ACATTCAAGCGCAGGAATGGAGGTCGCAACAAACACGGCCGCGGCCATGTCAAATTCATCCGATGCTCCAACTGCGGAAAATGCTGCCCCAAGgttgtttttattattatttatttcactttcttccaccttcaaattttttgtgcgaagcatttca--attaattg-aaaaaaataaaataat-aacag------------
|| |||||||| ||||| || || |||||||| ||||| |||||||| ||||| | ||| || |||||||||||||  || ||||| || ||||| |            |||  ||| ||||   ||   ||    | |  ||   ||| |    |    |||  || ||    ||    |  |   |              
ACGTTCAAGCGGAGGAACGGCGGACGCAACAAGCACGGGCGCGGCCACGTCAAGTACATACGCTGCTCCAACTGCGCCAAGTGCTGTCCAAAGgtagcc---------gtttccttccctttggaccgtatttgtttgtgatggatgaatcgagccgttgttagctgcaagggcatggcctcgttggccacattgtttagat

upper sequence: GLYMA14G38950.1 (Glycine max), 5'ss of exon 2
lower sequence: GRMZM5G827266_T03 (Zea mays), 5'ss of exon 2
ACATTCAAGCGCAGGAATGGAGGTCGCAACAAACACGGCCGCGGCCATGTCAAATTCATCCGATGCTCCAACTGCGGAAAATGCTGCCCCAAGgttgtttttattattatttatttcactttcttccaccttcaaattttttgtgcgaagcatttcaattaattgaaaaaaataaaataataacag
|| ||||||||| | || || || |||||||| || |||||||| || ||||| | |||||| ||||| |||||||  || |||||||||||||| |     ||   |    | |   |||||||   |  |  | ||    ||| |  | | | |  || ||    |        | |       
ACCTTCAAGCGCCGCAACGGCGGCCGCAACAAGCATGGCCGCGGTCACGTCAAGTACATCCGGTGCTCAAACTGCGCCAAGTGCTGCCCCAAGgt-gaggagatgcctccacagtcgcctttctttttctcttcatttacccgtgtggtggagtcc--ttgatcttgatgctcgttacag------

upper sequence: GLYMA14G38950.1 (Glycine max), 5'ss of exon 2
lower sequence: AT2G40590.1 (Arabidopsis thaliana), 5'ss of exon 2
ACATTCAAGCGCAGGAATGGAGGTCGCAACAAACACGGCCGCGGCCATGTCAAATTCATCCGATGCTCCAACTGCGGAAAATGCTGCCCCAAGgttgtttttattattatttatttcactttcttccaccttcaaattttttgtgcgaagcatttcaattaa--ttgaaaaaaataaaataataacag----
|| |||||||| ||||| || ||  | ||||| |||  | | || || |||||    ||| |||||||||||||||| ||||||||||| |||||  | | |       | | ||   |  ||   ||   || | |   |  |  |  | ||||  ||||    |        ||| ||||     |    
ACTTTCAAGCGAAGGAACGGTGGGAGGAACAAGCACAACAGAGGACACGTCAACCCAATCAGATGCTCCAACTGCGGCAAATGCTGCCCTAAGgtactctcttcctccttctcttctccaatcaatcaatctccagtaactcctatgtgg-attttgattagatcttgtggtggtaatataaatttggatag

upper sequence: GLYMA14G38950.1 (Glycine max), 5'ss of exon 2
lower sequence: Vv06s0004g07940.t01 (Vitis vinifera), 5'ss of exon 2
ACATTCAAGCGCAGGAATGGAGGTCGCAACAAACACGGCCGCGGCCATGTCAAATTCATCCGATGCTCCAACTGCGGAAAATGCTGCCCCAAGgttgtttttattattatttatttcactttcttccaccttcaaattttttgtg--cgaagcatttcaattaattgaaaaaaataaaataataacag------
|| |||||||| |||||||| ||||||||||| |||||||||||||| ||||| ||||| || ||||||||||| || ||||||||||| |||||  ||||| || |  ||   |  | |||| |  |  |||     ||| |||  |||   || || || ||    |  ||| ||||   | |         
ACGTTCAAGCGAAGGAATGGTGGTCGCAACAAGCACGGCCGCGGCCACGTCAAGTTCATTCGCTGCTCCAACTGTGGCAAATGCTGCCCTAAGgtactttttcttttgcttgcctcaattttcctttattttctttcgtttggtggccgagaaatatccat-aaccataggaaagaaaactttgaatctttttt

upper sequence: GLYMA14G38950.1 (Glycine max), 5'ss of exon 2
lower sequence: Vv13s0067g02700.t01 (Vitis vinifera), 5'ss of exon 3
ACATTCAAGCGCAGGAATGGAGGTCGCAACAAACACGGCCGCGGCCATGTCAAATTCATCCGATGCTCCAACTGCGGAAAATGCTGCCCCAAGgttgt-ttttattattattt--atttcactttcttccaccttcaaattttttgtgcgaagcatttcaattaattgaaaaaaataaaataataacag
|| ||||||||||| || || || |||||||| |||||||| || |||||||| |||||||| ||||| |||||||||||||||||||| |||||     |  |||  ||||   ||||     | ||  |   |||||   |  ||  |  | |||        ||   ||   |   || |      
ACGTTCAAGCGCAGAAACGGCGGCCGCAACAAGCACGGCCGTGGACATGTCAAGTTCATCCGCTGCTCAAACTGCGGAAAATGCTGCCCAAAGgtctcgctccatttgtattctgatttagtggttttgta---tcaaagcatcagta-gttgaattggtgcgtgtttggaattgtgtgatcag-----

upper sequence: GLYMA14G38950.1 (Glycine max), 5'ss of exon 2
lower sequence: EFJ33618 (Selaginella moellendorffii), 5'ss of exon 1
---ACATTCAAGCGCAGGAATGGAGGTCGCAACAAACACGGCCGCGGCCATGTCAAATTCATCCGATGCTCCAACTGCGGAAAATGCTGCCCCAAGgttgtttttattattatttatttcactttcttccaccttcaaattttttgtgcgaagcatttcaattaattgaaaaaaataaaataataacag
   ||  |||||||  ||||||| || |||||||| |||||||||||||||||| |    ||||| |||||||| || ||    |||  ||||||||    | | |    ||  | | ||  |  |  |     | | ||||    | |                                        
ATGACTGTCAAGCGGCGGAATGGCGGCCGCAACAAGCACGGCCGCGGCCATGTCGATCCAATCCGGTGCTCCAATTGTGGGCGCTGCGTCCCCAAGg----tatgacatctagatctctctttgccggcggagctgagatttcgcctccag--------------------------------------

upper sequence: GLYMA14G38950.1 (Glycine max), 5'ss of exon 2
lower sequence: EFJ36971 (Selaginella moellendorffii), 5'ss of exon 1
---ACATTCAAGCGCAGGAATGGAGGTCGCAACAAACACGGCCGCGGCCATGTCAAATTCATCCGATGCTCCAACTGCGGAAAATGCTGCCCCAAGgt----tgtttttattattatttatttcactttctt--ccaccttcaaattttttgtgcgaagcatttcaattaattgaaaaaaataaaataataacag
   ||  |||||||  ||||||| || |||||||| |||||||||||||||||| |    ||||| |||||||| || ||    |||  |||||||||      | |  |  ||| |  || || ||||     |     | | ||||    | |                                        
ATGACTGTCAAGCGGCGGAATGGCGGCCGCAACAAGCACGGCCGCGGCCATGTCGATCCAATCCGGTGCTCCAATTGTGGGCGCTGCGTCCCCAAGgtatgacatctagaggattttccatctctctttgccggcggagctgagatttcgcctccag--------------------------------------

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|298185816|gb|HO030977.1|HO030977
EST:     GCCATTTCAAATTCATCCGATGCTCCAACTGCGGAAAATGCTGCCCCAAG                         GACAAGGCCATCAAGAGGTTTTTGGTTAGGAACATTGTTGAACAGGCTGCA
genomic: GCCATGTCAAATTCATCCGATGCTCCAACTGCGGAAAATGCTGCCCCAAGgttgttttta ... ataataacagGACAAGGCCATCAAGAGGTTTTTGGTTAGGAACATTGTTGAACAGGCTGCA
EST: gi|7145743|gb|AW507665.1|AW507665
EST:     GCCATGTCAAATTCATCCGATGCTCCAACTGCGGAAAATGCTGCCCCAAG                         GACAAGGCCATCAAGAGGTTTTTGGTTAGGAACATTGTTGAACAGGCTGCA
genomic: GCCATGTCAAATTCATCCGATGCTCCAACTGCGGAAAATGCTGCCCCAAGgttgttttta ... ataataacagGACAAGGCCATCAAGAGGTTTTTGGTTAGGAACATTGTTGAACAGGCTGCA
EST: gi|193356347|gb|FK323060.1|FK323060
EST:     GCCATGTCAAATTCATCCGATGCTCCAACTGCGGAAAATGCTGCCCCAAG                         GACAAGGCCATCAAGAGGTTTTTGGTTAGGAACATTGTTGAACAGGCTGCA
genomic: GCCATGTCAAATTCATCCGATGCTCCAACTGCGGAAAATGCTGCCCCAAGgttgttttta ... ataataacagGACAAGGCCATCAAGAGGTTTTTGGTTAGGAACATTGTTGAACAGGCTGCA
EST: gi|5688292|gb|AI941307.1|AI941307
EST:     GCCTTGTCAAATTCATCCGATGCTCCAACTGCGGAAAATGCTGCCCCAAG                         GACAAGGCCATCAAGAGGTTTTTGGTTAGGAA
genomic: GCCATGTCAAATTCATCCGATGCTCCAACTGCGGAAAATGCTGCCCCAAGgttgttttta ... ataataacagGACAAGGCCATCAAGAGGTTTTTGGTTAGGAA
EST: gi|193558493|gb|FK515354.1|FK515354
EST:     GCCATGTCAAATTCATCCGATGCTCCAACTGCGGAAAATGCTGCCCCAAG                         GACAAGGCCATCAAGAGGTTTTTGGTTAGGAACATTGTTGAACAGGCTGCA
genomic: GCCATGTCAAATTCATCCGATGCTCCAACTGCGGAAAATGCTGCCCCAAGgttgttttta ... ataataacagGACAAGGCCATCAAGAGGTTTTTGGTTAGGAACATTGTTGAACAGGCTGCA
EST: gi|20449728|gb|BQ253860.1|BQ253860
EST:     GCCATGTCAAATTCATCCGATGCTCCAACTGCGGAAAATGCTGCCCCAAG                         GACAAGGCCATCAAGAGGTTTTTGGTTAGGAACATTGTTGAACAGGCTGCA
genomic: GCCATGTCAAATTCATCCGATGCTCCAACTGCGGAAAATGCTGCCCCAAGgttgttttta ... ataataacagGACAAGGCCATCAAGAGGTTTTTGGTTAGGAACATTGTTGAACAGGCTGCA
EST: gi|208238759|gb|GE036319.1|GE036319
EST:     CCATGTCAAATTCATCCGATGCTCCAACTGCGGAAAATGCTGCCCCAACG                         GACAAGGCCATCAAGAGGTTTTTGG
genomic: CCATGTCAAATTCATCCGATGCTCCAACTGCGGAAAATGCTGCCCCAA-Ggttgttttta ... ataataacagGACAAGGCCATCAAGAGGTTTTTGG
EST: gi|193661392|gb|FK601716.1|FK601716
EST:     GCCATGTCAAATTCATCCGATGCTCCAACTGCGGAAAATGCTGCCCCAAG                         GACAAGGCCATCAAGAGGTTTTTGGTTAGGAACATTGTTGAACAGGCTGCA
genomic: GCCATGTCAAATTCATCCGATGCTCCAACTGCGGAAAATGCTGCCCCAAGgttgttttta ... ataataacagGACAAGGCCATCAAGAGGTTTTTGGTTAGGAACATTGTTGAACAGGCTGCA
EST: gi|193344296|gb|FK312826.1|FK312826
EST:     CGGAAAATGCTGCCCCAAG                         GACAAGGCCATCAAGAGGTTTTTGGTTAGGAACATTGTTGAACAGGCTGCA
genomic: CGGAAAATGCTGCCCCAAGgttgttttta ... ataataacagGACAAGGCCATCAAGAGGTTTTTGGTTAGGAACATTGTTGAACAGGCTGCA
EST: gi|193644033|gb|FK593796.1|FK593796
EST:     GCCATGTCAAATTCATCCGATGCTCCAACTGCGGAAAATGCTGCCCCAAG                         GACAAGGCCATCAAGAGGTTTTTGGTTAGGAACATTGTTGAACAGGCTGCA
genomic: GCCATGTCAAATTCATCCGATGCTCCAACTGCGGAAAATGCTGCCCCAAGgttgttttta ... ataataacagGACAAGGCCATCAAGAGGTTTTTGGTTAGGAACATTGTTGAACAGGCTGCA
EST: gi|298193611|gb|HO040259.1|HO040259
EST:     GCCATGTCAAATTCATCCGATGCTCCAACTGCGGAAAATGCTGCCCCAAG                         GACAAGGCCATCAAGAGGTTTTTGGTTAGGAACATTGTTGAACAGGCTGCA
genomic: GCCATGTCAAATTCATCCGATGCTCCAACTGCGGAAAATGCTGCCCCAAGgttgttttta ... ataataacagGACAAGGCCATCAAGAGGTTTTTGGTTAGGAACATTGTTGAACAGGCTGCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACATTCAAGCGCAGGAATGGAGGTCGCAACAAACACGGCCGCGGCCATGTCAAATTCATCCGATGCTCCAACTGCGGAAAATGCTGCCCCAAGgttgtttttattattatttatttcactttcttccaccttcaaattttttgtgcgaagcatttcaattaattgaaaaaaataaaataataacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC