Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AACTGCATTCTGTCTTCTGTACAAGTTTTTTACTATGAAGCTCACCGTCAAGCAAATGCATGGGCTGTTAAAACACCTCGATTCTCCTTACATAAGAGCGgtatgtaggcgtgcctgacaatgtatatggggctttactgatttatttttttaggagtgaaaacattctgtgttcattatggtatgcttgtttgcgcttg...

Basic information

species Glycine max
transcript GLYMA02G40900.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G40900.1 (Glycine max), 5'ss of exon 2
lower sequence: LOC_Os05g08600.1 (Oryza sativa), 5'ss of exon 2
AACTGCATTCTGTCTTCTGTACAAGTTTTTTACTATGAAGCTCACCGTCAAGCAAATGCATGGGCTGTTAAAACACCTCGATTCTCCTTACATAAGAGCGgtatgtaggc-gtgcctgacaatgtatatggggctttact-gatttatttttttaggagtgaaaacattctgt-gttcattatggtatgcttgtttgcgcttg--
 |||||||||||||| || |||||||| || || |||||||| || ||||| || ||||||||  |||| || || |  ||||| || ||||| ||||| ||| ||     |  |||   ||  | |||    ||||| | ||||||   ||     | || |  | |||||| ||| || | | | |  | |  |||  |    
CACTGCATTCTGTCTCCTCTACAAGTTCTTCACCATGAAGCTTACTGTCAAACAGATGCATGGTTTGTTGAAGCATCCTGATTCCCCATACATTAGAGCTgtaagttctttgcccctattaacttttatcacactttattagatttaagatt-----aatgcatgctttctgttgtttatcaagttttattggagtgcaatgata

upper sequence: GLYMA02G40900.1 (Glycine max), 5'ss of exon 2
lower sequence: GRMZM2G092258_T04 (Zea mays), 5'ss of exon 2
AACTGCATTCTGTCTTCTGTACAAGTTTTTTACTATGAAGCTCACCGTCAAGCAAATGCATGGGCTGTTAAAACACCTCGATTCTCCTTACATAAGAGCGgtatgtaggcgtgcctgacaatgtatatggggctttactgatttatttttttaggagtgaaaacattctgtgttcattatggtatgcttgtttgcgcttg-
 ||||||||||||||||| |||||||| ||||| |||||||| || ||||| || ||||| ||  |||| || || |  || || ||  |||| ||||| ||| ||    ||  |   |  | | | |  |    | |||| |   ||  ||    |         | |   ||    |||   |   ||| ||    |  
CACTGCATTCTGTCTTCTATACAAGTTCTTTACCATGAAGCTTACTGTCAAACAGATGCACGGTTTGTTGAAGCATCCTGACTCCCCACACATTAGAGCTgtaagtttctgtttcctgccct-tctgtttgctgatgctgaatgtcttgcttcatggccctgtatctattcattaggcatgaggttagtgtatgaatctat

upper sequence: GLYMA02G40900.1 (Glycine max), 5'ss of exon 2
lower sequence: GRMZM2G173693_T02 (Zea mays), 5'ss of exon 2
AACTGCATTCTGTCTTCTGTACAAGTTTTTTACTATGAAGCTCACCGTCAAGCAAATGCATGGGCTGTTAAAACACCTCGATTCTCCTTACATAAGAGCGgtatgtaggcgtgcctgacaatgtatatggggctttactgatttatttttttag-gagtgaaaacattctgtgttcattatggtatgcttgtttgcgcttg------
  | || ||||| || || |||||||| || || |||||||||||||||||||| ||||| || ||| | || ||||  || || || ||||| ||||| ||| ||   | | | |  |  |     |||   | || | | | |||| |||   || |    |  | | |  | ||  |    ||  || ||  || |||      
CTCCGCCTTCTGCCTCCTCTACAAGTTATTCACCATGAAGCTCACCGTCAAGCAGATGCACGGCCTGCTCAAGCACCAGGACTCCCCCTACATCAGAGCTgtaagtgaacct-cttccctct-----tggttttctattcaatgatttctttgctgattctgcatgtaccgc-tgcaggaacagatttttcttgccgattgttacag

upper sequence: GLYMA02G40900.1 (Glycine max), 5'ss of exon 2
lower sequence: AT5G37370.3 (Arabidopsis thaliana), 5'ss of exon 2
AACTGCATTCTGTCTTCTGTACAAGTTTTTTACTATGAAGCTCACCGTCAAGCAAATGCATGGGCTGTTAAAACACCTCGATTCTCCTTACATAAGAGCGgtatgtaggcgtgcctgacaatgtatatggggctttactgatttatttttttaggagtgaaaacattctgtgttcattatggtatgcttgtttgcgcttg--
||| || |  |||||||| ||||| || ||||| ||||| || || || ||||| |||||||| |||||||| |||   ||||||||||| || ||||||||  ||     | | | || || | | | |   | |  |  |  ||    |  |   |      || || |   | || |  | |   | || |   |    
AACAGCGTATTGTCTTCTCTACAAATTCTTTACCATGAAACTTACAGTGAAGCAGATGCATGGACTGTTAAAGCACACAGATTCTCCTTATATTAGAGCGgtgagtgaatct-cttaaccatcttttttgcattattgtcctgcataaagtatgagctaccgtgatgctataacc-ttgtctttttggtattggttttctta

upper sequence: GLYMA02G40900.1 (Glycine max), 5'ss of exon 2
lower sequence: Vv04s0043g00270.t01 (Vitis vinifera), 5'ss of exon 2
AACTGCATTCTGTCTTCTGTACAAGTTTTTTACTATGAAGCTCACCGTCAAGCAAATGCATGGGCTGTTAAAACACCTCGATTCTCCTTACATAAGAGCGgtatgta-ggcgtgcctgacaatgtata----tggggcttt----actgatttatttttttaggagtgaaaacattctgtgttcattatggtatgcttgtttgcgcttg
 || ||||| || ||||| |||||||||||||| ||||||||||| || |||||||||||||| ||  |||| ||||  |||||||| || || ||||| ||  ||   || | | | | ||| |||     ||| |||||    | | | |  |||||||     | ||   | | | | | |||||    ||| |  |         
CACAGCATTTTGCCTTCTTTACAAGTTTTTTACAATGAAGCTCACTGTGAAGCAAATGCATGGACTACTAAAGCACCCAGATTCTCCCTATATTAGAGCTgtgagtctagccttcttcagaatttattaatttggtgcttttaacaattactactttttttttagtttaacttagtatctttgcattaattaatggtcat---------

upper sequence: GLYMA02G40900.1 (Glycine max), 5'ss of exon 2
lower sequence: EFJ33299 (Selaginella moellendorffii), 5'ss of exon 1
AACTGCATTCTGTCTTCTGTACAAGTTTTTTACTATGAAGCTCACCGTCAAGCAAATGCATGGGCTGTTAAAACACCTCGATTCTCCTTACATAAGAGCGgtatgtaggcgtgcctgacaatgtatatggggctttactgatttatttttttaggagtgaaaacattctgtgttcattatggtatgcttgtttgcgcttg
 || || || || || || ||||||||||| || |||||||||||||||||||| ||||| |||||  | || |||   ||||||||||||||  | ||||||||      |  ||    ||   |      |||    | ||| | |  ||             |||||| ||| |    |                  
GACAGCGTTTTGCCTCCTCTACAAGTTTTTCACCATGAAGCTCACCGTCAAGCAGATGCAGGGGCTTCTCAACCACGCTGATTCTCCTTACATTCGTGCGgtatg-----atctcttttcattccttcatttcttcgaagctttttctcatttc--------ttgttctgttttcctcgcag------------------

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|19347513|gb|BM892393.1|BM892393
EST:     AGCAAATGCATGGGCTGTTAAAACACCTCGATTCTCCTTACATAAGAGCG                         GTTGGATTTCTCTATCTGAGATATTGTGCTGATCCAAAGACACTATGG
genomic: AGCAAATGCATGGGCTGTTAAAACACCTCGATTCTCCTTACATAAGAGCGgtatgtaggc ... ttgtttatagGTTGGATTTCTCTATCTGAGATATTGTGCTGATCCAAAGACACTATGG
EST: gi|192304017|gb|FG995289.1|FG995289
EST:     AGCAAATGCATGGGCTGTTAAAACACCTCGATTCTCCTTACATAAGAGCG                         GTTGGATTTCTCTATCTGAGATATTGTGCTGATCCAAAGACACTATGGAAT
genomic: AGCAAATGCATGGGCTGTTAAAACACCTCGATTCTCCTTACATAAGAGCGgtatgtaggc ... ttgtttatagGTTGGATTTCTCTATCTGAGATATTGTGCTGATCCAAAGACACTATGGAAT
EST: gi|9987823|gb|BE661931.1|BE661931
EST:     AGCAAATGCATGGGCTGTTAAAACACCTCGATTCTCCTTACATAAGAGCG                         GTTGGATTTCTCTATCTGAGATATTGTGCTGATCCAAAGACACTATGGAAT
genomic: AGCAAATGCATGGGCTGTTAAAACACCTCGATTCTCCTTACATAAGAGCGgtatgtaggc ... ttgtttatagGTTGGATTTCTCTATCTGAGATATTGTGCTGATCCAAAGACACTATGGAAT
EST: gi|19270741|gb|BM886997.1|BM886997
EST:     AGCAAATGCATGGGCTGTTAAAACACCTCGATTCTCCTTACATAAGAGCG                         GTTGGATTTCTCTATCTGAGATATTGTGCTGATCCAAAGACACT
genomic: AGCAAATGCATGGGCTGTTAAAACACCTCGATTCTCCTTACATAAGAGCGgtatgtaggc ... ttgtttatagGTTGGATTTCTCTATCTGAGATATTGTGCTGATCCAAAGACACT
EST: gi|213591364|gb|DB955712.1|DB955712
EST:     AGCAAATGCATGGGCTGTTAAAACACCTCGATTCTCCTTACATAAGAGCG                         GTTGGATTTCTCTATCTGAGATATTGTGCTGATCCAAAGACACTATGGAAT
genomic: AGCAAATGCATGGGCTGTTAAAACACCTCGATTCTCCTTACATAAGAGCGgtatgtaggc ... ttgtttatagGTTGGATTTCTCTATCTGAGATATTGTGCTGATCCAAAGACACTATGGAAT
EST: gi|254343401|gb|GR857105.1|GR857105
EST:     AGCAAATGCATGGGCTGTTAAAACACCTCGATTCTCCTTACATAAGAGCG                         GTTGGATTTCTCTATCTGAGATATTGTGCTGATCCAAAGACACTATGGAAT
genomic: AGCAAATGCATGGGCTGTTAAAACACCTCGATTCTCCTTACATAAGAGCGgtatgtaggc ... ttgtttatagGTTGGATTTCTCTATCTGAGATATTGTGCTGATCCAAAGACACTATGGAAT
EST: gi|254318502|gb|GR832670.1|GR832670
EST:     AGCAAATGCATGGGCTGTTAAAACACCTCGATTCTCCTTACATAAGAGCG                         GTTGGATTTCTCTATCTGAGATATTGTGCTGATCCAAAGACACTATGGAAT
genomic: AGCAAATGCATGGGCTGTTAAAACACCTCGATTCTCCTTACATAAGAGCGgtatgtaggc ... ttgtttatagGTTGGATTTCTCTATCTGAGATATTGTGCTGATCCAAAGACACTATGGAAT
EST: gi|213595216|gb|DB962355.1|DB962355
EST:     AGCAAATGCATGGGCTGTTAAAACACCTCGATTCTCCTTACATAAGAGCG                         GTTGGATTTCTCTATCTGAGATATTGTGCTGATCCAAAGACACTATGGAAT
genomic: AGCAAATGCATGGGCTGTTAAAACACCTCGATTCTCCTTACATAAGAGCGgtatgtaggc ... ttgtttatagGTTGGATTTCTCTATCTGAGATATTGTGCTGATCCAAAGACACTATGGAAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AACTGCATTCTGTCTTCTGTACAAGTTTTTTACTATGAAGCTCACCGTCAAGCAAATGCATGGGCTGTTAAAACACCTCGATTCTCCTTACATAAGAGCGgtatgtaggcgtgcctgacaatgtatatggggctttactgatttatttttttaggagtgaaaacattctgtgttcattatggtatgcttgtttgcgcttg

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