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

...aggtaccctagaagttctttttcgttaacaacttgaggatacatgcgataatttctgtattattgcttagctggagagtgatttggatgcacatgcacagGTTTTGTTGTCGGTTCTTGATGAGCTTCAAGGATCAGAAGATGGGTATTATGTTGTGGTCGGAGGCATTACTCCGACTCCTCTCGGGGAAGGCAAATCTA

Basic information

species Glycine max
transcript GLYMA20G38740.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G13840.1 (Glycine max), 3'ss of exon 2
lower sequence: AT1G50480.1 (Arabidopsis thaliana), 3'ss of exon 1
-aggtaccctagaagttctt-tttcgttaacaacttgagga--tacatgcgataat--ttctgtattattgcttagctggagagtgatttggatgcacatgcacagGTTTTGTTGTCGGTTCTTGATGAGCTTCAAGGATCAGAAGATGGGTATTATGTTGTGGTCGGAGGCATTACTCCGACTCCTCTCGGGGAAGGCAAATCTA
  || |   | ||   | |  ||||   || ||| | || |  |   |     |||  ||| || || |    ||         |||||||             ||||||||||||| |   |||||||||||||||||  ||||||||| || |||||||| || ||||| |||||||| |||||||| || ||||||||   ||
tgggcaagattgatactttagtttcaccaaaaacatcagaagctggttaaaccaatggttcagtgttctgagctaatcaactgatgatttg------ttcttgtagGTTTTGTTGTCTGCGTTTGATGAGCTTCAAGGACAAGAAGATGGATACTATGTTGTTGTTGGAGGGATTACTCCTACTCCTCTTGGAGAAGGCAAGAGTA
















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|7233770|gb|AW569113.1|AW569113
EST:     TCAACCTTAGTCCCAATCACTATGACCTTTACGGTAAATACAAGGCTAAG                         GTTTTGTTGTCGGTTCTTGATGAGCTTCAAGGATCAGAAGATGGGTATTAT
genomic: TCAACCTTAGTCCCAATCACTATGACCTTTACGGTAAATACAAGGCTAAGgtaattaatc ... acatgcacagGTTTTGTTGTCGGTTCTTGATGAGCTTCAAGGATCAGAAGATGGGTATTAT
EST: gi|33390303|gb|CA853510.1|CA853510
EST:     TCAACCTTAGTCCCAATCACTATGACCTTTACGGTAAATACAAGGCTAAG                         GTTTTGTTGTCGGTTCTTGATGAGCTTCAAGGATCAGAAGATGGGTATTAT
genomic: TCAACCTTAGTCCCAATCACTATGACCTTTACGGTAAATACAAGGCTAAGgtaattaatc ... acatgcacagGTTTTGTTGTCGGTTCTTGATGAGCTTCAAGGATCAGAAGATGGGTATTAT
EST: gi|207806149|gb|GD777898.1|GD777898
EST:     TCAACCTTAGTCCCAATCACTATGACCTTTACGGTAAATACAAGGCTAAG                         GTTTTGTTGTCGGTTCTTGATGAGCTTCAAGGATCAGAAGATGGGTATTAT
genomic: TCAACCTTAGTCCCAATCACTATGACCTTTACGGTAAATACAAGGCTAAGgtaattaatc ... acatgcacagGTTTTGTTGTCGGTTCTTGATGAGCTTCAAGGATCAGAAGATGGGTATTAT
EST: gi|151393904|gb|EV263775.1|EV263775
EST:     TCAACCTTAGTCTCAATCACTATGACCTTTACGGTAAATACAAGGCTAAG                         GTTTTGTTGTCGGTTCTTGATGAGCTTCAAGGATCAGAAGATGGGTATTAT
genomic: TCAACCTTAGTCCCAATCACTATGACCTTTACGGTAAATACAAGGCTAAGgtaattaatc ... acatgcacagGTTTTGTTGTCGGTTCTTGATGAGCTTCAAGGATCAGAAGATGGGTATTAT
EST: gi|5752485|gb|AI959772.1|AI959772
EST:     TCAACCTTAGTCCCAATCACTATGACCTTTACGGTAAATACAAGGCTAAG                         GTTTTGTTGTCGGTTCTTGATGAGCTTCAAGGATCAGAAGATGGGTATTAT
genomic: TCAACCTTAGTCCCAATCACTATGACCTTTACGGTAAATACAAGGCTAAGgtaattaatc ... acatgcacagGTTTTGTTGTCGGTTCTTGATGAGCTTCAAGGATCAGAAGATGGGTATTAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgataatttctgtattattgcttagctggagagtgatttggatgcacatgcacagGTTTTGTTGTCGGTTCTTGATGAGCTTCAAGGATCAGAAGATGGGTATTATGTTGTGGTCGGAGGCATTACTCCGACTCCTCTCGGGGAAGGCAAATCTA
     atttctgtattatt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aggtaccctagaagttctttttcgttaacaacttgaggatacatgcgataatttctgtattattgcttagctggagagtgatttggatgcacatgcacagGTTTTGTTGTCGGTTCTTGATGAGCTTCAAGGATCAGAAGATGGGTATTATGTTGTGGTCGGAGGCATTACTCCGACTCCTCTCGGGGAAGGCAAATCTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC