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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GACTACGTGCCCACGGTTTTTGACAATTTCAGTGCTAATGTTGTGGTGGATGGAAGCACCGTAAACCTGGGGTTGTGGGATACTGCTGgtaattatgacaaccaattcagttatatagaatcgggtattatttttgactaattgtttgtttctggtggtttaacttgtttgattaacag

Basic information

species Glycine max
transcript GLYMA06G02580.2
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G02580.2 (Glycine max), 5'ss of exon 2
lower sequence: GRMZM5G803949_T02 (Zea mays), 5'ss of exon 2
GACTACGTGCCCACGGTTTTTGACAATTTCAGTGCTAATGTTGTGGTGGATGGAAGCACCGTAAACCTGGGGTTGTGGGATACTGCTGgtaatta----tgacaaccaattcagttatatagaatcgggtattatttttgactaattgtttgtttctggtggtttaacttgtttgattaacag-------------------------------
||||| || || ||||| |||||||| ||||||||||| |||||||| ||||| | ||| || ||||| ||  | ||||| ||||| ||| | ||    ||     |  | | ||  |      |  | |  | |||||  |   |  ||||       |  |||  |||  || || || |                                
GACTATGTTCCGACGGTGTTTGACAACTTCAGTGCTAACGTTGTGGTTGATGGTAACACTGTCAACCTCGGCCTCTGGGACACTGCAGgtgactagccgtgctgttctgtcctgtcctgctacttatgatgctttttttttcctttcctttgcgcgatatcctttttctttgttcatcaaaatggttgagcttccatctttgcaactgtaatag

upper sequence: GLYMA06G02580.2 (Glycine max), 5'ss of exon 2
lower sequence: Vv18s0001g14670.t01 (Vitis vinifera), 5'ss of exon 2
GACTACGTGCCCACGGTTTTTGACAATTTCAGTGCTAATGTTGTGGTGGATGGAAGCACCGTAAACCTGGGGTTGTGGGATACTGCTGgtaat--tatgacaaccaattcagttatatagaatcgggtattatttttgactaattgtttgtttctggtggtttaacttgtttgattaacag
|| || ||||| || |||||||||||||||||||| ||||| || || ||||| ||||| || ||  | ||||||||||||||||||||||||  |||||  | |  |   | | | | || ||   ||| | |||   || |||  |||||| |  | |  ||  ||   |  | |||||
GATTATGTGCCAACTGTTTTTGACAATTTCAGTGCAAATGTGGTTGTTGATGGGAGCACTGTCAATTTAGGGTTGTGGGATACTGCTGgtaatcttatgaacatccttctggatttcttgattcttttatcagtttc--ctcatttcttgtttttaattgactatattcgattttgaacag
















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|31561454|gb|CD487292.1|CD487292
EST:     TGTTGTGGTGGATGGAAGCACCGTAAACCTGGGGTTGTGGGATACTGCTG                         GTCAGGAGGATTATAATAGGCTTAGACCCTTGAGTTATCGAGGAGCTGATG
genomic: TGTTGTGGTGGATGGAAGCACCGTAAACCTGGGGTTGTGGGATACTGCTGgtaattatga ... tgattaacagGTCAGGAGGATTATAATAGGCTTAGACCCTTGAGTTATCGAGGAGCTGATG
EST: gi|4396727|gb|AI495724.1|AI495724
EST:     TGTTGTGGTGGATGGAAGCACCGTAAACCTGGGGTTGTGGGATACTGCTG                         GTCAGGAGGATTATAATAGGCTTAGACCCTTGAGTTATCGAGGAGCTGATG
genomic: TGTTGTGGTGGATGGAAGCACCGTAAACCTGGGGTTGTGGGATACTGCTGgtaattatga ... tgattaacagGTCAGGAGGATTATAATAGGCTTAGACCCTTGAGTTATCGAGGAGCTGATG
EST: gi|120533487|gb|EH261620.1|EH261620
EST:     TGTTGTGGTGGATGGAAGCACCGTAAACCTGGGGTTGTGGGATACTGCTG                         GTCAGGAGGATTATAATAGGCTTAGACCCTTGAGTTATCGAGGAGCTGATG
genomic: TGTTGTGGTGGATGGAAGCACCGTAAACCTGGGGTTGTGGGATACTGCTGgtaattatga ... tgattaacagGTCAGGAGGATTATAATAGGCTTAGACCCTTGAGTTATCGAGGAGCTGATG
EST: gi|4313831|gb|AI460950.1|AI460950
EST:     TGTTGTGGTGGATGGAAGCACCGTAAACCTGGGGTTGTGGGATACTGCTG                         GTCAGGAGGATTATAATAGGCTTAGACCCTTGAGTTATCGAGGAGCTGATG
genomic: TGTTGTGGTGGATGGAAGCACCGTAAACCTGGGGTTGTGGGATACTGCTGgtaattatga ... tgattaacagGTCAGGAGGATTATAATAGGCTTAGACCCTTGAGTTATCGAGGAGCTGATG
EST: gi|298164350|gb|HO013995.1|HO013995
EST:     TGTTGTGGTGGATGGAAGCACCGTAAACCTGGGGTTGTGGGATACTGCTG                         GTCAGGAGGATTATAATAGGCTTAGACCCTTGAGTTATCGAGGAGCTGATG
genomic: TGTTGTGGTGGATGGAAGCACCGTAAACCTGGGGTTGTGGGATACTGCTGgtaattatga ... tgattaacagGTCAGGAGGATTATAATAGGCTTAGACCCTTGAGTTATCGAGGAGCTGATG
EST: gi|16348169|gb|BI973764.1|BI973764
EST:     TGTTGTGGTGGATGGAAGCACCGTAAACCTGGGGTTGTGGGATACTGCTG                         GTCAGGAGGATTATAATAGGCTTAGACCCTTGAGTTATCGAGGAGCTGATG
genomic: TGTTGTGGTGGATGGAAGCACCGTAAACCTGGGGTTGTGGGATACTGCTGgtaattatga ... tgattaacagGTCAGGAGGATTATAATAGGCTTAGACCCTTGAGTTATCGAGGAGCTGATG
EST: gi|10845271|gb|BF068427.1|BF068427
EST:     TGTTGTGGTGGATGGAAGCACCGTAAACCTGGGGTTGTGGGATACTGCTG                         GTCAGGAGGATTATAATAGGCTTAGACCCTTGAGTTATCGAGGAGCTGATG
genomic: TGTTGTGGTGGATGGAAGCACCGTAAACCTGGGGTTGTGGGATACTGCTGgtaattatga ... tgattaacagGTCAGGAGGATTATAATAGGCTTAGACCCTTGAGTTATCGAGGAGCTGATG
EST: gi|6483101|gb|AW202293.1|AW202293
EST:     TGTTGTGGTGGATGGAAGCACCGTAAACCTGGGGTTGTGGGATACTGCTG                         GTCAGGAGGATTATAATAGGCTTAGACCCTTGAGTTATCGAGGAGCTGATG
genomic: TGTTGTGGTGGATGGAAGCACCGTAAACCTGGGGTTGTGGGATACTGCTGgtaattatga ... tgattaacagGTCAGGAGGATTATAATAGGCTTAGACCCTTGAGTTATCGAGGAGCTGATG
EST: gi|19269284|gb|BM885540.1|BM885540
EST:     TGTTGTGGTGGATGGAAGCACCGTAAACCTGGGGTTGTGGGATACTGCTG                         GTCAGGAGGATTATAATAGGCTTAGACCCTTGAGTTATCGAGGAGCTGATG
genomic: TGTTGTGGTGGATGGAAGCACCGTAAACCTGGGGTTGTGGGATACTGCTGgtaattatga ... tgattaacagGTCAGGAGGATTATAATAGGCTTAGACCCTTGAGTTATCGAGGAGCTGATG
EST: gi|17021451|gb|BM092485.1|BM092485
EST:     TGTTGTGGTGGATGGAAGCACCGTAAACCTGGGGTTGTGGGATACTGCTG                         GTCAGGAGGATTATAATAGGCTTAGACCCTTGAGTTATCGAGGAGCTGATG
genomic: TGTTGTGGTGGATGGAAGCACCGTAAACCTGGGGTTGTGGGATACTGCTGgtaattatga ... tgattaacagGTCAGGAGGATTATAATAGGCTTAGACCCTTGAGTTATCGAGGAGCTGATG
EST: gi|193378085|gb|FK344594.1|FK344594
EST:     TGTTGTGGTGGATGGAAGCACCGTAAACCTGGGGTTGTGGGATACTGCTG                         GTCAGGAGGATTATAATAGGCTTAGACCCTTGAGTTATCGAGGAGCTGATG
genomic: TGTTGTGGTGGATGGAAGCACCGTAAACCTGGGGTTGTGGGATACTGCTGgtaattatga ... tgattaacagGTCAGGAGGATTATAATAGGCTTAGACCCTTGAGTTATCGAGGAGCTGATG
EST: gi|19052868|gb|BM731535.1|BM731535
EST:     TGTTGTGGTGGATGGAAGCACCGTAAACCTGGGGTTGTGGGATACTGCTG                         GTCAGGAGGATTATAATAGGCTTAGACCCTTGAGTTATCGAGGAGCTGATG
genomic: TGTTGTGGTGGATGGAAGCACCGTAAACCTGGGGTTGTGGGATACTGCTGgtaattatga ... tgattaacagGTCAGGAGGATTATAATAGGCTTAGACCCTTGAGTTATCGAGGAGCTGATG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GACTACGTGCCCACGGTTTTTGACAATTTCAGTGCTAATGTTGTGGTGGATGGAAGCACCGTAAACCTGGGGTTGTGGGATACTGCTGgtaattatgacaaccaattcagttatatagaatcgggtattatttttgactaattgtttgtttctggtggtttaacttgtttgattaacag

- - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG