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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttttaacttagtgacagatattcattttaaagatacaagtgcaccaaccatgcattgactaatttttaagttgaatttttacagGCTTATTCTTATTGGCTTTACAACGTACCATGGGGCATGTACAAATCATTGATGTACATAAAGGAACGTTATGGAAACCCAACTGTGTTCTTATCCGAAA

Basic information

species Glycine max
transcript GLYMA07G11310.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G11310.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os03g49600.1 (Oryza sativa), 3'ss of exon 9
-------------------------------------------gtaa-gttttaacttagtgacagatattcattttaaagatacaagtgcaccaaccatgcattgactaatttttaagttg--aatttttacagGCTTATTCTTATTGGCTTTACAACGTACCATGGGGCATGTACAAATCATTGATGTACATAAAGGAACGTTATGGAAACCCAACTGTGTTCTTATCCGAAA
                                            ||    |  |   || ||||    |   |  | | | || ||   | | ||   |  |||  |    || || |       || |||||||||  ||||| |||||||||||| ||| |||||||| ||||||  ||   |||  ||||| ||| |    || || || || || ||  || || | ||||
gtatgcagtaatcagttgtatccttctccagcttcagattcttctagcactgcattctactgacgtg-accaaactgataaattcagaagtaaca-taactcataaaacctttgttgatccatcgatctttacagGCAAATTCTAATTGGCTTTACATCGTGCCATGGGGGATGTACGGATGTGTGAACTACATCAAGCAGAAGTACGGGAATCCGACAGTCGTCATAACTGAAA

upper sequence: GLYMA07G11310.1 (Glycine max), 3'ss of exon 9
lower sequence: AT3G18070.2 (Arabidopsis thaliana), 3'ss of exon 6
gtaagttttaacttagtgacagatattcattttaaagatacaagtgcaccaaccatgcattgactaatttt----taagttgaatttttacagGCTTATTCTTATTGGCTTTACAACGTACCATGGGGCATGTACAAATCATTGATGTACATAAAGGAACGTTATGGAAACCCAACTGTGTTCTTATCCGAAA
|| || |  ||  ||        | |   ||||    |  |      |  |    |   ||| || ||| |    |||  | | ||| | |||||  ||||  | ||| | ||||| || |||||||| ||||||||| | || ||||||||  ||||||||||||| ||||||||| || |  | |||||||
gtgagata-aatatatgttttcttctgagttttgttaactctctctgatgattgcttagttgtctgattatgaattaatctaattttattcagGCACATTCAGAATGGTTATACAATGTCCCATGGGGAATGTACAAAGCTTTAATGTACATTGAGGAACGTTATGGCAACCCAACTATGATTCTCTCCGAAA

upper sequence: GLYMA07G11310.1 (Glycine max), 3'ss of exon 9
lower sequence: AT3G18080.1 (Arabidopsis thaliana), 3'ss of exon 9
gtaagtttta-acttagtgacagatattcattttaaagatacaagtgcaccaacca-tgcattgactaatttttaagttgaat-ttttacagGCTTATTCTTATTGGCTTTACAACGTACCATGGGGCATGTACAAATCATTGATGTACATAAAGGAACGTTATGGAAACCCAACTGTGTTCTTATCCGAAA
|| || | || ||||  | | |  | ||  ||||      |  | |  |   || | ||  |    || |   |||      | | ||| ||||||| || | |||| | ||||||||||||||||| ||||||||  | |||||||| || ||||||||||| || ||||| ||| || || | || ||||
gtgagatatacacttgattatatgtttttttttttccctaagcaatatatatacaagtgtctaagttattaaataaaccacttatcttatagGCTTACTCGTCTTGGTTATACAACGTACCATGGGGAATGTACAAGGCCTTGATGTATATGAAGGAACGTTACGGCAACCCTACTATGATCCTCTCTGAAA

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|10847433|gb|BF070120.1|BF070120
EST:     ATGCAAAGAACGGAGTGCCTATTGGTCCAAGG                         GCTTATTCTTATTGGCTTTACAACGTACCATGGGGCATGTACAAAATCATT
genomic: ATGCAAAGAACGGAGTGCCTATTGGTCCAAGGgtaagtttta ... atttttacagGCTTATTCTTATTGGCTTTACAACGTACCATGGGGCATGTAC-AAATCATT
EST: gi|192318423|gb|FK006543.1|FK006543
EST:     ATGCAAAGAACGGAGTGCCTATTGGTCCAAGG                         GCTTATTCTTATTGGCTTTACAACGTGCCATGGGGCATGTACAAATCATTG
genomic: ATGCAAAGAACGGAGTGCCTATTGGTCCAAGGgtaagtttta ... atttttacagGCTTATTCTTATTGGCTTTACAACGTACCATGGGGCATGTACAAATCATTG
EST: gi|151405282|gb|EV275096.1|EV275096
EST:     ATGCAAAGAACGGAGTGCCTATTGGTCCAAGG                         GCTTATTCTTATTGGCTTTACAACGTACCATGGGGCATGTACAAATCATTG
genomic: ATGCAAAGAACGGAGTGCCTATTGGTCCAAGGgtaagtttta ... atttttacagGCTTATTCTTATTGGCTTTACAACGTACCATGGGGCATGTACAAATCATTG
EST: gi|193480632|gb|FK446394.1|FK446394
EST:     ATGCAAAGAACGGAGTGCCTATTGGTCCAAGG                         GCTTATTCTTATTGGCTTTACAACGTACCATGGGGCATGTACAAATCATTG
genomic: ATGCAAAGAACGGAGTGCCTATTGGTCCAAGGgtaagtttta ... atttttacagGCTTATTCTTATTGGCTTTACAACGTACCATGGGGCATGTACAAATCATTG
EST: gi|209698509|gb|BW656422.1|BW656422
EST:     ATGCAAAGAACGGAGTGCCTATTGGTCCAAGG                         GCTTATTCTTATTGGCTTTACAACGTACCATGGGGCATGTACAAATCATTG
genomic: ATGCAAAGAACGGAGTGCCTATTGGTCCAAGGgtaagtttta ... atttttacagGCTTATTCTTATTGGCTTTACAACGTACCATGGGGCATGTACAAATCATTG
EST: gi|192318424|gb|FK006544.1|FK006544
EST:     ATGCAAAGAACGGAGTGCCTATTGGTCCAAGG                         GCTTATTCTTATTGGCTTTACAACGTGCCATGGGGCATGTACAAATCATTG
genomic: ATGCAAAGAACGGAGTGCCTATTGGTCCAAGGgtaagtttta ... atttttacagGCTTATTCTTATTGGCTTTACAACGTACCATGGGGCATGTACAAATCATTG
EST: gi|193539494|gb|FK494754.1|FK494754
EST:     ATGCAAAGAACGGAGTGCCTATTGGTCCAAGG                         GCTTATTCTTATTGGCTTTACAACGTACCATGGGGCATGTACAAATCATTG
genomic: ATGCAAAGAACGGAGTGCCTATTGGTCCAAGGgtaagtttta ... atttttacagGCTTATTCTTATTGGCTTTACAACGTACCATGGGGCATGTACAAATCATTG
EST: gi|193426808|gb|FK397017.1|FK397017
EST:     ATGCAAAGAACGGAGTGACCTATTGGTCCAAGG                         GCTTATTCTTATTGGCTTTACAACGTACCATGGGGCATGTACAAATCATTG
genomic: ATGCAAAGAACGGAGTG-CCTATTGGTCCAAGGgtaagtttta ... atttttacagGCTTATTCTTATTGGCTTTACAACGTACCATGGGGCATGTACAAATCATTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagatacaagtgcaccaaccatgcattgactaatttttaagttgaatttttacagGCTTATTCTTATTGGCTTTACAACGTACCATGGGGCATGTACAAATCATTGATGTACATAAAGGAACGTTATGGAAACCCAACTGTGTTCTTATCCGAAA
                           gactaat  putative branch site (score: 2)
                                              tttttac  putative PPT
                        attgactaatttttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagttttaacttagtgacagatattcattttaaagatacaagtgcaccaaccatgcattgactaatttttaagttgaatttttacagGCTTATTCTTATTGGCTTTACAACGTACCATGGGGCATGTACAAATCATTGATGTACATAAAGGAACGTTATGGAAACCCAACTGTGTTCTTATCCGAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA