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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtggtgctaggacttaatgtttcaagcacaccatttatcttttctgttattaatcttgatagaaatcagcacacttacaaaatatctgattcttactcagGTTCGTGGAGCTAAAGGTCCAATTTTTGAAGATGGTCCCAATTTTGATTTGGCATTTAGGCTTTTCCACGGGAGTGATGGTGTAGTACCCTTATCTGACA

Basic information

species Glycine max
transcript GLYMA20G31850.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G31850.3 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os10g43060.1 (Oryza sativa), 3'ss of exon 2
gtggtgctaggacttaatgtttcaagcacaccat-ttatct----tttctgtta---ttaatct-tgatagaaatcagcacacttacaaaatatctgattcttactcagGTTCGTGGAGCTAAAGGTCCAATTTTTGAAGATGGTCCCAATTTTGATTTGGCATTTAGGCTTTTCCACGGGAGTGATGGTGTAGTACCCTTATCTGACA
     |  ||  ||| |  || ||  | ||  || |||||     ||||||  |   |  || | |  | ||   ||   | |    | |  || || | |||    |||   | ||||  || |||||||||||||||||||| |||||||||||  |||||||| |  ||||||| ||    ||||| || || ||  | ||  |  
-----gtaagccctttaccttccatcctcataatcttatcgcatgtttctgaaaaattggatgtattgtggatgccattgctcaactatatcatttgctgcttgtaaagGCAAGAGGAGACAAGGGTCCAATTTTTGAAGATGGACCCAATTTTGACATGGCATTTCGAGTTTTCCATGGCCAAGATGGGGTTGTTCCACTTTCACATG

upper sequence: GLYMA20G31850.3 (Glycine max), 3'ss of exon 2
lower sequence: AT4G25030.1 (Arabidopsis thaliana), 3'ss of exon 2
gtggtgctaggacttaatgtttcaagcacaccatttatcttttctgttattaatcttgatagaaatcagcacacttacaaaatatctgattct-tactcagGTTCGTGGAGCTAAAGGTCCAATTTTTGAAGATGGTCCCAATTTTGATTTGGCATTTAGGCTTTTCCACGGGAGTGATGGTGTAGTACCCTTATCTGACA
                       ||| | ||| | | |   |||  |     || |||| |    | |  | | |   |   | ||| ||  | ||   |||   | |  |  ||||| || || ||||||||||||||||||||||||  ||| |||||||||||||| ||    ||||| || || ||  | |||||||
---------------------gtaagta-accgtctgttggttcact---ccatattgacatttctta-tagattctgatcttgtctcatcatatatatagGCAAGAGCTGGGAAAGGACCTATATTTGAAGATGGTCCCAATTTTGATACGGCGTTTAGGCTTTTCCATGGCCAAGATGGAGTTGTCCCTCTCTCTGACA

upper sequence: GLYMA20G31850.3 (Glycine max), 3'ss of exon 2
lower sequence: Vv13s0019g03990.t01 (Vitis vinifera), 3'ss of exon 2
gtggtgctaggacttaatgttt-caagcacaccatttatcttttctgttattaatcttgatagaaatcagcacactta-caaaatatctgattct-tactcagGTTCGTGGAGCTAAAGGTCCAATTTTTGAAGATGGTCCCAATTTTGATTTGGCATTTAGGCTTTTCCACGGGAGTGATGGTGTAGTACCCTTATCTGACA
 |  ||  | |  |  ||| || ||    ||    | |  |  |   ||   |      ||   |||| | |||| ||   | || |||   | | | | ||||| |||||||| |||||||||||||||||||||||||||||||||||| ||||||| ||| ||||||| ||  |||| || || || ||  | ||||  |
-ttctgtgatgcttatatgattgcagaggcatgcctgacttggtgaattgccaga--aaattttaatcggaacacctaatgacatttctctctttctgcacagGTGCGTGGAGCAAAAGGTCCAATTTTTGAAGATGGTCCCAATTTTGATATGGCATTCAGGGTTTTCCATGGCCGTGACGGGGTTGTTCCACTTTCTGGAA

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|19935141|gb|BQ080171.1|BQ080171
EST:     ATGAGCCTACTAACTTCTCATTCTCTTCACCTTTGGCTTTACCAATGCCT                         GTTCGTGGAGCTAAAGGTCCAATTTTTGAAGATGGTCCCAATTTTGATTTG
genomic: ATGAGCCTACTAACTTCTCATTCTCTTCACCTTTGGCTTTACCAATGCCTgtaagttatc ... tcttactcagGTTCGTGGAGCTAAAGGTCCAATTTTTGAAGATGGTCCCAATTTTGATTTG
EST: gi|192299721|gb|FG993301.1|FG993301
EST:     ATGAGCCTACTAACTTCTCATTCTCTTCACCTTTGGCTTTACCAATGCCT                         GTTCGTGGAGCTAAAGGTCCAATTTTTGAAGATGGTCCCAATTTTGATTTG
genomic: ATGAGCCTACTAACTTCTCATTCTCTTCACCTTTGGCTTTACCAATGCCTgtaagttatc ... tcttactcagGTTCGTGGAGCTAAAGGTCCAATTTTTGAAGATGGTCCCAATTTTGATTTG
EST: gi|193420751|gb|FK390926.1|FK390926
EST:     ATTCTCTTCACCTTTGGCTTTACCAATGCCT                         GTTCGTGGAGCTAAAGGTCCAATTTTTGAAGATGGTCCCAATTTTGATTTG
genomic: ATTCTCTTCACCTTTGGCTTTACCAATGCCTgtaagttatc ... tcttactcagGTTCGTGGAGCTAAAGGTCCAATTTTTGAAGATGGTCCCAATTTTGATTTG
EST: gi|192330535|gb|FK022680.1|FK022680
EST:     ATGAGCCTACTAACTTCTCATTCTCTTCACCTTTGGCTTTACCAATGCCT                         GTTCGTGGAGCTAAAGGTCCAATTTTTGAAGATGGTCCCAATTTTGATTTG
genomic: ATGAGCCTACTAACTTCTCATTCTCTTCACCTTTGGCTTTACCAATGCCTgtaagttatc ... tcttactcagGTTCGTGGAGCTAAAGGTCCAATTTTTGAAGATGGTCCCAATTTTGATTTG
EST: gi|192300503|gb|FG988860.1|FG988860
EST:     ATGAGCCCACTAACTTCTCATTCTCTTCACCTTTGGCTTTACCAATGCCT                         GTTCGTGGAGCTAAAGGTCCAATTTTTGAAGATGGTCCCAATTTTGATTTG
genomic: ATGAGCCTACTAACTTCTCATTCTCTTCACCTTTGGCTTTACCAATGCCTgtaagttatc ... tcttactcagGTTCGTGGAGCTAAAGGTCCAATTTTTGAAGATGGTCCCAATTTTGATTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttattaatcttgatagaaatcagcacacttacaaaatatctgattcttactcagGTTCGTGGAGCTAAAGGTCCAATTTTTGAAGATGGTCCCAATTTTGATTTGGCATTTAGGCTTTTCCACGGGAGTGATGGTGTAGTACCCTTATCTGACA
                                            ttcttac  putative branch site (score: 2)
                                            ttcttactc  CT-rich tract
                             ttacaaaatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtggtgctaggacttaatgtttcaagcacaccatttatcttttctgttattaatcttgatagaaatcagcacacttacaaaatatctgattcttactcagGTTCGTGGAGCTAAAGGTCCAATTTTTGAAGATGGTCCCAATTTTGATTTGGCATTTAGGCTTTTCCACGGGAGTGATGGTGTAGTACCCTTATCTGACA

-tggtgct
- - - - - - - - - - - - agcacac
- - - - - - - - - - - - -gcacacc