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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaattgcgttttacacttctgaagcctctataaaattaagccatctatgatctatcaactaatattaaagtaatgaagcttcattctctgtagTTTGGTGATGCTAGTGGCATACAATCACCTGTTTCATTTGGTGGATTTGGAAGCTTGACCAGGCACCTGGGGAGACTGTCAGCTG

Basic information

species Glycine max
transcript GLYMA14G05100.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA14G05100.1 (Glycine max), 3'ss of exon 12
lower sequence: LOC_Os08g32630.5 (Oryza sativa), 3'ss of exon 10
gtaaattgcgttttacacttctgaagcctctataaaattaagccatctatgatctatcaactaatattaaagtaatgaagcttcattctctgtagTTTGGTGATGCTAGTGGCATACAATCACCTGTTTCATTTGGTGGATTTGGAAGCTTGACCAGGCACCTGGGGAGACTGTCAGCTG
| |       || |   |||| |||||||   |    |  | |||| | |   |  | ||||| ||   | |   |  |      | | ||  || |||||||||||||||| || || ||||||||||| ||||| || |||||||||||||| ||||| || ||  |  |||||  ||
gcatgccat-ttctctgcttcggaagcct--gttggctgtacccatttctccccc-ttaactagta---acgcccttcactgctttgcacttcagGTTGGTGATGCTAGTGGAATCCAGTCACCTGTTTCTTTTGGAGGTTTTGGAAGCTTGACAAGGCATCTTGGTCGTTTGTCAAATG

upper sequence: GLYMA14G05100.1 (Glycine max), 3'ss of exon 12
lower sequence: GRMZM5G851815_T02 (Zea mays), 3'ss of exon 11
gtaaattgcgttttacacttctgaagcctctataaaattaagcc--atctatgatctatcaactaatatta--aagtaatgaagcttcattctctgtagTTTGGTGATGCTAGTGGCATACAATCACCTGTTTCATTTGGTGGATTTGGAAGCTTGACCAGGCACCTGGGGAGACTGTCAGCTG
                 | | |||    ||| | ||   |||||  ||   |  |  | |  | | ||||   ||  | ||| |||   | |  |  || |||| ||||||||||| ||||| ||||||||||| ||||| || |||||||||||||| || || || ||  |  ||||   ||
----------------gcatgtgat-tttctcttaacagaagccttattactcctgcacctgcaagtattctcaatcactgatgctct-tgcatttcagGTTGGCGATGCTAGTGGAATACAGTCACCTGTTTCTTTTGGAGGTTTTGGAAGCTTGACGAGACATCTTGGCCGTTTGTCTAGTG

upper sequence: GLYMA14G05100.1 (Glycine max), 3'ss of exon 12
lower sequence: AT2G32640.1 (Arabidopsis thaliana), 3'ss of exon 11
gtaaattgcgttttacacttctgaagcctctataa--aattaagccatctatgatct-atcaactaat--attaaagtaatgaagcttcattctctgtagTTTGGTGATGCTAGTGGCATACAATCACCTGTTTCATTTGGTGGATTTGGAAGCTTGACCAGGCACCTGGGGAGACTGTCAGCTG
||   ||  |||      |    |||| || |  |  | ||     ||  || || | || ||||||   || ||||| |   |      || |    |||||||||||||||| || || |||||||||||||||||||| || |||||||| |||||||| ||||| || ||| ||||   ||
gttggtttggttcatttatatataagcttccaagataagtttgcggattgataatttgataaactaaataatcaaagttacttacaaattttttactcagTTTGGTGATGCTAGCGGTATTCAATCACCTGTTTCATTTGGGGGTTTTGGAAGTTTGACCAGACACCTTGGAAGATTGTCCAATG

upper sequence: GLYMA14G05100.1 (Glycine max), 3'ss of exon 12
lower sequence: Vv12s0059g01150.t01 (Vitis vinifera), 3'ss of exon 11
gtaaattgcgttttacacttctgaagcctctataaaattaagccatctatgatctatcaactaatattaaagtaatgaagcttcattctctgtagTTTGGTGATGCTAGTGGCATACAATCACCTGTTTCATTTGGTGGATTTGGAAGCTTGACCAGGCACCTGGGGAGACTGTCAGCTG
||   || | || || |||||| ||||||| |  | || | |       | |  |||||| |   ||  ||||  |  |   |||||||||| |||||||||||||||| |||||||| ||||| |||||||||||||| ||||| ||||||||||||||||| | |||  ||||| |||
gtgttttacattatatacttctaaagcctccaatagataatg------gtcacatatcaaatggaatggaagtgttacaaaatcattctctgcagTTTGGTGATGCTAGCGGCATACAGTCACCAGTTTCATTTGGTGGTTTTGGGAGCTTGACCAGGCACCTTGAGAGGTTGTCAACTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agccatctatgatctatcaactaatattaaagtaatgaagcttcattctctgtagTTTGGTGATGCTAGTGGCATACAATCACCTGTTTCATTTGGTGGATTTGGAAGCTTGACCAGGCACCTGGGGAGACTGTCAGCTG
                  aactaat  putative branch site (score: 2)
                                        cttcattctct  putative PPT
              tatcaactaatattaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaattgcgttttacacttctgaagcctctataaaattaagccatctatgatctatcaactaatattaaagtaatgaagcttcattctctgtagTTTGGTGATGCTAGTGGCATACAATCACCTGTTTCATTTGGTGGATTTGGAAGCTTGACCAGGCACCTGGGGAGACTGTCAGCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG