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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactgtttaatgcttaagatgttgatttgtttatgaatatacatgacttgtcccttcccttcaacttcatgctcaagcacaactctagaaaatatttggacatcactgattgacttgttctgtacattgtttcagAAATTGGTTATAACTCCAGTAAAGAAAGAGCTGGGTCTGGCATTCAAGGGGAACCAGAGGATGGTGGTTGAAGCACTTGAG

Basic information

species Glycine max
transcript GLYMA08G47890.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G47890.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os08g42560.1 (Oryza sativa), 3'ss of exon 6
gtactgtttaatgcttaagatgttgatttgtttatgaatatacatgacttgtcccttcccttcaacttcatgctcaagcacaactctagaaaatatttggacatcactgattgacttgttctgtacattgtttcagAAATTGGTTATAACTCCAGTAAAGAAAGAGCTGGGTCTGGCATTCAAGGGGAACCAGAGGATGGTGGTTGAAGCACTTGAG
     ||    |   |   ||||    || |||   | | | |   |   |||  ||     ||  || |       | |  |  || ||    |||||        ||     ||  | || | |||||   |||||| | ||||||   ||   ||||||||| ||||| || || || ||||||||||| | |||||||||||||||| | |||
-----gtgagttaactgtcatgtctgattctttggtattcttctgcaggagtcattttgtaacatattaaataatgtgtattagacttgagctaatttgcttgctgttg-----ctactactttccattg---cagAAACTTGTTATAGTGCCCTCAAAGAAAGACCTGGGGCTTGCTTTTAAGGGGAACCAAAAGATGGTGGTTGAAGCATTGGAG

upper sequence: GLYMA08G47890.1 (Glycine max), 3'ss of exon 4
lower sequence: AT1G29880.1 (Arabidopsis thaliana), 3'ss of exon 6
gtactgtttaatgcttaagatgttgatttgtttatgaatatacatgacttgtcccttcccttcaacttcatgctcaagcacaactctagaaaatatttggacatcactgattgacttgttctgtacattgtttcagAAATTGGTTATAACTCCAGTAAAGAAAGAGCTGGGTCTGGCATTCAAGGGGAACCAGAGGATGGTGGTTGAAGCACTTGAG
                                                               |  ||  ||  ||    ||    |        ||   || |  |   || || || | | |   || | ||||||| | || |||||||| || |||||||| |||||||| ||||||||||| || || | ||  ||||||||| |  | |||
-------------------------------------------------------------gtattttagtgaacagattcattcatctctgtctttattacttgtcc--ttaacatggt-tatcttttatatcagAAACTTGTGATAACTCCTGTGAAGAAAGAACTGGGTCTTGCATTCAAGGGAAATCAAAAGAATGTGGTTGAATCTTTGGAG

upper sequence: GLYMA08G47890.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv01s0150g00150.t01 (Vitis vinifera), 3'ss of exon 6
gtactgtttaatgcttaagatgttgatttgtttatgaatatacatgacttgtcccttcccttcaacttcatgctcaagcacaactctagaaaatatttggacatcactgattgacttg---ttctgtacattgtttcagAAATTGGTTATAACTCCAGTAAAGAAAGAGCTGGGTCTGGCATTCAAGGGGAACCAGAGGATGGTGGTTGAAGCACTTGAG
                                                            |    ||| ||||   | ||  |       |  | | | ||||  | ||  || ||||   ||  ||   |  || ||||||||||||||| || |||||||||| || |||||||| || |||| ||| || || | |||||||||||||||  | |||
-----------------------------------------------------------gtaatgctttatgcc--aacatcatagcgatagttctatagacacgattgcatggcttgatgtttggtgtgtgattccagAAATTGGTTATAGCTACAGTAAAGAAGGAACTGGGTCTTGCTTTCAGGGGTAATCAAAAGATGGTGGTTGAAGCTTTGGAG

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|193314660|gb|FK280894.1|FK280894
EST:     GTGTTCCGTTAGTGGCTCATGAAAAATTTGCAGAACCTAAGGAAGTGGAG                         AAATTGGTTATAACTCCAGTAAAGAAAGAGCTGGGTCTGGCATTCAAGGGG
genomic: GTGTTCCGTTAGTGGCTCATGAAAAATTTGCAGAACCTAAGGAAGTGGAGgtactgttta ... attgtttcagAAATTGGTTATAACTCCAGTAAAGAAAGAGCTGGGTCTGGCATTCAAGGGG
EST: gi|6916252|gb|AW397782.1|AW397782
EST:     GTGTTCCGTTAGTGGCTCATGAAAAATTTGCAGAACCTAAGGAAGTGGAG                         AAATTGGTTATAACTCCAGTAAAGAAAGAGCTGGGTCTGGCATTCAAGGGG
genomic: GTGTTCCGTTAGTGGCTCATGAAAAATTTGCAGAACCTAAGGAAGTGGAGgtactgttta ... attgtttcagAAATTGGTTATAACTCCAGTAAAGAAAGAGCTGGGTCTGGCATTCAAGGGG
EST: gi|208119562|gb|GD917411.1|GD917411
EST:     TGCAGAACCTAAGGAAGTGGAG                         AAATTGGTTATAACTCCAGTAAAGAAAGAGCTGGGTCTGGCATTCAAGGGG
genomic: TGCAGAACCTAAGGAAGTGGAGgtactgttta ... attgtttcagAAATTGGTTATAACTCCAGTAAAGAAAGAGCTGGGTCTGGCATTCAAGGGG
EST: gi|207703938|gb|GD685928.1|GD685928
EST:     AACCTAAGGAAGTGGAG                         AAATTGGTTATAACTCCAGTAAAGAAAGAGCTGGGTCTGGCATTCAAGGGG
genomic: AACCTAAGGAAGTGGAGgtactgttta ... attgtttcagAAATTGGTTATAACTCCAGTAAAGAAAGAGCTGGGTCTGGCATTCAAGGGG
EST: gi|192297232|gb|FG992371.1|FG992371
EST:     CTAAGGAAGTGGAG                         AAATTGGTTATAACTCCAGTAAAGAAAGAGCTGGGTCTGGCATTCAAGGGG
genomic: CTAAGGAAGTGGAGgtactgttta ... attgtttcagAAATTGGTTATAACTCCAGTAAAGAAAGAGCTGGGTCTGGCATTCAAGGGG
EST: gi|208079475|gb|GD877651.1|GD877651
EST:     TGCAGAACCTAAGGAAGTGGAG                         AAATTGGTTATAACTCCAGTAAAGAAAGAGCTGGGTCTGGCATTCAAGGGG
genomic: TGCAGAACCTAAGGAAGTGGAGgtactgttta ... attgtttcagAAATTGGTTATAACTCCAGTAAAGAAAGAGCTGGGTCTGGCATTCAAGGGG
EST: gi|16104863|gb|BI892603.1|BI892603
EST:     GTGTTCCGTTAGTGGCTCATGAAAAATTTGCAGAACCTAAGGAAGTGGAG                         AAATTGGTTATAACTCCAGTAAAGAAAGAGCTGGGTCTGGCATTCAAGGGG
genomic: GTGTTCCGTTAGTGGCTCATGAAAAATTTGCAGAACCTAAGGAAGTGGAGgtactgttta ... attgtttcagAAATTGGTTATAACTCCAGTAAAGAAAGAGCTGGGTCTGGCATTCAAGGGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aactctagaaaatatttggacatcactgattgacttgttctgtacattgtttcagAAATTGGTTATAACTCCAGTAAAGAAAGAGCTGGGTCTGGCATTCAAGGGGAACCAGAGGATGGTGGTTGAAGCACTTGAG
                           gattgac  putative branch site (score: 3)
                                              ttgtttc  putative PPT
     tagaaaatattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtactgtttaatgcttaagatgttgatttgtttatgaatatacatgacttgtcccttcccttcaacttcatgctcaagcacaactctagaaaatatttggacatcactgattgacttgttctgtacattgtttcagAAATTGGTTATAACTCCAGTAAAGAAAGAGCTGGGTCTGGCATTCAAGGGGAACCAGAGGATGGTGGTTGAAGCACTTGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC