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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagttgtgttcttgagaaaatatgtagtgttccatttgactactgttgtttcttggttggtaatattatgatgcttggttactgtagGAGGAAAGAAGAATGTCTTTGCCAAAATATCAGGTGCATGATGAAAGTAGCCAG

Basic information

species Glycine max
transcript GLYMA05G34280.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA05G34280.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os09g38790.1 (Oryza sativa), 3'ss of exon 5
----------------------gtgagttgtgttcttgagaaaatatgtagtgt-tccatttgactact-gttgtttcttggttggtaatatta--tgatgcttggttactgtagGAGGAAAGAAGAATGTCTTTGCCAAAATATCAGGTGCATGATGAAAGTAGCCAG----------------------------------------------
                          ||| |  || | ||| |  || | || | |   ||  | |||| | | |   || |  ||| || | |  |  |  |||  |  ||||||||||||||||| ||||  | || || ||||||||||||||||||| |||||||                                              
gtatattttccatcctctctttagttgttattctcattagagatcatttggtatatatgttacattactagatatgagtttgagggttatctcaaatatttgttgacttgtgtagGAGGAAAGAAGATTGTCGCTACCCAAGTATCAGGTGCATGATGAAACTAGCCAGGTAAGTTCTGATTTTTATAATTTTATATCTGTAATATTAATGATAT

upper sequence: GLYMA05G34280.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os09g38790.3 (Oryza sativa), 3'ss of exon 5
----------------------gtgagttgtgttcttgagaaaatatgtagtgt-tccatttgactact-gttgtttcttggttggtaatatta--tgatgcttggttactgtagGAGGAAAGAAGAATGTCTTTGCCAAAATATCAGGTGCATGATGAAAGTAGCCAG
                          ||| |  || | ||| |  || | || | |   ||  | |||| | | |   || |  ||| || | |  |  |  |||  |  ||||||||||||||||| ||||  | || || ||||||||||||||||||| |||||||
gtatattttccatcctctctttagttgttattctcattagagatcatttggtatatatgttacattactagatatgagtttgagggttatctcaaatatttgttgacttgtgtagGAGGAAAGAAGATTGTCGCTACCCAAGTATCAGGTGCATGATGAAACTAGCCAG

upper sequence: GLYMA05G34280.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G081812_T02 (Zea mays), 3'ss of exon 5
--gtgagttgtgttcttgagaaaatatgtagtgttccatttgactactgttgtttcttg-------gttggtaatattatgatgct--tggttactgtagGAGGAAAGAAGAATGTCTTTGCCAAAATATCAGGTGCATGATGAAAGTAGCCAG
   ||  |       |     | || | |  |  |  | |||   |  |   | | |         |||  |||| | |   |  |  ||  |  ||||||||||||||||  |||| |||||||| ||||||||||||||||||| |||||||
gtatgcttctaaccatcatctatatgtcttttagtttacttgtgcatagcgatatatgattgaaatgttaataatctcaattttttgctgtcttttgtagGAGGAAAGAAGGTTGTCGTTGCCAAAGTATCAGGTGCATGATGAAACTAGCCAG

upper sequence: GLYMA05G34280.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G081812_T01 (Zea mays), 3'ss of exon 5
--gtgagttgtgttcttgagaaaatatgtagtgttccatttgactactgttgtttcttg-------gttggtaatatta--tgatgcttggttactgtagGAGGAAAGAAGAATGTCTTTGCCAAAATATCAGGTGCATGATGAAAGTAGCCAG----------------------------------------------
   ||  |       |     | || | |  |  |  | |||   |  |   | | |         |||  |||| | |  |  |   ||  |  ||||||||||||||||  |||| |||||||| ||||||||||||||||||| |||||||                                              
gtatgcttctaaccatcatctatatgtcttttagtttacttgtgcatagcgatatatgattgaaatgttaataatctcaattttttgctgtcttttgtagGAGGAAAGAAGGTTGTCGTTGCCAAAGTATCAGGTGCATGATGAAACTAGCCAGGTAAGTTGTGTTTCTTATGATACTATTATTGTAGTTTCTCAAACAA

upper sequence: GLYMA05G34280.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv03s0017g02160.t01 (Vitis vinifera), 3'ss of exon 5
gtgagttgt--gtt-cttgagaaaatatgtagtgttccatttgactactgttgtttcttggttggtaatattatga----tgcttgg--ttactgtagGAGGAAAGAAGAATGTCTTTGCCAAAATATCAGGTGCATGATGAAAGTAGCCAG
|| ||||||  ||| | |      || | |  ||  | || |      || |||   ||||||    | | | | |    || |||   |  ||  ||||||||||||| ||||| || |  || ||||||||||||||||||| |||||||
gttagttgttagttacctttctggatgtatcatgc-caatcttttggatgctgtactttggtttaacacactttaaattgtgtttgaaatatctacagGAGGAAAGAAGGATGTCATTACTGAAGTATCAGGTGCATGATGAAACTAGCCAG

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|254326254|gb|GR840846.1|GR840846
EST:     CTGCCACCAACGAAGTCTACTTGGTTTGGGATGATGAGGCAATGTCCATG                         GAGGAAAGAAGAATGTCTTTGCCAAAATATCAGGTGCATGATGAAAGTAGC
genomic: CTGCCACCAACGAAGTCTACTTGGTTTGGGATGATGAGGCAATGTCCATGgtgagttgtg ... gttactgtagGAGGAAAGAAGAATGTCTTTGCCAAAATATCAGGTGCATGATGAAAGTAGC
EST: gi|6095024|gb|AW119691.1|AW119691
EST:     CTGCCACCAACGAAGTCTACTTGGTTTGNGATGATGAGGCAATGTCCATG                         GAGGAAAGAAGAATGTC
genomic: CTGCCACCAACGAAGTCTACTTGGTTTGGGATGATGAGGCAATGTCCATGgtgagttgtg ... gttactgtagGAGGAAAGAAGAATGTC
EST: gi|6846393|gb|AW348683.1|AW348683
EST:     CTGCCACCAACGAAGTCTACTTGGTTTGGGATGATGAGGCAATGTCCATG                         GAGGAAAGAAGAATGTCTTTGCCAAAATATCAGGTGCATGATGAAAGTAGC
genomic: CTGCCACCAACGAAGTCTACTTGGTTTGGGATGATGAGGCAATGTCCATGgtgagttgtg ... gttactgtagGAGGAAAGAAGAATGTCTTTGCCAAAATATCAGGTGCATGATGAAAGTAGC
EST: gi|7042083|gb|AW471977.1|AW471977
EST:     CTGCCACCAACGAAGTCTACTTGGTTTGGGATGATGAGGCAATGTCCATG                         GAGGAAAGAAGAATGTCTTTGCCAAAATATCAGGTGCATGATGAAAGTAGC
genomic: CTGCCACCAACGAAGTCTACTTGGTTTGGGATGATGAGGCAATGTCCATGgtgagttgtg ... gttactgtagGAGGAAAGAAGAATGTCTTTGCCAAAATATCAGGTGCATGATGAAAGTAGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catttgactactgttgtttcttggttggtaatattatgatgcttggttactgtagGAGGAAAGAAGAATGTCTTTGCCAAAATATCAGGTGCATGATGAAAGTAGCCAG
 atttgac  putative branch site (score: 4)
                            taatattatgat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagttgtgttcttgagaaaatatgtagtgttccatttgactactgttgtttcttggttggtaatattatgatgcttggttactgtagGAGGAAAGAAGAATGTCTTTGCCAAAATATCAGGTGCATGATGAAAGTAGCCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG