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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcctgtgttaatttaaattggagtacaaaacaattttgtatctttgcacgctagtaactttgaatctagttctaagcccctctttacttggcaattatagTTTATGCGGATGGCAGTATATGCTTGGACATTTTACAAAATCAGTGGAGCCCTATATATGATGTAGCTGCAATTCTTACCTCAATCCAG

Basic information

species Glycine max
transcript GLYMA08G40860.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G40860.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os05g08960.2 (Oryza sativa), 3'ss of exon 4
----tcctgtgttaatttaaat-tggagtacaaaacaattttgtatctttgcacgctagtaactttgaatctagttctaagcccctctttacttggcaattatagTTTATGCGGATGGCAGTATATGCTTGGACATTTTACAAAATCAGTGGAGCCCTATATATGATGTAGCTGCAATTCTTACCTCAATCCAG
     | |||||  |   |  | || |    | || |   |  |||  ||| |      |   ||| | | |    ||||     || ||  ||  ||  || ||||||||| ||||| || |||||||| || ||  ||||||| ||||||||||| ||||||||||||||||| || || || || ||||||
tgctacttgtgtggaagcacttatgtaccttagaatagcatgatattgttgtatctccatttgttttacttt---cctaacattttcctt--ttatcatgtacagTTTATGCTGATGGGAGCATATGCTTAGATATACTACAAAACCAGTGGAGCCCCATATATGATGTAGCTGCTATACTCACATCCATCCAG

upper sequence: GLYMA08G40860.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G110983_T02 (Zea mays), 3'ss of exon 3
tcctgtgttaatttaaattggagtacaaaacaattttgtatctttgcacgctagtaactttgaatctagttctaagcccctctttacttggcaattatagTTTATGCGGATGGCAGTATATGCTTGGACATTTTACAAAATCAGTGGAGCCCTATATATGATGTAGCTGCAATTCTTACCTCAATCCAG
                         |  ||| || |  |     |     ||| |  |     || |   ||    |||     |  ||  ||  |  ||||||||| ||||| || |||||||| || ||  | || ||||||||||| || ||||||||||||||||| || || || |||||||||
------------------------tcttaactatatgatggtactatcttctaatgcccacttatatgtgtc---accctgacatttttctcatatgcagtttatgctgatggaagcatatgcttagATATCCTGCAGAATCAGTGGAGTCCGATATATGATGTAGCTGCGATACTCACGTCAATCCAG

upper sequence: GLYMA08G40860.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G110983_T03 (Zea mays), 3'ss of exon 2
---tcctgtgttaatttaaattggagtacaaaacaattttgtatctttgcacgctagtaactttgaatctagttctaagcccctctttacttggcaattatagTTTATGCGGATGGCAGTATATGCTTGGACATTTTACAAAATCAGTGGAGCCCTATATATGATGTAGCTGCAATTCTTACCTCAATCCAG
     |||  ||| | | |         |  ||| || |  |     |     ||| |  |     || |   ||    |||     |  ||  ||  |  ||||||||| ||||| || |||||||| || ||  | || ||||||||||| || ||||||||||||||||| || || || |||||||||
ctcctctggcttattctgatacaactctcttaactatatgatggtactatcttctaatgcccacttatatgtgtc---accctgacatttttctcatatgcagTTTATGCTGATGGAAGCATATGCTTAGATATCCTGCAGAATCAGTGGAGTCCGATATATGATGTAGCTGCGATACTCACGTCAATCCAG

upper sequence: GLYMA08G40860.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv01s0026g01770.t01 (Vitis vinifera), 3'ss of exon 5
tcctgtgttaat--ttaaattggagtacaaaacaattttgt---atctttgcacgctagtaactt--tgaatctagttctaagcccctctttacttggcaattatagTTTATGCGGATGGCAGTATATGCTTGGACATTTTACAAAATCAGTGGAGCCCTATATATGATGTAGCTGCAATTCTTACCTCAATCCAG
     || | ||  | |   |   ||    | |  |||||    | ||   |    || ||  ||  ||   || | ||||||  |   |   |||     |   ||||||||||||||| || || ||||| |||||| |||||||||||||||| || || |||||||||||||| || ||||| || ||||||
---catgatgatgatcatcataatgtttttagcttttttgaggaaactaaactaagtattattttgctgttgctggctctaagttctcttaatcttt----tgtcagTTTATGCGGATGGAAGCATTTGCTTAGACATTCTACAAAATCAGTGGAGTCCAATTTATGATGTAGCTGCCATACTTACATCCATCCAG

upper sequence: GLYMA08G40860.1 (Glycine max), 3'ss of exon 4
lower sequence: EFJ16328 (Selaginella moellendorffii), 3'ss of exon 3
tcctgtgttaatttaaattggagtacaaaacaattttgtatctttgcacgctagtaactttgaatctagttctaagcccctctttacttggcaatt-atagTTTATGCGGATGGCAGTATATGCTTGGACATTTTACAAAATCAGTGGAGCCCTATATATGATGTAGCTGCAATTCTTACCTCAATCCAG
                                    ||  ||  |    |||  |  |||||| | |  |  |       |  |||||   |  ||   ||||||||| ||||| ||||| ||| | |||||| | |||||||| ||||| || || || ||||| || ||||||||||| || || |||
-----------------------------------gtgagtccct---tgcttctttctttgagtttcttctt------tttcttactcatctcttcgcagTTTATGCTGATGGAAGTATTTGCCTCGACATTCTGCAAAATCAATGGAGTCCGATCTACGATGTTGCGGCAATTCTTACGTCCATACAG

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|48575511|gb|CO036440.1|CO036440
EST:     TAATAAACCACCTACTGTGCGCTTTGTTTCTCGAATGTTTCATCCTAACA                         TTTATGCGGATGGCAGTATATGCTTGGACATTTTACAAAATCAGTGGAGCC
genomic: TAATAAACCACCTACTGTGCGCTTTGTTTCTCGAATGTTTCATCCTAACAgtgagtacaa ... gcaattatagTTTATGCGGATGGCAGTATATGCTTGGACATTTTACAAAATCAGTGGAGCC
EST: gi|192333434|gb|FK023963.1|FK023963
EST:     TAATAAACCACCTACTGTGCGCTTTGTTTCTCGAATGTTTCATCCTAACA                         TTTATGCGGATGGCAGTATATGCTTGGACATTTTACAAAATCAGTGGAGCC
genomic: TAATAAACCACCTACTGTGCGCTTTGTTTCTCGAATGTTTCATCCTAACAgtgagtacaa ... gcaattatagTTTATGCGGATGGCAGTATATGCTTGGACATTTTACAAAATCAGTGGAGCC
EST: gi|10233426|gb|BE802314.1|BE802314
EST:     TAATAAACCACCTACTGTGCGCTTTGTTTCTCGAATGTTTCATCCTAACA                         TTTATGCGGATGGCAGTATATGCTTGGACATTTTACAAAATCAGTGGAGCC
genomic: TAATAAACCACCTACTGTGCGCTTTGTTTCTCGAATGTTTCATCCTAACAgtgagtacaa ... gcaattatagTTTATGCGGATGGCAGTATATGCTTGGACATTTTACAAAATCAGTGGAGCC
EST: gi|192297623|gb|FG989571.1|FG989571
EST:     TAATAAACCACCTACTGTGCGCTTTGTTTCTCGAATGTTTCATCCTAACA                         TTTATGCAGATGGCAGTATATGCTTGGACATTTTACAAAATCAGTGGAGCC
genomic: TAATAAACCACCTACTGTGCGCTTTGTTTCTCGAATGTTTCATCCTAACAgtgagtacaa ... gcaattatagTTTATGCGGATGGCAGTATATGCTTGGACATTTTACAAAATCAGTGGAGCC
EST: gi|192306185|gb|FG995035.1|FG995035
EST:     TAATAAACCACCTACTGTGCGCTTTGTTTCTCGAATGTTTCATCCTAACA                         TTTATGCGGATGGCAGTATATGCTTGGACATTTTACAAAATCAGTGGAGCC
genomic: TAATAAACCACCTACTGTGCGCTTTGTTTCTCGAATGTTTCATCCTAACAgtgagtacaa ... gcaattatagTTTATGCGGATGGCAGTATATGCTTGGACATTTTACAAAATCAGTGGAGCC
EST: gi|192306775|gb|FG998142.1|FG998142
EST:     TGTTTCATCCTAACA                         TTTATGCGGATGGCAGTATATGCTTGGACATTTTACAAAATCAGTGGAGCC
genomic: TGTTTCATCCTAACAgtgagtacaa ... gcaattatagTTTATGCGGATGGCAGTATATGCTTGGACATTTTACAAAATCAGTGGAGCC
EST: gi|209721200|gb|BW665731.1|BW665731
EST:     TAATAAACCACCTACTG--CGCTTTGTTTCTCGAATGTTTCATCCTAACA                         TTTATGCGGATGGCAGTATATGCTTGGACATTTTACAAAATCAGTGGAGCC
genomic: TAATAAACCACCTACTGTGCGCTTTGTTTCTCGAATGTTTCATCCTAACAgtgagtacaa ... gcaattatagTTTATGCGGATGGCAGTATATGCTTGGACATTTTACAAAATCAGTGGAGCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcacgctagtaactttgaatctagttctaagcccctctttacttggcaattatagTTTATGCGGATGGCAGTATATGCTTGGACATTTTACAAAATCAGTGGAGCCCTATATATGATGTAGCTGCAATTCTTACCTCAATCCAG
      tagtaac  putative branch site (score: 1)
                                               aattata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcctgtgttaatttaaattggagtacaaaacaattttgtatctttgcacgctagtaactttgaatctagttctaagcccctctttacttggcaattatagTTTATGCGGATGGCAGTATATGCTTGGACATTTTACAAAATCAGTGGAGCCCTATATATGATGTAGCTGCAATTCTTACCTCAATCCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC