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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttagtcagttattaaaagattaagcatatgcttttcattgtataactccttttttttttcaatatgatctttgactctcttacattcatgtattttacagGCTGGTCTATTTGTGTATGACATTTTCTGGGTTTTCTTCACCCCAGTGATGGTCAGCGTTGCAAAATCATTTGATGCTCCAATAAAG

Basic information

species Glycine max
transcript GLYMA04G08510.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G08510.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os02g02530.3 (Oryza sativa), 3'ss of exon 6
-ttagtcagttattaaaagattaagcatatgctt--ttcattgtataactccttttttttttcaatatgatctttgactctcttacattcatgtattttacagGCTGGTCTATTTGTGTATGACATTTTCTGGGTTTTCTTCACCCCAGTGATGGTCAGCGTTGCAAAATCATTTGATGCTCCAATAAAG
  |  |   ||  || ||  |   |||  |||||  |  | | | ||| ||  | ||   ||   ||     | ||  || |     ||| | | |  | |||||||| || ||| | ||||| |||||||||||||||||||| || || |||||||| |||||||||||||||||||| || ||||||
cctgttatatttgtagaaactattgcac-tgcttgctgtactttgtaaatcactattaagtt--gtaacgcttatgtatcacgggatttcctttttgattcagGCTGGCCTCTTTTTCTATGATATTTTCTGGGTTTTCTTCACTCCTGTTATGGTCAGTGTTGCAAAATCATTTGATGCACCGATAAAG

upper sequence: GLYMA04G08510.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os05g36070.2 (Oryza sativa), 3'ss of exon 7
--ttagtcagttattaaaagattaagcatatgctttt-cattgtataactccttttttttttcaatatgatctttgactctctta-cattcatgtattttacagGCTGGTCTATTTGTGTATGACATTTTCTGGGTTTTCTTCACCCCAGTGATGGTCAGCGTTGCAAAATCATTTGATGCTCCAATAAAG
  ||    | |||         |  | |||  |      ||||| |||  | |||||  |||     | |  ||||  | || |   ||||   | |  | |||   || || ||| | ||||| ||||||||||| |||||||| ||||| |||||||| ||||| || |||||||||||||||||||||
gcttgcgaaattaaagtccatatttgtatacaccaccgtattgtgtaaagcatttttaattt----gtaacttttgtgtatcgtggtattcccttttaattcagAGCGGACTCTTTTTCTATGATATTTTCTGGGTCTTCTTCACTCCAGTTATGGTCAGTGTTGCCAAGTCATTTGATGCTCCAATAAAG

upper sequence: GLYMA04G08510.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G044348_T04 (Zea mays), 3'ss of exon 7
-----ttagtcagttattaaaagattaagcatatgcttttcattgtataactccttttttttttcaatatgatctttgactctcttacattcatgtattttacagGCTGGTCTATTTGTGTATGACATTTTCTGGGTTTTCTTCACCCCAGTGATGGTCAGCGTTGCAAAATCATTTGATGCTCCAATAAAG
     |  | |      |   |  || ||   ||     | ||| |||   || ||  ||   |  |||||    |  |  |  ||    |  |   |||| |||| ||| || ||||||||||||||||||||||| |||||||| ||||| |||||||| || || ||||| || |||||||||||||||
gtaattggggctagcccttgcattttgagagcatctgaattattttatg-ttcattaattacattcatatg----taaatgcatttttccttttcctttttccagGGTGGACTTTTTGTGTATGACATTTTCTGGGTGTTCTTCACTCCAGTTATGGTCAGTGTGGCTAAATCTTTCGATGCTCCAATAAAG

upper sequence: GLYMA04G08510.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G150251_T01 (Zea mays), 3'ss of exon 7
ttagtcagttattaaaagattaagcatatgcttttcattgtataactccttttttttttcaatatg-atctttgact-ctcttacattcatgtattttacagGCTGGTCTATTTGTGTATGACATTTTCTGGGTTTTCTTCACCCCAGTGATGGTCAGCGTTGCAAAATCATTTGATGCTCCAATAAAG
  |||   ||  |   |  |    ||      |  || || || | ||  | ||  ||   | ||| || | ||| | |  ||    |  |  ||||  |||| ||| || ||||||||||||||||||||||| |||||||| ||||| |||||||| || || ||||| ||||||||||| ||||||
-gagttgatttcttctacttgtttcaacattgtgccagtgaatcattctctgttcattattacatgcatatgtgaatgcaattgtccttttccatttc-cagGGTGGACTTTTTGTGTATGACATTTTCTGGGTGTTCTTCACTCCAGTTATGGTCAGTGTGGCTAAATCTTTTGATGCTCCTATAAAG

upper sequence: GLYMA04G08510.1 (Glycine max), 3'ss of exon 7
lower sequence: AT2G03120.1 (Arabidopsis thaliana), 3'ss of exon 6
-----------------ttagt-cagttattaaaagattaagcatatgcttttcattgtataactccttttttttttca--atatgatctttgactctcttacattcatgtattttacagGCTGGTCTATTTGTGTATGACATTTTCTGGGTTTTCTTCACCCCAGTGATGGTCAGCGTTGCAAAATCATTTGATGCTCCAATAAAG
                 | | | |  || || |||  ||  |  |   ||| |   || | |     ||  |||    |  |    ||| ||   | | |   || | ||    || ||||| || |||||| | ||||| || |||||||||||||| || ||||| ||||| || ||||| ||||| || ||||||||||| |||
gtaagaactgcatcttttgaatgctattcttgaaaactt--gtttggacttctagatgaaaagaaaattcgtttgaaaatgactcaatcattcggtgtttgttatgcttga--cttgcagGCAGGACTATTTTTCTATGATATCTTCTGGGTTTTCTTTACTCCAGTTATGGTTAGTGTTGCCAAATCCTTCGATGCTCCAATTAAG

upper sequence: GLYMA04G08510.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv06s0009g03520.t01 (Vitis vinifera), 3'ss of exon 7
ttagt--cagt-tattaaaagattaagcatatgcttttcattgtata-actccttttttttttcaatatgatctttgactctcttacattcatgtattttacagGCTGGTCTATTTGTGTATGACATTTTCTGGGTTTTCTTCACCCCAGTGATGGTCAGCGTTGCAAAATCATTTGATGCTCCAATAAAG
||  |  |||| | ||      | |    ||||| | |   || ||  | |   ||| |  ||| |  |||| ||||||     |   | | ||    || ||||| || || ||||| ||||| ||||||||||| |||||||| |||||||||||||| |||||||| || || |||||||| || |||
ttgatgccagtatttttgtccctcatatctatgcctgttcctgcattcagtttgtttgtacttctaagtgatttttgaca----tgggtacttgcgaattgcagGCAGGACTTTTTGTTTATGATATTTTCTGGGTCTTCTTCACTCCAGTGATGGTCAGTGTTGCAAAGTCCTTCGATGCTCCTATTAAG

upper sequence: GLYMA04G08510.1 (Glycine max), 3'ss of exon 7
lower sequence: EFJ18240 (Selaginella moellendorffii), 3'ss of exon 6
ttagtcagttattaaaagattaagcatatgcttttcattgtataactccttttttttttcaatatgatctt--tgactctcttacattcatgtattttacagGCTGGTCTATTTGTGTATGACATTTTCTGGGTTTTCTTCACCCCAGTGATGGTCAGCGTTGCAAAATCATTTGATGCTCCAATAAAG
                                          || |   ||   ||    || |  |  ||  ||| |   || |  ||      |   ||||| || ||||| || |||||||| |||||||| |||||||| || |||||||||| |||||| || || ||||||||||| || |||
-----------------------------------------gtaccgtgttcacttacaaaacaacactttgatgatttgttttctctctctgtctcgccagGCCGGGCTATTCGTATATGACATCTTCTGGGTATTCTTCACTCCTGTGATGGTCACCGTTGCGAAGTCCTTTGATGCTCCCATCAAG

upper sequence: GLYMA04G08510.1 (Glycine max), 3'ss of exon 7
lower sequence: EFJ21978 (Selaginella moellendorffii), 3'ss of exon 6
ttagtcagttattaaaagattaagcatatgcttttcattgtataactccttttttttttcaatatgatctt--tgactctcttacattcatgtattttacagGCTGGTCTATTTGTGTATGACATTTTCTGGGTTTTCTTCACCCCAGTGATGGTCAGCGTTGCAAAATCATTTGATGCTCCAATAAAG
                                          || |   ||   ||    || |  |  ||  | | ||  || |  ||      |   ||||| || ||||| || |||||||| |||||||| |||||||| || |||||||||| |||||| || || ||||||||||| || |||
-----------------------------------------gtaccgtgttcacttacaaaacaacactttgatcattcgttttctctctctgtctcgccagGCCGGGCTATTCGTATATGACATCTTCTGGGTATTCTTCACTCCTGTGATGGTCACCGTTGCGAAGTCCTTTGATGCTCCCATCAAG

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|207703563|gb|GD686545.1|GD686545
EST:     GAATTGAAATGCTTTCTCTTGGGTCTTTCAAGACTGGTGCTATTCTCTTG                         GCTGGTCTATTTGTGTATGACATTTTCTGGGTTTTCTTCACCCCAGTGATG
genomic: GAATTGAAATGCTTTCTCTTGGGTCTTTCAAGACTGGTGCTATTCTCTTGgtaggtgttt ... tattttacagGCTGGTCTATTTGTGTATGACATTTTCTGGGTTTTCTTCACCCCAGTGATG
EST: gi|26267892|gb|CA818955.1|CA818955
EST:     GAATTGAAATGCTTTCTCTTGGGTCTTTCAAGACTGGTGCTATTCTCTTG                         GCTGGTCTATTTGTGTATGACATTTTCTGGGTTTTCTTCACCCCAGTGATG
genomic: GAATTGAAATGCTTTCTCTTGGGTCTTTCAAGACTGGTGCTATTCTCTTGgtaggtgttt ... tattttacagGCTGGTCTATTTGTGTATGACATTTTCTGGGTTTTCTTCACCCCAGTGATG
EST: gi|6481874|gb|AW201145.1|AW201145
EST:     GAATTGAAATGCTTTCTCTTGGGTCTTTCAAGACTGGTGCTATTCTCTTG                         GCTGGTCTATTTGTGTATGACATT
genomic: GAATTGAAATGCTTTCTCTTGGGTCTTTCAAGACTGGTGCTATTCTCTTGgtaggtgttt ... tattttacagGCTGGTCTATTTGTGTATGACATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctccttttttttttcaatatgatctttgactctcttacattcatgtattttacagGCTGGTCTATTTGTGTATGACATTTTCTGGGTTTTCTTCACCCCAGTGATGGTCAGCGTTGCAAAATCATTTGATGCTCCAATAAAG
                               ctcttac  putative branch site (score: 3)
     tttttttttcaatatg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttagtcagttattaaaagattaagcatatgcttttcattgtataactccttttttttttcaatatgatctttgactctcttacattcatgtattttacagGCTGGTCTATTTGTGTATGACATTTTCTGGGTTTTCTTCACCCCAGTGATGGTCAGCGTTGCAAAATCATTTGATGCTCCAATAAAG

- - - - - - - - - - - -gcatatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -acattca