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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cctctttacttgtaaatttgattggttctcattccaactgtgttcgtgcatgcattgtcacagctaactctattgagatatgttccttgacctgataaagATATTGTTACGAGGATGATTGCACAAAAGAGGACCCCTTATCACAGGAGGCTTTCCGCACACTAGCCATGCCATTACCATATTCAAAGCAGCATCACTCT

Basic information

species Glycine max
transcript GLYMA20G38660.1
intron # 5
splice site 3'
intron type U12 (go to U12 genes for details)

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G38660.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv13s0067g03560.t01 (Vitis vinifera), 3'ss of exon 5
cctctttacttgtaaatttgattggttctcattccaactgtgttc-gtgcatgcattgtcacagctaa---ctctattgagatatgtt-ccttgacctgataaagATATTGTTACGAGGATGATTGCACAAAAGAGGACCCCTTATCACAGGAGGCTTTCCGCACACTAGCCATGCCATTACCATATTCAAAGCAGCATCACTCT
     ||| ||||  ||     |  |   | ||      |||||  |||||||  ||    | | |||   || | |  ||   | || || |||||||||  ||||| |||||| | ||||| ||||| |||||||| || || |||||||| |  ||||| | ||| ||| |||||||||| || ||||||||||||||||| 
-----ttagttgtggatgctcattttcacctttgtgctggtgttttgtgcatgagttacggctggtaatttctttttccagtcgttttaccctgacctgatttagATACTGTTACCAAGATGACTGCACCAAAGAGGATCCTTTGTCACAGGACGGATTCCGGAAACTTGCCTTGCCATTACCCTACTCAAAGCAGCATCACTCG
















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|15001094|gb|BI321908.1|BI321908
EST:     AATATCTATCTGCAAGCTGGCCTTTCTGCTCTCAAGACACC                         ATATTGTTATGAGGATGATTGCACAAAAGAGGACCCCTTATCACAGGAGGC
genomic: AATATCTATCTGCAAGCTGGCCTTTCTGCTCTCAAGACACCgtatccttta ... cctgataaagATATTGTTACGAGGATGATTGCACAAAAGAGGACCCCTTATCACAGGAGGC
EST: gi|5666950|gb|AI930986.1|AI930986
EST:     CCCTTGCTCAATATCTATCTGCAAGCTGGCCTTTCTGCTCTCAAGACACC                         ATATTGTTATGAGGATGATTGCACAAAAGAGGACCCCTTATCACAGGAGGC
genomic: CCCTTGCTCAATATCTATCTGCAAGCTGGCCTTTCTGCTCTCAAGACACCgtatccttta ... cctgataaagATATTGTTACGAGGATGATTGCACAAAAGAGGACCCCTTATCACAGGAGGC
EST: gi|208045200|gb|GD839734.1|GD839734
EST:     CCCTTGCTCAATATCTATCTGCAAGCTGGCCTTTCTGCTCTCAAGACACC                         ATATTGTTACGAGGATGATTGCACAAAAGAGGACCCCTTATCACAGGAGGC
genomic: CCCTTGCTCAATATCTATCTGCAAGCTGGCCTTTCTGCTCTCAAGACACCgtatccttta ... cctgataaagATATTGTTACGAGGATGATTGCACAAAAGAGGACCCCTTATCACAGGAGGC
EST: gi|15662642|gb|BI700013.1|BI700013
EST:     CCCTTGCTCAATATCTATCTGCAAGCTGGCCTTTCTGCTCTCAAGACACC                         ATATTGTTATGAGGATGATTGCACAAAAGAGGACCCCTTATCACAGGAGGC
genomic: CCCTTGCTCAATATCTATCTGCAAGCTGGCCTTTCTGCTCTCAAGACACCgtatccttta ... cctgataaagATATTGTTACGAGGATGATTGCACAAAAGAGGACCCCTTATCACAGGAGGC
EST: gi|207815488|gb|GD788667.1|GD788667
EST:     TCTGCAAGCTGGCCTTTCTGCTCTCAAGACACC                         ATATTGTTACGAGGATGATTGCACAAAAGAGGACCCCTTATCACAGGAGGC
genomic: TCTGCAAGCTGGCCTTTCTGCTCTCAAGACACCgtatccttta ... cctgataaagATATTGTTACGAGGATGATTGCACAAAAGAGGACCCCTTATCACAGGAGGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgcatgcattgtcacagctaactctattgagatatgttccttgacctgataaagATATTGTTACGAGGATGATTGCACAAAAGAGGACCCCTTATCACAGGAGGCTTTCCGCACACTAGCCATGCCATTACCATATTCAAAGCAGCATCACTCT
                                     ttccttgac  putative branch site 
                                atatgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cctctttacttgtaaatttgattggttctcattccaactgtgttcgtgcatgcattgtcacagctaactctattgagatatgttccttgacctgataaagATATTGTTACGAGGATGATTGCACAAAAGAGGACCCCTTATCACAGGAGGCTTTCCGCACACTAGCCATGCCATTACCATATTCAAAGCAGCATCACTCT

- - - - - - - - - - - - - - - - tccaact
- - - - - - - - - - - - - - - - - - - - - - - -gcatgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtcaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gctaact