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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aatttttcagaatcacttaattaagttcttttataactctttggaaaatcaatatggatctgtaaagactttctaatatattgctttccatgacatccagACGCAGACAGTTTCCGAGTTGAAGGACTTTGTGAAAAAGCTGAACTCATTGCCAGAGATGACC

Basic information

species Glycine max
transcript GLYMA10G35210.1
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G35210.2 (Glycine max), 3'ss of exon 12
lower sequence: AT3G54860.1 (Arabidopsis thaliana), 3'ss of exon 12
-----aatttttcagaatcacttaattaagttcttttataactctttggaaaatcaatatggatctgtaaagactttctaatatattgctttccatgacatccagACGCAGACAGTTTCCGAGTTGAAGGACTTTGTGAAAAAGCTGAACTCATTGCCAGAGATGACC
|| | || | | | | | || | | || | || | || | | | | | | | ||| | || || | ||||| ||||||||||| ||| ||||||||||||| || ||||| |||||| | |||||||||||
catgttatgccttaggaatgatcagcc---tattcatagagtttactgttagattattagttgtatccagatatctaatggggtatgg--ttatataatgcacagACCCAGACAGTTTCTGAGCTGAAGGACTTTGTTAAGAAGCTTAACTCACTACCAGAGATGACA

upper sequence: GLYMA10G35210.2 (Glycine max), 3'ss of exon 12
lower sequence: Vv13s0019g04720.t01 (Vitis vinifera), 3'ss of exon 12
--aatttttcagaatcacttaatta----agttcttttataactctttggaaaatcaatatggatctgtaaagactttctaatatattgctttccatgacatccagACGCAGACAGTTTCCGAGTTGAAGGACTTTGTGAAAAAGCTGAACTCATTGCCAGAGATGACC
| || | | |||| | | || ||| ||||| | | | || | | | | || | ||||| ||| | | | || | | ||||| |||||||| || || || ||||||||||| |||||||| || ||||||||||| || ||
tgccctgttatgttttgcttagaaactgcatctcggttacttgtcttttggaga-cagt-taatttgatcaacaatttct--tatgaggttccctataa--tgcagACTCAGACAGTGTCTGAATTAAAGGACTTTGTCAAAAAGCTCAATTCATTGCCAGAAATTACT
















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|207780159|gb|GD753088.1|GD753088
EST:     GCCAAAAAGCTACTTCCATGAAGCAAGACTACACAGAAATGACAACTACT                         ACGCAGACAGTTTCCGAGTTGAAGGACTTTGTGAAAAAGCTGAACTCATTG
genomic: GCCAAAAAGCTACTTCCATGAAGCAAGACTACACAGAAATGACAACTACTgtaaggagat ... tgacatccagACGCAGACAGTTTCCGAGTTGAAGGACTTTGTGAAAAAGCTGAACTCATTG
EST: gi|193322483|gb|FK289433.1|FK289433
EST:     GCCAAAAAGCTACTTCCATGAAGCAAGACTACACAGAAATGACAACTACT                         ACGCAGACAGTTTCCGAGTTGAAGGACTTTGTGAAAAAGCTGAACCCATTG
genomic: GCCAAAAAGCTACTTCCATGAAGCAAGACTACACAGAAATGACAACTACTgtaaggagat ... tgacatccagACGCAGACAGTTTCCGAGTTGAAGGACTTTGTGAAAAAGCTGAACTCATTG
EST: gi|207757763|gb|GD730609.1|GD730609
EST:     GCCAAAAAGCTACTTCCATGAAGCAAGACTACACAGAAATGACAACTACT                         ACGCAGACAGTTTCCGAGTTGAAGGACTTTGTGAAAAAGCTGAACTCATTG
genomic: GCCAAAAAGCTACTTCCATGAAGCAAGACTACACAGAAATGACAACTACTgtaaggagat ... tgacatccagACGCAGACAGTTTCCGAGTTGAAGGACTTTGTGAAAAAGCTGAACTCATTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaatcaatatggatctgtaaagactttctaatatattgctttccatgacatccagACGCAGACAGTTTCCGAGTTGAAGGACTTTGTGAAAAAGCTGAACTCATTGCCAGAGATGACC
                         ttctaat  putative branch site (score: 2)
 ctttccat  putative PPT
 actttctaatatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aatttttcagaatcacttaattaagttcttttataactctttggaaaatcaatatggatctgtaaagactttctaatatattgctttccatgacatccagACGCAGACAGTTTCCGAGTTGAAGGACTTTGTGAAAAAGCTGAACTCATTGCCAGAGATGACC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - -gaaaatc