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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggtttaatttcaatgttggaatagctataatgatgtttctacaaagtctgagttatggtgttatcttcctgcactcattgcttcaatttgttggcagGTATATATCCATGGCAAGAGATTACATTGGTGAAGAAAGTTAAATACGACGATGCCCTGGTTGAGGCAGCATGGCCCCTAGGCAGCGCCATTGAAGCTGT

Basic information

species Glycine max
transcript GLYMA16G04790.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G04790.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv05s0094g01630.t01 (Vitis vinifera), 3'ss of exon 8
--------------------------gtaggtttaatttcaatgttggaatagctataatgatgtttctacaaagtctgagttatggtgttatcttcctgcactcattgcttcaatttgttgg-cagGTATATATCCATGGCAAGAGATTACATTGGTGAAGAAAGTTAAATACGACGATGCCCTGGTTGAGGCAGCATGGCCCCTAGGCAGCGCCATTGAAGCTGT
                            | |  |  | | ||  | | | | |   | ||| || || |  | | ||  | |     | | | |         |   |||||   ||| |||| ||||  || |||| |||||||| ||||||||||||||| | |||||||| | ||||||||| ||||| ||||||||||| ||||| || |||||||| || ||
gtaagctccacgcccatttgagtgtctcatgcatcctcttaac-tggaagtggtattgatgttgcttgttaacattcatattagaattctgaaccatgcattttggctgcttgtgtttcttggacagGCCTAGATCCCTGGCAAGAAATTACATTGGTGAAGCAGGTTAAATATGGCGATGCCCTTGTTGAAGCAGCATGGCCACTAGGGAGTGCCATTGATGCCGT
















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|16344845|gb|BI970440.1|BI970440
EST:     TCTTTGCATGGATCTTATATACCAGTATACACTACTCGTTGATGGGTTTG                         GTATATATCCATGGCAAGAGATTACATTGGTGAAGAAAGTTAAATACGACG
genomic: TCTTTGCATGGATCTTATATACCAGTATACACTACTCGTTGATGGGTTTGgtaggtttaa ... ttgttggcagGTATATATCCATGGCAAGAGATTACATTGGTGAAGAAAGTTAAATACGACG
EST: gi|7233645|gb|AW568917.1|AW568917
EST:     GCATGGATCTTATATACCAGTATACACTACTCGTTGATGGGTTTG                         GTATATATCCATGGCAAGAGATTACATTGGTGAAGAAAGTTAAATACGACG
genomic: GCATGGATCTTATATACCAGTATACACTACTCGTTGATGGGTTTGgtaggtttaa ... ttgttggcagGTATATATCCATGGCAAGAGATTACATTGGTGAAGAAAGTTAAATACGACG
EST: gi|192322324|gb|FK014565.1|FK014565
EST:     TCTTTGCATGGATCTTATATACCAGTATACACTACTCGTTGATGGGTTTG                         GTATATATCCATGGCAAGAGATTACATTGGTGAAGAAAGTTAAATACGACG
genomic: TCTTTGCATGGATCTTATATACCAGTATACACTACTCGTTGATGGGTTTGgtaggtttaa ... ttgttggcagGTATATATCCATGGCAAGAGATTACATTGGTGAAGAAAGTTAAATACGACG
EST: gi|51337808|gb|CO981674.1|CO981674
EST:     TCTTTGCATGGATCTTATATACCAGTATACACTACTCGTTGATGGGTTTG                         GTATATATCCATGGCAAGAGATTACATTGGTGAAGAAAGTTAAATACGACG
genomic: TCTTTGCATGGATCTTATATACCAGTATACACTACTCGTTGATGGGTTTGgtaggtttaa ... ttgttggcagGTATATATCCATGGCAAGAGATTACATTGGTGAAGAAAGTTAAATACGACG
EST: gi|57575136|gb|CX548111.1|CX548111
EST:     TCTTTGCATGGATCTTATATACCAGTATACACTACTCGTTGATGGGTTTG                         GTATATATCCATGGCAAGAGATTACATTGGTGAAGAAAGTTAAATACGACG
genomic: TCTTTGCATGGATCTTATATACCAGTATACACTACTCGTTGATGGGTTTGgtaggtttaa ... ttgttggcagGTATATATCCATGGCAAGAGATTACATTGGTGAAGAAAGTTAAATACGACG
EST: gi|31306230|gb|CD391433.1|CD391433
EST:     TCTTTGCATGGATCTTATATACCAGTATACACTACTCGTTGATGGGTTTG                         GTATATATCCCATGGCAAGAGATTACATTGGTGAAGAAAGTTAAATACGAC
genomic: TCTTTGCATGGATCTTATATACCAGTATACACTACTCGTTGATGGGTTTGgtaggtttaa ... ttgttggcagGTATATAT-CCATGGCAAGAGATTACATTGGTGAAGAAAGTTAAATACGAC
EST: gi|207835642|gb|GD805639.1|GD805639
EST:     TCTTTGCATGGATCTTATATACCAGTATACACTACTCGTTGATGGGTTTG                         GTATATATCCATGGCAAGAGATTACATTGGTGAAGAAAGTTAAATACGACG
genomic: TCTTTGCATGGATCTTATATACCAGTATACACTACTCGTTGATGGGTTTGgtaggtttaa ... ttgttggcagGTATATATCCATGGCAAGAGATTACATTGGTGAAGAAAGTTAAATACGACG
EST: gi|4297390|gb|AI442611.1|AI442611
EST:     TCTTTGCATGGATCTTATATACCAGTATACACTACTCGTTGATGGGTTTG                         GTATATATCCATGGCAAGAGATTACATTGGTGAAGAAAGTTAAATACGACG
genomic: TCTTTGCATGGATCTTATATACCAGTATACACTACTCGTTGATGGGTTTGgtaggtttaa ... ttgttggcagGTATATATCCATGGCAAGAGATTACATTGGTGAAGAAAGTTAAATACGACG
EST: gi|6072975|gb|AW102362.1|AW102362
EST:     TCTTTGCATGGATCTTATATACCAGTATACACTACTCGTTGATGGGTTTG                         GTATATATCCATGGCAAGAGATTACATTGGTGAAGAAAGTTAAATACGACG
genomic: TCTTTGCATGGATCTTATATACCAGTATACACTACTCGTTGATGGGTTTGgtaggtttaa ... ttgttggcagGTATATATCCATGGCAAGAGATTACATTGGTGAAGAAAGTTAAATACGACG
EST: gi|6846435|gb|AW348725.1|AW348725
EST:     TCTTTGCATGGATCTTATATACCAGTATACACTACTCGTTGATGGGTTTG                         GTATATATCCATGGCAAGAGATTACATTGGTGAAGAAAGTTAAATACGACG
genomic: TCTTTGCATGGATCTTATATACCAGTATACACTACTCGTTGATGGGTTTGgtaggtttaa ... ttgttggcagGTATATATCCATGGCAAGAGATTACATTGGTGAAGAAAGTTAAATACGACG
EST: gi|207709188|gb|GD691962.1|GD691962
EST:     TCTTTGCATGGATCTTATATACCAGTATACACTACTCGTTGATGGGTTTG                         GTATATATCCATGGCAAGAGATTACATTGGTGAAG-AAGTTAAATACGACG
genomic: TCTTTGCATGGATCTTATATACCAGTATACACTACTCGTTGATGGGTTTGgtaggtttaa ... ttgttggcagGTATATATCCATGGCAAGAGATTACATTGGTGAAGAAAGTTAAATACGACG
EST: gi|16342247|gb|BI967842.1|BI967842
EST:     TCTTTGCATGGATCTTATATACCAGTATACACTACTCGTTGATGGGTTTG                         GTATATATCCATGGCAAGAGATTACATTGGTGAAGAAAGTTAAATACGACG
genomic: TCTTTGCATGGATCTTATATACCAGTATACACTACTCGTTGATGGGTTTGgtaggtttaa ... ttgttggcagGTATATATCCATGGCAAGAGATTACATTGGTGAAGAAAGTTAAATACGACG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaagtctgagttatggtgttatcttcctgcactcattgcttcaatttgttggcagGTATATATCCATGGCAAGAGATTACATTGGTGAAGAAAGTTAAATACGACGATGCCCTGGTTGAGGCAGCATGGCCCCTAGGCAGCGCCATTGAAGCTGT
                                       ttcaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaggtttaatttcaatgttggaatagctataatgatgtttctacaaagtctgagttatggtgttatcttcctgcactcattgcttcaatttgttggcagGTATATATCCATGGCAAGAGATTACATTGGTGAAGAAAGTTAAATACGACGATGCCCTGGTTGAGGCAGCATGGCCCCTAGGCAGCGCCATTGAAGCTGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG