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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taactgcatatcaagaaaaccagttagttttttctttttttgtgtgaaatgttttatctttgtaataagttgttgacgactgcactgtgttcatggtgaaGGTAAAAACTTGGGCAGAATTGTTGAATACATTCTGCACCAGCGGGAAACTTGAGCTGGAGCTGATGTACAAAGTACAGATGCAATGCTATGAGGATGCT

Basic information

species Glycine max
transcript GLYMA18G47780.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G47780.1 (Glycine max), 3'ss of exon 6
lower sequence: AT1G65220.1 (Arabidopsis thaliana), 3'ss of exon 6
taactgcatatcaagaaaaccagttagttttttctttttttgtg---tgaaatgttttatctttgtaataagttgttgacgactgcactgtgttcatggtgaaGGTAAAAACTTGGGCAGAATTGTTGAATACATTCTGCACCAGCGGGAAACTTGAGCTGGAGCTGATGTACAAAGTACAGATGCAATGCTATGAGGATGCT-
                     ||||  |||| | |||| || ||     | ||  | |   |||||   ||| |        ||   |  ||||  ||  | |||| ||||| ||||||    |  |||| ||  | || | || ||||||  | ||| |||| |||||||| |||||||||||||||||||||||||||||  
------------------gtgagttgattttctattttattttgaagcaagattatgttgttttgttcaaagctaagctaagctagccgctgttt-tgtggtagGTGAAAACATGGGCACCCCTTCTGAACACGCTGTGTAGCACCGGGAACATGGAGATGGAACTGATGTATAAAGTACAGATGCAATGCTATGAGGATGCAA

upper sequence: GLYMA18G47780.1 (Glycine max), 3'ss of exon 6
lower sequence: AT5G36230.1 (Arabidopsis thaliana), 3'ss of exon 6
taactgcatatcaagaaaaccagttagttttttctttttttgtgtgaaatgttttatctttgtaataagttgttgacgactgcactgtgttcatggtgaaGGTAAAAACTTGGGCAGAATTGTTGAATACATTCTGCACCAGCGGGAAACTTGAGCTGGAGCTGATGTACAAAGTACAGATGCAATGCTATGAGGATGCT-
| | |   ||     ||   |  ||  | |  | ||    |      ||| | | |||  | | ||      || |   ||  | ||| |     ||| |||| ||||| |||||   | |  |||| || ||||| |||||||| || || |||||||| |||||||||||||| || ||||||||||||||||||||  
tgaatcactaatgcaaatcgcttttgatgtcatattagcgttgaaataatatgtgatccctcttatggtcactttatctcttga-tgtttgatctgtgtagGTGAAAACATGGGCTCCACTTCTGAACACGTTCTGTACCAGCGGAAAGCTAGAGCTGGAACTGATGTACAAAGTCCAAATGCAATGCTATGAGGATGCAA

upper sequence: GLYMA18G47780.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv04s0023g00670.t01 (Vitis vinifera), 3'ss of exon 7
taactgcatatcaagaaaaccagttagttttttctttttttgtgtgaaatgttttatctttgtaataagttgttgacg--actgcactgtgttcatggtgaaGGTAAAAACTTGGGCAGAATTGTTGAATACATTCTGCACCAGCGGGAAACTTGAGCTGGAGCTGATGTACAAAGTACAGATGCAATGCTATGAGGATGCT-
    |   | |||    ||||  |   || |||  |||| | |          || | ||    | | |   |  |     |||          ||  |  |||| ||| | |||||| || |  |||| || ||||||||||  ||||| || || || |||||| |||||||||| ||||| |||||||||||||||||  
---ttttgtttcagaggaacctttcttttcttttcttttcttttcttttcccattgttttaaagaaatgccctctatattgctgagagtctcctattttacagGTGAAAGCATGGGCAAAACTTCTGAACACCTTCTGCACCAATGGGAAGCTCGAACTAGAGCTGTTGTACAAAGTTCAGATCCAATGCTATGAGGATGCCA

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|193556907|gb|FK512340.1|FK512340
EST:     CAGTGGTCTGGAAAAAATCAGCAACAGAATGCCAATGCAGCCCTTCGTCA                         GGTAAAAACTTGGGCAGAATTGTTGAATACATTCTG
genomic: CAGTGGTCTGGAAAAAATCAGCAACAGAATGCAAATGCAGCCCTTCGTCAggtatccttt ... tcatggtgaaGGTAAAAACTTGGGCAGAATTGTTGAATACATTCTG
EST: gi|14990170|gb|BI315843.1|BI315843
EST:     CAGCCCTTCGTCA                         GGTAAAAACTTGGGCAGAATTGTTGAATACATTCTGCACCAGCGGGAAACT
genomic: CAGCCCTTCGTCAggtatccttt ... tcatggtgaaGGTAAAAACTTGGGCAGAATTGTTGAATACATTCTGCACCAGCGGGAAACT
EST: gi|151401127|gb|EV270941.1|EV270941
EST:     CAGTGGTCTGGAAAAAATCAGCAACAGAATGCAAATGCAGCCCTTCGTCA                         GGTAAAAACTTGGGCAGAATTGTTGAATACATTCTGCACCAGCGGGAAACT
genomic: CAGTGGTCTGGAAAAAATCAGCAACAGAATGCAAATGCAGCCCTTCGTCAggtatccttt ... tcatggtgaaGGTAAAAACTTGGGCAGAATTGTTGAATACATTCTGCACCAGCGGGAAACT
EST: gi|10846257|gb|BF071303.1|BF071303
EST:     CAGTGGTCTGGAAAAAATCAGCAACAGAATGCAAATGCAGCCCTTCGTCA                         GGTAAAAACTTGGGCAGAATTGTTGAATACATTCTGCACCAGCGGGAAACT
genomic: CAGTGGTCTGGAAAAAATCAGCAACAGAATGCAAATGCAGCCCTTCGTCAggtatccttt ... tcatggtgaaGGTAAAAACTTGGGCAGAATTGTTGAATACATTCTGCACCAGCGGGAAACT
EST: gi|193490663|gb|FK453422.1|FK453422
EST:     CAGTGGTCTGGAAAAAATCAGCAACAGAATGCAAATGCAGCCCTTCGTCA                         GGTAAAAACTTGGGCAGAATTGTTGAATACATTCTGCACCAGCGGGAAACT
genomic: CAGTGGTCTGGAAAAAATCAGCAACAGAATGCAAATGCAGCCCTTCGTCAggtatccttt ... tcatggtgaaGGTAAAAACTTGGGCAGAATTGTTGAATACATTCTGCACCAGCGGGAAACT
EST: gi|19347148|gb|BM892028.1|BM892028
EST:     CAGTGGTCTGGAAAAAATCAGCAACAGAATGCAAATGCAGCCCTTCGTCA                         GGTAAAAACTTGGGCAGAATTGTTGAATACATTCTGCACCAGCGGGAAACT
genomic: CAGTGGTCTGGAAAAAATCAGCAACAGAATGCAAATGCAGCCCTTCGTCAggtatccttt ... tcatggtgaaGGTAAAAACTTGGGCAGAATTGTTGAATACATTCTGCACCAGCGGGAAACT
EST: gi|31456738|gb|CD398766.1|CD398766
EST:     GAATGCAAATGCAGCCCTTCGTCA                         GGTAAAAACTTGGGCAGAATTGTTGAATACATTCTGCACCAGCGGGAAACT
genomic: GAATGCAAATGCAGCCCTTCGTCAggtatccttt ... tcatggtgaaGGTAAAAACTTGGGCAGAATTGTTGAATACATTCTGCACCAGCGGGAAACT
EST: gi|27426423|gb|CA937943.1|CA937943
EST:     CAGTGGTCTGGAAAAAATCAGCAACAGAATGCAAATGCAGCCCTTCGTCA                         GGTAAAAACTTGGGCAGAATTGTTGAATACATTCTGCACCAGCGGGAAACT
genomic: CAGTGGTCTGGAAAAAATCAGCAACAGAATGCAAATGCAGCCCTTCGTCAggtatccttt ... tcatggtgaaGGTAAAAACTTGGGCAGAATTGTTGAATACATTCTGCACCAGCGGGAAACT
EST: gi|24135580|gb|BU926090.1|BU926090
EST:     CAGTGGTCTGGAAAAAATCAGCAACAGAATGCTAATGCAGTGCTTCGTCA                         GGCAAAAACTTGGGCAGAATTGTTGAATACATTCTGCACCAGCGGGAAACT
genomic: CAGTGGTCTGGAAAAAATCAGCAACAGAATGCAAATGCAGCCCTTCGTCAggtatccttt ... tcatggtgaaGGTAAAAACTTGGGCAGAATTGTTGAATACATTCTGCACCAGCGGGAAACT
EST: gi|192327753|gb|FK022382.1|FK022382
EST:     CAGTGGTCTGGAAAAAATCAGCAACAGAATGCAAATGCAGCCCTTCGTCA                         GGTAAAAACTTGGGCAGAATTGTTGAATACATTCTGCACCAGCGGGAAACT
genomic: CAGTGGTCTGGAAAAAATCAGCAACAGAATGCAAATGCAGCCCTTCGTCAggtatccttt ... tcatggtgaaGGTAAAAACTTGGGCAGAATTGTTGAATACATTCTGCACCAGCGGGAAACT
EST: gi|18734887|gb|BM528442.1|BM528442
EST:     CAGTGGTCTGGAAAAAATCAGCAACAGAATGCAAATGCAGCCCTTCGTCA                         GGTAAAAACTTGGGCAGAATTGTTGAATACATTCTGCACCAGCGGGAAACT
genomic: CAGTGGTCTGGAAAAAATCAGCAACAGAATGCAAATGCAGCCCTTCGTCAggtatccttt ... tcatggtgaaGGTAAAAACTTGGGCAGAATTGTTGAATACATTCTGCACCAGCGGGAAACT
EST: gi|22927121|gb|BU544260.1|BU544260
EST:     CAGTGGTCTGGAAAAAATCAGCAACAGAATGCAAATGCAGCCCTTCGTCA                         GGTAAAAACTTGGGCAGAATTGTTGAATACATTCTGCACCAGCGGGAAACT
genomic: CAGTGGTCTGGAAAAAATCAGCAACAGAATGCAAATGCAGCCCTTCGTCAggtatccttt ... tcatggtgaaGGTAAAAACTTGGGCAGAATTGTTGAATACATTCTGCACCAGCGGGAAACT
EST: gi|14990964|gb|BI316637.1|BI316637
EST:     CAGTGGTCTGGAAAAAATCAGCAACAGAATGCAAATGCAGCCCTTCGTCA                         GGTAAAAACTTGGGCAGAATTGTTGAATACATTCTGCACCAGCGGGAAACT
genomic: CAGTGGTCTGGAAAAAATCAGCAACAGAATGCAAATGCAGCCCTTCGTCAggtatccttt ... tcatggtgaaGGTAAAAACTTGGGCAGAATTGTTGAATACATTCTGCACCAGCGGGAAACT
EST: gi|120533169|gb|EH261302.1|EH261302
EST:     CAGTGGTCTGGAAAAAATCAGCAACAGAATGCAAATGCAGCCCTTCGTCA                         GGTAAAAACTTGGGCAGAATTGTTGAATACATTCTGCACCAGCGGGAAACT
genomic: CAGTGGTCTGGAAAAAATCAGCAACAGAATGCAAATGCAGCCCTTCGTCAggtatccttt ... tcatggtgaaGGTAAAAACTTGGGCAGAATTGTTGAATACATTCTGCACCAGCGGGAAACT
EST: gi|254321640|gb|GR824957.1|GR824957
EST:     CAGTGGTCTGGAAAAAATCAGCAACAGAATGCAAATGCAGCCCTTCGTCA                         GGTAAAAACTTGGGCAGAATTGTTGAATACATTCTGCACCAGCGGGAAACT
genomic: CAGTGGTCTGGAAAAAATCAGCAACAGAATGCAAATGCAGCCCTTCGTCAggtatccttt ... tcatggtgaaGGTAAAAACTTGGGCAGAATTGTTGAATACATTCTGCACCAGCGGGAAACT
EST: gi|15337352|gb|BI498008.1|BI498008
EST:     CAGTGGTCTGGAAAAAATCAGCAACAGAATGCAAATGCAGCCCTTCGTCA                         GGTAAAAACTTGGGCAGAATTGTTGAATACATTCTGCACCAGCGGGAAACT
genomic: CAGTGGTCTGGAAAAAATCAGCAACAGAATGCAAATGCAGCCCTTCGTCAggtatccttt ... tcatggtgaaGGTAAAAACTTGGGCAGAATTGTTGAATACATTCTGCACCAGCGGGAAACT
EST: gi|17518869|gb|BM187911.1|BM187911
EST:     CAGTGGTCTGGAAAAAATCAGCAACAGAATGCAAATGCAGCCCTTCGTCA                         GGTAAAAACTTGGGCAGAATTGTTGAATACATTCTGCACCAGC
genomic: CAGTGGTCTGGAAAAAATCAGCAACAGAATGCAAATGCAGCCCTTCGTCAggtatccttt ... tcatggtgaaGGTAAAAACTTGGGCAGAATTGTTGAATACATTCTGCACCAGC
EST: gi|18730241|gb|BM525765.1|BM525765
EST:     CAGTGGTCTGGAAAAAATCAGCAACATAATGCAAATGCAGCCCTTCGTCA                         GGTAAAAACTTGGGCAGAATTGTTGAATACATTCTGCACCAGCGGGAAACT
genomic: CAGTGGTCTGGAAAAAATCAGCAACAGAATGCAAATGCAGCCCTTCGTCAggtatccttt ... tcatggtgaaGGTAAAAACTTGGGCAGAATTGTTGAATACATTCTGCACCAGCGGGAAACT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaaatgttttatctttgtaataagttgttgacgactgcactgtgttcatggtgaaGGTAAAAACTTGGGCAGAATTGTTGAATACATTCTGCACCAGCGGGAAACTTGAGCTGGAGCTGATGTACAAAGTACAGATGCAATGCTATGAGGATGCT
                         tgttgac  putative branch site (score: 3)
      ttttatctttgtaata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taactgcatatcaagaaaaccagttagttttttctttttttgtgtgaaatgttttatctttgtaataagttgttgacgactgcactgtgttcatggtgaaGGTAAAAACTTGGGCAGAATTGTTGAATACATTCTGCACCAGCGGGAAACTTGAGCTGGAGCTGATGTACAAAGTACAGATGCAATGCTATGAGGATGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - tgcatat
- - - - - - aagaaaa
- - - - - - - - - - - - - - - - - - - - tgtgtga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgttgac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgcactg