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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cttaggaagcctgtatagtgtatatatcctttaattgtttgccaatgtctttttagttgccagttctcattgattcgactttggttgcatatttctttagGTAGTTCCATTAACTGCTGCTGTAATTGTTACCACTCCTCAAAAGCTGTCGTTCATTGATGTTGCAAAAGGAGTTCGGATGTTTTCAAAACTTAAG

Basic information

species Glycine max
transcript GLYMA07G09820.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G09820.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os01g52170.1 (Oryza sativa), 3'ss of exon 8
cttaggaagcctgtatagtgtatatatcctttaattgtttgccaatgtctttttagttgccagttctcattgattcgactttggttgcatatttctttagGTAGTTCCATTAACTGCTGCTGTAATTGTTACCACTCCTCAAAAGCTGTCGTTCATTGATGTTGCAAAAGGAGTTCGGATGTTTTCAAAACTTAAG
     |  |    | |||  |   |||  |  || |         |  | |      |||  ||   || || |   | ||    ||  |    | | ||||||  ||||| ||||| ||||| ||||||||||| ||||| |||||  | ||||| ||||||||||| |||||| | |||||||| || || |||
-----gtggtacctctagcctgagtattgtacaaatcacacgtggtaacatcaaccatgcttgtaggcactg-tgaaatttaacatgtctgaaacatcagGTAGCCCCATTGACTGCAGCTGTCATTGTTACCACCCCTCAGAAGCTTGCTTTCATCGATGTTGCAAAGGGAGTTAGAATGTTTTCCAAGCTGAAG

upper sequence: GLYMA07G09820.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G129208_T01 (Zea mays), 3'ss of exon 7
----cttaggaagcctgtatagtgtatatatcctttaattgtttgccaatgtctttttagttgccagttctcattgattcgactttggttgcatatttctttagGTAGTTCCATTAACTGCTGCTGTAATTGTTACCACTCCTCAAAAGCTGTCGTTCATTGATGTTGCAAAAGGAGTTCGGATGTTTTCAAAACTTAAG
           ||||| | |  |||| | ||| | |       |   ||  ||     |  | |   |||  |    | |||  |     |  |      | |||| | |||||| ||||| || || ||||||||||| |||||||||||| | |||||||||||||| || |||||  ||||||| || ||||| |||
gtgctaccaccagcctctgtgctgtacaaatcgtatg------tagtaacatc-----aaatactccttcaaagcattgcgaaatataacgtctgaaatatcagGTGGCTCCATTGACTGCAGCAGTGATTGTTACCACCCCTCAAAAGCTGGCTTTCATTGATGTTGCCAAGGGAGTAAGGATGTTCTCTAAACTGAAG

upper sequence: GLYMA07G09820.1 (Glycine max), 3'ss of exon 8
lower sequence: AT3G24430.1 (Arabidopsis thaliana), 3'ss of exon 7
---cttaggaagcctgtatagtgtatatatcctttaattgtttgccaatgtctttttagttgccagttctcattgattcgactttggttgcatatttctttagGTAGTTCCATTAACTGCTGCTGTAATTGTTACCACTCCTCAAAAGCTGTCGTTCATTGATGTTGCAAAAGGAGTTCGGATGTTTTCAAAACTTAAG
   | |   |   ||| |||   |   || |   | |    |    |||   || |||  | |   |  |   || |  |||| |  | |    |    | |||| |  ||||| || || || |||||||| ||||| ||||||||| || |||| ||||||||||||||||| ||  ||||||| ||||||||||||
ttgcatgtaacaactgaataactttgctagcaactgaaatatgatgaata--ttattaaattcttctgttagatgctatgactataat-gttcttggtatcagGTTGCGCCATTGACAGCAGCGGTAATTGTCACCACCCCTCAAAAGTTGGCGTTTATTGATGTTGCAAAAGGTGTAAGGATGTTCTCAAAACTTAAG

upper sequence: GLYMA07G09820.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv11s0016g04250.t01 (Vitis vinifera), 3'ss of exon 7
----cttaggaagcctgtatagtgtatatatcctttaattgtttgccaatgtctttttagttgccagttctcattgattcgactttggttgcat--atttctttagGTAGTTCCATTAACTGCTGCTGTAATTGTTACCACTCCTCAAAAGCTGTCGTTCATTGATGTTGCAAAAGGAGTTCGGATGTTTTCAAAACTTAAG
     ||| |||     |    || |||  || | | | |     | ||    |  ||||||      |  |    ||| || || | |    |  |  | || |||| |||||| |||| ||||| || ||||||||||| || || |||||  | ||||||||||||||||||||||| || ||||||||||||||||||
ctattttatgaaaatcttcc--tgcatagctcatctgaatc----ctaagaattccttagttcagtacttcctacaatttgagttggatgaatttcaacttttcagGTTGTTCCACTAACAGCTGCGGTTATTGTTACCACCCCACAGAAGCTAGCCTTCATTGATGTTGCAAAAGGAGTCCGTATGTTTTCAAAACTTAAG

upper sequence: GLYMA07G09820.1 (Glycine max), 3'ss of exon 8
lower sequence: EFJ08337 (Selaginella moellendorffii), 3'ss of exon 7
cttaggaagcctgtatagtgtatatatcctttaattgtttgccaatgtctttttagttgccagttctcattgattcgactttggttgcatatttctttagGTAGTTCCATTAACTGCTGCTGTAATTGTTACCACTCCTCAAAAGCTGTCGTTCATTGATGTTGCAAAAGGAGTTCGGATGTTTTCAAAACTTAAG
                                        |  | | ||||        | || | |          |  || |||     ||||   |||| || || || || || ||||| || ||||| || || || |||||  | |||||||| ||||| |||||||| || ||||||||||| ||||||
----------------------------------------gttactatcttcg-----actagcttttggcatactaatctttgtta-gcttttcggcagGTTGTGCCTTTGACAGCAGCTGTTATAGTTACGACGCCACAGAAGCTTGCATTCATTGACGTTGCCAAAGGAGTGCGAATGTTTTCAAAGCTTAAG

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|51345383|gb|CO986116.1|CO986116
EST:     TTATTGACATGCCTCCTGGAACTGGAGATATTCAACTCACATTATGCCAG                         GTAGTTCCATTAACTGCTGCTGTAATTGTTACCACTCCTCAAAAGCTGTCG
genomic: TTATTGACATGCCTCCTGGAACTGGAGATATTCAACTCACATTATGCCAGgttctggtcc ... atttctttagGTAGTTCCATTAACTGCTGCTGTAATTGTTACCACTCCTCAAAAGCTGTCG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtctttttagttgccagttctcattgattcgactttggttgcatatttctttagGTAGTTCCATTAACTGCTGCTGTAATTGTTACCACTCCTCAAAAGCTGTCGTTCATTGATGTTGCAAAAGGAGTTCGGATGTTTTCAAAACTTAAG
                      cattgat  putative branch site (score: 4)
                                            tatttcttt  putative PPT
                                           atatttcttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cttaggaagcctgtatagtgtatatatcctttaattgtttgccaatgtctttttagttgccagttctcattgattcgactttggttgcatatttctttagGTAGTTCCATTAACTGCTGCTGTAATTGTTACCACTCCTCAAAAGCTGTCGTTCATTGATGTTGCAAAAGGAGTTCGGATGTTTTCAAAACTTAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - -agcctgt
- - - - - - - - - - - - - - - - - -tgtttgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - -gttgcca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tggttgc