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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgagatttgtgattttgttacttacccaaacttggctctaagatgtttatgctaaactcagtttgaaattttcagGACTGTTTGGGAGATTAAGCAAAAGACATTGGTTGATATGGCTGTTGATAGAGGATGCTACATAGACCAGAGTCAGAGCTTGAATATTCACATGGATCAA

Basic information

species Glycine max
transcript GLYMA05G32070.1
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA05G32070.1 (Glycine max), 3'ss of exon 14
lower sequence: LOC_Os06g07210.1 (Oryza sativa), 3'ss of exon 14
gtatgagatttgtgattttgttacttacccaaacttggctcta--------agatgtttat---gctaaac--tcagtttgaaat-tttcagGACTGTTTGGGAGATTAAGCAAAAGACATTGGTTGATATGGCTGTTGATAGAGGATGCTACATAGACCAGAGTCAGAGCTTGAATATTCACATGGATCAA
|||||   ||  |  |  |   |  | |  |  ||  | ||||        |||| || ||    ||||||  | |   | || | || ||| || ||||||||||| ||||| || ||  | ||||| |||||||||||| | ||||||||||| || ||||| |||||  | ||| |||||||||| |||
gtatgttgttcattgtccta--aactcctaatgctatgttctaccagatgcagatattcatttatctaaacgtttaacctcaattgttccagAACGGTTTGGGAGATAAAGCAGAAAACGCTTGTTGACATGGCTGTTGATCGTGGATGCTACATTGATCAGAGCCAGAGTCTTAATGTTCACATGGAACAA

upper sequence: GLYMA05G32070.1 (Glycine max), 3'ss of exon 14
lower sequence: GRMZM2G340527_T01 (Zea mays), 3'ss of exon 14
gtatgagatttg---tgattttgttacttaccc--aaacttggct-ctaa---gatgtttatg---ctaaactcagtttgaaatttt-----cagGACTGTTTGGGAGATTAAGCAAAAGACATTGGTTGATATGGCTGTTGATAGAGGATGCTACATAGACCAGAGTCAGAGCTTGAATATTCACATGGATCAA
|||||   ||      |||    ||| || |    ||| | |  | ||||     |||||  |   ||||| |   | |  |||| |     |||||||||||||||||| ||||| || || || ||||||||||| |||||  | |||||||| || |||||||| |||||| | ||  | |||||||| |||
gtatgtatttcaaccagatgccattatttcctataaaattcgattactaatttactgtttgagcttctaaagtttatatacaattattgcaccagGACTGTTTGGGAGATCAAGCAGAAAACTTTAGTTGATATGGCGGTTGACCGTGGATGCTATATTGACCAGAGCCAGAGCCTCAACGTCCACATGGAGCAA

upper sequence: GLYMA05G32070.1 (Glycine max), 3'ss of exon 14
lower sequence: Vv07s0031g01990.t01 (Vitis vinifera), 3'ss of exon 14
--------gtatgag--atttgtgattttgttacttacccaaacttggctctaagatgtttatgctaaactcagtttgaaattttcagGACTGTTTGGGAGATTAAGCAAAAGACATTGGTTGATATGGCTGTTGATAGAGGATGCTACATAGACCAGAGTCAGAGCTTGAATATTCACATGGATCAA
         ||| |    ||| |  | ||  |  ||||||| | ||    ||    | | | | ||||   || |||       ||||||||||||||||||| ||||||||||||||||||||||||||||| ||  | ||||||||||||||||||||||| ||| ||||||| |||||||| |||
gtatgtatttatcatttgtttcttgtctttctttttacccacattttatactcc--tttctgtactaaga-caatttcttgcaatcagGACTGTTTGGGAGATCAAGCAAAAGACATTGGTTGATATGGCTGTGGACCGTGGATGCTACATAGACCAGAGTCAAAGCCTGAATATACACATGGACCAA

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|51345093|gb|CO985826.1|CO985826
EST:     TCAGTTCAGAAAATCCCAGAAATACCTGATGATCTGAAAATCATATACAA                         GACTGTTTGGGAGATTAAGCAAAAGACATTGGTTGATATGGCTGTTGATAG
genomic: TCAGTTCAGAAAATCCCAGAAATACCTGATGATCTGAAAATCATATACAAgtatgagatt ... aaattttcagGACTGTTTGGGAGATTAAGCAAAAGACATTGGTTGATATGGCTGTTGATAG
EST: gi|58022119|gb|CX708860.1|CX708860
EST:     TCAGTTCAGAAAATCCCAGAAATACNTGATGATCTGAAAATCATATACAA                         GACTGTTTGGGAGATTAAGCAAAAGACATTGGTTGATATGGCTGTTGATAG
genomic: TCAGTTCAGAAAATCCCAGAAATACCTGATGATCTGAAAATCATATACAAgtatgagatt ... aaattttcagGACTGTTTGGGAGATTAAGCAAAAGACATTGGTTGATATGGCTGTTGATAG
EST: gi|192296534|gb|FG991640.1|FG991640
EST:     TCAGTTCAGAAAATCCCAGAAATACCTGATGATCTGAAAATCATATACAA                         GACTGTTTGGGAGATTAAGCAAAAGACATTGGTTGATATGGCTGTTGATAG
genomic: TCAGTTCAGAAAATCCCAGAAATACCTGATGATCTGAAAATCATATACAAgtatgagatt ... aaattttcagGACTGTTTGGGAGATTAAGCAAAAGACATTGGTTGATATGGCTGTTGATAG
EST: gi|208201785|gb|GE000965.1|GE000965
EST:     CTGAAAATCATATACAA                         GACTGTTTGGGAGATTAAGCAAAAGACATTGGTTGATATGGCTGTTGATAG
genomic: CTGAAAATCATATACAAgtatgagatt ... aaattttcagGACTGTTTGGGAGATTAAGCAAAAGACATTGGTTGATATGGCTGTTGATAG
EST: gi|13791431|gb|BG654022.1|BG654022
EST:     TCAGTTCAGAAAATCCCAGAAATACCTGATGATCTGAAAATCATATACAA                         GACTGTTTGGGAGATTAAGCAAAAGACATTGGTTGATATGGCTGTTGATAG
genomic: TCAGTTCAGAAAATCCCAGAAATACCTGATGATCTGAAAATCATATACAAgtatgagatt ... aaattttcagGACTGTTTGGGAGATTAAGCAAAAGACATTGGTTGATATGGCTGTTGATAG
EST: gi|58018661|gb|CX705403.1|CX705403
EST:     TCAGTTCAGAAAATCCCAGAAATACCTGATGATCTGAAAATCATATACAA                         GACTGTTTGGGAGATTAAGCAAAAGACATTGGTTGATATGGCTGTTGATAG
genomic: TCAGTTCAGAAAATCCCAGAAATACCTGATGATCTGAAAATCATATACAAgtatgagatt ... aaattttcagGACTGTTTGGGAGATTAAGCAAAAGACATTGGTTGATATGGCTGTTGATAG
EST: gi|58024594|gb|CX711335.1|CX711335
EST:     TCAGTTCAGAAAATCCCAGAAATACCTGATGATCTGAAAATCATATACAA                         GACTGTTTGGGAGATTAAGCAAAAGACATTGGTTGATATGGCTGTTGATAG
genomic: TCAGTTCAGAAAATCCCAGAAATACCTGATGATCTGAAAATCATATACAAgtatgagatt ... aaattttcagGACTGTTTGGGAGATTAAGCAAAAGACATTGGTTGATATGGCTGTTGATAG
EST: gi|192293903|gb|FG986112.1|FG986112
EST:     TCAGTTCAGAAAATCCCAGAAATACCTGATGATCTGAAAATCATATACAA                         GACTGTTTGGGAGATTAAGC--AAGACATTGGTTGATATGGCTGTTGATAG
genomic: TCAGTTCAGAAAATCCCAGAAATACCTGATGATCTGAAAATCATATACAAgtatgagatt ... aaattttcagGACTGTTTGGGAGATTAAGCAAAAGACATTGGTTGATATGGCTGTTGATAG
EST: gi|51335204|gb|CO979070.1|CO979070
EST:     TCAGTTCAGAAAATCCCAGAAATACCTGATGATCTGAAAATCATATACAA                         GACTGTTTGGGAGATTAAGCAAAAGACATTGGTTGATATGGCTGTTGATAG
genomic: TCAGTTCAGAAAATCCCAGAAATACCTGATGATCTGAAAATCATATACAAgtatgagatt ... aaattttcagGACTGTTTGGGAGATTAAGCAAAAGACATTGGTTGATATGGCTGTTGATAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttacccaaacttggctctaagatgtttatgctaaactcagtttgaaattttcagGACTGTTTGGGAGATTAAGCAAAAGACATTGGTTGATATGGCTGTTGATAGAGGATGCTACATAGACCAGAGTCAGAGCTTGAATATTCACATGGATCAA
                                                ttttc  CT-rich tract
                                         tttgaaatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgagatttgtgattttgttacttacccaaacttggctctaagatgtttatgctaaactcagtttgaaattttcagGACTGTTTGGGAGATTAAGCAAAAGACATTGGTTGATATGGCTGTTGATAGAGGATGCTACATAGACCAGAGTCAGAGCTTGAATATTCACATGGATCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA