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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...actagatgtcaatagtgcatcatgtgagtttattaaaaaaaaaaaaaaagagagcacagttgtcattctgctccttactttttgaggcaacattatgcagGATATCTGTAACTTTTATTGATAAGGACGGTGAGGAGAAGCATATCAAAGTCCCTGTTGGAATGTCTATGTTAGAAGCTGCTCATGAAAACGACATAGAA

Basic information

species Glycine max
transcript GLYMA17G05130.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G05130.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os07g01930.1 (Oryza sativa), 3'ss of exon 4
actagatgtcaatagtgcatca-tgtgagtttattaaaaaaaaaaaaaaagagagcacagttgtcattctgctccttactttttgaggcaacattatgcagGATATCTGTAACTTTTATTGATAAGGACGGTGAGGAGAAGCATATCAAAGTCCCTGTTGGAATGTCTATGTTAGAAGCTGCTCATGAAAACGACATAGAA
  |  | |    |  | | ||| | |     |  ||  ||| |        | |  || | | | ||| | ||  | |     |          |   |||||| |||||||| ||| |  | ||||| ||    ||| ||   ||||  ||||||||||||||||| || |||||||||||||||||||| ||||| |||
ctttaaaggggcttctccttcagtttttccctcctaggaaatagctgtccaaaacaaccgat-taatttttctaatgagcaaatttctttgtgctgcacagGATCTCTGTAACATTTGTGAACAAGGATGGCACAGAGCAGACAATCAGTGTCCCTGTTGGAATGTCCATCTTAGAAGCTGCTCATGAAAATGACATCGAA

upper sequence: GLYMA17G05130.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os09g26650.1 (Oryza sativa), 3'ss of exon 3
actagatgtcaatagtgcatcatgtgagtttattaaaaaaaaaaaaaaagagagcacagttgtcattctgctccttactttttgaggcaaca--tta---tgcagGATATCTGTAACTTTTATTGATAAGGACGGTGAGGAGAAGCATATCAAAGTCCCTGTTGGAATGTCTATGTTAGAAGCTGCTCATGAAAACGACATAGAA
  |   | ||  |  ||  ||||||| | || ||    | |||    | |       | |   || | ||  | | | | |   |    | |  |||   |||||||||||||| |||||| |||||||||| || ||||| |||| | | ||||| ||| | |||||||| ||| |||| || || ||||| || |||||||||
--tttttatctgt--tggctcatgtgtgatt-ttggttataaagtccatgttgttttattctacaatttgaacttgaatatcaaatattataatttaatttgcagGATATCTGTGACTTTTGTTGATAAGGATGGCGAGGAAAAGCTTGTTAAAGTACCTATAGGAATGTCAATGCTAGAGGCAGCACATGAGAATGACATAGAA

upper sequence: GLYMA17G05130.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G013607_T02 (Zea mays), 3'ss of exon 4
actagatgtcaatagtgcatcatgtgagtttattaaaaaaaaaaaaaaagag-agcacagttgtcattctgctccttactttttgaggcaacattatgcagGATATCTGTAACTTTTATTGATAAGGACGGTGAGGAGAAGCATATCAAAGTCCCTGTTGGAATGTCTATGTTAGAAGCTGCTCATGAAAACGACATAGAA
| |     | ||| ||   |  || |  || | |||  |   |    |  || ||  |  |  | ||| |     ||| ||||      |   | |  ||| || || ||||| ||| |  | ||||| ||    || |||   ||    || || ||||||||||| |||||||||||||||||||||||||||||||| 
agttttactgaattgttagtgttgagctttcaataattatttagggtagaagcagtcctctgatgattgttgaggttatttttctccatactgtga-acagAATCTCGGTAACATTTGTCAACAAGGATGGCTCAGAAAAGACAATATGTGTTCCAGTTGGAATGTCCATGTTAGAAGCTGCTCATGAAAACGACATAGAG

upper sequence: GLYMA17G05130.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv11s0016g00530.t01 (Vitis vinifera), 3'ss of exon 4
actagatgtcaatagtgcatcatgtgagtttattaaaaaaaaaaaaaaaga-gagcacag-ttgtcattctgctccttactttttg-aggcaacattatgcagGATATCTGTAACTTTTATTGATAAGGACGGTGAGGAGAAGCATATCAAAGTCCCTGTTGGAATGTCTATGTTAGAAGCTGCTCATGAAAACGACATAGAA
     || | | |    |||||||    |  |||       ||   |     |     || ||  | |  || | |||    ||   |      ||| ||||||||||||||  | ||| |||||||||| || |||||  | || || |  |||||  |||||||||||||||||||||||||||||||||| || ||||||
---caatcttagttacacatcatggttctacatttcctcttaactcatttctgcatgtagattaccctggtgtttcttctcattcatatatttaattgtgcagGATATCTGTGTCATTTGTTGATAAGGATGGAGAGGAACATCACATTAGGGTCCCCATTGGAATGTCTATGTTAGAAGCTGCTCATGAAAATGATATAGAA

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|10231340|gb|BE800228.1|BE800228
EST:     ACAATGACTACTAACAACACTACCAAGGAAAGGAGTGAACAAGAACAAGC                         GATATCTGTAACTTTTATTGATAAGGACGGTGAGGAGAAGCATATCAAAGT
genomic: ACAATGACTACTAACAACACTACCAAGGAAAGGAGTGAACAAGAACAAGCgtaagttctt ... cattatgcagGATATCTGTAACTTTTATTGATAAGGACGGTGAGGAGAAGCATATCAAAGT
EST: gi|192322757|gb|FK014448.1|FK014448
EST:     ACAATGACTACTAACAACACTACCAAGGAAAGGAGTGAACAAGAACAAGC                         GATATCTGTAACTTTTATTGATAAGGACGGTGAGGAGAAGCATATCAAAGT
genomic: ACAATGACTACTAACAACACTACCAAGGAAAGGAGTGAACAAGAACAAGCgtaagttctt ... cattatgcagGATATCTGTAACTTTTATTGATAAGGACGGTGAGGAGAAGCATATCAAAGT
EST: gi|254345030|gb|GR855687.1|GR855687
EST:     AACACTACCAAGGAAAGGAGTGAACAAGAACAAGC                         GATATCTGTAACTTTTATTGATAAGGACGGTGAGGAGAAGCATATCAAAGT
genomic: AACACTACCAAGGAAAGGAGTGAACAAGAACAAGCgtaagttctt ... cattatgcagGATATCTGTAACTTTTATTGATAAGGACGGTGAGGAGAAGCATATCAAAGT
EST: gi|6070770|gb|AW100157.1|AW100157
EST:     CAATGACTACTAACAACACTACCAAGGGAAAGGAGTGAACAAGAACAAGC                         GATATCTGTAACTTTTATTGATAAGGACGGTGAGGAGAAGCATATCAAAGT
genomic: CAATGACTACTAACAACACTACCAA-GGAAAGGAGTGAACAAGAACAAGCgtaagttctt ... cattatgcagGATATCTGTAACTTTTATTGATAAGGACGGTGAGGAGAAGCATATCAAAGT
EST: gi|298179386|gb|HO027857.1|HO027857
EST:     ACAATGACTACTAACAACACTACCAAGGAAAGGAGTGAACAAGAACAAGC                         GATATCTGTAACTTTTATTGATAAGGACGGTGAGGAGAAGCTTATCAAAGT
genomic: ACAATGACTACTAACAACACTACCAAGGAAAGGAGTGAACAAGAACAAGCgtaagttctt ... cattatgcagGATATCTGTAACTTTTATTGATAAGGACGGTGAGGAGAAGCATATCAAAGT
EST: gi|14259415|gb|BG882323.1|BG882323
EST:     ACAATGACTACTAACAACACTACCAAGGAAAGGAGTGAACAAGAACAAGC                         GATATCTGTAACTTTTATTGATAAGGACGGTGAGGAGAAGCATATCAAAGT
genomic: ACAATGACTACTAACAACACTACCAAGGAAAGGAGTGAACAAGAACAAGCgtaagttctt ... cattatgcagGATATCTGTAACTTTTATTGATAAGGACGGTGAGGAGAAGCATATCAAAGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaaagagagcacagttgtcattctgctccttactttttgaggcaacattatgcagGATATCTGTAACTTTTATTGATAAGGACGGTGAGGAGAAGCATATCAAAGTCCCTGTTGGAATGTCTATGTTAGAAGCTGCTCATGAAAACGACATAGAA
                          tccttac  putative branch site (score: 2)
                             ttacttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
actagatgtcaatagtgcatcatgtgagtttattaaaaaaaaaaaaaaagagagcacagttgtcattctgctccttactttttgaggcaacattatgcagGATATCTGTAACTTTTATTGATAAGGACGGTGAGGAGAAGCATATCAAAGTCCCTGTTGGAATGTCTATGTTAGAAGCTGCTCATGAAAACGACATAGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - -tcatgtg
- - - - - - - - - - - - - - - - - aaaaaaa