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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cttaacaatattttgttgccttatctaattcaactactgcattaccgtatttgatatggcacacttttaaacttgagttttgctgtcaattctctgacagATAGTTTTCAGAGAGGATTTTGGAACTGATGGCCGTGGTGGATATTTTGACCAATATGG

Basic information

species Glycine max
transcript GLYMA19G24250.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G24250.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os04g40874.1 (Oryza sativa), 3'ss of exon 7
cttaacaatat---tttgttgc-cttatctaattcaactactgcattaccgtatttgatatggcacacttttaaacttgagttttgctgtcaattc--tctgacagATAGTTTTCAGAGAGGATTTTGGAACTGATGGCCGTGGTGGATATTTTGACCAATATGG
   || |||||   | | || |  || |   |||  |  | |  ||| ||       ||||||||  |  |   |  ||   |||    ||||| |  ||   ||||| || ||||| ||||| ||||| ||||| || ||||||||||||||||| ||||||||
---aaaaatataggtatatttcatttgtactattttaacagtatattgccaa---caatatggcatgccatagtagctgcaatttataatcaatacaatcctgcagATTGTATTCAGGGAGGACTTTGGGACTGACGGGCGTGGTGGATATTTTGATCAATATGG

upper sequence: GLYMA19G24250.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G031107_T01 (Zea mays), 3'ss of exon 7
-------------------------------------------------------------------------------------------------cttaacaatattttgttgccttatctaattcaactactgcattaccgtatttgatatggcacacttttaaacttgagttttgctgtcaattctctgacagATAGTTTTCAGAGAGGATTTTGGAACTGATGGCCGTGGTGGATATTTTGACCAATATGG
                                                                                                 || || |||    |      | || | |   | ||      || | ||| ||  | || |  || | |   ||||  | |        | | |||| ||||| || || |  ||||| ||||||||||| || ||||| ||||||||||| ||||||||
gtaagatcctttcctaggtggttacagtattttttttatttctttataaatcatggttggctgttataagttgataacacatcttttgtcagtttgtctgaagaattaaataaaat-tgatgtcaaaaagctgtattttttcagtaattattgtgcctaacatatgttcttgcatgtaatgaatgaat-tctg-cagATCGTATTTAAGGAGGACTTTGGAACTGAAGGACGTGGAGGATATTTTGATCAATATGG

upper sequence: GLYMA19G24250.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G130230_T03 (Zea mays), 3'ss of exon 7
---cttaacaatattttgttgccttatctaattcaactactgcat-taccgtatttgatatggcacacttttaaacttgagttttgctgtcaattctctgacagATAGTTTTCAGAGAGGATTTTGGAACTGATGGCCGTGGTGGATATTTTGACCAATATGG
     |||||||    |   |  | |  | | ||||  |||| |  ||   ||  ||| |  | ||| | | ||      |   ||||    | |      ||||| || ||||| || || ||||| ||||| || ||||| ||||||||||||||||||||
tattgtaacaattgactacagtttgaaatgagtcaa--actgaacctaagataactgaaa--gtacagtatcaatgacatggcatgctaattactacactgcagATTGTATTCAGGGAAGACTTTGGTACTGAAGGGCGTGGAGGATATTTTGACCAATATGG

upper sequence: GLYMA19G24250.1 (Glycine max), 3'ss of exon 7
lower sequence: AT5G40760.1 (Arabidopsis thaliana), 3'ss of exon 7
cttaacaatattttgttgccttatctaattcaactactgcattaccgtatttgatatggcacacttttaaacttgagttttgctgtcaattctctgacagATAGTTTTCAGAGAGGATTTTGGAACTGATGGCCGTGGTGGATATTTTGACCAATATGG
          |        | || ||||  ||   |  |    || || | | || | |        | || |    |||| |      || |||  ||||| |||||||| || |||||||||||||| || ||||| |||||||||||| |||||||
---------gtgagagctgcatagctaagacagaaatagtcagactgtttgttatttagag------tcaattcacatttt-caaatgcttttcttgcagATTGTTTTCAGGGAAGATTTTGGAACTGAAGGGCGTGGCGGATATTTTGACGAATATGG

upper sequence: GLYMA19G24250.1 (Glycine max), 3'ss of exon 7
lower sequence: AT3G27300.1 (Arabidopsis thaliana), 3'ss of exon 7
cttaacaatattttgttgccttatctaattcaactactgcattaccgtatttgatatggcacacttttaaacttgagttttgctgtcaattctctgacagATAGTTTTCAGAGAGGATTTTGGAACTGATGGCCGTGGTGGATATTTTGACCAATATGG
      |   |||  | || |     || |  | | ||  | |   ||||    |      ||       || | | | |  ||      | | || ||||| ||||||||||| |||||||||||||| || || ||||||||||||||  |||| ||
---gtgagagtttgatcgcttagcacaaat--atttctaaacttttgtatagagttgaatccatcc----acataaatct--ctaatttctttttg-cagATCGTTTTCAGAGAAGATTTTGGAACTGAAGGTCGCGGTGGATATTTTGATGAATACGG

upper sequence: GLYMA19G24250.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv14s0171g00490.t01 (Vitis vinifera), 3'ss of exon 7
cttaacaatattttgttgccttatctaattcaactactgcattaccgtatttgatatggcacacttttaaacttg-agttttgctgtcaattctctgacagATAGTTTTCAGAGAGGATTTTGGAACTGATGGCCGTGGTGGATATTTTGACCAATATGG
  | ||   |   |||||   | ||| || |   | ||   | |   ||  | ||||| || |   |||| | ||  | | |  | |   |||| || ||||| || ||||| ||||||||||||||||| || |||||||||||||||||  |||||||
ggttacctcaaaatgttgaagtctctgat-cgttttctatttcaaaataagtaatatgccataaacttaagcatgtggctattattttttttctttggcagATTGTGTTCAGGGAGGATTTTGGAACTGAAGGTCGTGGTGGATATTTTGATGAATATGG

upper sequence: GLYMA19G24250.1 (Glycine max), 3'ss of exon 7
lower sequence: EFJ23968 (Selaginella moellendorffii), 3'ss of exon 6
cttaacaatattttgttgccttatctaattcaactactgcattaccgtatttgatatggcacacttttaaacttgagttttgctgtcaattctctgacagATAGTTTTCAGAGAGGATTTTGGAACTGATGGCCGTGGTGGATATTTTGACCAATATGG
                                              ||||  |  |      ||   | | |   ||| ||      |     |   ||||| || ||||| ||| |||||||||||||||| || ||||| || |||||| |||||||
----------------------------------------------gtatgggtgacaatg-acaaatcatcgctagtgttctaaatagcatacatgcagATTGTGTTCAGGGAGAATTTTGGAACTGATGGTCGCGGTGGCTACTTTGACGAATATGG

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|18040428|gb|BM308722.1|BM308722
EST:     ATCGGTTTTTCTTGCCACTTTGGAACCGCGACAACATTGACAACGTACAG                         ATAGTTTTCAGAGAGGATTTTGGAACTGATGGCCGTGGTGGATATTTTGAC
genomic: ATCGGTTTTTCTTGCCACTTTGGAACCGCGACAACATTGACAATGTACAGgtgagaattt ... tctctgacagATAGTTTTCAGAGAGGATTTTGGAACTGATGGCCGTGGTGGATATTTTGAC
EST: gi|254338293|gb|GR849818.1|GR849818
EST:     ATCGGTTTTTCTTGCCACTTTGGAACCGCGACAACATTGACAATGTACAG                         ATAGTTTTCAGAGAGGATTTTGGAACTGATGGCCGTGGTGGATATTTTGAC
genomic: ATCGGTTTTTCTTGCCACTTTGGAACCGCGACAACATTGACAATGTACAGgtgagaattt ... tctctgacagATAGTTTTCAGAGAGGATTTTGGAACTGATGGCCGTGGTGGATATTTTGAC
EST: gi|16279238|gb|BI943331.1|BI943331
EST:     ATCGGTTTTTCTTGCCACTTTGGAACCGCGACAACATTGACAACGTACAG                         ATAGTTTTCAGAGAGGATTTTGGAACTGATGGCCGTGGTGGATATTTTGAC
genomic: ATCGGTTTTTCTTGCCACTTTGGAACCGCGACAACATTGACAATGTACAGgtgagaattt ... tctctgacagATAGTTTTCAGAGAGGATTTTGGAACTGATGGCCGTGGTGGATATTTTGAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgtatttgatatggcacacttttaaacttgagttttgctgtcaattctctgacagATAGTTTTCAGAGAGGATTTTGGAACTGATGGCCGTGGTGGATATTTTGACCAATATGG
   atttgat  putative branch site (score: 5)
                                            ttctct  putative PPT
                   ttttaaactt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cttaacaatattttgttgccttatctaattcaactactgcattaccgtatttgatatggcacacttttaaacttgagttttgctgtcaattctctgacagATAGTTTTCAGAGAGGATTTTGGAACTGATGGCCGTGGTGGATATTTTGACCAATATGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA