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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cttttgatggtttagtttagtatttccagacctcagtatcattttttttgttgcaattgtatattgtggttacattaatttctgtgaatttcaactgcagACAATGACAACTTTCATGCCACCTCCACCAGCTGCTACATTTCTTGCATTTCATCCTCAAGACAACAATATTATTGCTATTGGCATGGAGGACTCTTCCA

Basic information

species Glycine max
transcript GLYMA13G22720.1
intron # 21
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G22720.1 (Glycine max), 3'ss of exon 21
lower sequence: Vv11s0016g05620.t01 (Vitis vinifera), 3'ss of exon 21
cttttgatggtttagtttagtatttccagacctcagtatcattttttttgttgcaattgtatattgtggttacattaatttctgtgaatttcaactgcagACAATGACAACTTTCATGCCACCTCCACCAGCTGCTACATTTCTTGCATTTCATCCTCAAGACAACAATATTATTGCTATTGGCATGGAGGACTCTTCCA
                                                                                                  |||| |||||||| || ||||| || |||||||| || |||||| | ||||| |||||||||||||| ||||| ||||| || ||||||||||||||||| |
nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnagACCATGACAACATTTATGCCCCCACCACCAGCAGCAACATTTTTGGCATTCCATCCTCAAGACAATAATATCATTGCCATAGGCATGGAGGACTCTTCTA

upper sequence: GLYMA13G22720.1 (Glycine max), 3'ss of exon 21
lower sequence: PP1S316_34V6.1 (Physcomitrella patens), 3'ss of exon 20
cttttgatggtttagtttagtatttccagacctcagtatcattttttttgttgcaattgtatattgtggttacattaatt-tctgtgaatttcaactgcagACAATGACAACTTTCATGCCACCTCCACCAGCTGCTACATTTCTTGCATTTCATCCTCAAGACAACAATATTATTGCTATTGGCATGGAGGACTCTTCCA
  ||  |    ||       | |||    |    |  || | | |  | ||     ||| | || |  |||     | ||  ||  | |||   | | |||   ||||| || |||||||| || || ||||| ||||| |||||||| || ||||| ||||||||||| || ||||| || || |||||||| ||  | |
tattaaaaaaattgaagccattttttattattaaaaaattactctgctggtgatgcttgaacatggcagttctgacagttgccttcggattgtgatt-cagGTCATGACGACATTCATGCCGCCACCTCCAGCAGCTACTTTTCTTGCGTTCCATCCCCAAGACAACAACATCATTGCCATAGGAATGGAGGATTCAACAA

upper sequence: GLYMA13G22720.1 (Glycine max), 3'ss of exon 21
lower sequence: PP1S99_260V6.1 (Physcomitrella patens), 3'ss of exon 20
--------------------------cttttgatggtttagtttagtatttcca-gacctcagtatcatttttt----ttgttgcaattgtatattgtggttacattaattt-ctgtgaatttcaactgcagACAATGACAACTTTCATGCCACCTCCACCAGCTGCTACATTTCTTGCATTTCATCCTCAAGACAACAATATTATTGCTATTGGCATGGAGGACTCTTCCA
                            ||| ||  |||  | || || |     ||     || |  |||||     || |  || ||||  ||| |  ||       ||| ||  | ||||  ||| |||   ||||| || ||||||||||| || ||||| ||||| ||||||||||||||||| |||||||||||||| |||||||| || ||||| || ||  | |
gtaaagtccgcgaatcatgaggagtctattttattctttgttctaataatatggtgagaagcgttttgtttttggtaattttgacagttgtcaatttttattctgacgcttttcttcggattttgact-cagGTCATGACGACATTCATGCCACCACCTCCAGCAGCTACTTTTCTTGCATTTCATCCACAAGACAACAATATCATTGCTATCGGAATGGAAGATTCGACAA

upper sequence: GLYMA13G22720.1 (Glycine max), 3'ss of exon 21
lower sequence: EFJ17248 (Selaginella moellendorffii), 3'ss of exon 20
cttttgatggtttagtttagtatttccagacctcagtatcattttttttgttgcaattgtatattgtggttacattaatttctgtgaatttcaactgcagACAATGACAACTTTCATGCCACCTCCACCAGCTGCTACATTTCTTGCATTTCATCCTCAAGACAACAATATTATTGCTATTGGCATGGAGGACTCTTCCA
                                   ||||       ||||||||  || | |   ||| | | |  | | ||   |||         ||||  ||||||   |||||||| ||||| ||||| || ||||| || || ||||||||||| || || ||| |||||||||| || |||||||| ||  | |
-----------------------------------gtatg--ccgatttgttgct-ttttctccagtgatgaaaccattgtc---gaa--------acagATTATGACACAATTCATGCCGCCTCCGCCAGCAGCAACATTCCTCGCTTTTCATCCTCAGGATAATAATTTTATTGCTATCGGTATGGAGGATTCGGCTA

upper sequence: GLYMA13G22720.1 (Glycine max), 3'ss of exon 21
lower sequence: EFJ30926 (Selaginella moellendorffii), 3'ss of exon 20
cttttgatggtttagtttagtatttccagacctcagtatcattttttttgttgcaattgtatattgtggttacattaatttctgtgaatttcaactgcagACAATGACAACTTTCATGCCACCTCCACCAGCTGCTACATTTCTTGCATTTCATCCTCAAGACAACAATATTATTGCTATTGGCATGGAGGACTCTTCCA
                                   ||||       ||||||||  || | |   ||| | | |  | | ||   |||         ||||  ||||||   |||||||| ||||| ||||| || ||||| || || ||||||||||| || || ||| |||||||||| || |||||||| ||    |
-----------------------------------gtatg--ccgatttgttgctctt-tctccagtgatgaaaccattgtc---gaa--------acagATTATGACACAATTCATGCCGCCTCCGCCAGCAGCAACATTCCTCGCTTTTCATCCTCAGGATAATAATTTTATTGCTATCGGTATGGAGGATTCGGTTA

upper sequence: GLYMA13G22720.1 (Glycine max), 3'ss of exon 21
lower sequence: EFJ32018 (Selaginella moellendorffii), 3'ss of exon 20
cttttgatggtttagtttagtatttccagacctcagtatcattttttttgttgcaattgtatattgtggttacattaatttctgt--gaattt--caactgcagACAATGACAACTTTCATGCCACCTCCACCAGCTGCTACATTTCTTGCATTTCATCCTCAAGACAACAATATTATTGCTATTGGCATGGAGGACTCTTCCA
                                                         || | ||| |   | | || |    |||  ||| ||  ||  | |||   |||||| | ||||||||||| |||||||| || || || || || ||||| ||||||||||||||||| || || ||||| ||||| || ||| | |
------------------------------------------------------gtatgcacatttttccttc-ttgaccggtgtaagaacttgccatgtccagGTGATGACAGCATTCATGCCACCGCCACCAGCAGCAACGTTCCTGGCTTTTCACCCTCAAGACAACAATATCATAGCGATTGGAATGGAAGATTCTACAA

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|11412135|gb|BF424146.1|BF424146
EST:     CTCTATTCAATATGATGACATTTAAG                         ACAATGACAACTTTCATGCCACCTCCACCAGCTGCTACATTTCTTGCATTT
genomic: CTCTATTCAATATGATGACATTTAAGgtatgtggct ... tcaactgcagACAATGACAACTTTCATGCCACCTCCACCAGCTGCTACATTTCTTGCATTT
EST: gi|7795165|gb|AW780562.1|AW780562
EST:     TGTCTGCTTCATGGGGAAAAATTTCTCTATTCAATATGATGACATTTAAG                         ACAATGACAACTTTCATGCCACCTCCACCAGCTGCTACATTTCTTGCATTT
genomic: TGTCTGCTTCAGGGGGAAAAATTTCTCTATTCAATATGATGACATTTAAGgtatgtggct ... tcaactgcagACAATGACAACTTTCATGCCACCTCCACCAGCTGCTACATTTCTTGCATTT
EST: gi|23731795|gb|BU764044.1|BU764044
EST:     TGTCTGCTTCAGGGGGGAAAATTTCTCTATTCAATATGATGACATTTAAG                         ACAATGACAACTTTCATGCCACCTCCACCAGCTGCGACATTTCTTGCATTT
genomic: TGTCTGCTTCAGGGGGAAAAATTTCTCTATTCAATATGATGACATTTAAGgtatgtggct ... tcaactgcagACAATGACAACTTTCATGCCACCTCCACCAGCTGCTACATTTCTTGCATTT
EST: gi|16349478|gb|BI975073.1|BI975073
EST:     TGTCTGCTTCAGGGGGGAAAATTTCTCTATTCAATATGATGACATTTAAG                         ACAATGACAACTTTCATGCCACCTCCACCAGCTGCGACATTTCTTGCATTT
genomic: TGTCTGCTTCAGGGGGAAAAATTTCTCTATTCAATATGATGACATTTAAGgtatgtggct ... tcaactgcagACAATGACAACTTTCATGCCACCTCCACCAGCTGCTACATTTCTTGCATTT
EST: gi|14990529|gb|BI316202.1|BI316202
EST:     TGTCTGCTTCAGGGGGGAAAATTTCTCTATTCAATATGATGACATTTAAG                         ACAATGACAACTTTCATGCCACCTCCACCAGCTGCGACATTTCTTGCATTT
genomic: TGTCTGCTTCAGGGGGAAAAATTTCTCTATTCAATATGATGACATTTAAGgtatgtggct ... tcaactgcagACAATGACAACTTTCATGCCACCTCCACCAGCTGCTACATTTCTTGCATTT
EST: gi|6482921|gb|AW202189.1|AW202189
EST:     TGTCTGC-TCAGGGGGAAAAATTTCTCTATTCAATATGATGACATTTAAG                         ACAATGACAACTTTCATGCCACCTCCACCAGCTGCTACATTTCTTGCATTT
genomic: TGTCTGCTTCAGGGGGAAAAATTTCTCTATTCAATATGATGACATTTAAGgtatgtggct ... tcaactgcagACAATGACAACTTTCATGCCACCTCCACCAGCTGCTACATTTCTTGCATTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttgttgcaattgtatattgtggttacattaatttctgtgaatttcaactgcagACAATGACAACTTTCATGCCACCTCCACCAGCTGCTACATTTCTTGCATTTCATCCTCAAGACAACAATATTATTGCTATTGGCATGGAGGACTCTTCCA
                           cattaat  putative branch site (score: 3)
                        ttacattaatttct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cttttgatggtttagtttagtatttccagacctcagtatcattttttttgttgcaattgtatattgtggttacattaatttctgtgaatttcaactgcagACAATGACAACTTTCATGCCACCTCCACCAGCTGCTACATTTCTTGCATTTCATCCTCAAGACAACAATATTATTGCTATTGGCATGGAGGACTCTTCCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - -gatggtt
- - - - - - - - - - - - -ccagacc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgtggtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttctgtg