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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagttgaacaatttttagaaaaacacatacaattttctatctctttttaattcccttatctatctgagcaccactgcatacactcctgctcccaagaagcttccttgtcagttgctggttctaactttcgtattaccgctgttggctcagGTATATCAATTTGTAGGACTAACAGAACTTTATTACGCTGGTAGTCATGGAATGGACATCATTGGCCCTGTTAGACAATCTGTATCTGATAATCACCTAA

Basic information

species Glycine max
transcript GLYMA09G36570.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G36570.2 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os10g40555.1 (Oryza sativa), 3'ss of exon 3
gtagttgaacaatttttagaaaaacacatacaattttctatctctttttaattcccttatctatctgagcaccactgcata-cactcctgctcccaagaagcttccttgtcagttgctggttctaactttcgtattaccgctgt-tggctcagGTATATCAATTTGTAGGACTAACAGAACTTTATTACGCTGGTAGTCATGGAATGGACATCATTGGCCCTGTTAGACAATCTGTATCTGATAATCACCTAA
                                                        | |   || |  |  |   || | |  |||||  || | ||     | | || |    |  | |||    || || |||    | | | |   | |||| | | | |||||   |||||| ||||| ||||||||||| |||||||||||||| ||||| || ||||||||  | ||||  ||   |  ||| |   
-------------------------------------------------------gtaaggaatttatgttcacatgtaaaatactccccctgctaaccttttgcatttttcactctttgttgactctctcttatgtgtgttttgttctttagGTTTTTGACTTTGTGAAACTAACTGAACTGTATTACGCTGGAAGTCATGGAATGGATATCATGGGGCCTGTTAGGAAGTCTGATTCGAGTGGTCAGCATG

upper sequence: GLYMA09G36570.2 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os07g30160.1 (Oryza sativa), 3'ss of exon 4
gtagttgaacaatttttagaaaaacacatacaattttctatctctttttaattcccttatctatctgagcaccactgcatacactcctgctcccaagaagcttccttgtcagttgctggttctaactttcgtattaccgctgttggctcagGTATATCAATTTGTAGGACTAACAGAACTTTATTACGCTGGTAGTCATGGAATGGACATCATTGGCCCTGTTAGACAATCTGTATCTGATAATCACCTAA
                                    |  || | || || |     || || |  | | ||    |||  | |     |         |  ||   ||||| |  ||| | |||||| |    ||   |        | |||| | | | |||||   |||||||||| | || || |||||||| ||||||||||||||||| || || ||| |  ||  ||  || | || | |||  |
-----------------------------------gtgcatatgttatttaaaaggtt-tcgacgtaatcattg-tgctgatataatagtaaattgatatgttatctgtcatt--ctgatactaactgt-acctttttgtatcaattttagGTGTTTGATTTTGTTAAACTAACAGAATTGTACTATGCTGGTAGCCATGGAATGGACATCATGGGTCCAGTTGGGGAACATGATTCAGTTACTAACCATA

upper sequence: GLYMA09G36570.2 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G178546_T01 (Zea mays), 3'ss of exon 4
gtagttgaacaatttttagaaaaacacatacaattttctatctctttttaattcccttatctatctgagcaccactgcatacactcctgctcccaagaagcttccttgtcagttgctggttctaactttcgtattaccgctgttggctcagGTATATCAATTTGTAGGACTAACAGAACTTTATTACGCTGGTAGTCATGGAATGGACATCATTGGCCCTGTTAGACAATCTGTATCTGATAATCACCTAA
                                                                    | |  || |  |  | |  |  |  ||  ||     | | ||||    | |   |   ||||  |||    || ||     |||| | | | |||||    ||||  ||| | || |||||||| || |||||||||||||| || |||||||||||  |  ||         |||  | |  
--------------------------------------------------------------------gtat-acagtgt-tattgttcattgcacaaataactcctatcagcattttgcatt---tttctcattgtttctttt-----agGTTTTTGACTTTGTGAAGCTAAATGAATTGTACTACGCTGGAAGCCATGGAATGGACATAATGGGCCCTGTTAGGAAGACTACTGACTCCAATGGCGTGG

upper sequence: GLYMA09G36570.2 (Glycine max), 3'ss of exon 3
lower sequence: AT5G51460.1 (Arabidopsis thaliana), 3'ss of exon 4
gtagttgaacaatttttagaaaaacacatacaattttctatctctttttaattcccttatctatctgagcaccactgcatacactcctgctcccaagaagcttccttgtcagttgctggttctaactttcgtattaccgctgttggctcagGTATATCAATTTGTAGGACTAACAGAACTTTATTACGCTGGTAGTCATGGAATGGACATCATTGGCCCTGTTAGACAATCTGTATCTGATAATCACCTAA
                                                        | |||| |||         ||  |    | || |  | |  |   || |||||  ||       | |||   | |||  |      ||     |||| ||| | |||||     | |  |||||||||||||| || || |||||||||||||||||  | || |   || ||||| ||    || | ||     
-------------------------------------------------------gtaatctttctaca------tgttttattttcttcatcaagaacattttcttgt--gtgatctaatgtaataatagtac-attttgcttcatctagGTGTATGAGTTTGTTAATTTGAGTGAACTTTATTACGCCGGAAGCCATGGAATGGACATCATGAGTCCCGCAGGAGAATCTTTAAACCATGAACATAGCC

upper sequence: GLYMA09G36570.2 (Glycine max), 3'ss of exon 3
lower sequence: Vv16s0022g00660.t01 (Vitis vinifera), 3'ss of exon 3
gtagttgaacaatttttagaaaaacacatacaattttctatctctttttaattcccttatctatctgagcaccactgcatacactcctgctcccaagaagcttccttgtcagttgctggttctaactttcgtattaccgctgttggctcagGTATATCAATTTGTAGGACTAACAGAACTTTATTACGCTGGTAGTCATGGAATGGACATCATTGGCCCTGTTAGACAATCTGTATCTGATAATCACCTAA
            |  || | |        |   | | ||||   |||  |||     |  | || |   | |   |  ||    |     ||   ||| | ||  |  ||  |  |||  |     || ||||   |  || ||   | |||| ||| | ||||| ||||||||||| || || ||||||||||||||||| ||||||||||| |||||||| ||||| ||  | ||| || | || | ||
-----------gtaattggcaggcttttgagtgtgtgctattattttaaaatcattatggcaatttcctcccatttatatcagttttccttctatagatggtttttcatct-tcactgactt---gttacgtaac-ctactattcatttagGTGTATAATTTTGTGGGACTAACAGAGCTCTACTACGCTGGTAGTCATGGGATGGACATCATGGGCCCTGTCAGACACTCCATTTCTAATGACCATCCAA

upper sequence: GLYMA09G36570.2 (Glycine max), 3'ss of exon 3
lower sequence: PP1S46_31V6.1 (Physcomitrella patens), 3'ss of exon 4
gtagttgaacaatttttagaaaaacacatacaattttctatctctttttaattcccttatctatctgagcaccactgcatacactcctgctcccaagaagcttccttgtcagttgctggttctaactttcgtattaccgctgttggctcagGTATATCAATTTGTAGGACTAACAGAACTTTATTACGCTGGTAGTCATGGAATGGACATCATTGGCCCTGTTAGACAATCTGTATCTGATAATCACCTAA--
                                               |  ||   |  |  | | || ||     || ||  |    ||     | | || |       || ||    | |||   | | ||     || | ||||  ||||| | | | |||||   | | |||||||| ||||||||||| |||||||| ||||| ||||| || ||||  | | | |    ||  | ||   |   ||  
-----------------------------------------------tggatcttcagaaat-tttgtgcgaagttg-atttaggtttgtg--aagggagttgaagctacaattaagaggtcttcttgtggttgcttcgattttggagcagGTGTTTGAGTTTGTGCAATTGACAGAACTATATTACGCTGGAAGTCATGGCATGGATATCATGGGACCTGC-AAAGAGTTCAGATG-GGTATCGAGTGAAGG

upper sequence: GLYMA09G36570.2 (Glycine max), 3'ss of exon 3
lower sequence: PP1S227_48V6.1 (Physcomitrella patens), 3'ss of exon 3
gtagttgaacaatttttagaaaaacacatacaattttctatctctttttaattcccttatctatctgagcaccactgcatacactcctgctcccaagaagcttccttgtcagttgctggttctaactttcgtattaccgctgttggctcagGTATATCAATTTGTAGGACTAACAGAACTTTATTACGCTGGTAGTCATGGAATGGACATCATTGGCCCTGTTAGACAATCTGTATCTGATAATCACCTAA--
                                              |  |  |   ||     | | | ||  | ||  |    |      |    |||   | |   |  |  ||  | ||  |  ||    |||  | | ||||  ||||| | | | |||||   | | |||||||| ||||||||||| |||||||| ||||| ||||| ||||||| || | |    | ||  | |    |  |||  
----------------------------------------------tggatctattttgagattttaatcaggattgattttggtgagatgcatgcgaaagcttcaattaggaggcgtgctcacagctt----ttatggtt-ttggagcagGTGTTTGATTTTGTGCAATTGACAGAACTGTATTACGCTGGGAGTCATGGCATGGATATCATGGGCCCTGCTAAA-AGCTCGGATG-GTTTCCGAGTTAAGG

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|6566157|gb|AW233794.1|AW233794
EST:     GAAGTCGTGATAAG                         GTATATCAATTTGTAGGACTAACAGAACTTTATTACGCTGGTAGTCATGGA
genomic: GAAGTCGTGATAAGgtagttgaac ... gttggctcagGTATATCAATTTGTAGGACTAACAGAACTTTATTACGCTGGTAGTCATGGA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaagcttccttgtcagttgctggttctaactttcgtattaccgctgttggctcagGTATATCAATTTGTAGGACTAACAGAACTTTATTACGCTGGTAGTCATGGAATGGACATCATTGGCCCTGTTAGACAATCTGTATCTGATAATCACCTAA
                       ttctaac  putative branch site (score: 1)
                          taacttt  TA-rich tract