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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cacaaagctcagaaaaaaataattatttttctaaaataagctgaaccagacattatcttatttcagtactgtatggtattaattctctacacttttttagGTTGTTGGGTTGGATTTGGTTGATGATGAAAGCAAACCTGAAAGACGGCCAACAAAACACATGCCTACACCTGAGCAATGGACTAATGTTTTCAATCCGG

Basic information

species Glycine max
transcript GLYMA01G29470.1
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA01G29470.1 (Glycine max), 3'ss of exon 13
lower sequence: LOC_Os05g28180.3 (Oryza sativa), 3'ss of exon 4
cacaaagctcagaaaaaaataattatttttctaaaataagctgaaccagacattatcttat--ttcagtactgtatggtattaa-----ttctctacacttttttagGTTGTTGGGTTGGATTTGGTTGATGATGAAAGCAAACCTGAAAGACGGCCAACAAAACACATGCCTACACCTGAGCAATGGACTAATGTTTTCAATCCGG
      |   ||  ||   | ||| || ||  ||| ||  || ||   |  | ||||  |    |||  |          |||      |  | |      ||  ||||||| ||||| ||||||||||||||||| || ||||||||||| || |||||||| || |||||||||||||| |||||||| ||||| ||||| || |
-----ggactaggtaatttttatttttatttaaaacta--ctaaatatgttaatatcgcacacatcacaagcaggcaactttaggatactcttttttggccttgcagGTTGTAGGGTTAGATTTGGTTGATGATGAGAGTAAACCTGAAAGGCGTCCAACAAAGCATATGCCTACACCTGAACAATGGACCAATGTCTTCAACCCAG

upper sequence: GLYMA01G29470.1 (Glycine max), 3'ss of exon 13
lower sequence: GRMZM2G416667_T01 (Zea mays), 3'ss of exon 12
cacaaagctcagaaaaaaataattatttttctaaaataagctgaaccagacattatcttatttcagtactgt-atggtattaattctctacactt-----ttttagGTTGTTGGGTTGGATTTGGTTGATGATGAAAGCAAACCTGAAAGACGGCCAACAAAACACATGCCTACACCTGAGCAATGGACTAATGTTTTCAATCCGG
 |  |   |    |     |||| ||  ||   ||||| | |       |  |||||| |  |   |  | | |     | ||||  ||     |     ||  ||||||| ||||||||  |||||||||||||||| ||||| ||||| || |||||||| |||||||| |||||||| || ||||| ||||| ||||| || |
-attagttttttcag----taatgataattgagaaatacgttcgcatgtat-ttatctcagatacatgatatcacaacttcaattgactctttctgggccttgcagGTTGTAGGGTTGGACCTGGTTGATGATGAAAGTAAACCAGAAAGGCGTCCAACAAAGCACATGCCCACACCTGAACAGTGGACCAATGTGTTCAACCCTG

upper sequence: GLYMA01G29470.1 (Glycine max), 3'ss of exon 13
lower sequence: AT2G38280.1 (Arabidopsis thaliana), 3'ss of exon 12
-----cacaaagctcagaaaaaaataattatttttctaaaataagctgaaccagacattatcttatttcagtactgtatggtattaattctctacacttttttagGTTGTTGGGTTGGATTTGGTTGATGATGAAAGCAAACCTGAAAGACGGCCAACAAAACACATGCCTACACCTGAGCAATGGACTAATGTTTTCAATCCGG
     ||   |  ||   ||| ||    || |   |     |   |  ||  |    ||   ||   |   | |||| |  | ||           || ||| |||||||||| || ||||||||||||||||||||||||||||||||||| || |||||||||||||| || || |  ||||||||||| |  |||||||| |
gttagcattcatatcttcaaataacctctaatccgcatgtctttacacaataaagagttggtttgactggttgctgtctcttgtt---------tgctatttcagGTTGTTGGATTTGATTTGGTTGATGATGAAAGCAAACCTGAAAGACGTCCCACAAAACACATGCCCACTCCAGCTCAATGGACTAACGCATTCAATCCTG

upper sequence: GLYMA01G29470.1 (Glycine max), 3'ss of exon 13
lower sequence: Vv08s0105g00570.t01 (Vitis vinifera), 3'ss of exon 12
---cacaaagctcagaaaaaaataattatttttctaaaataagctgaaccagacattatcttatttcagtact-gtatgg-tattaattctctacacttttttagGTTGTTGGGTTGGATTTGGTTGATGATGAAAGCAAACCTGAAAGACGGCCAACAAAACACATGCCTACACCTGAGCAATGGACTAATGTTTTCAATCCGG
   |     | | | |  | |     |   || ||        ||||| ||   |||| |||  |   ||| | |  |   ||||| |||  |  |  |||| ||||||||||  |||| || || ||||||||||||||||| |||||||| || |||||||| |||||||| || |  || ||||| |||| ||||||||| |
ttgcttttggtttacattagatc--ctggcttactttttccctctgaatcaagaatta-cttgctatggtatttgagtaactattatttcattgga--ttttcagGTTGTTGGCCTGGACTTAGTGGATGATGAAAGCAAACCAGAAAGACGTCCTACAAAACATATGCCTACTCCAGCTCAGTGGACCAATGCTTTCAATCCTG

upper sequence: GLYMA01G29470.1 (Glycine max), 3'ss of exon 13
lower sequence: PP1S168_82V6.1 (Physcomitrella patens), 3'ss of exon 12
-------------------------------------------------------cacaaagctcagaaaaaaataattatttttctaaaataagctgaaccagacattatcttatttcagtactgt-atggtatta-attctctacactttttt-----------agGTTGTTGGGTTGGATTTGGTTGATGATGAAAGCAAACCTGAAAGACGGCCAACAAAACACATGCCTACACCTGAGCAATGGACTAATGTTTTCAATCCGG
                                                         || |  | ||  |     || ||   ||  |  |   |||    ||  |  |    | |   |  |  || ||| || ||   | | ||| ||||  |           |||| || || || ||  |||| |||||||||||||| |||||||| ||||||||||| |||||||   ||||||   |||||   ||   ||| |||||||
gtgagttgaaaaaactactaaattactgttcttctcagttttgcatcttcattcttgcacacattagccatctg-aactacgattgcatgaggtgctccttcatgcggtgctctgtcatacaaaagtcatgatactatggtttgtacgctttcctttgtgcgtactagGTGGTGGGATTTGACATGGTGGATGATGAAAGCAAGCCTGAAAGGCGGCCAACAAAGCACATGCAACCACCTGCAAAATGGGACAACCCTTTTAATCCGG

upper sequence: GLYMA01G29470.1 (Glycine max), 3'ss of exon 13
lower sequence: PP1S77_89V6.1 (Physcomitrella patens), 3'ss of exon 12
------------------------------------------------------------cacaaagctcagaaaaaaataatta---tttttctaaaataagctgaa----ccagacattatcttatttcagtactgtatggtattaattctctacacttttt----------tagGTTGTTGGGTTGGATTTGGTTGATGATGAAAGCAAACCTGAAAGACGGCCAACAAAACACATGCCTACACCTGAGCAATGGACTAATGTTTTCAATCCGG
                                                            | |      ||     | |  |||    ||| ||    ||  |  |||    || || | | |  | |  || |    |    |  |  ||   | || |||||          ||||||||||| || ||| |||| |||||||| ||||| |||||||| |||||||| || |||||||   |||||| | |||||  ||||  ||||||||| |
gttggtcaaaagcaaaaccaaacccccagcgtcatgcgtcttttcgtttacattcttgtccgctttctccaactggatacgatttgcttttgtcgcgtattggtcgaaataacctgataatttgctttcccattgggtttcaatccttctttcatgcattttttgttaaatgaatagGTTGTTGGATTCGATATGGTGGATGATGAGAGCAAGCCTGAAAGGCGGCCAACGAAGCACATGCAACCACCTGCGAAATGGGATAATCCTTTCAATCCAG

upper sequence: GLYMA01G29470.1 (Glycine max), 3'ss of exon 13
lower sequence: EFJ30909 (Selaginella moellendorffii), 3'ss of exon 11
cacaaagctcagaaaaaaataattatttttctaaaataagctgaaccagacattatcttatttcagtactgta-tggtattaattctctacacttttt-tagGTTGTTGGGTTGGATTTGGTTGATGATGAAAGCAAACCTGAAAGACGGCCAACAAAACACATGCCTACACCTGAGCAATGGACTAATGTTTTCAATCCGG
                                                   ||||  || | |   |   | | | |   | | || ||  ||||| |  ||||||| || || ||  |||| || |||||||||||||| |||||||||||||| || || ||||  || || || || |||   | |  ||||||||| |
-------------------------------------------------gtattactttgtgttcatctcgaactagagcttaatcactgaactttatgcagGTTGTCGGTTTTGACATGGTGGACGATGAAAGCAAACCCGAAAGACGGCCAACTAAGCATATGCAGACTCCCGAACAGTGGCAAATTTCTTTCAATCCAG

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|7925052|gb|AW831078.1|AW831078
EST:     TCACTGTCAACCCAGATTCACATCCTCAGCTGCATGTTTTCCTGAAACAG                         GTTGTTGGGTTGGATTTGGTTGATGATGAAAGCAAACCTGANAGACGGCCA
genomic: TCACTGTCAACCCAGATTCACATCCTCAGCTGCATGTTTTCCTGAAACAGgtgtgttatt ... acttttttagGTTGTTGGGTTGGATTTGGTTGATGATGAAAGCAAACCTGAAAGACGGCCA
EST: gi|254332340|gb|GR846385.1|GR846385
EST:     TCACTGTCAACCCAGATTCACATCCTCAGCTGCATGTTTTCCTGAAACAG                         GTTGTTGGGTTGGATTTGGTTGATGATGAAAGCAAACCTGAAAGACGGCCA
genomic: TCACTGTCAACCCAGATTCACATCCTCAGCTGCATGTTTTCCTGAAACAGgtgtgttatt ... acttttttagGTTGTTGGGTTGGATTTGGTTGATGATGAAAGCAAACCTGAAAGACGGCCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccagacattatcttatttcagtactgtatggtattaattctctacacttttttagGTTGTTGGGTTGGATTTGGTTGATGATGAAAGCAAACCTGAAAGACGGCCAACAAAACACATGCCTACACCTGAGCAATGGACTAATGTTTTCAATCCGG
                               tattaat  putative branch site (score: 2)
                                     ttctctacactttttt  CT-rich tract
      attatcttatttca  TA-rich tract