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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTTTCTTGCTTCGTGCTGCTGGATTTCTATTACCTTGCTACATCATGGCTTGGGCAATCAGTATTCTGCAGCGTCGGCGACAAAGACAAgtcagtcttaattatagttatcaatattttcagttttgcttgcatgtgtttggtttcacgttacagaattgattctgagtgcagaattgattttagacag...

Basic information

species Glycine max
transcript GLYMA01G05800.1
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA01G05800.1 (Glycine max), 5'ss of exon 7
lower sequence: LOC_Os11g38800.1 (Oryza sativa), 5'ss of exon 7
CTTTTCTTGCTTCGTGCTGCTGGATTTCTATTACCTTGCTACATCATGGCTTGGGCAATCAGTATTCTGCAGCGTCGGCGACAAAGACAAgtcagtcttaat---tatagttatcaat-attttcagttttgcttgcatgtgtttggtttcacgttaca--gaattgattctgagtgcagaat-tgattttagacag
|| ||  | ||||| ||||||||||||||  | || ||||| ||||||||||||  | |||||||| |||| || |||||||||||||| ||   ||| | |   ||| | | ||| | ||| ||| |         ||  |  |  | | | |    |  ||| |||||    ||| |  || ||||  ||     
CTCTTTCTACTTCGAGCTGCTGGATTTCTGCTGCCATGCTATATCATGGCTTGGATATTCAGTATTTTGCATCGCCGGCGACAAAGACAGgtacttctaattctgtatggatctcattgattgtcaataaaatcattattgggctattcttatggaggaatgaaatgatt---ggtggaccatctgatcctaa----

upper sequence: GLYMA01G05800.1 (Glycine max), 5'ss of exon 7
lower sequence: GRMZM2G113619_T04 (Zea mays), 5'ss of exon 9
CTTTTCTTGCTTCGTGCTGCTGGATTTCTATTACCTTGCTACATCATGGCTTGGGCAATCAGTATTCTGCAGCGTCGGCGACAAAGACAAgtcagtct-taattatagttatcaatattttcagttttgcttgcatgtgtttggtttcacgttacagaattgattctgagtgcagaattgattttagacag-----
|||||  || | ||||||||||| || ||  | || | |||||||||||||||||||||||||||  ||||||| ||  |||| ||||| ||||||   |||||       | ||||||| ||  ||   || | | | ||| |    | ||| | | |   |  |  |  | |    |     || || |     
CTTTTTCTGTTGCGTGCTGCTGGTTTCCTGCTTCCGTTCTACATCATGGCTTGGGCAATCAGTATCTTGCAGCGCCGCAGACAGAGACAGgtcagttaataatttctaaagtgaatatttgcatcttccttttcttattttttga---aggttccggga---acacctaacgtatttcttgccatacaccgaatac

upper sequence: GLYMA01G05800.1 (Glycine max), 5'ss of exon 7
lower sequence: GRMZM2G303431_T01 (Zea mays), 5'ss of exon 7
CTTTTCTTGCTTCGTGCTGCTGGATTTCTATTACCTTGCTACATCATGGCTTGGGCAATCAGTATTCTGCAGCGTCGGCGACAAAGACAAgtcagtcttaattatagttatcaatattttcagttttgct--tgcatgtgtttggtttcacgtta-cagaattgattctgagtgcagaattgattttag-acag--------------------------------------------------------------------------------------------------
|||||  ||||||| |||||||| |||||  | || |||||||||||||| |||  | |||||||| |||| || || ||||||||||| ||    || | ||   |  |||   |      || ||| |  || |      | ||| ||  |   ||  || |  |  || |    | |  |   ||| | |                                                                                                   
CTTTTTCTGCTTCGAGCTGCTGGGTTTCTGCTGCCGTGCTACATCATGGCATGGATATTCAGTATTTTGCATCGCCGTCGACAAAGACAGgt--acctcatttgacgcaatctcgagagatggtgttggtcatgaaaaaaacttgttccaaatcgtcatcatagtgtaggaataggaagtccaccgtagtatattttttaactatatgtggctcctggtcctaaatctgtcgatgatatggcacaccatccatctaagttctctgtgcttcttcttcttcctttgtctgcag

upper sequence: GLYMA01G05800.1 (Glycine max), 5'ss of exon 7
lower sequence: AT2G02960.2 (Arabidopsis thaliana), 5'ss of exon 7
CTTTTCTTGCTTCGTGCTGCTGGATTTCTATTACCTTGCTACATCATGGCTTGGGCAATCAGTATTCTGCAGCGTCGGCGACAAAGACAAgtcagtcttaattatagttat-caatatttt-------cagttttgcttgcatgtgtttggtttcacgttacagaattgattctgagtgcagaattgattttagacag--------
||| || |||| || ||||||||||||||  | || ||||| |||||||||||||| ||||||||||| ||||| ||  |||| ||||| || |||  ||     | | || |||   |||       |||| ||  ||   | |   || ||| | |   || | |   |     ||   || || || | |  |          
CTTGTCCTGCTCCGAGCTGCTGGATTTCTTCTTCCATGCTATATCATGGCTTGGGCCATCAGTATTCTACAGCGCCGAAGACAGAGACAGgttagtagtataagaactcatgcaaggatttttccggacagtcttttttttttcttactg-ttttatgaatcaaactgagtcactggtatcgacttaatgtaacccgattgaacag

upper sequence: GLYMA01G05800.1 (Glycine max), 5'ss of exon 7
lower sequence: AT2G02960.5 (Arabidopsis thaliana), 5'ss of exon 5
----------CTTTTCTTGCTTCGTGCTGCTGGATTTCTATTACCTTGCTACATCATGGCTTGGGCAATCAGTATTCTGCAGCGTCGGCGACAAAGACAAgtcagtcttaattatagttat-caatatttt-------cagttttgcttgcatgtgtttggtttcacgttacagaattgattctgagtgcagaattgattttagacag--------
          ||| || |||| || ||||||||||||||  | || ||||| |||||||||||||| ||||||||||| ||||| ||  |||| ||||| || |||  ||     | | || |||   |||       |||| ||  ||   | |   || ||| | |   || | |   |     ||   || || || | |  |          
CTTATTTTAGCTTGTCCTGCTCCGAGCTGCTGGATTTCTTCTTCCATGCTATATCATGGCTTGGGCCATCAGTATTCTACAGCGCCGAAGACAGAGACAGgttagtagtataagaactcatgcaaggatttttccggacagtcttttttttttcttactg-ttttatgaatcaaactgagtcactggtatcgacttaatgtaacccgattgaacag

upper sequence: GLYMA01G05800.1 (Glycine max), 5'ss of exon 7
lower sequence: Vv01s0026g02470.t01 (Vitis vinifera), 5'ss of exon 9
CTTTTCTTGCTTCGTGCTGCTGGATTTCTATTACCTTGCTACATCATGGCTTGGGCAATCAGTATTCTGCAGCGTCGGCGACAAAGACAAgtcagt--cttaat----tatagttatcaatattttcagt---tttgcttgcatgtgtttggtttcacgttacagaattgattctgagtgcagaattgattttagacag
|||||||||||||| |||||||| ||| || | || |||||||| ||||| ||||| || |||||  ||||||||||  |||| || || || |||  ||  ||    | | |||| | ||| ||    |   ||  | |  |  ||| |  | |  | || |  |  ||   ||   |      |||           
CTTTTCTTGCTTCGGGCTGCTGGGTTTTTACTGCCCTGCTACATTATGGCCTGGGCCATTAGTATCTTGCAGCGTCGAAGACAGAGGCAGgttagtgtctccatattttgtggttaaccataattcttatacattcccatcaacatgtcttttcttccttttcctatctg-ccctttctcttcctttgtac--------

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|254321831|gb|GR837245.1|GR837245
EST:     ACATCATGGCTTGGGCAATCAGTATTCTGCAGCGTCGGCGACAAAGACAA                         GAGGCTGCAGCACTAGCGGCAACCCAAGTTGCTTTTGTTCTACAATCTGGT
genomic: ACATCATGGCTTGGGCAATCAGTATTCTGCAGCGTCGGCGACAAAGACAAgtcagtctta ... ggtgaaacagGAGGCTGCAGCACTAGCGGCAACCCAAGTTGCTTTTGTTCTACAATCTGGT
EST: gi|31471470|gb|CD413498.1|CD413498
EST:     ACATCATGGCTTGGGCAATCAGTATTCTGCAGCGTCGGCGACAAAGACAA                         GAGGCTGCAGCACTAGCGGCAACCCAAGTTGCTTTTGTTCTACAATCTGGT
genomic: ACATCATGGCTTGGGCAATCAGTATTCTGCAGCGTCGGCGACAAAGACAAgtcagtctta ... ggtgaaacagGAGGCTGCAGCACTAGCGGCAACCCAAGTTGCTTTTGTTCTACAATCTGGT
EST: gi|151400968|gb|EV270782.1|EV270782
EST:     ACATCATGGCTTGGGCAATCAGTATTCTGCAGCGTCGGCGACAAAGACAA                         GAGGCTGCAGCACTAGCGGCAACCCAAGTTGCTTTTGTTCTACAATCTGGT
genomic: ACATCATGGCTTGGGCAATCAGTATTCTGCAGCGTCGGCGACAAAGACAAgtcagtctta ... ggtgaaacagGAGGCTGCAGCACTAGCGGCAACCCAAGTTGCTTTTGTTCTACAATCTGGT
EST: gi|15001277|gb|BI322091.1|BI322091
EST:     ACATCATGGCTTGGGCAATCAGTATTCTGCAGCGTCGGCGACAAAGACAA                         GAGGCTGCAGCACTAGCGGCAACCCAAGTTGCTTTTGTTCTACAATCTGGT
genomic: ACATCATGGCTTGGGCAATCAGTATTCTGCAGCGTCGGCGACAAAGACAAgtcagtctta ... ggtgaaacagGAGGCTGCAGCACTAGCGGCAACCCAAGTTGCTTTTGTTCTACAATCTGGT
EST: gi|9987060|gb|BE661168.1|BE661168
EST:     GGCAATCAGTATTCTGCAGCGTCGGCGACAAAGACAA                         GAGGCTGCAGCACTAGCGGCAACCCAAGTTGCTTTTGTTCTACAATCTGGT
genomic: GGCAATCAGTATTCTGCAGCGTCGGCGACAAAGACAAgtcagtctta ... ggtgaaacagGAGGCTGCAGCACTAGCGGCAACCCAAGTTGCTTTTGTTCTACAATCTGGT
EST: gi|254340833|gb|GR854561.1|GR854561
EST:     ACATCATGGCTTGGGCAATCAGTATTCTGCAGCGTCGGCGACAAAGACAA                         GAGGCTGCAGCACTAGCGGCAACCCAAGTTGCTTTTGTTCTACAATCTGGT
genomic: ACATCATGGCTTGGGCAATCAGTATTCTGCAGCGTCGGCGACAAAGACAAgtcagtctta ... ggtgaaacagGAGGCTGCAGCACTAGCGGCAACCCAAGTTGCTTTTGTTCTACAATCTGGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTTTTCTTGCTTCGTGCTGCTGGATTTCTATTACCTTGCTACATCATGGCTTGGGCAATCAGTATTCTGCAGCGTCGGCGACAAAGACAAgtcagtcttaattatagttatcaatattttcagttttgcttgcatgtgtttggtttcacgttacagaattgattctgagtgcagaattgattttagacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG