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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGAGAAGGGAATTGGGGATGGAACTGTTAGCTATGGAATGGATGACGCTGACGACATATACATGCAATCTTGGACTGGGACTATCATTGGGCCCCCTGGTgtaagctgctctctgcttttctgaaataataatttatttttcttttattagttatttttgacacattggaatctccagctaacatccctatcagcttcta...

Basic information

species Glycine max
transcript GLYMA09G22600.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G22600.1 (Glycine max), 5'ss of exon 2
lower sequence: LOC_Os03g50440.1 (Oryza sativa), 5'ss of exon 2
TGAGAAGGGAATTGGGGATGGAACTGTTAGCTATGGAATGGATGACGCTGACGACATATACATGCAATCTTGGACTGGGACTATCATTGGGCCCCCTGGTgtaagctgctctctgcttttctg-aaataataatttatttttcttttattagttatttttgacacattggaatctccagctaacatccctatcagcttcta
||||||||| ||||| ||||| || || ||||||||||||||||| ||||| |||||||| ||||  || ||||| || ||||||||||| || |||  |||| | ||       |   |  | | ||| ||| |   ||| ||| | |  | |     |||   ||     | | ||   ||  |  ||  |||      
TGAGAAGGGCATTGGTGATGGGACAGTGAGCTATGGAATGGATGATGCTGATGACATATATATGCGTTCCTGGACAGGAACTATCATTGGCCCTCCTAATgtatgttgtataacacccattagtagatattaactgcatttgcttctgtatgctcaaactgaatgatct---tttacattcaatttgtcttgcag------

upper sequence: GLYMA09G22600.1 (Glycine max), 5'ss of exon 2
lower sequence: GRMZM2G090172_T02 (Zea mays), 5'ss of exon 2
TGAGAAGGGAATTGGGGATGGAACTGTTAGCTATGGAATGGATGACGCTGACGACATATACATGCAATCTTGGACTGGGACTATCATTGGGCCCCCTGGTgtaagctgctct--ctgcttttctgaaata-ataatttatttttcttttattagttatttttgacacattggaatctccagctaacatccctatcagcttcta
||||||||| ||||| ||||||||||| |||||||| |||||||| ||||| |||||||| ||||  || ||||| || ||||||||||| || ||   |||| |||||        |  |  ||| ||| |||||  |||||  ||       |||||||  | || |  ||   |  |       |   |  |||      
TGAGAAGGGCATTGGTGATGGAACTGTGAGCTATGGGATGGATGATGCTGATGACATATATATGCGGTCCTGGACAGGAACTATCATTGGTCCTCCCAATgtatgctgcagaaatacccatagtgagatacataatacattttcttt------attattttcaa-acctgagaggttttactgcgtttattttgcag------

upper sequence: GLYMA09G22600.1 (Glycine max), 5'ss of exon 2
lower sequence: GRMZM2G022859_T01 (Zea mays), 5'ss of exon 2
TGAGAAGGGAATTGGGGATGGAACTGTTAGCTATGGAATGGATGACGCTGACGACATATACATGCAATCTTGGACTGGGACTATCATTGGGCCCCCTGGTgtaagctgctctctgcttttctgaaataataatttatttttcttttattagttatttttgacacattggaatctccagctaacatccctatcagcttcta
||||||||| ||||| ||||||||||| |||||||| ||||| || ||||| |||||||  ||||  || ||||| || ||||||||||| || ||    ||| ||| |       |   |  || ||   |  || |    || | || |||||| |  |  |  ||  || |    ||  |||   |  |||      
TGAGAAGGGCATTGGTGATGGAACTGTGAGCTATGGGATGGACGATGCTGATGACATATTTATGCGGTCCTGGACAGGAACTATCATTGGTCCTCCCAACgtatgctacaga--aatacccataactagatacataatgcatttgtttt-gttattctcaaacc--tgagatgtttcactg-catttttcgcag------

upper sequence: GLYMA09G22600.1 (Glycine max), 5'ss of exon 2
lower sequence: AT1G23260.1 (Arabidopsis thaliana), 5'ss of exon 2
TGAGAAGGGAATTGGGGATGGAACTGTTAGCTATGGAATGGATGACGCTGACGACATATACATGCAATCTTGGACTGGGACTATCATTGGGCCCCCTGGTgtaagctgctctctgcttttctgaaataataatttatttttcttttattagttatttttgacacattggaatctccagct--aacatccctatcagcttcta-----
|||||| || ||||| ||||| ||||||||||||||||||||||| ||||| || || || ||||||||||||||||| || ||  |||| || |||  |||| |   ||||||     |||   |      ||| ||||   |||||    | | ||||| | | |  |    | |  |  ||||    | | ||    |      
TGAGAAAGGTATTGGAGATGGTACTGTTAGCTATGGAATGGATGATGCTGATGATATTTATATGCAATCTTGGACTGGCACCATTCTTGGTCCTCCTAATgtatgtatctctctatcgatctctga----gttttgttttagatttatc---tgtgtttgatagagtaaagatgcaatttttaacacttttgtgagagaattgttgg

upper sequence: GLYMA09G22600.1 (Glycine max), 5'ss of exon 2
lower sequence: AT1G70660.1 (Arabidopsis thaliana), 5'ss of exon 2
TGAGAAGGGAATTGGGGATGGAACTGTTAGCTATGGAATGGATGACGCTGACGACATATACATGCAATCTTGGACTGGGACTATCATTGGGCCCCCTGGTgtaagctgctctctgct---tttctgaaataataatttatttttcttttatta-gttatttttgacacattggaatctccagctaacatccctatcagcttcta
|||||| |||||||| ||||| || || || |||||||||||||| ||||| || || |  ||||||||||||||||| || ||  |||| || | |  ||| || |    ||| ||   | | |    | ||  ||| |||  |||  || |   ||| | ||  | ||| ||||    |     |||   |    |||    
TGAGAAAGGAATTGGAGATGGGACAGTGAGTTATGGAATGGATGATGCTGATGATATTTTGATGCAATCTTGGACTGGTACCATTCTTGGTCCTCATAATgttagttttcttcttctcaatctatctcttcatcttttgtttaacttaaatgataatatctatggtagatttgaat---aaagatgcattttttaatgctaaa-

upper sequence: GLYMA09G22600.1 (Glycine max), 5'ss of exon 2
lower sequence: Vv01s0011g05630.t01 (Vitis vinifera), 5'ss of exon 2
TGAGAAGGGAATTGGGGATGGAACTGTTAGCTATGGAATGGATGACGCTGACGACATATACATGCAATCTTGGACTGGGACTATCATTGGGCCCCCTGGTgtaagctgctctctgcttttctgaaata--ataatttatttttctt-ttattagttatttttgacacattggaatctccagctaacatccctatcagcttcta
 || ||||||||||| ||||||||||| || |||||||||||||| ||||| || ||||||||||| || |||||||||||||||||||| || |||  ||| || |  | |||  ||  |  || |   || || || |   ||  |||   |||   | |  ||  | |   |    |  | |  |   |   |   ||  
GGAAAAGGGAATTGGCGATGGAACTGTCAGTTATGGAATGGATGATGCTGATGATATATACATGCAGTCGTGGACTGGGACTATCATTGGTCCTCCTAATgtgagtt-ttttctttttcacacaattttcatgatataatgaactccttacaggttgaatctctcaactagatgttaagaatttatgtggttggtattatc--

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|298168826|gb|HO009756.1|HO009756
EST:     ACGACATATACATGCAATCTTGGACTGGGACTATCATTGGGCCCCCTGGT                         ACTGTTCATGAAGGGCGTATCCACCAGTTGAAATTGTTTTGTGGCAAGGAT
genomic: ACGACATATACATGCAATCTTGGACTGGGACTATCATTGGGCCCCCTGGTgtaagctgct ... tttttaccagACTGTTCATGAAGGGCGTATCCACCAGTTGAAATTGTTTTGTGGCAAGGAT
EST: gi|6071962|gb|AW101349.1|AW101349
EST:     ACGACATATACATGCAATCTTGGACTGGGACTATCATTGGGCCCCCTGGT                         ACTGTTCATGAAGGGCGTATCCACCAGTTGAAATTGTTTTGTGGCAAGGAT
genomic: ACGACATATACATGCAATCTTGGACTGGGACTATCATTGGGCCCCCTGGTgtaagctgct ... tttttaccagACTGTTCATGAAGGGCGTATCCACCAGTTGAAATTGTTTTGTGGCAAGGAT
EST: gi|33387487|gb|CA850694.1|CA850694
EST:     ACGACATATACATGCAATCTTGGACTGGGACTATCATTGGGCCCCCTGGT                         ACTGTTCATGAAGGGCGTATCCACCAGTTGAAATTGTTTTGTGGCAAGGAT
genomic: ACGACATATACATGCAATCTTGGACTGGGACTATCATTGGGCCCCCTGGTgtaagctgct ... tttttaccagACTGTTCATGAAGGGCGTATCCACCAGTTGAAATTGTTTTGTGGCAAGGAT
EST: gi|298193121|gb|HO033555.1|HO033555
EST:     ACGACATATACATGCAATCTTGGACTGGGACTATCATTGGGCCCCCTGGT                         ACTGTTCATGAAGGGCGTATCCACCAGTTGAAATTGTTTTGTGGCAAGGAT
genomic: ACGACATATACATGCAATCTTGGACTGGGACTATCATTGGGCCCCCTGGTgtaagctgct ... tttttaccagACTGTTCATGAAGGGCGTATCCACCAGTTGAAATTGTTTTGTGGCAAGGAT
EST: gi|21285722|gb|BQ473593.1|BQ473593
EST:     ACGACATATACATGCAATCTTGGACTGGGACTATCATTGGGCCCCCTGGT                         ACTGTTCATGAAGGGCGTATCCACCAGTTGAAATTGTTTTGTGGCAAGGAT
genomic: ACGACATATACATGCAATCTTGGACTGGGACTATCATTGGGCCCCCTGGTgtaagctgct ... tttttaccagACTGTTCATGAAGGGCGTATCCACCAGTTGAAATTGTTTTGTGGCAAGGAT
EST: gi|193401185|gb|FK365466.1|FK365466
EST:     ACGACATATACATGCAATCTTGGACTGGGACTATCATTGGGCCCCCTGGT                         ACTGTTCATGAAGG
genomic: ACGACATATACATGCAATCTTGGACTGGGACTATCATTGGGCCCCCTGGTgtaagctgct ... tttttaccagACTGTTCATGAAGG
EST: gi|9898614|gb|BE607582.1|BE607582
EST:     ACGACATATACATGCAATCTTGGACTGGGACTATCATTGGGCCCCCTGGT                         ACTGTTCATGAAGGGCGTATCCACCAGTTGAAATTGTTTTGTGGCAAGGAT
genomic: ACGACATATACATGCAATCTTGGACTGGGACTATCATTGGGCCCCCTGGTgtaagctgct ... tttttaccagACTGTTCATGAAGGGCGTATCCACCAGTTGAAATTGTTTTGTGGCAAGGAT
EST: gi|22522487|gb|BU081298.1|BU081298
EST:     ACGACATATACATGCAATCTTGGACTGGGACTATCATTGGGCCCCCTGGT                         ACTGTTCATGAAGGGCGTATCCACCAGTTGAAATTGTTTTGTGGCAAGGAT
genomic: ACGACATATACATGCAATCTTGGACTGGGACTATCATTGGGCCCCCTGGTgtaagctgct ... tttttaccagACTGTTCATGAAGGGCGTATCCACCAGTTGAAATTGTTTTGTGGCAAGGAT
EST: gi|19269626|gb|BM885882.1|BM885882
EST:     ACGACATATACATGCAATCTTGGACTGGGACTATCATTGGGCCCCCTGGT                         ACTGTTCATGAAGGGCGTATCCACCAGTTGAAATTGTTTTGTGGCAAGGAT
genomic: ACGACATATACATGCAATCTTGGACTGGGACTATCATTGGGCCCCCTGGTgtaagctgct ... tttttaccagACTGTTCATGAAGGGCGTATCCACCAGTTGAAATTGTTTTGTGGCAAGGAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGAGAAGGGAATTGGGGATGGAACTGTTAGCTATGGAATGGATGACGCTGACGACATATACATGCAATCTTGGACTGGGACTATCATTGGGCCCCCTGGTgtaagctgctctctgcttttctgaaataataatttatttttcttttattagttatttttgacacattggaatctccagctaacatccctatcagcttcta

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctctctgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tccctatc