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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCTCGCAAAGTACAAGCTGGTGTTCTTGGGTGATCAGTCCGTTGGGAAAACCAGCATCATCACTCGCTTCATGTACGACAAATTCGACAACACTTATCAGgtcttcttctttcagatccaatctcactttcactatttcattgcatttccattattattttcaaaacattcaagagatcacggttttatcgtgggatggg...

Basic information

species Glycine max
transcript GLYMA05G05860.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA05G05860.1 (Glycine max), 5'ss of exon 1
lower sequence: LOC_Os07g31370.1 (Oryza sativa), 5'ss of exon 1
TCTCGCAAAGTACAAGCTGGTGTTCTTGGGTGATCAGTCCGTTGGGAAAACCAGCATCATCACTCGCTTCATGTACGACAAATTCGACAACACTTATCAGgtc--ttcttctttcagatccaatctcactttcactatttcattgcatttccattattattttcaaaacattcaagagatcacggttttatcgtgggatggg--
 ||||| |||||||||||||||||| | || || |||||||| || || |||||||||||||| ||||||||||||||||| ||||||||||| || |||||   ||||||||    |||   | || |  ||  |  |    |   ||       ||    |   | |      | |  || | |      ||||        
GCTCGCCAAGTACAAGCTGGTGTTCCTCGGCGACCAGTCCGTCGGCAAGACCAGCATCATCACCCGCTTCATGTACGACAAGTTCGACAACACCTACCAGgtgcgttcttcttctctatc-ggtttcgccgtc--tgctcgcctctcttcggggggttggggttggatctgatcgggggcca-gatccggcggtggcgccctgg

upper sequence: GLYMA05G05860.1 (Glycine max), 5'ss of exon 1
lower sequence: GRMZM2G075719_T01 (Zea mays), 5'ss of exon 1
TCTCGCAAAGTACAAGCTGGTGTTCTTGGGTGATCAGTCCGTTGGGAAAACCAGCATCATCACTCGCTTCATGTACGACAAATTCGACAACACTTATCAGgtcttcttctttcagatccaatctcactttcactatttcattgcatttccattattattttcaaaacattcaagagatcacggttttatcgtgggatggg---
 ||||| ||||||||||| || ||| |||| || |||||||| || || |||||||||||||| |||||||||||||| || |||||||||||||| |||||               ||  ||  |     |    | | | || |  |  ||  | || ||    |      | | |   |||||    || ||||      
GCTCGCCAAGTACAAGCTCGTCTTCCTGGGGGACCAGTCCGTCGGCAAGACCAGCATCATCACCCGCTTCATGTACGATAAGTTCGACAACACTTACCAGgtacgacggcccgcacgcctctccgatcccgatcgatccctcgcgtg-ctgttcgtgttatcttcccgcgtcggggttg--ggtttgtgggttggatccaatc

upper sequence: GLYMA05G05860.1 (Glycine max), 5'ss of exon 1
lower sequence: GRMZM2G169694_T01 (Zea mays), 5'ss of exon 1
TCTCGCAAAGTACAAGCTGGTGTTCTTGGGTGATCAGTCCGTTGGGAAAACCAGCATCATCACTCGCTTCATGTACGACAAATTCGACAACACTTATCAGgt-cttcttctttcagatccaatctcactttcact-atttcattgcatttccattattattttcaaaacatt---caagagatcacggttttatcgtgggatggg
 ||||| ||||||||||| || ||| |||| || |||||||| || || || ||||||||||| ||||||||||||||||| ||||| ||||| || ||||| |  |  |   ||   ||    || ||  | |  ||  |  |  ||  |     |  | |||    |||    |  | | |   ||     | |||||     
GCTCGCCAAGTACAAGCTCGTCTTCCTGGGGGACCAGTCCGTCGGCAAGACGAGCATCATCACCCGCTTCATGTACGACAAGTTCGATAACACCTACCAGgtacgacggcccgcaccgcctccttctctggctccgatcccgatcgatccctcgcgtgctgttcgtgtcatctcccccgcgttgggggcgggttagtggg-----

upper sequence: GLYMA05G05860.1 (Glycine max), 5'ss of exon 1
lower sequence: AT2G44610.1 (Arabidopsis thaliana), 5'ss of exon 1
TCTCGCAAAGTACAAGCTGGTGTTCTTGGGTGATCAGTCCGTTGGGAAAACCAGCATCATCACTCGCTTCATGTACGACAAATTCGACAACACTTATCAGgt----cttcttctttcagatccaatctcactttcactatttcattgcatttccattattattttcaaaacattcaagagatcacggttttatcgtgggatggg
 ||||| ||||| |||||||||||  |||| ||||| ||||| || |||||||| ||||| ||||| ||||||||||||||||||||||||||||| |||||     | | |  |||| ||| |       | ||     | ||   | ||| | |   ||||||  |   |||  ||     |   |   |  ||  ||| | 
ACTCGCTAAGTATAAGCTGGTGTTTCTGGGAGATCAATCCGTCGGCAAAACCAGTATCATTACTCGATTCATGTACGACAAATTCGACAACACTTACCAGgtaaatttccattgttcaaatctaggtattatctcgacgatgcacgacgtttgcttc--tatttt-gagggattatagtcgggaaaatcccagggtttgattg-

upper sequence: GLYMA05G05860.1 (Glycine max), 5'ss of exon 1
lower sequence: EFJ30542 (Selaginella moellendorffii), 5'ss of exon 1
TCTCGCAAAGTACAAGCTGGTGTTCTTGGGTGATCAGTCCGTTGGGAAAACCAGCATCATCACTCGCTTCATGTACGACAAATTCGACAACACTTATCAGgtcttcttctttcagatccaatctcactttcactatttcattgcatttccattattattttcaaaacattcaagagatcacggttttatcgtgggatggg
 || |||||||||||||| || ||  | || |||||||| || ||||| || ||||||||||| || |||||||| || || || |||||||| || ||||| |     |   || | |    || || ||||| |  ||    | ||  |     ||||||||                                    
GCTTGCAAAGTACAAGCTCGTCTTTCTCGGCGATCAGTCTGTGGGGAAGACGAGCATCATCACGCGATTCATGTATGATAAGTTTGACAACACATACCAGgtatgagattacgagtttc---ttctctctcactttggca----aattggaa----attttcaag-----------------------------------

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|7146015|gb|AW507937.1|AW507937
EST:     CCAGCATCATCACTCGCTTTATGTACGACAAATTCGACAACACTTATCAG                         GCTACAATCGGTATCGATTTTCTGTCAAAAACTATGTATCTTGAAGATCGA
genomic: CCAGCATCATCACTCGCTTCATGTACGACAAATTCGACAACACTTATCAGgtcttcttct ... tgctaaacagGCTACAATCGGTATCGATTTTCTGTCAAAAACTATGTATCTTGAAGATCGA
EST: gi|21995147|gb|BQ786675.1|BQ786675
EST:     CCAGCATCATCACTCGCTTCATGTACGACAAATTCGACAACACTTATCAG                         GCTACAATCGGTATCGATTTTCTGTCAAAAACTATGTATCTTGAAGATCGA
genomic: CCAGCATCATCACTCGCTTCATGTACGACAAATTCGACAACACTTATCAGgtcttcttct ... tgctaaacagGCTACAATCGGTATCGATTTTCTGTCAAAAACTATGTATCTTGAAGATCGA
EST: gi|8284612|gb|BE022171.1|BE022171
EST:     CCAGCATCATCACTCGCTTCATGTACGACAAATTCGACAACACTTATCAG                         GCTACAATCGGTATCGATTTTCTGTCAAAAACTATGTATCTTGAAGATCGA
genomic: CCAGCATCATCACTCGCTTCATGTACGACAAATTCGACAACACTTATCAGgtcttcttct ... tgctaaacagGCTACAATCGGTATCGATTTTCTGTCAAAAACTATGTATCTTGAAGATCGA
EST: gi|192325163|gb|FK017534.1|FK017534
EST:     ACTCGCTTCATGTACGACAAATTCGACAACACTTATCAG                         GCTACAATCGGTATCGATTTTCTGTCAAAAACTATGTATCTTGAAGATCGA
genomic: ACTCGCTTCATGTACGACAAATTCGACAACACTTATCAGgtcttcttct ... tgctaaacagGCTACAATCGGTATCGATTTTCTGTCAAAAACTATGTATCTTGAAGATCGA
EST: gi|298193040|gb|HO033474.1|HO033474
EST:     CCAGCATCATCACTCGCTTCATGTACGACAAATTCGACAACACTTATCAG                         GCTACAATCGGTATCGATTTTCTGTCAAAAACTATGTATCTTGAAGATCGA
genomic: CCAGCATCATCACTCGCTTCATGTACGACAAATTCGACAACACTTATCAGgtcttcttct ... tgctaaacagGCTACAATCGGTATCGATTTTCTGTCAAAAACTATGTATCTTGAAGATCGA
EST: gi|192321239|gb|FK014329.1|FK014329
EST:     CATCATCACTCGCTTCATGTACGACAAATTCGACAACACTTATCAG                         GCTACAATCGGTATCGATTTTCTGTCAAAAACTATGTATCTTGAAGATCGA
genomic: CATCATCACTCGCTTCATGTACGACAAATTCGACAACACTTATCAGgtcttcttct ... tgctaaacagGCTACAATCGGTATCGATTTTCTGTCAAAAACTATGTATCTTGAAGATCGA
EST: gi|193335501|gb|FK300201.1|FK300201
EST:     CCAGCATCATCACTCGCTTCATGTACGACAAATTCGACAACACTTATCAG                         GCTACAATCGGTATCGATTTTCTGTCAAAAACTATGTATCTTGAAGATCGA
genomic: CCAGCATCATCACTCGCTTCATGTACGACAAATTCGACAACACTTATCAGgtcttcttct ... tgctaaacagGCTACAATCGGTATCGATTTTCTGTCAAAAACTATGTATCTTGAAGATCGA
EST: gi|192322379|gb|FK014620.1|FK014620
EST:     CCAGCATCATCACTCGCTTCATGTACGACAAATTCGACAACACTTATCAG                         GCTACAATCGGTATCGATTTTCTGTCAAAAACTATGTATCTTGAAGATCGA
genomic: CCAGCATCATCACTCGCTTCATGTACGACAAATTCGACAACACTTATCAGgtcttcttct ... tgctaaacagGCTACAATCGGTATCGATTTTCTGTCAAAAACTATGTATCTTGAAGATCGA
EST: gi|192321240|gb|FK014330.1|FK014330
EST:     CCAGCATCATCACTCGCTTCATGTACGACAAATTCGACAACACTTATCAG                         GCTACAATCGGTATCGATTTTCTGTCAAAAACTATGTATCTTGAAGATCGA
genomic: CCAGCATCATCACTCGCTTCATGTACGACAAATTCGACAACACTTATCAGgtcttcttct ... tgctaaacagGCTACAATCGGTATCGATTTTCTGTCAAAAACTATGTATCTTGAAGATCGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCTCGCAAAGTACAAGCTGGTGTTCTTGGGTGATCAGTCCGTTGGGAAAACCAGCATCATCACTCGCTTCATGTACGACAAATTCGACAACACTTATCAGgtcttcttctttcagatccaatctcactttcactatttcattgcatttccattattattttcaaaacattcaagagatcacggttttatcgtgggatggg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gggatgg