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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGTGGATATGTTGCTGGTGTACTTTGTGCAATTGTGTCTCATCCTGCTGATAATCTTGTCTCTTTTCTGAACAATGCAAAAGGAGCAACAGTTGGTGATgtgagtttcagacttggtgcatgtttagtgtcattgttttgtattacatctgtttttgacgagtttctttgattttatatactatataatgcag

Basic information

species Glycine max
transcript GLYMA19G27380.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G27380.1 (Glycine max), 5'ss of exon 4
lower sequence: LOC_Os06g10810.1 (Oryza sativa), 5'ss of exon 4
TGGTGGATATGTTGCTGGTGTACTTTGTGCAATTGTGTCTCATCCTGCTGATAATCTTGTCTCTTTTCTGAACAATGCAAAAGGAGCAACAGTTGGTGATgtgagtttcagacttggtgca-tg-tttagtgtcattgttttgtattacatctgtttttgacgagtttctttgat--tttatatactata-taatgcag--------
|||||| ||  |||| |||||  | ||||| ||||| ||||| || || |||||||| |||||||| ||||||||||| || || || ||||| ||||||||||||||   ||||  | || || | | || | | ||  ||||  | | | || ||||||  |||||  |||||     |   | || | | ||| |         
TGGTGGTTACATTGCCGGTGTCTTCTGTGCTATTGTTTCTCACCCGGCAGATAATCTAGTCTCTTTCCTGAACAATGCCAAGGGTGCTACAGTGGGTGATgtgagtttattacttattacaatgctctggtattaatgcattgtggtgc-tttgcttttga--agttttgttgatgagcaactgattacagttatgtatttctgtag

upper sequence: GLYMA19G27380.1 (Glycine max), 5'ss of exon 4
lower sequence: LOC_Os04g37600.1 (Oryza sativa), 5'ss of exon 4
TGGTGGATATGTTGCTGGTGTACTTTGTGCAATTGTGTCTCATCCTGCTGATAATCTTGTCTCTTTTCTGAACAATGCAAAAGGAGCAACAGTTGGTGATgtgagtttcagacttggtgcatgtttagtgtcattgttttgtattacatctgtttttgacgagtttctttgattttatatactatataatgcag
 ||||| ||  |||| || ||  | |||||||| || || || ||||| || |||||||| ||||| || |||||||| || || ||||||||||| ||||| |||||   | |      |   |       |  || || | ||  || | || ||      | |  |||  |||| |               
AGGTGGTTACATTGCAGGGGTGTTCTGTGCAATAGTTTCACACCCTGCGGACAATCTTGTGTCTTTCCTCAACAATGCCAAGGGCGCAACAGTTGGCGATgtaagttttgtaatcaccataccatcttctgtaacgtgtt-tgttggatttattatt------tcttgttgcatttacag--------------

upper sequence: GLYMA19G27380.1 (Glycine max), 5'ss of exon 4
lower sequence: GRMZM2G015401_T01 (Zea mays), 5'ss of exon 4
TGGTGGATATGTTGCTGGTGTACTTTGTGCAATTGTGTCTCATCCTGCTGATAATCTTGTCTCTTTTCTGAACAATGCAAAAGGAGCAACAGTTGGTGATgtgagtttcagacttggtgcatgt-ttagtgtcattgttttgtattacatctgtttttgacgagtttctttgattttatatactatataatgcag
|||||| || ||||| |||||  | ||||| ||||| ||||| || ||||| || ||||| ||||| ||||||||||| || ||||| ||||| || ||||| ||  |      | |  ||||  | |      |      || ||  | ||  |    |   |||   |    ||  |||| | |    |||||
TGGTGGTTACGTTGCCGGTGTCTTCTGTGCTATTGTTTCTCACCCGGCTGACAACCTTGTGTCTTTCCTGAACAATGCCAAGGGAGCTACAGTGGGAGATgtaagcatatattcttgctcatgcatcaaacatgtatcgacgtcttgtacctactagctattggttatatattgttgctatattct----tgcag

upper sequence: GLYMA19G27380.1 (Glycine max), 5'ss of exon 4
lower sequence: GRMZM2G152827_T01 (Zea mays), 5'ss of exon 4
TGGTGGATATGTTGCTGGTGTACTTTGTGCAATTGTGTCTCATCCTGCTGATAATCTTGTCTCTTTTCTGAACAATGCAAAAGGAGCAACAGTTGGTGATgtgagtttcagacttggtgcatgt-ttagtgtcattgttttgtattacatctgtttttgacgagtttctttgattttatatactatataatgcag
|||||| ||  |||| |||||  | ||||| ||||| ||||| || ||||| || ||||| ||||| ||||||||||| || ||||| ||||| || ||||| ||  |      | |  ||||  | |      |   |  || ||  | ||  |    |   |||   |    ||  |||| | |    |||||
TGGTGGTTACATTGCCGGTGTCTTCTGTGCTATTGTTTCTCACCCGGCTGACAACCTTGTGTCTTTCCTGAACAATGCCAAGGGAGCTACAGTGGGAGATgtaagcatatattcttgctcatgcatcaaacatgtatctacgtcttgtacctactagctattggttatatattgttgctatattct----tgcag

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|207679443|gb|GD662119.1|GD662119
EST:     ATAATCTTGTCTCTTTTCTGAACAATGCAAAAGGAGCAACAGTTGGTGAT                         GCGGTGAAGAAGCTTGGTTTGTGGGGTCTCTTTACGCGTGGTC
genomic: ATAATCTTGTCTCTTTTCTGAACAATGCAAAAGGAGCAACAGTTGGTGATgtgagtttca ... tataatgcagGCGGTGAAGAAGCTTGGTTTGTGGGGTCTCTTTACGCGTGGTC
EST: gi|10845648|gb|BF068722.1|BF068722
EST:     TAATCTTGTCTTTTTTCTGAACAATGCAAAAAGAGCAACTAGT-GGTGAT                         GCTGTGAAGAAGCTTGGCTTGTGG
genomic: TAATCTTGTCTCTTTTCTGAACAATGCAAAAGGAGCAAC-AGTTGGTGATgtgagtttca ... tataatgcagGCGGTGAAGAAGCTTGGTTTGTGG
EST: gi|298168584|gb|HO009514.1|HO009514
EST:     ATAATCTTGTCTCTTTTCTGAACAATGCAAAAGGAGCAACAGTTGGTGAT                         GCGGTGAAGAAGCTTGGTTTGTGGGGTCTCTTTACGCGTGGTCTCCCCCTC
genomic: ATAATCTTGTCTCTTTTCTGAACAATGCAAAAGGAGCAACAGTTGGTGATgtgagtttca ... tataatgcagGCGGTGAAGAAGCTTGGTTTGTGGGGTCTCTTTACGCGTGGTCTCCCCCTC
EST: gi|213596228|gb|DB981816.1|DB981816
EST:     GAACAATGCAAAAGGAGCAACAGTTGGTGAT                         GCGGTGAAGAAGCTTGGTTTGTGGGGTCTCTTTACGCGTCGTTTCCCCTTT
genomic: GAACAATGCAAAAGGAGCAACAGTTGGTGATgtgagtttca ... tataatgcagGCGGTGAAGAAGCTTGGTTTGTGGGGTCTCTTTACGCGTGGTCTCCCCCTC
EST: gi|192295707|gb|FG990561.1|FG990561
EST:     ATAATCTTGTCTCTTTTCTGAACAATGCAAAAGGAGCAACAGTTGGTGAT                         GCGGTGAAGAAGCTTGGTTTGTGGGGTCTCTTTACGCGTGGTCTCCCCCTC
genomic: ATAATCTTGTCTCTTTTCTGAACAATGCAAAAGGAGCAACAGTTGGTGATgtgagtttca ... tataatgcagGCGGTGAAGAAGCTTGGTTTGTGGGGTCTCTTTACGCGTGGTCTCCCCCTC
EST: gi|213597197|gb|DB981589.1|DB981589
EST:     GAACAATGCAAAAGGAGCAACAGTTGGTGAT                         GCGGTGAAGAAGCTTGGTTTGTGGGGTCTCTTTACGCCTGGTCTCCCCCTC
genomic: GAACAATGCAAAAGGAGCAACAGTTGGTGATgtgagtttca ... tataatgcagGCGGTGAAGAAGCTTGGTTTGTGGGGTCTCTTTACGCGTGGTCTCCCCCTC
EST: gi|22927800|gb|BU544939.1|BU544939
EST:     ACAATGCAAAAGGAGCAACAGTTGGTGAT                         GCGGTGAAGAAGCTTGGTTTGTGGGGTCTCTTTACGCGTGGTCTNNNNNNN
genomic: ACAATGCAAAAGGAGCAACAGTTGGTGATgtgagtttca ... tataatgcagGCGGTGAAGAAGCTTGGTTTGTGGGGTCTCTTTACGCGTGGTCTCCCCCTC
EST: gi|58024028|gb|CX710769.1|CX710769
EST:     ATAATCTTGTCTCTTTTCTGAACAATGCAAAAGGAGCAACAGTTGGTGAT                         GCGGTGAAGAAGCTTGGTTTGTGGGGTCTCTTTACGCGTGGTCTCCCCCTC
genomic: ATAATCTTGTCTCTTTTCTGAACAATGCAAAAGGAGCAACAGTTGGTGATgtgagtttca ... tataatgcagGCGGTGAAGAAGCTTGGTTTGTGGGGTCTCTTTACGCGTGGTCTCCCCCTC
EST: gi|254314924|gb|GR829917.1|GR829917
EST:     ATAATCTTGTCTCTTTTCTGAACAATGCAAAAGGAGCAACAGTTGGTGAT                         GCGGTGAAGAAGCTTGGTTTGTGGGGTCTCTTTACGCGTGGTCTCCCCCTC
genomic: ATAATCTTGTCTCTTTTCTGAACAATGCAAAAGGAGCAACAGTTGGTGATgtgagtttca ... tataatgcagGCGGTGAAGAAGCTTGGTTTGTGGGGTCTCTTTACGCGTGGTCTCCCCCTC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGGTGGATATGTTGCTGGTGTACTTTGTGCAATTGTGTCTCATCCTGCTGATAATCTTGTCTCTTTTCTGAACAATGCAAAAGGAGCAACAGTTGGTGATgtgagtttcagacttggtgcatgtttagtgtcattgttttgtattacatctgtttttgacgagtttctttgattttatatactatataatgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA