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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGTTCTTTCAAAGAACAACTTCAACAGCATGTCCGGGTCCATGCAATGGAAGCAGTCATGGCTTGTTGGGAGATCGAGCAATCCTTACAAAGTTTAACAGgtacaacgatagtctttttagtgatttttgcatctcaacataaaaataaactaataaaggttagttgcccttccatgataaaatggaaataacttgattc...

Basic information

species Glycine max
transcript GLYMA06G06890.2
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G06890.1 (Glycine max), 5'ss of exon 2
lower sequence: LOC_Os02g08544.2 (Oryza sativa), 5'ss of exon 2
TGTTCTTTCAAAGAACAACTTCAACAGCATGTCCGGGTCCATGCAATGGAAGCAGTCATGGCTTGTTGGGAGATCGAGCAATCCTTACAAAGTTTAACAGgtacaacgatagtctttttagtgatttttgcatctcaacataaaa-ataaactaataaaggttagttgcccttccatgataaaatggaaataacttgattc-
|| || ||||| ||||||||||| |||||||| || || ||||||||||||||||| ||||  || |||||  | || || || ||||||||| ||||||||| | | |   |  | |   || ||    ||  ||| || |    | ||| |   |||  |    |    ||   | ||   || || |  | |       
TGCTCATTCAAGGAACAACTTCAGCAGCATGTGCGTGTTCATGCAATGGAAGCAGTGATGGGGTGCTGGGAACTTGAACAGTCTTTACAAAGTCTAACAGgtagaccaaagcttctatc--tgcttgaatcagttcagcaaatggtagaaaatttcaaacatacactttttttttgttatttcattgataatattcaggcaa

upper sequence: GLYMA06G06890.1 (Glycine max), 5'ss of exon 2
lower sequence: LOC_Os06g43860.2 (Oryza sativa), 5'ss of exon 2
TGTTCTTTCAAAGAACAACTTCAACAGCATGTCCGGGTCCATGCAATGGAAGCAGTCATGGCTTGTTGGGAGATCGAGCAATCCTTACAAAGTTTAACAGgtacaacgatag--tctttttagtgatttttgcatctcaacataaaaataaactaataaaggttagttgcccttccatgataaaatggaaataacttgattc
||||| ||||| |||||||| || || ||||| || || ||||||||||||||||| |||||||| |||||  | || ||| | ||||| ||  | |||||||  || | |   |||  ||  | ||| ||  |  | |  |||        || ||    |  ||     |||  |      | |         || ||| 
TGTTCGTTCAAGGAACAACTACAGCAACATGTGCGTGTTCATGCAATGGAAGCAGTAATGGCTTGCTGGGAACTTGAACAAACTTTACAGAGCCTTACAGgtagcacaaaaaaatctagttgat-attattcaacatgagaatagtggactcctgattttaggaagagaaacttaaagttattatttctctctgtttaatt-

upper sequence: GLYMA06G06890.1 (Glycine max), 5'ss of exon 2
lower sequence: GRMZM2G055243_T01 (Zea mays), 5'ss of exon 2
TGTTCTTTCAAAGAACAACTTCAACAGCATGTCCGGGTCCATGCAATGGAAGCAGTCATGGCTTGTTGGGAGATCGAGCAATCCTTACAAAGTTTAACAGgtacaacgatagtctttttagtgatttttgcatctcaacataaaaataaactaataaaggttagttgcccttccatgataaaatggaaataacttgattc-------
||||| ||||| |||||||| || |||||||| || || ||||||||||||||||||||||||||||||||| |||| ||| | ||||||||  | |||||||   |   ||  || |     | |||   || |  | |  |||||    ||        |  |||   |    |      |     | ||||   | |       
TGTTCATTCAAGGAACAACTCCAGCAGCATGTGCGTGTTCATGCAATGGAAGCAGTCATGGCTTGTTGGGAGCTCGAACAAACTTTACAAAGCCTTACAGgta--gctgaagctttct-----actttaatatttttagaggaaaatgctttagctgcccctttttggagtctgcttgatgtacaagtacaactccctacttaatat

upper sequence: GLYMA06G06890.1 (Glycine max), 5'ss of exon 2
lower sequence: GRMZM2G370332_T01 (Zea mays), 5'ss of exon 2
TGTTCTTTCAAAGAACAACTTCAACAGCATGTCCGGGTCCATGCAATGGAAGCAGTCATGGCTTGTTGGGAGATCGAGCAATCCTTACAAAGTTTAACAGgtacaacgatag-tctttttagtgatttttgcatctcaacataaaaataaactaataaaggttagttgcccttccatgataaaatggaaataacttgattc-
|| || ||||| |||||||| || |||||||| || || ||||||||||||||||| |||| ||| |||||| | || ||||| ||||||||  ||||||||| |  | |   | |||||| |  | | |  ||    | |      | ||    | |    ||  |  | | |  | || |  |   ||||| |  |  | 
TGCTCATTCAAGGAACAACTCCAGCAGCATGTACGTGTTCATGCAATGGAAGCAGTGATGGGTTGCTGGGAGCTTGAACAATCTTTACAAAGCCTAACAGgtagattgttttctttttttaatcttgtgttaattcagaaacgtgcctgaagctttcagatatacatcacttgcttttatcatttc--aataattgcagcct

upper sequence: GLYMA06G06890.1 (Glycine max), 5'ss of exon 2
lower sequence: GRMZM2G433591_T02 (Zea mays), 5'ss of exon 3
TGTTCTTTCAAAGAACAACTTCAACAGCATGTCCGGGTCCATGCAATGGAAGCAGTCATGGCTTGTTGGGAGATCGAGCAATCCTTACAAAGTTTAACAGgtacaacgatagtctttttagtgatttttgcatctcaacataaaaat-----aaactaataaaggttagttgcccttccatgataaaatggaaataacttgattc-
|| || ||||| ||||| || || |||||||| || || ||||||||||||||||| |||| ||| |||||| | || ||||||||||||||  ||||||||     ||| || |||||  | | | | || |     || |||  |     || ||   | |  |    | |       |   |  ||   ||||| |  |    
TGCTCATTCAAGGAACAGCTGCAGCAGCATGTACGTGTTCATGCAATGGAAGCAGTGATGGGTTGCTGGGAGCTTGAACAATCCTTACAAAGCCTAACAGgtg----gattgttttttt--taaatctcgcgttaattcagaaacttggctgaagctttcatatatacactacttgcttttatcatcatttcaataattgtagcat

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|105633903|gb|DW247266.1|DW247266
EST:     AGCAGTCATGGCTTGTTGGGAGATTGAGCAATCCTTACAAAGTTTAACAG                         GAGTTTCACCCGGGGAAGGT
genomic: AGCAGTCATGGCTTGTTGGGAGATCGAGCAATCCTTACAAAGTTTAACAGgtacaacgat ... gatttaacagGAGTTTCACCCGGGGAAGGT
EST: gi|105633102|gb|DW246627.1|DW246627
EST:     AGCAGTCATGGCTTGTTGGGAGATTGAGCAATCCTTACAAAGTTCAACAG                         GAGTTTCACCCGGGGAAGGT
genomic: AGCAGTCATGGCTTGTTGGGAGATCGAGCAATCCTTACAAAGTTTAACAGgtacaacgat ... gatttaacagGAGTTTCACCCGGGGAAGGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGTTCTTTCAAAGAACAACTTCAACAGCATGTCCGGGTCCATGCAATGGAAGCAGTCATGGCTTGTTGGGAGATCGAGCAATCCTTACAAAGTTTAACAGgtacaacgatagtctttttagtgatttttgcatctcaacataaaaataaactaataaaggttagttgcccttccatgataaaatggaaataacttgattc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC