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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTAGCTCTGGAGCTGTTAATGATGTGGCAAATACAATTATGCAAAAATTTTGGGACTCAGCTTTTAATCTAGAACCACCGGAAGATTCTGATACTCATAGgtaatcttgttgtgtagacatttaaacacaagatttgttttgttctgatccttgaatcagcctatatgatgttctattgcag

Basic information

species Glycine max
transcript GLYMA08G00560.3
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G00560.1 (Glycine max), 5'ss of exon 10
lower sequence: LOC_Os11g06930.1 (Oryza sativa), 5'ss of exon 10
GTAGCTCTGGAGCTGTTAATGATGTGGCAAATACAATTATGCAAAAATTTTGGGACTCAGCTTTTAATCTAGAACCACCG---GAAGATTCTGATACTCATAGgtaatcttgttgtgtagacatttaaacacaagatttgttttgttctgatccttgaatca-gcctatatgatgttctattgcag
   |  |||   |    |||| ||||||||| ||||| |||||||| ||||||||||||||| ||  | | || || ||    || || | ||||| ||  |||| |  ||   |  |     |||   |       |  | || |||  ||     | ||   |||  ||  |    |  | |||
---GTCCTGAGACCACGAATGGTGTGGCAAACACAATAATGCAAAAGTTTTGGGACTCAGCTCTTGCTTTGGAGCCCCCAGATGAGGAATTTGATAGTCGCAGgttaa-ttaacgcttccttttttgtcctttg---tcctctttttcaaatttgcaattcttacctgcatttttgcattgttcag

upper sequence: GLYMA08G00560.1 (Glycine max), 5'ss of exon 10
lower sequence: GRMZM2G031609_T01 (Zea mays), 5'ss of exon 10
---GTAGCTCTGGAGCTGTTAATGATGTGGCAAATACAATTATGCAAAAATTTTGGGACTCAGCTTTTAATCTAGAACCACCGGAAGATTCTGATACTCATAGgtaatcttgttgtgtagacatttaaacacaagatttgtttt--gttctgatccttgaatcagcctatatgatgttctattgcag--
   |  |  |||| |  |  |||||||||||||| ||||| ||||| ||||| |||||||| ||  |  | |     |||   || |||| ||||| ||| ||||    ||  | | |   | |||     |    | ||| ||   ||   |        | | |||  ||  ||||  ||||||   
AAGGAGGTCCTGGTGGCGCAAATGATGTGGCAAACACAATAATGCAGAAATTCTGGGACTCTGCACTAGAGCCT---CCAGATGAGGATTTTGATAGTCACAGgtttagttaatattt---cctttgggttccttctatgtcttccctttcaaatgcaaggttatcctgaat--tgttgcattgcacag

upper sequence: GLYMA08G00560.1 (Glycine max), 5'ss of exon 10
lower sequence: GRMZM2G177485_T01 (Zea mays), 5'ss of exon 5
-----GTAGCTCTGGAGCTGTTAATGATGTGGCAAATACAATTATGCAAAAATTTTGGGACTCAGCTTTTAATCTAGAACCACCGGAAGATTCTGATACTCATAGgtaatcttgttgtgtagacatttaaacacaagatttgttttg--ttctgatccttgaatcagcctatatgatgttctattgcag
     |  |   ||| ||    |||||||||||||| | ||| ||||||||||| |||||||| ||  |  | | |   |||   || |||| ||||| ||| | ||    ||  | | |   | |||     |    | ||| ||   ||   |        | | |||  ||  ||||  |||||| 
TGAAGGAGGTCGTGGTGCCACAAATGATGTGGCAAACATAATAATGCAAAAATTCTGGGACTCTGCACTAGAGCCA---CCAGATGAGGATTTTGATAGTCACatgtttagttaatattt---cctttgggttccttctatgtcttccctttcaaattcaaggttatcctgaat--tgttgcattgcac

upper sequence: GLYMA08G00560.1 (Glycine max), 5'ss of exon 10
lower sequence: Vv07s0031g02750.t01 (Vitis vinifera), 5'ss of exon 10
GTAGCTCTGGAGCTGTTAATGATGTGGCAAATACAATTATGCAAAAATTTTGGGACTCAGCTTTTAATCTAGAACCACCGGAAGATTCTGATACTCATAGgtaatcttgttgtgtagacatttaaacacaagat-ttgttttgttc-tgatccttgaatcagcctatatgatgttctattgcag
 ||||||||||||||||||||| ||  ||||||| || |||||||| |||||||| ||| |  ||  |||||| ||||| || |||| ||| || || |||||    | |||     | | |||      | || ||| |    |  |  | |   ||  || |    ||||||| | |  |||
ATAGCTCTGGAGCTGTTAATGAGGTCACAAATACGATAATGCAAAAGTTTTGGGATTCAACACTTGCTCTAGAGCCACCAGATGATTATGACACCCAGAGgtatctcttttgctaccataattatttgttatatgttggtaaactggtagttcaataactagtcctgttgatgttatgt-acag

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|27427474|gb|CA938994.1|CA938994
EST:     TGGGACTCAGCTTTTAATCTAGAACCACCGGAAGATTCTGATACTCATAG                         TGAACTTTCTGGGCTAGTGATGTCAGATGGGGCTGATACATCAAAGTCTGG
genomic: TGGGACTCAGCTTTTAATCTAGAACCACCGGAAGATTCTGATACTCATAGgtaatcttgt ... tctattgcagTGAACTTTCTGGGCTAGTGATGTCAGATGGGGCTGATACATCAAAGTCTGG
EST: gi|31312544|gb|CD397747.1|CD397747
EST:     GATTCTGATACTCATAG                         TGAACTTTCTGGGCTAGTGATGTCAGATGGGGCTGATACATCAAAGTCTGG
genomic: GATTCTGATACTCATAGgtaatcttgt ... tctattgcagTGAACTTTCTGGGCTAGTGATGTCAGATGGGGCTGATACATCAAAGTCTGG
EST: gi|254333300|gb|GR850550.1|GR850550
EST:     TGGGACTCAGCTTTTAATCTAGAACCACCGGAAGATTCTGATACTCATAG                         TGAACTTTCTGGGCTAGTGATGTCAGATGGGGCTGATACATCAAAGTCTGG
genomic: TGGGACTCAGCTTTTAATCTAGAACCACCGGAAGATTCTGATACTCATAGgtaatcttgt ... tctattgcagTGAACTTTCTGGGCTAGTGATGTCAGATGGGGCTGATACATCAAAGTCTGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTAGCTCTGGAGCTGTTAATGATGTGGCAAATACAATTATGCAAAAATTTTGGGACTCAGCTTTTAATCTAGAACCACCGGAAGATTCTGATACTCATAGgtaatcttgttgtgtagacatttaaacacaagatttgttttgttctgatccttgaatcagcctatatgatgttctattgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA