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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agggaagatagtgtactttacacttttatttttctttgatgacagaagcttctagtgatttgataagttgccctaatttttttaaaataaactcacctagGTCTGCAAGTCAGCTGATGTTGCAAGCAGGGTTGAGAGCCAGCTGAAGCTAGTGATTAGGCCCATGTACTCAAGTCCTCCCATTCATGGTGCATCCATTG

Basic information

species Glycine max
transcript GLYMA06G08670.2
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G08670.2 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os01g55540.2 (Oryza sativa), 3'ss of exon 8
agggaagatagtgtactttacacttttatttttctttgatgacag--aagcttctagtgatttgataagttgccctaatttttttaaaataaactcacct--------agGTCTGCAAGTCAGCTGATGTTGCAAGCAGGGTTGAGAGCCAGCTGAAGCTAGTGATTAGGCCCATGTACTCAAGTCCTCCCATTCATGGTGCATCCATTG
          ||  |  ||| | ||| ||| |   |||||| |     || |  || |    |  | ||||||    |     | ||   ||  | || |        |||| ||       |||||||| ||   ||||||||| || || || ||||| || |||||||| ||||| ||||  ||||| |||||||||||||| || |
----------gttgaaattaaattttgattctaagttgatgccgacccagataataatatcctatttagttgcatagaaaaactgaacggaatgtaactttgtatttcagGTTTGTGGAAGTGCTGATGTAGCTGTCAGGGTTGAAAGTCAACTTAAGCTTGTAATTAGGCCTATGTATTCAAACCCTCCTATTCATGGTGCATCTATCG

upper sequence: GLYMA06G08670.2 (Glycine max), 3'ss of exon 8
lower sequence: EFJ08853 (Selaginella moellendorffii), 3'ss of exon 8
agggaagatagtgtactttacacttttatttttctttgatgacagaagcttctagtgatttgataagttgccctaattttt----ttaaaataaactcacct---agGTCTGCAAGTCAGCTGATGTTGCAAGCAGGGTTGAGAGCCAGCTGAAGCTAGTGATTAGGCCCATGTACTCAAGTCCTCCCATTCATGGTGCATCCATTG
                                                      || | || | | || |||  | || |      | | || || |  | |   ||||||  || ||   ||  |||||||  ||||| || |||||| ||||||| || || || || |||||||||| ||||||||||||||| || || || |
------------------------------------------------------gtaagtttaaaggtagcctgacttatggaggctgatatcaagtttcttttcagGTCTCGAAATCTAGTGGAGTTGCAACGAGGGTCGAAAGCCAGTTGAAGCTCGTCATCAGACCAATGTACTCAAATCCTCCCATTCATGGGGCTTCAATCG

upper sequence: GLYMA06G08670.2 (Glycine max), 3'ss of exon 8
lower sequence: EFJ09053 (Selaginella moellendorffii), 3'ss of exon 8
agggaagatagtgtactttacacttttatttttctttgatgacagaagcttctagtgatttgataagttgccctaatttttttaaaataaactcacctagGTCTGCAAGTCAGCTGATGTTGCAAGCAGGGTTGAGAGCCAGCTGAAGCTAGTGATTAGGCCCATGTACTCAAGTCCTCCCATTCATGGTGCATCCATTG
                                             ||| |    ||    |||    ||        |  | | || |    |  |  |||||   || ||   ||  |||||||  ||||| || |||||| ||||||| || || || || |||||||||| ||||||||||||||| || || || |
-------------------------------------------gtaagttaaaggtagcctgac---ttatggaggctgatatcaagtttcttttc--agGTCACGAAATCTAGTGGAGTTGCAACGAGGGTCGAAAGCCAGTTGAAGCTCGTCATCAGACCAATGTACTCAAATCCTCCCATTCATGGGGCTTCAATCG

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|19346696|gb|BM891576.1|BM891576
EST:     ATGCAAAGAATCTGGGTCTTTATGGGGAACGTGTTGGCGCCTTAAGCATT                         GTCTGCAAGTCAGCTGATGTTGCAAGCAGGGTTGAGAGCCAGCTGAAGCTA
genomic: ATGCAAAGAATCTGGGTCTTTATGGGGAACGTGTTGGCGCCTTAAGCATTgtaagaactt ... actcacctagGTCTGCAAGTCAGCTGATGTTGCAAGCAGGGTTGAGAGCCAGCTGAAGCTA
EST: gi|7686676|gb|AW757333.1|AW757333
EST:     ATGCACAGAATCTGAGTCTTTATGGTGAACGTGTTGGCGCCTTAAGCATT                         GGCTGCAAGTCAGCTGATGTGGCAAGCAGGTTTGAGAGCCAGCTGAAGCTA
genomic: ATGCAAAGAATCTGGGTCTTTATGGGGAACGTGTTGGCGCCTTAAGCATTgtaagaactt ... actcacctagGTCTGCAAGTCAGCTGATGTTGCAAGCAGGGTTGAGAGCCAGCTGAAGCTA
EST: gi|254323227|gb|GR840032.1|GR840032
EST:     ATGCAAAGAATCTGGGTCTTTATGGGGAACGTGTTGGCGCCTTAAGCATT                         GTCTGCAAGTCAGCTGATGTTGCAAGCAGGGTTGAGAGCCAGCTGAAGCTA
genomic: ATGCAAAGAATCTGGGTCTTTATGGGGAACGTGTTGGCGCCTTAAGCATTgtaagaactt ... actcacctagGTCTGCAAGTCAGCTGATGTTGCAAGCAGGGTTGAGAGCCAGCTGAAGCTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagcttctagtgatttgataagttgccctaatttttttaaaataaactcacctagGTCTGCAAGTCAGCTGATGTTGCAAGCAGGGTTGAGAGCCAGCTGAAGCTAGTGATTAGGCCCATGTACTCAAGTCCTCCCATTCATGGTGCATCCATTG
                                            aactcac  putative branch site (score: 2)
                                              ctcacct  CT-rich tract
                            taatttttttaaaata  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agggaagatagtgtactttacacttttatttttctttgatgacagaagcttctagtgatttgataagttgccctaatttttttaaaataaactcacctagGTCTGCAAGTCAGCTGATGTTGCAAGCAGGGTTGAGAGCCAGCTGAAGCTAGTGATTAGGCCCATGTACTCAAGTCCTCCCATTCATGGTGCATCCATTG

- - - gatagtg
- - - - - - - - - - - - - - - - - - tgatgac
- - - - - - - - - - - - - - - - - - - - - - - -gcttcta
- - - - - - - - - - - - - - - - - - - - - - - - - - - -tgatttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttgccct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaataa