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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagctgtacattgttgatttgtagtactctatggtcccgtccttcataacttcaaattgtagttgcctacgtttgttgatttgatagtgtcacttccattattagGCAATCAAAAGGGATTCTTCCTTTGCAAGCAAAGTGAAGAGAATAGTTATACTTGGTGGTGCATTCTTTGCCTTGGGGAATGTGAATCCTGCTGCAGAAG

Basic information

species Glycine max
transcript GLYMA03G35170.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G35170.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os08g44370.1 (Oryza sativa), 3'ss of exon 4
gtaagctgtacattgttgatttgtagtactctatggtcccgtccttcataacttcaaattgtagttgcctacgtttgttgatttgatagtgtcacttccattattagGCAATCAAAAGGGATTCTTCCTTTGCAAGCAAAGTGAAGAGAATAGTTATACTTGGTGGTGCATTCTTTGCCTTGGGGAATGTGAATCCTGCTGCAGAAG
                   | ||      | ||  |      |||   || | |     | ||  ||||   |   |  |||  |   || |   |||  || |||||| |||||||||||  ||||||||||||| || ||||||| ||||||| |||| |||||||| ||||||||    || ||||| |  || ||||| ||||
------------------gtatgcttccatttacaggataaacctgtttagcatgttgctttatatgcc-gtgacagaggataagtctgtctgtgttct-ttcttagGCCATCAAAAGGGACCCTTCCTTTGCAAGTAAGGTGAAGAAAATAGTTGTACTGGGTGGTGCTTTCTTTGCGGCTGGAAATGTCAGCCCAGCTGCTGAAG

upper sequence: GLYMA03G35170.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G015344_T02 (Zea mays), 3'ss of exon 4
gtaagctgtacattgttgatttgtagtactctatggtcccgtccttcataacttcaaattgtagttgcctacgtttgttgatttgatagtgtcacttccattattagGCAATCAAAAGGGATTCTTCCTTTGCAAGCAAAGTGAAGAGAATAGTTATACTTGGTGGTGCATTCTTTGCCTTGGGGAATGTGAATCCTGCTGCAGAAG
       |||  ||   |||   ||| |||  |    ||  |   || |    |    || |  |   |||  | |  | | |   | || ||  |||  |  |||||| |||||||| ||  |||||||||||||||| || |||| ||||||| |||| ||||| || ||||||||    || ||||| || |||||||| ||||
-------gtatgttcaggatc-ataggactaaa----cctatttatcgtgctgt----ttatgctgtgctatatgttataagtcagt-gtctctgttctttgcttagGCCATCAAAAGAGACCCTTCCTTTGCAAGCAAGGTTAAGAAAATAGTTGTACTGGGTGGAGCTTTCTTTGCGGCTGGAAATGTCAACCCTGCTGCTGAAG

upper sequence: GLYMA03G35170.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv08s0007g03690.t01 (Vitis vinifera), 3'ss of exon 4
gtaagctgtacattgttgatttgtagtactctatggtcccgtccttcataacttcaaattgtagttgcctacgtttgttgatttgatagtgtcacttccattattagGCAATCAAAAGGGATTCTTCCTTTGCAAGCAAAGTGAAGAGAATAGTTATACTTGGTGGTGCATTCTTTGCCTTGGGGAATGTGAATCCTGCTGCAGAAG
||||| ||     |  ||   | |   | |  |       |   |||||    | |  |      ||| |||  || | |       | |||   ||   | ||||||| || |||||||| || |||||||| ||||| |||||||   | ||  ||||||||||||| ||||||||  |||| ||||| ||||||||||| ||||
gtaagttgcggtatcctgtccttt--cagttcaattctgtgattttcatggtctgagttctgcaatgcataccattctggtcacacaaatgtatttttattgattagGCTATTAAAAGGGACTCGTCCTTTGCGAGCAAGGTGAAGAAGGTGGTCGTACTTGGTGGTGCTTTCTTTGCACTGGGAAATGTCAATCCTGCTGCCGAAG

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|16347635|gb|BI973230.1|BI973230
EST:     ACAAATTTGGCTTTG                         GCAATCAAAAGGGATTCTTCCTTTGCAAGCAAAGTGAAGAGAATAGTTATA
genomic: ACAAATTTGGCTTTGgtaagctgta ... ccattattagGCAATCAAAAGGGATTCTTCCTTTGCAAGCAAAGTGAAGAGAATAGTTATA
EST: gi|16105461|gb|BI893201.1|BI893201
EST:     CTGGTGAAGTATCTGTGCTAGCACTTGGACCACTAACAAATTTGGCTTTG                         GCAATCAAAAGGGATTCTTCCTTTGCAAGCAAAGTGAAGAGAATAGTTATA
genomic: CTGGTGAAGTATCTGTGCTAGCACTTGGACCACTAACAAATTTGGCTTTGgtaagctgta ... ccattattagGCAATCAAAAGGGATTCTTCCTTTGCAAGCAAAGTGAAGAGAATAGTTATA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcaaattgtagttgcctacgtttgttgatttgatagtgtcacttccattattagGCAATCAAAAGGGATTCTTCCTTTGCAAGCAAAGTGAAGAGAATAGTTATACTTGGTGGTGCATTCTTTGCCTTGGGGAATGTGAATCCTGCTGCAGAAG
                                       tcacttcc  CT-rich tract
                                               attatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagctgtacattgttgatttgtagtactctatggtcccgtccttcataacttcaaattgtagttgcctacgtttgttgatttgatagtgtcacttccattattagGCAATCAAAAGGGATTCTTCCTTTGCAAGCAAAGTGAAGAGAATAGTTATACTTGGTGGTGCATTCTTTGCCTTGGGGAATGTGAATCCTGCTGCAGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG