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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtacttttatacacatacacacaagagaatgaaatgaaattatatattctttccataaaattttctttctgatgctaatgtctgctatttctgtttccccttactagGTGAGGATTTTGATCAAAGAATAATGGAGTACTTCATTAAATTGATCAAGAAAAAGCATGGAAAGGATATTAGCAAGGACAACAGAGCACTTGGAAAGCT

Basic information

species Glycine max
transcript GLYMA08G02940.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G02940.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os02g02410.1 (Oryza sativa), 3'ss of exon 4
gtgagtacttttatacacatacacacaagagaatgaaatgaaattatatattctttccataaaattttctttctgatgctaatgtctgctatttctgtttccccttactagGTGAGGATTTTGATCAAAGAATAATGGAGTACTTCATTAAATTGATCAAGAAAAAGCATGGAAAGGATATTAGCAAGGACAACAGAGCACTTGGAAAGCT
        ||||| ||  ||    ||| |    |   |   | ||     |  |    ||     |      |||    | || | ||      |||| ||  ||    ||||||||| ||||| || ||||| |||||||||||||| || ||||||||||| ||| |  | ||||| || |||||||||||| | || |||||||||||
--------ttttaaactaatg---acatgccttttgtagttagttggtcgtcttgattatctggatagtgcactgtgattcatatttgactgaactgtctcatctcttcagGTGAGGACTTTGACCAGAGAATCATGGAGTACTTCATCAAGTTGATCAAGAAGAAGTACAGCAAGGACATCAGCAAGGACAACCGTGCTCTTGGAAAGCT

upper sequence: GLYMA08G02940.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G114793_T01 (Zea mays), 3'ss of exon 4
gtgagtacttttatacacatacacacaagagaatgaaatgaaattatatattctttccataaaattttctttctgatgctaatgtctgctatttctgtttccccttactagGTGAGGATTTTGATCAAAGAATAATGGAGTACTTCATTAAATTGATCAAGAAAAAGCATGGAAAGGATATTAGCAAGGACAACAGAGCACTTGGAAAGCT
   | |  |  ||||     |  ||  |   |     |  |  |  | |   ||| |  |  || || | |  | |||      |  ||| | ||   | | | ||   ||||||||| ||||| || || || |||||||||||||| || ||||||||||| ||| |  | ||||| || |||||||||||| | || |||||||||||
---attgttgatatattt-catgcatgatctatcagcac-atttcctgtgagcttgcactgtaacttgcctatttatgac----tgagctgtatcacctcctcatt--cagGTGAGGACTTTGACCAGAGGATCATGGAGTACTTCATCAAGTTGATCAAGAAGAAGTACAGCAAGGACATCAGCAAGGACAACCGTGCTCTTGGAAAGCT

upper sequence: GLYMA08G02940.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G415007_T01 (Zea mays), 3'ss of exon 4
gtgagtacttttatacacatacacacaagagaatgaaatgaaattatatattctttccataaaattttctttctgatgctaatgtctgctatttctgtttccccttactagGTGAGGATTTTGATCAAAGAATAATGGAGTACTTCATTAAATTGATCAAGAAAAAGCATGGAAAGGATATTAGCAAGGACAACAGAGCACTTGGAAAGCT
        |   |   ||||  |||||   |  |  | ||   ||    |   || |  | |  ||   | |||  | || |  |   || | ||   |   | ||   ||||||||||||||| || || || ||||| |||||||| || ||||||||||| ||| |  | ||||| ||  ||||||||||| | || |||||||||||
------tttagaagttacatggacacacttgcttttagtg---ttgagcacatttcctgtgagcttgcatatctatttctgacttgaactgtatcacctcttcatt--cagGTGAGGATTTTGACCAGAGGATCATGGAATACTTCATCAAGTTGATCAAGAAGAAGTACAGCAAGGACATCGGCAAGGACAACCGTGCTCTTGGAAAGCT

upper sequence: GLYMA08G02940.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv16s0098g01580.t01 (Vitis vinifera), 3'ss of exon 4
gtgagtacttttatacacatacacacaagagaatgaaatgaaattatatattctttccataaaattttctttctgatgctaatgtctgctatttctgtttccccttact--agGTGAGGATTTTGATCAAAGAATAATGGAGTACTTCATTAAATTGATCAAGAAAAAGCATGGAAAGGATATTAGCAAGGACAACAGAGCACTTGGAAAGCT
           || |   |      |||  |  |||||   ||  |  | ||   | | ||||||  |  |    ||    | ||     | || ||||     || ||  |||||||||||||||||| ||||| ||||| |||||||| |||||||||||||| |||||||||||||| || |||||||||||||||||  |||| ||| |
----------atagaattacggtggcaaatgggtgaaacccaaccaagtttttgcttc-taaaatgatgatc--aattgggaagtagaaaacttatgttcattttttctgcagGTGAGGATTTTGATCAGAGAATCATGGAATACTTCATCAAATTGATCAAGAAGAAGCATGGAAAGGACATCAGCAAGGACAACAGAGCTATTGGGAAGTT

upper sequence: GLYMA08G02940.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv02s0025g02140.t01 (Vitis vinifera), 3'ss of exon 4
gtgagtacttttatacacatacacacaagagaatgaaatgaaattatatatt---------ctttccataaaattttctttctgatgctaatgtctgctatttctgtttccccttactagGTGAGGATTTTGATCAAAGAATAATGGAGTACTTCATTAAATTGATCAAGAAAAAGCATGGAAAGGATATTAGCAAGGACAACAGAGCACTTGGAAAGCT
||||| | |||| |    |   |  |      ||         ||  | |||          || | | |  |   |  || |  ||   |||       || |  ||    | | | ||||||||||||||| || || || ||||||||||| || || ||||| ||||| ||||| |||||||| || ||||||||||||||||| ||||| |||||
GTGAGGATTTTTTTCTCTACTGATGCTCTTTCATCTTTGCTCTTTGCACATTGAAAGAAAATTTACGAGAGGAAAGTTATTATACTGTGGATGCTCAAGGTT-CAATTCTTTCCTGC-AGGTGAGGATTTTGACCAGAGGATTATGGAGTACTTTATCAAGTTGATTAAGAAGAAGCACGGAAAGGACATCAGCAAGGACAACAGAGCTCTTGGGAAGCT

upper sequence: GLYMA08G02940.1 (Glycine max), 3'ss of exon 4
lower sequence: EFJ29073 (Selaginella moellendorffii), 3'ss of exon 4
gtgagtacttttatacacatacacacaagagaatgaaatgaaattatatattctttccataaaattttctttctgatgctaatgtct-gctatttctgtttccccttactagGTGAGGATTTTGATCAAAGAATAATGGAGTACTTCATTAAATTGATCAAGAAAAAGCATGGAAAGGATATTAGCAAGGACAACAGAGCACTTGGAAAGCT
                                                || | |   || |   || || || |  | || |   || |  | |    | | ||  | | ||||||||| || ||||| ||| | ||||| |||||||| ||  | |||||||| |||||    |||||||| |||||||||||| | || |||||||||||
-----------------------------------------------gtactttgatcaaagccttctccttttctttcttacagctcgaaactaacatctaccaatgc-agGTGAGGACTTCGATCAGAGAGTGATGGACTACTTCATCAAGCTCATCAAGAAGAAGCACAACAAGGATATCAGCAAGGACAACCGGGCTCTTGGAAAGCT

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|17400539|gb|BM177321.1|BM177321
EST:     TAACGGTGTTTTTGAAGTTCTTGCTACAAATGGAGATACTCATCTTGGAG                         GTGAGGATTTTGATCAAAGAATAATGGAGTACTTCATTAAATTGATCAAGA
genomic: TAACGGTGTTTTTGAAGTTCTTGCTACAAATGGAGATACTCATCTTGGAGgtgagtactt ... cccttactagGTGAGGATTTTGATCAAAGAATAATGGAGTACTTCATTAAATTGATCAAGA
EST: gi|17400598|gb|BM177380.1|BM177380
EST:     TAACGGTGTTTTTGAAGTTCTTGCTACAAATGGAGATACTCATCTTGGAG                         GTGAGGATTTTGATCAAAGAATAATGGAGTACTTCATTAAATTGATCAAGA
genomic: TAACGGTGTTTTTGAAGTTCTTGCTACAAATGGAGATACTCATCTTGGAGgtgagtactt ... cccttactagGTGAGGATTTTGATCAAAGAATAATGGAGTACTTCATTAAATTGATCAAGA
EST: gi|16284523|gb|BI946135.1|BI946135
EST:     TAACGGTGTTTTTGAAGTTCTTGCTACAAATGGAGATACTCATCTTGGAG                         GTGAGGATTTTGATCAAAGAATAATGGAGTACTTCATTAAATTGATCAAGA
genomic: TAACGGTGTTTTTGAAGTTCTTGCTACAAATGGAGATACTCATCTTGGAGgtgagtactt ... cccttactagGTGAGGATTTTGATCAAAGAATAATGGAGTACTTCATTAAATTGATCAAGA
EST: gi|298177863|gb|HO027416.1|HO027416
EST:     TAACGGTGTTTTTGAAGTTCTTGCTACAAATGGAGATACTCATCTTGGAG                         GTGAGGATTTTGATCAAAGAATAATGGAGTACTTCATTAAATTGATCAAGA
genomic: TAACGGTGTTTTTGAAGTTCTTGCTACAAATGGAGATACTCATCTTGGAGgtgagtactt ... cccttactagGTGAGGATTTTGATCAAAGAATAATGGAGTACTTCATTAAATTGATCAAGA
EST: gi|298166661|gb|HO010100.1|HO010100
EST:     GGAGATACTCATCTTGGAG                         GTGAGGATTTTGATCAAAGAATAATGGAGTACTTCATTAAATTGATCAAGA
genomic: GGAGATACTCATCTTGGAGgtgagtactt ... cccttactagGTGAGGATTTTGATCAAAGAATAATGGAGTACTTCATTAAATTGATCAAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccataaaattttctttctgatgctaatgtctgctatttctgtttccccttactagGTGAGGATTTTGATCAAAGAATAATGGAGTACTTCATTAAATTGATCAAGAAAAAGCATGGAAAGGATATTAGCAAGGACAACAGAGCACTTGGAAAGCT
                    tgctaat  putative branch site (score: 2)
                            tctgctatttctgttt  CT-rich tract
     aaattttcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtacttttatacacatacacacaagagaatgaaatgaaattatatattctttccataaaattttctttctgatgctaatgtctgctatttctgtttccccttactagGTGAGGATTTTGATCAAAGAATAATGGAGTACTTCATTAAATTGATCAAGAAAAAGCATGGAAAGGATATTAGCAAGGACAACAGAGCACTTGGAAAGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA