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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgactcatatcatgtgtgcatagttttttgttcactgttcctaaagtcctaaacactttgatggacagtttctgattgttcagcattcttgtgatatagGCCGTCAGACTTTCCTAAACACATCAAAGTGGATTGAAGAGGTGCGCAGTGAAAGAGGCAGCGATGTTATTGTTGTTCTTGTTGGGAACAAAACTGATCT

Basic information

species Glycine max
transcript GLYMA17G16200.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G16200.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os07g31370.1 (Oryza sativa), 3'ss of exon 3
ttgactcatatcatgtgtgcatagttt--tttgttcactgttcctaaagtcctaaacactttgatggacagtttctgattgttcagcattcttgtgatatagGCCGTCAGACTTTCCTAAACACATCAAAGTGGATTGAAGAGGTGCGCAGTGAAAGAGGCAGCGATGTTATTGTTGTTCTTGTTGGGAACAAAACTGATCT
 ||| |  ||  |    ||     |||  || |||     ||   ||||  ||     || |  ||     ||| |  ||        ||    || | ||||| | ||| ||||||||||||| ||||| ||||| || || ||  | | ||| || ||||| ||||||||  |||| || ||||||||||||||||||||
atgatttttaatagcaatgtcatttttaattcgttttgcattataaaagctctt--tcctatcctgcctcctttttccttaaatttgttttacatgctgtagGCAGACAGTCTTTCCTAAACACTTCAAAATGGATAGAGGAAGTTAGAACTGAGAGGGGCAGTGATGTTATCATTGTGCTGGTTGGGAACAAAACTGATCT

upper sequence: GLYMA17G16200.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G075719_T02 (Zea mays), 3'ss of exon 3
--------------------------------------------------------------ttgactcatatca-tgtgtgcatagttttttgttcactgttcctaaagtcctaaacactttgatggacagtttctgattgtt-----cagcattcttgtgatatagGCCGTCAGACTTTCCTAAACACATCAAAGTGGATTGAAGAGGTGCGCAGTGAAAGAGGCAGCGATGTTATTGTTGTTCTTGTTGGGAACAAAACTGATCT
                                                                ||  || |||| |     ||  |  |         | |   | |||   |||  || |  ||    | | | | ||| ||      |    | |  || | ||||| | ||| ||||| |||| ||||| |||||||| || || || |||| ||| || ||||| ||||||||  |||| |||||||||||||||||||| ||
gtaatctctctctgtctctctcgcacacacaaacacacattctttaggaaaaaaaatggtatcagatgcacatcagtagcaacaatgactaggaagttttatcttttaaggattaaggacataaatttttactattttattcttacctttatttgtttcatgttgtagGCAGGCAGTCTTTCTTAAATACATCCAAGTGGATAGATGAAGTTCGCACTGAGAGGGGCAGTGATGTTATCATTGTGCTTGTTGGGAACAAAACTGACCT

upper sequence: GLYMA17G16200.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G169694_T01 (Zea mays), 3'ss of exon 3
------------------------------------------------ttgactcatatcatgtgtgcatagttttttg---ttcactgttcctaaagtcctaaacactttgatggacagtttctgattgttcag------cattcttgt-----gatatagGCCGTCAGACTTTCCTAAACACATCAAAGTGGATTGAAGAGGTGCGCAGTGAAAGAGGCAGCGATGTTATTGTTGTTCTTGTTGGGAACAAAACTGATCT
                                                  ||| || |||| ||    | | |   | |    | |    |  |||||   ||| |  ||      | |   | | | | ||  |      | || ||||     | | ||||| | ||| | ||| |||| ||||| |||||||| || || || |||| ||| || ||||| ||||||||  |||| |||||||||||||||||||| ||
gtaatctccctctctcatacacacacattctatagaaatagttgttgtcagacgcacatca-gtaacaacaatgactaggaacttatatcttttaaaggtttaagcctttaaggacataaacttttactattttgttcttacctttttgtttcatgttgtagGCAGGCAGTCCTTCTTAAATACATCTAAGTGGATAGAGGAAGTTCGCACTGAGAGGGGCAGTGATGTTATCATTGTGCTTGTTGGGAACAAAACTGACCT

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|31307061|gb|CD392264.1|CD392264
EST:     AAGCTACATTAGGGACTCATCTGTTGCTGTCATTGTTTATGATGTTGCAA                         GCCGTCAGACTTTCCTANACACATCAAAGTGGATTGAAGAGGTGCGCAGTG
genomic: AAGCTACATTAGGGACTCATCTGTTGCTGTCATTGTTTATGATGTTGCAAgtatgccatt ... tgtgatatagGCCGTCAGACTTTCCTAAACACATCAAAGTGGATTGAAGAGGTGCGCAGTG
EST: gi|192323740|gb|FK016046.1|FK016046
EST:     AAGCTACATTAGGGACTCATCTGTTGCTGTCATTGTTTATGATGTTGCAA                         GCCGTCAGACTTTCCTAAACACATCAAAGTGGATTGAAGAGGTGCGCAGTG
genomic: AAGCTACATTAGGGACTCATCTGTTGCTGTCATTGTTTATGATGTTGCAAgtatgccatt ... tgtgatatagGCCGTCAGACTTTCCTAAACACATCAAAGTGGATTGAAGAGGTGCGCAGTG
EST: gi|298166624|gb|HO010063.1|HO010063
EST:     AAGCTACATTAGGGACTCATCTGTTGCTGTCATTGTTTATGATGTTGCAA                         GCCGTCAGACTTTCCTAAACACATCAAAGTGGATTGAAGAGGTGCGCAGTG
genomic: AAGCTACATTAGGGACTCATCTGTTGCTGTCATTGTTTATGATGTTGCAAgtatgccatt ... tgtgatatagGCCGTCAGACTTTCCTAAACACATCAAAGTGGATTGAAGAGGTGCGCAGTG
EST: gi|120529270|gb|EH257404.1|EH257404
EST:     AAGCTACATTAGGGACTCATCTGTTGCTGTCATTGTTTATGATGTTGCAA                         GCCGTCAGACTTTCCTAAACACATCAAAGTGGATTGAAGAGGTGCGCAGTG
genomic: AAGCTACATTAGGGACTCATCTGTTGCTGTCATTGTTTATGATGTTGCAAgtatgccatt ... tgtgatatagGCCGTCAGACTTTCCTAAACACATCAAAGTGGATTGAAGAGGTGCGCAGTG
EST: gi|298177779|gb|HO027332.1|HO027332
EST:     AAGCTACATTAGGGACTCATCTGTTGCTGTCATTGTTTATGATGTTGCAA                         GCCGTCAGACTTTCCTAAACACATCAAAGTGGATTGAAGAGGTGCGCAGTG
genomic: AAGCTACATTAGGGACTCATCTGTTGCTGTCATTGTTTATGATGTTGCAAgtatgccatt ... tgtgatatagGCCGTCAGACTTTCCTAAACACATCAAAGTGGATTGAAGAGGTGCGCAGTG
EST: gi|14991048|gb|BI316721.1|BI316721
EST:     AAGCTACATTAGGGACTCATCTGTTGCTGTCATTGTTTATGATGTTGCAA                         GCCGTCAAACTTTCCCTAAA-ACTTCAAA
genomic: AAGCTACATTAGGGACTCATCTGTTGCTGTCATTGTTTATGATGTTGCAAgtatgccatt ... tgtgatatagGCCGTCAGACTTTCC-TAAACACATCAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtcctaaacactttgatggacagtttctgattgttcagcattcttgtgatatagGCCGTCAGACTTTCCTAAACACATCAAAGTGGATTGAAGAGGTGCGCAGTGAAAGAGGCAGCGATGTTATTGTTGTTCTTGTTGGGAACAAAACTGATCT
                                       cattctt  CT-rich tract
                                               tgatata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgactcatatcatgtgtgcatagttttttgttcactgttcctaaagtcctaaacactttgatggacagtttctgattgttcagcattcttgtgatatagGCCGTCAGACTTTCCTAAACACATCAAAGTGGATTGAAGAGGTGCGCAGTGAAAGAGGCAGCGATGTTATTGTTGTTCTTGTTGGGAACAAAACTGATCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - catatca
- - - - - - -tgtgtgc
- - - - - - - - - - - - - - - - - -ctgttcc
- - - - - - - - - - - - - - - - - - - - - - - - -ctaaaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttgatgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcattct