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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtgctctacacttccttgctagtgtgggtgcattttgggaactgcatattgcacatgacggtttttgttaaccaccttagttattgtagGTTCATTCAATTCGTGAAGCAGCTGCTAACAACTTGAAACGCCTTGCTGAAGAATTTGGTCCTGAGTGGGCTATGCAGCACATAATTCCTCAG

Basic information

species Glycine max
transcript GLYMA10G42250.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G42250.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os09g07510.1 (Oryza sativa), 3'ss of exon 9
----gttt-gtgctc-tacacttccttgctagtgt-gggtgcattt-tgggaactgcatattgcacatgacggtttttgttaaccaccttagttattgtagGTTCATTCAATTCGTGAAGCAGCTGCTAACAACTTGAAACGCCTTGCTGAAGAATTTGGTCCTGAGTGGGCTATGCAGCACATAATTCCTCAG
    |||  ||| |  || | ||  ||  || ||  |  || |    ||| |  |  |   |||   | | | | ||| |||||    |   | ||| |||||    |||||  | || || ||||| ||||||||||| ||||| ||||| || |||||||| || ||||| |||||||| ||||| ||||||
ttgtgttcagtgattatatagtttttttttaatgcagaatggacaagtggtatttataacctgctatttaagatgttt-ttaactggatctttaattttagGTCTTCTCAATCAGAGATGCTGCTGCAAACAACTTGAAGCGCCTAGCTGAGGAGTTTGGTCCAGAATGGGCGATGCAGCATATAATCCCTCAG

upper sequence: GLYMA10G42250.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G164352_T04 (Zea mays), 3'ss of exon 9
-----------------------------------------gtttgtgctctacacttccttgcta---gtgtgggtgcattttgggaactgca---tattgcacatgacggt---ttttgttaaccaccttagttattgtagGTTCATTCAATTCGTGAAGCAGCTGCTAACAACTTGAAACGCCTTGCTGAAGAATTTGGTCCTGAGTGGGCTATGCAGCACATAATTCCTCAG
                                            |||   |  |   |   |  ||      || |||||| ||||    || |   |||||   |  |  ||   |||   |||| |   |    |||  ||||   ||||||  | || || || |||||||||||||| |||||||| ||||| |||||||| |||||||| |||||||| ||||| ||||||
gtttgtatcattagggttatgtcaaaacagtatctctttggagctgtctccagcgtctttatcttatatccttgagtgcatattggactttgtaatgtattgactaaaattgtcagtttaactaactaaaatttggatttcagGTCTTTTCAATCAGAGATGCTGCCGCTAACAACTTGAAGCGCCTTGCAGAAGAGTTTGGTCCAGAGTGGGCAATGCAGCATATAATCCCTCAG

upper sequence: GLYMA10G42250.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G122135_T04 (Zea mays), 3'ss of exon 9
---------------------------------------------gtttgtgc-tctacacttccttgctagtgt----gggtgcattttgggaactgc-atattgcacatgacggtttttgttaaccaccttagtt----attgtagGTTCATTCAATTCGTGAAGCAGCTGCTAACAACTTGAAACGCCTTGCTGAAGAATTTGGTCCTGAGTGGGCTATGCAGCACATAATTCCTCAG
                                               |   || |||   ||| |   || || |    | |||||| | ||  | ||  || |      | | |||||   ||||| | |  |  |    |||  ||||    |||||  | || || || || ||||||||||| |||||||| ||||| || ||||| |||||||| |||||||| ||||||||||||
gttcgtatcactagacttatgtcaaaacagtaacgctgtggggctactcaagcatctttcctttccatcttgtatcctcgagtgcatataggacattgtgatgtattgactaatggtttagattaactaaccaaaatttggatttcagGTCTTCTCAATCAGAGATGCTGCCGCCAACAACTTGAAGCGCCTTGCGGAAGAGTTCGGTCCAGAGTGGGCAATGCAGCATATAATTCCTCAG

upper sequence: GLYMA10G42250.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G102858_T01 (Zea mays), 3'ss of exon 9
----------------------------------------------------------------gtttgtgctc-tacacttccttgctagtgtgggt-gcattttggg--aactgcatattgcacatgacggtttttgttaaccaccttagttattgtagGTTCATTCAATTCGTGAAGCAGCTGCTAACAACTTGAAACGCCTTGCTGAAGAATTTGGTCCTGAGTGGGCTATGCAGCACATAATTCCTCAG
                                                                 ||| |  |  |   |||  | |    | |  || | ||| | |    | |  || |     |  |  |  |      ||||      |   |  |||||   || ||  | || || | ||| || || || || ||  |  | || |||||||| ||||||||||| ||||| || ||||||||||||
gtgcataaataatttcaccaaccattattacacaagttccattaatgcagaaaccatgcatactatttctaatgatggtctttttagtctatataagttgaattcttgattgattctatgtaatgtaatagtgactcaaaataccaaacatttggcttcagGTTTTCTCGATCAGAGATGCTGGTGCCAATAATTTAAAGCGTTTGACAGAGGAATTTGGCCCTGAGTGGGCGATGCAACATATAATTCCTCAG

upper sequence: GLYMA10G42250.1 (Glycine max), 3'ss of exon 9
lower sequence: AT1G13320.2 (Arabidopsis thaliana), 3'ss of exon 9
---gtttgtgctctacacttccttgctagtgtgggtgcattttgggaactgcatattgcacatgacggtttttgttaaccaccttagttattgtagGTTCATTCAATTCGTGAAGCAGCTGCTAACAACTTGAAACGCCTTGCTGAAGAATTTGGTCCTGAGTGGGCTATGCAGCACATAATTCCTCAG
     |  | ||||||  |   |   |  |   | |  ||          |  | |    | |||   |||    |||  |  | | || |   ||||||| ||||| |||||||| ||||| |||||  |||| || ||||||||||| ||||||||||| ||||| |||||||| ||| ||||||||
gtccctcattctctaccttcattgaatcatccagataaataa-atttgtcgtctctactgcttgaaattttgaaataatta--taaattgt--cagGTTCACTCAATCCGTGAAGCTGCTGCAAACAATCTGAAGCGTCTTGCTGAAGAGTTTGGTCCTGAATGGGCAATGCAGCATATAGTTCCTCAG

upper sequence: GLYMA10G42250.1 (Glycine max), 3'ss of exon 9
lower sequence: AT3G25800.1 (Arabidopsis thaliana), 3'ss of exon 8
-------------------gtttgtgctctacacttccttgctagtgtgggtgc-attttgggaactgcatattgcacatgacggtttttgttaaccaccttagttattg-------tagGTTCATTCAATTCGTGAAGCAGCTGCTAACAACTTGAAACGCCTTGCTGAAGAATTTGGTCCTGAGTGGGCTATGCAGCACATAATTCCTCAG
                     || | ||    |    |    ||    |  |   ||||   ||| |  || ||     |     ||||| ||       || |    ||       |||||||| ||||| || || || |||||||||||  | || || |||||||| |||||||||||||| ||||| ||||| || ||| ||||||||
gtatttctttctctctcttacttttactgggaatgatcagattataccgcttcttatttatagaaattgatttttttttttttttttttttttttttttttttgcggatgctctcattagGTTCACTCAATCCGCGATGCTGCTGCTAACAATCTCAAGCGGCTTGCTGAGGAATTTGGTCCTGAATGGGCAATGCAACATATAGTTCCTCAG

upper sequence: GLYMA10G42250.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv01s0011g03280.t01 (Vitis vinifera), 3'ss of exon 8
------gtttgtgctctacacttccttgctagtgtgggtgcattttgggaactgcatatt-gcacatgacggtttttgttaaccaccttagttattgtagGTTCATTCAATTCGTGAAGCAGCTGCTAACAACTTGAAACGCCTTGCTGAAGAATTTGGTCCTGAGTGGGCTATGCAGCACATAATTCCTCAG
          | ||| |   | || |||  |  ||        | ||  | ||   ||||     |   |          ||     | |  |  || ||||| | || |||||||| || |||||||||||||| || |||||||| ||||||||||||||||| ||||| ||||||||| ||||||| |||
tattttaagagggctttcatcatctttgtcatcgttttctttgtctgtcatctatgtatttatgtagttcaaaagggacaaatattatcatgttgtgcagGTTTACTCCATTCGTGATGCTGCTGCTAACAACTTAAAGCGCCTTGCAGAAGAATTTGGTCCTGACTGGGCAATGCAGCACTTAATTCCACAG

upper sequence: GLYMA10G42250.1 (Glycine max), 3'ss of exon 9
lower sequence: PP1S214_34V6.1 (Physcomitrella patens), 3'ss of exon 8
------------------------------------gtttgtgctctacacttccttgctagtgtgggtgcattttgggaactgcatattgcacatgacggtttttgt-taaccaccttagttattg------tagGTTCATTCAATTCGTGAAGCAGCTGCTAACAACTTGAAACGCCTTGCTGAAGAATTTGGTCCTGAGTGGGCTATGCAGCACATAATTCCTCAG
                                    ||||||| || | |    | | ||      | |   ||||   |  ||| | ||    |  |      |  | |||   | ||  || |||      |||||  | || || || || |||||||| |||||  | || || ||||| ||||| |||||||||||||||||  |||||||||| ||||| |||
gttcatatattcccatcaagcaatgtttcgatggtggtttgtg-tcgagatggtcgtcctcaatcagatctcttttcatatttgcttctttagaactagttcagtaatataatttcattcttttttggattaatagGTGTACTCTATCCGAGAGGCAGCTGCCAACAATCTCAAGCGTCTTGCCGAAGAGTTTGGTCCTGAGTGGGCATTGCAGCACATCATTCCACAG

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|151403929|gb|EV273739.1|EV273739
EST:     TTTTCGATGACAAGCTTGGTGCTCTTTGCATGCAGTGGTTACAGGATAAG                         GTTCATTCAATTCGTGAAGCAGCTGCTAACAACTTGAAACGCCTTGCTGAA
genomic: TTTTCGATGACAAGCTTGGTGCTCTTTGCATGCAGTGGTTACAGGATAAGgtttgtgctc ... gttattgtagGTTCATTCAATTCGTGAAGCAGCTGCTAACAACTTGAAACGCCTTGCTGAA
EST: gi|208302617|gb|GE099962.1|GE099962
EST:     TTTTCGATGACAAGCTTGGTGCTCTTTGCATGCAGTGGTTACAGGATAAG                         GTTCATTCAATTCGTGAAGCAGCTGCTGACAACTTGAA
genomic: TTTTCGATGACAAGCTTGGTGCTCTTTGCATGCAGTGGTTACAGGATAAGgtttgtgctc ... gttattgtagGTTCATTCAATTCGTGAAGCAGCTGCTAACAACTTGAA
EST: gi|151407658|gb|EV277473.1|EV277473
EST:     TTTTCGATGACAAGCTTGGTGCTCTTTGCATGCAGTGGTTACAGGATAAG                         GTTCATTCAATTCGTGAAGCAGCTGCTAACAACTTGAAACGCCTTGCTGAA
genomic: TTTTCGATGACAAGCTTGGTGCTCTTTGCATGCAGTGGTTACAGGATAAGgtttgtgctc ... gttattgtagGTTCATTCAATTCGTGAAGCAGCTGCTAACAACTTGAAACGCCTTGCTGAA
EST: gi|17153685|gb|BM143618.1|BM143618
EST:     TTTTCGATGACAAGCTTGGTGCTCTTTGCATGCAGTGGTTACAGGATAAG                         GTTCATTCAATTCGTGAAGCAGCTGCTAACAACTTGAAACGCCTTGCTGAA
genomic: TTTTCGATGACAAGCTTGGTGCTCTTTGCATGCAGTGGTTACAGGATAAGgtttgtgctc ... gttattgtagGTTCATTCAATTCGTGAAGCAGCTGCTAACAACTTGAAACGCCTTGCTGAA
EST: gi|14012021|gb|BG726943.1|BG726943
EST:     TTTTCGATGACAAGCTTGGTGCTCTTTGCATGCAGTGGTTACAGGATAAG                         GTTCATTCAATTCGTGAAGCAGCTGCTAACAACTTGAAACGCCTTGCTGAA
genomic: TTTTCGATGACAAGCTTGGTGCTCTTTGCATGCAGTGGTTACAGGATAAGgtttgtgctc ... gttattgtagGTTCATTCAATTCGTGAAGCAGCTGCTAACAACTTGAAACGCCTTGCTGAA
EST: gi|254343718|gb|GR857474.1|GR857474
EST:     GGTGCTCTTTGCATGCAGTGGTTACAGGATAAG                         GTTCATTCAATTCGTGAAGCAGCTGCTAACAACTTGAAACGCCTTGCTGAA
genomic: GGTGCTCTTTGCATGCAGTGGTTACAGGATAAGgtttgtgctc ... gttattgtagGTTCATTCAATTCGTGAAGCAGCTGCTAACAACTTGAAACGCCTTGCTGAA
EST: gi|254331030|gb|GR842295.1|GR842295
EST:     TTTTCGATGACAAGCTTGGTGCTCTTTGCATGCAGTGGTTACAGGATAAG                         GTTCATTCAATTCGTGAAGCAGCTGCTAACAACTTGAAACGCCTTGCTGAA
genomic: TTTTCGATGACAAGCTTGGTGCTCTTTGCATGCAGTGGTTACAGGATAAGgtttgtgctc ... gttattgtagGTTCATTCAATTCGTGAAGCAGCTGCTAACAACTTGAAACGCCTTGCTGAA
EST: gi|19270079|gb|BM886335.1|BM886335
EST:     TTTTCGATGACAAGCTTGGTGCTCTTTGCATGCAGTGGTTACAGGATAAG                         GTTCATTCAATTCGTGAAGCAGCTGCTAACAACTTGAAACGCCTTGCTGAA
genomic: TTTTCGATGACAAGCTTGGTGCTCTTTGCATGCAGTGGTTACAGGATAAGgtttgtgctc ... gttattgtagGTTCATTCAATTCGTGAAGCAGCTGCTAACAACTTGAAACGCCTTGCTGAA
EST: gi|16105352|gb|BI893092.1|BI893092
EST:     TTTTCGATGACAAGCTTGTTGTTCTTTGCATGCAGTGGTTACAGGATAAG                         GTTCATTCAATTCGTGAAGCAGCTGCTAACAACTTGAAACGCCTTGCTGAA
genomic: TTTTCGATGACAAGCTTGGTGCTCTTTGCATGCAGTGGTTACAGGATAAGgtttgtgctc ... gttattgtagGTTCATTCAATTCGTGAAGCAGCTGCTAACAACTTGAAACGCCTTGCTGAA
EST: gi|7926502|gb|AW832528.1|AW832528
EST:     CTTTCGATGACAAGCTTGGTGCTCTATGCATGCAGTGGTTACAGGATAAG                         GTTCATTCAATTCGTGAAGCAGCTGCTAACAACTTGAAACGCCTTGCTGAA
genomic: TTTTCGATGACAAGCTTGGTGCTCTTTGCATGCAGTGGTTACAGGATAAGgtttgtgctc ... gttattgtagGTTCATTCAATTCGTGAAGCAGCTGCTAACAACTTGAAACGCCTTGCTGAA
EST: gi|208055523|gb|GD854618.1|GD854618
EST:     TTTTCGATGACAAGCTTGGTGCTCTTTGCATGCAGTGGTTACAGGATAAG                         GTTCATTCAATT
genomic: TTTTCGATGACAAGCTTGGTGCTCTTTGCATGCAGTGGTTACAGGATAAGgtttgtgctc ... gttattgtagGTTCATTCAATT
EST: gi|254343474|gb|GR857230.1|GR857230
EST:     TTTTCGATGACAAGCTTGGTGCTCTTTGCATGCAGTGGTTACAGGATAAG                         GTTCATTCAATTCGTGAAGCAGCTGCTAACAACTTGAAACGCCTTGCTGAA
genomic: TTTTCGATGACAAGCTTGGTGCTCTTTGCATGCAGTGGTTACAGGATAAGgtttgtgctc ... gttattgtagGTTCATTCAATTCGTGAAGCAGCTGCTAACAACTTGAAACGCCTTGCTGAA
EST: gi|254343473|gb|GR857229.1|GR857229
EST:     TTTTCGATGACAAGCTTGGTGCTCTTTGCATGCAGTGGTTACAGGATAAG                         GTTCATTCAATTCGTGAAGCAGCTGCTAACAACTTGAAACGCCTTGCTGAA
genomic: TTTTCGATGACAAGCTTGGTGCTCTTTGCATGCAGTGGTTACAGGATAAGgtttgtgctc ... gttattgtagGTTCATTCAATTCGTGAAGCAGCTGCTAACAACTTGAAACGCCTTGCTGAA
EST: gi|17400839|gb|BM177621.1|BM177621
EST:     TTTTCGATGACAAGCTTGGTGCTCTTTGCATGCAGTGGTTACAGGATAAG                         GTTCATTCAATTCGTGAAGCAGCTGCTAACAACTTGAAACGCCTTGCTGAA
genomic: TTTTCGATGACAAGCTTGGTGCTCTTTGCATGCAGTGGTTACAGGATAAGgtttgtgctc ... gttattgtagGTTCATTCAATTCGTGAAGCAGCTGCTAACAACTTGAAACGCCTTGCTGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgggaactgcatattgcacatgacggtttttgttaaccaccttagttattgtagGTTCATTCAATTCGTGAAGCAGCTGCTAACAACTTGAAACGCCTTGCTGAAGAATTTGGTCCTGAGTGGGCTATGCAGCACATAATTCCTCAG
                               tgttaac  putative branch site (score: 2)
                           tttttgttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgtgctctacacttccttgctagtgtgggtgcattttgggaactgcatattgcacatgacggtttttgttaaccaccttagttattgtagGTTCATTCAATTCGTGAAGCAGCTGCTAACAACTTGAAACGCCTTGCTGAAGAATTTGGTCCTGAGTGGGCTATGCAGCACATAATTCCTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA