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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattataaattactgtcaccatagtcgtgttttggaaacgagtgaatgtgaaaaagcatctaagttacttgtgtcagcatctggttctggccatgatattcgccgtaacatatttgaaaattttaattttatttcagGTCTGGTTGCTGATATTGATATCGAGTCTGAAAAGTATAGGTGGATGGGAAGTGCTCGTATTGATTTTTAT

Basic information

species Glycine max
transcript GLYMA08G06300.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G06300.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os01g57350.2 (Oryza sativa), 3'ss of exon 6
gtaattataaattactgtcaccatagtcgtgttttggaaacgagtgaatgtgaaaaagcatctaagttacttgtgtcagcatctggttctggccatgatattcgccgtaacat-atttgaaaattttaat--tttatttcagGTCTGGTTGCTGATATTGATATCGAGTCTGAAAAGTATAGGTGGATGGGAAGTGCTCGTATTGATTTTTAT
                                                | ||  | |   |   | ||| |||  ||   |||||  |    |  |  |      | |  ||  ||||    ||  ||||  |  ||||||||| |||| |||||||| ||||| |||||||| ||||| ||||||||||||||||| ||  ||||||| |||
-----------------------------------------------gtatgccacaagcttggaattagttg-atcga-atctgaatgatactttcttggctctcatctcaccatttagggataataataatacatttcagGTTTGGTGGCTGATATAGATATTGAGTCTGAGAAGTACAGGTGGATGGGAAGTGCACGCTTTGATTTCTAT

upper sequence: GLYMA08G06300.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os07g37580.2 (Oryza sativa), 3'ss of exon 5
gta-attataaattactgtcaccatagtcgtgttttggaaacgag-tgaatgtgaaaaagcatctaa-----gttacttgtgtcagcatctggttctggccatgatattcgccgtaaca-tatttgaaaattttaattttatttcagGTCTGGTTGCTGATATTGATATCGAGTCTGAAAAGTATAGGTGGATGGGAAGTGCTCGTATTGATTTTTAT
|||     |  ||||   | |   ||  | | |||        |  |  | ||  | |  |   |||       |     | |||| | || |||||  |  |     |  | |   || ||   |||||   |   |  | | |||||||||| |||||||| ||||| ||||| || ||||| ||||||||||| ||||||||| |||| || |||
gtatgccgtgtattagcttgatgctaagcttttttctctcttaaactacacgtctatacccccataacactgactgtcactctcag-agcttgttctcccactatctatttctggggcactaagagaaaacgatttatgaactgcagGTCTGGTAGCTGATATCGATATTGAGTCAGAGAAGTACAGGTGGATGGGCAGTGCTCGTCTTGACTTCTAT

upper sequence: GLYMA08G06300.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G057475_T03 (Zea mays), 3'ss of exon 6
gtaattataaattactgtcaccatagtcgtgttttggaaacga-----gtgaatgtgaaaaagcatctaagttacttgtgtcagcatctggt-tctggccatgata----ttcgccg-----taacatatttgaaaattttaattttatttcagGTCTGGTTGCTGATATTGATATCGAGTCTGAAAAGTATAGGTGGATGGGAAGTGCTCGTATTGATTTTTAT
|||  |  |   ||   |  | ||  |     |||| |||| |     | |||     |  | | ||        |||   || ||  |  | | | |||    ||    ||    |     | |||    |||||||  ||  |  | | |||||||||| |||||| ||||||| || || || ||||||||||||||||||||||||||  |||| ||||||
gta--tgcagcatataatttctatgctaactatttgaaaacaacagctgagaacacagaccaccttcctcagagattgctccatcactttctcttttgccgcagtaaaatttaattgacaactgacaagcctgaaaatgatatatgaactgcagGTCTGGTGGCTGATGTTGATATTGAATCGGAGAAGTATAGGTGGATGGGAAGTGCTCGCCTTGAATTTTAT

upper sequence: GLYMA08G06300.1 (Glycine max), 3'ss of exon 6
lower sequence: AT4G21534.1 (Arabidopsis thaliana), 3'ss of exon 6
gtaattataaattactgtcaccatagtcgtgttttggaaacgagtgaatgtgaaaaagcatctaagttacttgtgtcagcatctggttctggccatgatattcgccgtaacatatttgaaaattttaattttatttcagGTCTGGTTGCTGATATTGATATCGAGTCTGAAAAGTATAGGTGGATGGGAAGTGCTCGTATTGATTTTTAT
          ||  | || |           |||||  |      || |    |||   || |  |  | |      |  |  ||    ||   |   || ||   ||   ||   |||  | |  |  |||||||||||| |  | |||||||| || |||||||| || ||||  || ||||||||||||||||||||||| ||||||
--------gtatgccagtaaattctacttctttttgctatgtccagagttcagaaagttattt--gcaaatgaaagtaatacatgagcttgctgaacgtactctttgttgtat---tgattagtcca--tttatttcagGTTTAATAGCTGATATAGACATCGAGTCAGAGAAGTTCAGATGGATGGGAAGTGCTCGTATTGACTTTTAT

upper sequence: GLYMA08G06300.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv00s0181g00250.t01 (Vitis vinifera), 3'ss of exon 6
-----------------------------------------gtaattataaattactgtcaccatagtcgtgttttggaaacgag-tgaatgtgaaaaagcatctaagtt-acttgtgtcagcat-ctggt-------tctggccatgata--ttcgccgtaacatatttg-aaaattttaattttatttcagGTCTGGTTGCTGATATTGATATCGAGTCTGAAAAGTATAGGTGGATGGGAAGTGCTCGTATTGATTTTTAT
                                         | || |  || | |||||      |   |  ||||  | || || |   |  ||| | || |||   || ||| |  | ||| | || ||       | ||    |||||  |   |  |  | || |   | |||||||    |||| |||||||||| || |||||||| || ||||||||||| |||||||||||||||||||||||| | ||||| || 
gtatgaccaaaatttccaccacttgtttatgccatactcttggaactgcaagtgactgttg----aactggatttttaagacaagctttctaagaatatgcctctggatttactagaataagctttctagtggatttgtttgattttgatagctctactttgccttactgacagaattttag---tattccagGTCTGGTGGCAGATATTGACATTGAGTCTGAAAAATATAGGTGGATGGGAAGTGCTCGTTTAGATTTCTAC

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|151397505|gb|EV267378.1|EV267378
EST:     CATCACACAAGGGGAGACCAGATTTTTCAGTGTGTTGATGCTTGCATGGG                         GTCTGGTTGCTGATATTGATATCGAGTCTGAAAAGTATAGGTGGATGGGAA
genomic: CATCACACAAGGGGAGACCAGATTTTTCAGTGTGTTGATGCTTGCATGGGgtaattataa ... tttatttcagGTCTGGTTGCTGATATTGATATCGAGTCTGAAAAGTATAGGTGGATGGGAA
EST: gi|19271300|gb|BM887556.1|BM887556
EST:     CATCACACAAGGGGAGACCAGATTTTTCAGTGTGTTGATGCTTGCATGGG                         GTCTGGTTGCTGATATTGATATCGAGTCTGAAAAGTATAGGTGGATGGGAA
genomic: CATCACACAAGGGGAGACCAGATTTTTCAGTGTGTTGATGCTTGCATGGGgtaattataa ... tttatttcagGTCTGGTTGCTGATATTGATATCGAGTCTGAAAAGTATAGGTGGATGGGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggttctggccatgatattcgccgtaacatatttgaaaattttaattttatttcagGTCTGGTTGCTGATATTGATATCGAGTCTGAAAAGTATAGGTGGATGGGAAGTGCTCGTATTGATTTTTAT
                                      ttttaat  putative branch site (score: 3)
                                            ttttatttc  CT-rich tract
                       taacatatttgaaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaattataaattactgtcaccatagtcgtgttttggaaacgagtgaatgtgaaaaagcatctaagttacttgtgtcagcatctggttctggccatgatattcgccgtaacatatttgaaaattttaattttatttcagGTCTGGTTGCTGATATTGATATCGAGTCTGAAAAGTATAGGTGGATGGGAAGTGCTCGTATTGATTTTTAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA