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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtgtaattcctgagctaatctataggttcagttggggtcattatatcaataggaccagtcaatttaacatatctgtatgttttccctatgatttctgcagATTTTCTTTAATCCTGAGATATATAGTAGTGACTTTACTACCCCTTTGCCAGTTGTAATAGACAAATGCATTCAGTCTGCGCCAATTGACACAAGGAGAT

Basic information

species Glycine max
transcript GLYMA08G13780.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G13780.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os08g03440.1 (Oryza sativa), 3'ss of exon 6
-gtgtaattcctgagctaa-tctataggttcagttggggtcattatatcaataggaccagtcaatttaacata--tctgtatgttttccctatgatttctgcagATTTTCTTTAATCCTGAGATATATAGTAGTGACTTTACTACCCCTTTGCCAGTTGTAATAGACAAATGCATTCAGTCTGCGCCAATTGACACAAGGAGAT
| | ||| | ||| | || | || ||||| | | | | || | ||||| | || | || || ||| ||||||| ||||| |||| ||||| || | ||||| | || ||| | || | |||| || | || |||| ||||||||||||||||||||||||
cattttattgacatttggactcttcaccttgaaatga---cattaaaaggagaaaaaca-tgaatttgatgtaatttactaaccttctactagcgcaaatgcagATCTTCTTCCATCCCGAGATTTACTCTGCCGACTTCTCCACTCCTCTACCTGAACTAATTGATAGCTGTGTTCAATCTGCGCCAATTGACACAAGGAGAG

upper sequence: GLYMA08G13780.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G305332_T01 (Zea mays), 3'ss of exon 1
-gtgtaattcctgagctaatctataggttcagttggg-gtcattatatcaataggaccagtcaatttaacatatctgtatgttttccctatgatttctgcagATTTTCTTTAATCCTGAGATATATAGTAGTGACTTTACTACCCCTTTGCCAGTTGTAATAGACAAATGCATTCAGTCTGCGCCAATTGACACAAGGAGAT
||| | | | | ||||||||| | ||| | | | ||| ||||| | | | | | | | ||||||| ||||| ||||||||||| || | ||||| | || ||||| || | | || || || || |||||||||| ||||||||||||||||||
tttgttagaataaacttttaacttgttttcagttggtcatgattttttttaagaagtcag--aatttggtgtgcgtctctaatcatctagcaacaaatgcagATCTTCTTCAATCCTGAGATTTACTCTGCCGACTTCTCCACTCCTTTACCTGAGTTGATTGATAACTGTGTTCAGTCTGCACCAATTGACACAAGGAGAG

upper sequence: GLYMA08G13780.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G136662_T01 (Zea mays), 3'ss of exon 5
gtgtaattcctgag-ctaatcta-taggttca-gttggggtcattatatcaataggaccagtcaatttaacatatctgtatgttttccctatgatttctgcagATTTTCTTTAATCCTGAGATATATAGTAGTGACTTTACTACCCCTTTGCCAGTTGTAATAGACAAATGCATTCAGTCTGCGCCAATTGACACAAGGAGAT
| | | || | |||| | || ||| | || | | | || | | | ||| |||| | | | | | | ||||||| ||||| ||||||||||| || | || || | || |||||||| | | || ||||| || |||||||||| ||||||||||||||||||
-taacttgcttgggactaaaagactatgttgatgtacagttggtcatgttttttaggtcag--aattaggtgtgcatctctaatcatttaccaacaaatgcagATCTTCTTCAATCCTGAGATTTACTCTGCCGATTTCTCCACTCCTTTGCCCGAGTTGATTGACAACTGTGTTCAGTCTGCACCAATTGACACAAGGAGAG

upper sequence: GLYMA08G13780.1 (Glycine max), 3'ss of exon 5
lower sequence: AT1G13180.1 (Arabidopsis thaliana), 3'ss of exon 5
-----gtgtaattcctgagctaatctataggttcagttggggtcattatatcaataggaccagtcaatttaacatatctgta-tgttttccctatgatttctgcagATTTTCTTTAATCCTGAGATATATAGTAGTGACTTTACTACCCCTTTGCCAGTTGTAATAGACAAATGCATTCAGTCTGCGCCAATTGACACAAGGAGAT
| |||| | || | | ||| ||| || || || | | | | | | | || || ||| |||| | || | | ||| | ||||||||||| |||||||| || | |||||| || || |||| |||| ||| ||||||||||| ||||||||||| |||||||||||| | |||
caagagagtaactggaaagtggaac-ataatttcctttattgttcttgcgttttt--gttctgctatt---accgatgagtaatgttgagattttgtgtgttacagGTGTTCTTTAATCCAGAGATATACAGCAATGACTTCACAACTACTTTACCAGCTGTGATAGACAAATGTATTCAGTCTGCACCAATTGACACACGAAGAG

upper sequence: GLYMA08G13780.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv01s0137g00280.t01 (Vitis vinifera), 3'ss of exon 5
-gtgtaattcctgagctaatctataggttcagttggggtcattata--tcaataggaccagtcaatttaacatatctgtatgttttccctatgatttctgcagATTTTCTTTAATCCTGAGATATATAGTAGTGACTTTACTACCCCTTTGCCAGTTGTAATAGACAAATGCATTCAGTCTGCGCCAATTGACACAAGGAGAT
|| || || | || | || || | | ||| || | | | ||||| | | || || | || ||||||||||||| ||||||||||| || || || || ||| | |||||||| |||| |||||||||||| || ||||||||||| |||||||||||||| ||
tgtttacttgtgcattgcatttcatctactagatgatgctttgataagtcttttaaaaaaaggaattt---gtttttgatgattaatctggctgattatgcagATTTTCTTCAATCCTGAGATCTACAGCAGCGATTTTGCAACCCCTTTACCAGCTGTAATAGACAAGTGTATTCAGTCTGCACCAATTGACACAAGAAGGG

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|10238544|gb|BE807432.1|BE807432
EST:     GGGCACCATATTCATGTGATATTGGCTATGAGCGATTTCTTGGCCCTGAG                         ATTTTCTTTAATCCTGAGATATATAGTAGTGACTTTACTACCCCTTTGCCA
genomic: GGGCACCATATTCATGTGATATTGGCTATGAGCGATTTCTTGGCCCTGAGgtttgttcta ... atttctgcagATTTTCTTTAATCCTGAGATATATAGTAGTGACTTTACTACCCCTTTGCCA
EST: gi|208073296|gb|GD869929.1|GD869929
EST:     CTTGGCCCTGAG                         ATTTTCTTTAATCCTGAGATATATAGTAGTGACTTTACTACCCCTTTGCCA
genomic: CTTGGCCCTGAGgtttgttcta ... atttctgcagATTTTCTTTAATCCTGAGATATATAGTAGTGACTTTACTACCCCTTTGCCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcaataggaccagtcaatttaacatatctgtatgttttccctatgatttctgcagATTTTCTTTAATCCTGAGATATATAGTAGTGACTTTACTACCCCTTTGCCAGTTGTAATAGACAAATGCATTCAGTCTGCGCCAATTGACACAAGGAGAT
                atttaac  putative branch site (score: 3)
 tttctgc  putative PPT
 tcaatttaacatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgtaattcctgagctaatctataggttcagttggggtcattatatcaataggaccagtcaatttaacatatctgtatgttttccctatgatttctgcagATTTTCTTTAATCCTGAGATATATAGTAGTGACTTTACTACCCCTTTGCCAGTTGTAATAGACAAATGCATTCAGTCTGCGCCAATTGACACAAGGAGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - -attcctg
- - - - - - - - - - - - - - - gttgggg
- - - - - - - - - - - - - - - - - - - - - - - - - - - ccagtca