Sequence
atgc intronic sequence ATGC exonic sequencegtattttatctaattttgatattattattgaatagtaaattctaatacatattgctgtgaatcaaaaaaactttccagggacaatttttattctcctttacttggattaaagtttctctcgatcatacatgttatgtgtgatctttcaaatgagtttatatgttagagtttgtagttactgactcatttaaaatatgcagTTATGAAGGGAGATGTGGCTTGCCTACTAATTTTGATGCTACTTATTGCTATGCTCTGGGTTATGGTGCTGGAGCCCTCCTTCATAGTGGGAAGACTGGA
Basic information
species | Glycine max |
transcript | GLYMA09G01050.1 |
intron # | 11 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G01050.1 (Glycine max), 3'ss of exon 11
lower sequence: LOC_Os06g13810.1 (Oryza sativa), 3'ss of exon 11
gtattttatctaattttgatattattattgaatagtaaattctaatacatattgctgtgaatcaaaaaaactttccagggacaatttttattctcctttacttggattaaagtttctctcgatcatacatgttatgtgtgatctttcaaatgagt--ttatatgttagagtttgtagttactgactcatttaaaatatgcagTTATGAAGGGAGATGTGGCTTGCCTACTAATTTTGATGCTACTTATTGCTATGCTCTGGGTTATGGTGCTGGAGCCCTCCTTCATAGTGGGAAGACTGGA
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--------------------------------------------------------------------------------------------------------------------------gtatgtatgaattgttgcattttccaaaaaaataattccatctctaa---tgctgttgctgtgtaattt------tgcagATATGAAGGAAGATGTGGCCTTCCTACTATTTTTGATTCTAACTATTGCTATGCGTTAGGCTACGGTTCTGGGGCACTTCTCCAATGTGGGAAGACAGGA
upper sequence: GLYMA09G01050.1 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM2G143862_T01 (Zea mays), 3'ss of exon 4
gtattttatctaattttgatattatta-ttgaatagtaaatt--ctaatacatattgctgtgaatcaaaaaaactttccagggacaatttttattctcctttacttggattaaagtttctctcgatcatacatgttatgtgtgatctttcaaatgagtttatatgttagagtttgtagttactgactcatttaaaatatgcagTTATGAAGGGAGATGTGGCTTGCCTACTAATTTTGATGCTACTTATTGCTATGCTCTGGGTTATGGTGCTGGAGCCCTCCTTCATAGTGGGAAGACTGGA
||| | | |||| || || | | ||| | ||| || | || | | | ||| | || || | ||| || |||| || || | || | | |||| | || | | | | | | | || ||| || ||||| || ||||| ||||| ||| | ||||||||||||||| ||| ||||||||||| | || ||||||||||| ||||| || || ||||||||||| |||
gtaagcgttttttttttaattttgtgaactgagcaataacttggttggtagacttcccactgag--gaggccacccctgagaattagtttcagggagttccctggccagctagggttttgggtactc-cacttttttaatacaaagcc----atgaaatgtcatctccaactctctcatg--tagct--tttgttat-tgcagGTACGAAGGAAGATGCGGCCTTCCTACTAATTTTGATTCTAACTATTGCTATGCATTAGGCTATGGTGCTGGTGCCCTTCTCCAAAGTGGGAAGACAGGA
upper sequence: GLYMA09G01050.1 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM2G059151_T01 (Zea mays), 3'ss of exon 11
gtattttatctaattttgatattattattgaatagtaaattctaatacatattgctgtgaatcaaaaaaactttccagggacaatttttattctcctttacttggattaaagtttctctcgatcatacatgttatgtgtgatctttcaaatgagtttatatgttagagtttgtagttactgactcatttaaaatatgcagTTATGAAGGGAGATGTGGCTTGCCTACTAATTTTGATGCTACTTATTGCTATGCTCTGGGTTATGGTGCTGGAGCCCTCCTTCATAGTGGGAAGACTGGA
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-------------------------------------------------------------------------gccagggaa---tgtcatctccctgtggt-ggttt----tttctattaattttgcgt-------------ttccaaat----ttttctttccaactctctcatg--cagcttctttgctatttgcagGTACGAAGGAAGATGCGGCCTTCCTACTAATTTTGATTCTAACTATTGCTATGCATTAGGCTATGGCGCTGGTGCCCTTCTCCAAAGTGGGAAGACAGGA
upper sequence: GLYMA09G01050.1 (Glycine max), 3'ss of exon 11
lower sequence: AT1G12000.1 (Arabidopsis thaliana), 3'ss of exon 11
gtattttatctaattttgatattattattgaatagtaaattctaatacatattgctgtgaatcaaaaaaactttccagggacaatttttattctcctttacttggattaaagtttctctcgatcatacatgttatgtgtgatctttcaaatgagtttatatgttagagtttgtagttactgactcatttaaaatatgcagTTATGAAGGGAGATGTGGCTTGCCTACTAATTTTGATGCTACTTATTGCTATGCTCTGGGTTATGGTGCTGGAGCCCTCCTTCATAGTGGGAAGACTGGA
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-------------------------------------------------------------------------gtaagttacgcaatttgttct--ttcagtta-accaaa---tcgttatataatacattgcttatttattgatgtgaataa---tacaagcttga-tttatggtttgtaatcaacttgaa---tacagGTATGAAGGAAGATGCGGCTTGCCCACAAATTTTGATGCCACATACTGTTATGCACTTGGTTATGGCGCTGGAGTACTCCTCAACAGTGGGAAGACCGGA
upper sequence: GLYMA09G01050.1 (Glycine max), 3'ss of exon 11
lower sequence: Vv10s0116g00360.t01 (Vitis vinifera), 3'ss of exon 11
gtattttatctaattttgatattattattgaatagtaaattctaatacatattgctgtgaatcaaaaaaactttccagggacaatttttattctcctttacttggattaaagtttctctcgatcatacatgttatgtgtgatctttcaaatgagtttatatgttagagtttgtagttactgactcatttaaaatatgcagTTATGAAGGGAGATGTGGCTTGCCTACTAATTTTGATGCTACTTATTGCTATGCTCTGGGTTATGGTGCTGGAGCCCTCCTTCATAGTGGGAAGACTGGA
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--------------gtatgtaccatcttttgatgaaaaag---gatata-gctattttgagtcacata----tttcaattacaagtaatgacatgatattctt--actcaaat---tgttgaacctaccccc-----acaacaatttatgttagtt---atgacactatgttttgtttctgg--catccctgatgtgcagATATGAAGGGAGGTGTGGTTTTCCAACTAACTTCGATGCTGCCTACTGCTATGCATTGGGTTTTGCTGCTGGAGCTCTCCTTCACTGTGGGAAAACTGGGMapped 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|4313688|gb|AI460807.1|AI460807EST: CAAGAAGGCAAATACAAAGGCGAATTTAAAGGGCAATCCCACTTCTTCGG TTATGAAGGGAGATGTGGCTTGCCTACTAATTTTGATGCTACTTATTGCTA
genomic: CAAGAAGGCAAATACAAAGGCGAATTTAAAGGGCAATCCCACTTCTTCGGgtattttatc ... aaatatgcagTTATGAAGGGAGATGTGGCTTGCCTACTAATTTTGATGCTACTTATTGCTA
EST:
gi|4313720|gb|AI460839.1|AI460839EST: CAAGAAGGCAAATACAAAGGCGAATTTAAAGGGCAATCCCACTTCTTCGG TTATGAAGGGAGATGTGGCTTGCCTACTAATTNTGATGCTACTTATTGCTA
genomic: CAAGAAGGCAAATACAAAGGCGAATTTAAAGGGCAATCCCACTTCTTCGGgtattttatc ... aaatatgcagTTATGAAGGGAGATGTGGCTTGCCTACTAATTTTGATGCTACTTATTGCTA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcaaatgagtttatatgttagagtttgtagttactgactcatttaaaatatgcagTTATGAAGGGAGATGTGGCTTGCCTACTAATTTTGATGCTACTTATTGCTATGCTCTGGGTTATGGTGCTGGAGCCCTCCTTCATAGTGGGAAGACTGGA
tactgac putative branch site (score: 1)
actcatttaaaatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtattttatctaattttgatattattattgaatagtaaattctaatacatattgctgtgaatcaaaaaaactttccagggacaatttttattctcctttacttggattaaagtttctctcgatcatacatgttatgtgtgatctttcaaatgagtttatatgttagagtttgtagttactgactcatttaaaatatgcagTTATGAAGGGAGATGTGGCTTGCCTACTAATTTTGATGCTACTTATTGCTATGCTCTGGGTTATGGTGCTGGAGCCCTCCTTCATAGTGGGAAGACTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA