Sequence
atgc intronic sequence ATGC exonic sequencegtatgttagatattccctttttccacaaagcaagagcctctctctctttttctctctagcagttcttttgattattgatcaaccattaattgtgatgaaattcagGGTGAGAAAGATGACAAGATAATTGCTGTCTGTGCTGATGATCCTGAGTATAGGCATTACAATGATATCAAGGACCTTCCTCCTCACCGTTTAGCTGAAA
Basic information
species | Glycine max |
transcript | GLYMA10G05130.2 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA10G05130.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os01g74350.1 (Oryza sativa), 3'ss of exon 7
gtatgttagatattccctttttccacaaagcaagagcctctctctctttttctctctagcagttcttttg--attattgatcaaccattaattgtgatgaaatt-----cagGGTGAGAAAGATGACAAGATAATTGCTGTCTGTGCTGATGATCCTGAGTATAGGCATTACAATGATATCAAGGACCTTCCTCCTCACCGTTTAGCTGAAA
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------------------------------------gtttggtccctactcaacaagtgcgctttcttcagaatgaatgaacagattctaaa-gtggtaaggttttatccagGGAGAGGCAGATGATAAGATTATTGCAGTCTGTGCTGATGATCCTGAGTACAAGCATTACAACGATATCAAGGACCTCCCACCTCACCGCTTAGCTGAAA
upper sequence: GLYMA10G05130.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os05g02310.1 (Oryza sativa), 3'ss of exon 6
gtatgttagatattccctttttccacaaagcaagagcctctctctctttttctctctagcagttcttttgattattgatcaaccattaattgtgatgaaattcagGGTGAGAAAGATGACAAGATAATTGCTGTCTGTGCTGATGATCCTGAGTATAGGCATTACAATGATATCAAGGACCTTCCTCCTCACCGTTTAGCTGAAA
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--gtttggcttcattccaacatttacaaagtcc-agcgaaatgctattctgatcccca-----tgtttctatt-ctgaccccatgtttgtt----tgaa---cagGGAGAGGCAGATGACAAGATTATTGCCGTTTGTGCTGATGATCCTGAGTACAAGCATTACAATGATATCAAGGAGCTCCCACCTCACCGCTTGGCTGAAA
upper sequence: GLYMA10G05130.1 (Glycine max), 3'ss of exon 6
lower sequence: AT3G53620.1 (Arabidopsis thaliana), 3'ss of exon 6
gtatgttagatattccctttttccacaaagcaagagcctctctctctttttctctctagcagttcttttgattattgatcaaccattaattgtgatgaaattcagGGTGAGAAAGATGACAAGATAATTGCTGTCTGTGCTGATGATCCTGAGTATAGGCATTACAATGATATCAAGGACCTTCCTCCTCACCGTTTAGCTGAAA
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----gttagatatt-----------caacgta-----cttgtcatattagtacttataaaagtaacagagattga-aactagaagctctttctgcttgaat--agGGTGAGAAAGACGACAAGATCATTGCTGTCTGCGCTGACGATCCAGAGTATCGCCATTACAACGACATCAGTGAGCTTCCGCCTCATCGTATGGCTGAGA
upper sequence: GLYMA10G05130.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv08s0040g02470.t01 (Vitis vinifera), 3'ss of exon 6
gtatgttagatattccctttttccacaaagcaagagcctctctctctttttctctctagcagtt-cttttgattattgatcaaccattaattgtgatgaaattcagGGTGAGAAAGATGACAAGATAATTGCTGTCTGTGCTGATGATCCTGAGTATAGGCATTACAATGATATCAAGGACCTTCCTCCTCACCGTTTAGCTGAAA
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--------------------------gtagaaaaagatgacaagatatatttcctctcccaattacttctaaaccttgaattaatcttgaccttgattaa-cacagGGAGAGAAAGATGACAAGATAATTGCAGTTTGTGCTGATGATCCTGAGTACCGACACTACACTGATATCAATGAGCTCCCTCCGCACCGTTTGGCTGAGA
upper sequence: GLYMA10G05130.1 (Glycine max), 3'ss of exon 6
lower sequence: PP1S46_53V6.1 (Physcomitrella patens), 3'ss of exon 7
------gtatgttagatattccctttttccacaaagcaag--agcctctctctctttttctctctagcagttctt--ttgattatt-----------gatcaaccattaa--ttgtgatgaaattcagGGTGAGAAAGATGACAAGATAATTGCTGTCTGTGCTGATGATCCTGAGTATAGGCATTACAATGATATCAAGGACCTTCCTCCTCACCGTTTAGCTGAAA
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gtgagggactattatgccgtactctttgacggaaaccaaactagcttgtattgatcatgttctcatattgttcgtacctaatcatccactatatgtaaatctaatgttaaatttgtaaggacctgtagGGAGAGAAGGATGACAAGATCATCGCTGTCTGTGCTGACGATCCGGAGTATAGACACTTCAAAGACATCAATGAGTTTCCTCCACATCGACTTGCCGAAAMapped 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|13480494|gb|BG509837.1|BG509837EST: GTTGCTTTCTACGGGCCAAAGCTATTGGACTCATGCCTATGATTGATCAG GGTGAGAAAGATGACAAGATAATTGCTGTCTGTGCTGATGATCCTGAGTAT
genomic: GTTGCTTTCTACGGGCCAAAGCTATTGGACTCATGCCTATGATTGATCAGgtatgttaga ... tgaaattcagGGTGAGAAAGATGACAAGATAATTGCTGTCTGTGCTGATGATCCTGAGTAT
EST:
gi|192331411|gb|FK022716.1|FK022716EST: GTTGCTTTCTACGGGCCAAAGCTATTGGACTCATGCCTATGATTGATCAG GGTGAGAAAGATGACAAGATAATTGCTGTCTGTGCTGATGATCCTGAGTAT
genomic: GTTGCTTTCTACGGGCCAAAGCTATTGGACTCATGCCTATGATTGATCAGgtatgttaga ... tgaaattcagGGTGAGAAAGATGACAAGATAATTGCTGTCTGTGCTGATGATCCTGAGTAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctctctagcagttcttttgattattgatcaaccattaattgtgatgaaattcagGGTGAGAAAGATGACAAGATAATTGCTGTCTGTGCTGATGATCCTGAGTATAGGCATTACAATGATATCAAGGACCTTCCTCCTCACCGTTTAGCTGAAA
cattaat putative branch site (score: 3)
ttcttttgattatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgttagatattccctttttccacaaagcaagagcctctctctctttttctctctagcagttcttttgattattgatcaaccattaattgtgatgaaattcagGGTGAGAAAGATGACAAGATAATTGCTGTCTGTGCTGATGATCCTGAGTATAGGCATTACAATGATATCAAGGACCTTCCTCCTCACCGTTTAGCTGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA