Sequence
atgc intronic sequence ATGC exonic sequencegtaagctcaagcttcaaatagtcatgttacaccatgaaaatcttattatattaatcttatggtggtctttttttcttgcacatcaaaaaaggtataatattcttattttgatatgcattccagAGATATCAAGCCTGACAATTTGCTGCTAGATAGAAATGGTCACATGAAATTATCAGACTTTGGATTATGTAAACCACTGGACTGCAGTAATCTTCAGGAA
Basic information
species | Glycine max |
transcript | GLYMA10G32480.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA10G32480.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os10g33640.1 (Oryza sativa), 3'ss of exon 4
gtaagctcaagcttcaaatagtcatgttacaccatgaaaatcttattatattaatcttatggtggtctttttttcttgcacatcaaaaaaggtataatattcttattttgatatgcattccagAGATATCAAGCCTGACAATTTGCTGCTAGATAGAAATGGTCACATGAAATTATCAGACTTTGGATTATGTAAACCACTGGACTGCAGTAATCTTCAGGAA
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--------------------------------------gtgtgtatatttgtagcttcatatcagcttcttcttaccgctgtt--gagatgttctgatgaacttagc---acatgattttcagAGATATCAAGCCTGATAATCTTTTATTAGATAGACATGGTCACTTAAGACTGTCAGATTTTGGATTATGCAAACCACTAGATTATTCCAACTTCCCAGAC
upper sequence: GLYMA10G32480.1 (Glycine max), 3'ss of exon 4
lower sequence: AT4G14350.3 (Arabidopsis thaliana), 3'ss of exon 5
gtaagctcaagcttcaaatagtcatgttacaccatgaaaatcttattatattaatcttatggtggtctttttttcttgcacatcaaaaaaggtataatattcttattttgatatgcattccagAGATATCAAGCCTGACAATTTGCTGCTAGATAGAAATGGTCACATGAAATTATCAGACTTTGGATTATGTAAACCACTGGACTGCAGTAATCTTCAGGAA
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------------------------------gtca-gtgaagcagaatatat-gatttagttctagctcccattgttattttgttctaaacg------tctttttttctcca-atgtgatacagAGATATCAAGCCTGATAATCTGCTACTTGACAAAGACGGCCACATGAAATTGTCAGATTTTGGATTATGTAAACCATTAGACTGTAGTAATCTTCAAGAG
upper sequence: GLYMA10G32480.1 (Glycine max), 3'ss of exon 4
lower sequence: AT3G23310.1 (Arabidopsis thaliana), 3'ss of exon 5
gtaagctcaagcttcaaatagtcatgttacaccatgaaa-atcttattatattaatcttatggtggtctttttttcttgcacatcaaaaaaggtataatattcttattttgatatgcattccagAGATATCAAGCCTGACAATTTGCTGCTAGATAGAAATGGTCACATGAAATTATCAGACTTTGGATTATGTAAACCACTGGACTGCAGTAATCTTCAGGAA
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--------------------gtctagtgaagcaatcaactatctgagtaaatttgtagcgta-tcatttttcttttttggtgttctgaccatccat----ttacttctccaatttg--ttacagAGATATCAAGCCTGATAATCTGCTACTCGACAGAAGCGGTCACATGAAGTTATCCGATTTTGGATTATGTAAGCCATTAGATTGTAGTATTCTCCAGGAA
upper sequence: GLYMA10G32480.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv05s0049g01220.t01 (Vitis vinifera), 3'ss of exon 4
gtaagctcaagcttcaaatagtcatgttacaccatgaaaatcttat-tatattaatcttatggtggtctttttttcttgcacatcaaaaaaggtataatattcttattttgatatgcattccagAGATATCAAGCCTGACAATTTGCTGCTAGATAGAAATGGTCACATGAAATTATCAGACTTTGGATTATGTAAACCACTGGACTGCAGTAATCTTCAGGAA
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-------------------gtttgtgtaagattttatcatgattgtatgtgggaaccatatg-catgcttctgatcatg---acttaagaagcaataaccctctccatatt-tacttattacagAGATATCAAGCCCGACAATTTACTGCTCGATAGATATGGACATATGAAATTGTCAGATTTTGGATTATGTAAACCATTGGATTGCAGTAATCTTCATGAG
upper sequence: GLYMA10G32480.1 (Glycine max), 3'ss of exon 4
lower sequence: PP1S22_429V6.1 (Physcomitrella patens), 3'ss of exon 4
gtaagctcaagcttcaaatagtcatgttacaccatgaaaatcttattatattaatcttatggtggtctttttttcttgcacatcaaaaaaggtataatattcttattttgatatgcattccagAGATATCAAGCCTGACAATTTGCTGCTAGATAGAAATGGTCACATGAAATTATCAGACTTTGGATTATGTAAACCACTGGACTGCAGTAATCTTCAGGAA
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----gcttg-gtatgaaggactctctcgtgttcactgatgcctgtttatttgaaatt---gatgttccgcttacttttgactccaaca---------------tctactggtttgtgtaccagAGATATCAAACCGGACAACTTGCTGTTAGATAAGAATGGGCACATGAAGTTATCTGATTTTGGCCTCTGTAAGCCTTTGGACTGCTCCAACTTGCCTGCC
upper sequence: GLYMA10G32480.1 (Glycine max), 3'ss of exon 4
lower sequence: EFJ28086 (Selaginella moellendorffii), 3'ss of exon 4
gtaagctcaagcttcaaatagtcatgttacaccatgaaaatcttattatattaatcttatggtggtctttttttcttgcacatcaaaaa---aggtataatattcttattttgatatgcattc----cagAGATATCAAGCCTGACAATTTGCTGCTAGATAGAAATGGTCACATGAAATTATCAGACTTTGGATTATGTAAACCACTGGACTGCAGTAATCTTCAGGAA
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----------------------------------------------------------------------gtatgttgcgagtcgagaacatggcttgaacttaccagtttttctgtgtcttctgtgcagGGATATCAAGCCTGATAATCTTCTACTTGATAAGAATGGTCACATGAAATTGTCAGACTTCGGGTTGTGTAAACCCCTAGACTGCTCTAACTTACCAGCTMapped 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|13563179|gb|BG551399.1|BG551399EST: GTCGATTCATAAACATAATTATATTCATAG AGATATCAAGCCTGACAATTTGCTGCTAGATAGAAATGGTCACATGAAATT
genomic: GTCGATTCATAAACATAATTATATTCATAGgtaagctcaa ... tgcattccagAGATATCAAGCCTGACAATTTGCTGCTAGATAGAAATGGTCACATGAAATT
EST:
gi|192294765|gb|FG986614.1|FG986614EST: GAGACTGTCTTAGCTATAGAGTCGATTCATAAACATAATTATATTCATAG AGATATCAAGCCTGACAATTTGCTGCTAGATAGAAATGGTCACATGAAATT
genomic: GAGACTGTCTTAGCTATAGAGTCGATTCATAAACATAATTATATTCATAGgtaagctcaa ... tgcattccagAGATATCAAGCCTGACAATTTGCTGCTAGATAGAAATGGTCACATGAAATT
EST:
gi|16346917|gb|BI972512.1|BI972512EST: GAGACTGTCTTAGCTATAGAGTCGATTCATAAACATAATTATATTCATAG AGATATCAAGCCTGACAATTTGCTGCTAGATAGAAATGGTCACATGAAATT
genomic: GAGACTGTCTTAGCTATAGAGTCGATTCATAAACATAATTATATTCATAGgtaagctcaa ... tgcattccagAGATATCAAGCCTGACAATTTGCTGCTAGATAGAAATGGTCACATGAAATT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttttcttgcacatcaaaaaaggtataatattcttattttgatatgcattccagAGATATCAAGCCTGACAATTTGCTGCTAGATAGAAATGGTCACATGAAATTATCAGACTTTGGATTATGTAAACCACTGGACTGCAGTAATCTTCAGGAA
ttttgat putative branch site (score: 4)
aaaaaaggtataatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagctcaagcttcaaatagtcatgttacaccatgaaaatcttattatattaatcttatggtggtctttttttcttgcacatcaaaaaaggtataatattcttattttgatatgcattccagAGATATCAAGCCTGACAATTTGCTGCTAGATAGAAATGGTCACATGAAATTATCAGACTTTGGATTATGTAAACCACTGGACTGCAGTAATCTTCAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG