Sequence
atgc intronic sequence ATGC exonic sequence...aatagctagtatttattttgaaattcacttacattaattaaggccgttgtaacaatttcaacattttcccattgtttccttgatatttattcttgtgaagGTACCTGGAGAATAGTGGCTGTGTTGGAATGTGTGTCAATATGTGCAAGATTCCTACCCAAGATTTTTTCACTAATGAATTTGGACTTCCGTTAACAATG
Basic information
species | Glycine max |
transcript | GLYMA13G10340.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G10340.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os08g02210.1 (Oryza sativa), 3'ss of exon 2
aatagctagtatttattttgaaattcacttacattaattaaggccgttgtaacaatttcaacattttcccattgtttccttgatatttattcttgtga-agGTACCTGGAGAATAGTGGCTGTGTTGGAATGTGTGTCAATATGTGCAAGATTCCTACCCAAGATTTTTTCACTAATGAATTTGGACTTCCGTTAACAATG
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----------gtaagacggacgattcaactgtgttcgtcttggatttcaagcgagattcagtaa------aaaattcagaaaacattcatctccgtttcagGTACCTGGAGAACAGCGGCTGCGTCGGAATGTGCGTCAACATGTGCAAAATTCCGACGCAAAACTTCTTCACCAACGAGTTCGGACTCCCTCTCACCATG
upper sequence: GLYMA13G10340.1 (Glycine max), 3'ss of exon 4
lower sequence: AT1G64680.1 (Arabidopsis thaliana), 3'ss of exon 1
aatagctagtatttattttgaaattcacttacattaattaaggccgttgtaacaatttcaacattttcccattgtttccttgatatttattcttgtgaagGTACCTGGAGAATAGTGGCTGTGTTGGAATGTGTGTCAATATGTGCAAGATTCCTACCCAAGATTTTTTCACTAATGAATTTGGACTTCCGTTAACAATG
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-gtaacaagtgaattccatcaaaatgactattactagttg----tcttgt-------tcaaaatgtgacagacttgctcctactgttgatt-----gaagGTATCTGGAGAACAGTGGGTGTGTAGGAATGTGTGTGAATATGTGCAAGATTCCAACCCAAGATTTCTTCACCAATGAGTTTGGCCTCCCACTCACCATG
upper sequence: GLYMA13G10340.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv02s0025g02640.t01 (Vitis vinifera), 3'ss of exon 3
--aatagc-tagtatttattttgaaattcactt-acattaattaaggccgttgtaacaatttcaacattttcccattgtttccttgatatttattcttgtgaagGTACCTGGAGAATAGTGGCTGTGTTGGAATGTGTGTCAATATGTGCAAGATTCCTACCCAAGATTTTTTCACTAATGAATTTGGACTTCCGTTAACAATG
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catatgtcacagtaaccaaatttcaatatattagaaataaaataatgtccaactactaatctt----tcttttttttctttttctgacaaattctcctatcaagGTACCTGGAGAACAGTGGGTGTGTGGGAATGTGCGTGAATATGTGCAAAATTCCTACTCAAGATTTCTTCACCAACGAATTCGGGCTTCCTTTAACTATG
upper sequence: GLYMA13G10340.1 (Glycine max), 3'ss of exon 4
lower sequence: PP1S6_190V6.1 (Physcomitrella patens), 3'ss of exon 4
aatagctagtatttattttgaaattcacttacatta-attaaggccgttgtaacaatttcaacattt-------tcccattgtttccttgatatttattcttgtgaa--gGTACCTGGAGAATAGTGGCTGTGTTGGAATGTGTGTCAATATGTGCAAGATTCCTACCCAAGATTTTTTCACTAATGAATTTGGACTTCCGTTAACAATG
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-gtacttgccatttttttccactcttgttttccctctattctgcttatcttgaatctgtcaagtgttgtagaggtggtactaatgacacaatagctgcggatgagaacagATACCTAGAAAATAGTGGATGCGTCGGGATGTGCGTCAATATGTGCAAAATCCCGACCCAGGATTTCTTCACCAATGAATTCGGTCTTCCACTTACTATG
upper sequence: GLYMA13G10340.1 (Glycine max), 3'ss of exon 4
lower sequence: EFJ23359 (Selaginella moellendorffii), 3'ss of exon 4
aatagctagtatttattttgaaattcacttacattaattaaggccgttgtaacaatttcaacattttcccattgtttccttgatatttattcttgtgaagGTACCTGGAGAATAGTGGCTGTGTTGGAATGTGTGTCAATATGTGCAAGATTCCTACCCAAGATTTTTTCACTAATGAATTTGGACTTCCGTTAACAATG
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------------------------------------------------gtga-gatttctacaaagaagagaactaagcatg-taaaaatacgtttccagGTATCTAGAGAACAGCAACTGTGTTGGAATGTGCGTAAATATGTGTAAAATTCCCACCCAGGATTTCTTCACAAATGACTTTGGGTTGCCTCTCACCATG
upper sequence: GLYMA13G10340.1 (Glycine max), 3'ss of exon 4
lower sequence: EFJ25335 (Selaginella moellendorffii), 3'ss of exon 4
aatagctagtatttattttgaaattcacttacattaattaaggccgttgtaacaatttcaacattttcccattgtttccttgatatttattcttgtgaagGTACCTGGAGAATAGTGGCTGTGTTGGAATGTGTGTCAATATGTGCAAGATTCCTACCCAAGATTTTTTCACTAATGAATTTGGACTTCCGTTAACAATG
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------------------------------------------------gtgagatttctacaaagaagagaactaagcatgtaaaactacgtttcc--agGTATCTAGAGAACAGCAATTGTGTTGGAATGTGCGTAAATATGTGTAAAATTCCCACCCAGGATTTCTTCACAAATGACTTTGGGTTGCCTCTCACCATG
upper sequence: GLYMA13G10340.1 (Glycine max), 3'ss of exon 4
lower sequence: EFJ23185 (Selaginella moellendorffii), 3'ss of exon 3
aatagctagtatttattttgaaattcacttacattaattaaggccgttgtaacaatttca-acattttcccattgtttccttgatatttattcttgtgaagGTACCTGGAGAATAGTGGCTGTGTTGGAATGTGTGTCAATATGTGCAAGATTCCTACCCAAGATTTTTTCACTAATGAATTTGGACTTCCGTTAACAATG
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------------------------------------------------gtaagaattctacaaagaagaaaagtgcgcatgtaaaaattgcttttcc--agGTATTTAGAGAACAGCTCCTGTGCTGGAATGTGCGTAAATGTGTGTAAAATTCCCACCCAAGATTTATTCACAAATGACTTTGGACTGCCTCTGACCATG
upper sequence: GLYMA13G10340.1 (Glycine max), 3'ss of exon 4
lower sequence: EFJ25185 (Selaginella moellendorffii), 3'ss of exon 3
aatagctagtatttattttgaaattcacttacattaattaaggccgttgtaacaatttcaacattttcccattgtttccttgatatttattcttgtgaagGTACCTGGAGAATAGTGGCTGTGTTGGAATGTGTGTCAATATGTGCAAGATTCCTACCCAAGATTTTTTCACTAATGAATTTGGACTTCCGTTAACAATG
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---------------------------------gtaag-aaatctacaaagaagaaaactacgcatgtaaaaatgtgttttgcttttgatttcc----agGTATTTAGAGAACAGCTCCTGTGCTGGAATGTGCGTAAATGTGTGTAAAATTCCCACCCAAGATTTATTCACAAATGACTTTGGACTGCCTCTGACCATGMapped 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|22522530|gb|BU081341.1|BU081341EST: GAGATAAATGGAGTGAAGCAAAAAAGTGGCGTGC--ATAAAGAAGTGCAG GTACCTGGAGAATAGTGGCTGTGTTGGAATGTGTGTCAATATGTGCAAGAT
genomic: GAGATAAATGGAGTGAAGCAAAAAAGTGGCGTGCATATAAAGAAGTGCAGgtagatttca ... tcttgtgaagGTACCTGGAGAATAGTGGCTGTGTTGGAATGTGTGTCAATATGTGCAAGAT
EST:
gi|22932678|gb|BU549817.1|BU549817EST: GAGATAAATGGAGTGAAGCAAAAAAGTGGCGTGCATATAAAGAAGTGCAG GTACCTGGAGAATAGTGGCTGTGTTGGAATGTGTGTCAATATGTGCAAGAT
genomic: GAGATAAATGGAGTGAAGCAAAAAAGTGGCGTGCATATAAAGAAGTGCAGgtagatttca ... tcttgtgaagGTACCTGGAGAATAGTGGCTGTGTTGGAATGTGTGTCAATATGTGCAAGAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gttgtaacaatttcaacattttcccattgtttccttgatatttattcttgtgaagGTACCTGGAGAATAGTGGCTGTGTTGGAATGTGTGTCAATATGTGCAAGATTCCTACCCAAGATTTTTTCACTAATGAATTTGGACTTCCGTTAACAATG
tttattctt CT-rich tract
ttgatatttattctt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aatagctagtatttattttgaaattcacttacattaattaaggccgttgtaacaatttcaacattttcccattgtttccttgatatttattcttgtgaagGTACCTGGAGAATAGTGGCTGTGTTGGAATGTGTGTCAATATGTGCAAGATTCCTACCCAAGATTTTTTCACTAATGAATTTGGACTTCCGTTAACAATG
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