Sequence
atgc intronic sequence ATGC exonic sequence...tatatgattctgctggctcagcactcagcatcaaacctgaattttttatgaaagggattttaaggataacctacatatacttgttttttggtcatttcagGCTTGGATGGCTTATTCGTTTCATTAGCCATTCAGTGATATCTGGCTTTACAACCGCTTCAGCTATTGTCATTGGTTTATCTCAAGCAAAATACTTCTTG
Basic information
species | Glycine max |
transcript | GLYMA02G10590.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA02G10590.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os09g06499.2 (Oryza sativa), 3'ss of exon 4
tatatgattctgctggctcagcactcagcatcaaacctgaattttttatgaaagg---gattttaaggataacctacatatacttgttttttggtc--attt-cagGCTTGGATGGCTTATTCGTTTCATTAGCCATTCAGTGATATCTGGCTTTACAACCGCTTCAGCTATTGTCATTGGTTTATCTCAAGCAAAATACTTCTTG
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------aaactatcttctaagttttagggggcaaaaccaaaatcatttagatatgcttaatttttactatagttatgttgccaatgatatgtgttcttatttacagGCTCGGTTGGCTTATTCGATTTATTAGCCATTCTGTCATATCTGGCTTCACTACTGCTTCAGCTATTGTAATTGGTCTGTCACAGATCAAGTATTTCTTG
upper sequence: GLYMA02G10590.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G068212_T01 (Zea mays), 3'ss of exon 3
tatatgattctgctggctcagcactcagcatcaaacctgaattttttatgaaagggattt-taaggataacctaca--tatacttgttttttggtcatttcagGCTTGGATGGCTTATTCGTTTCATTAGCCATTCAGTGATATCTGGCTTTACAACCGCTTCAGCTATTGTCATTGGTTTATCTCAAGCAAAATACTTCTTG
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---aatattttcttaatttgatagtagaacaaatacacaatcttggtatgcttgttctctgtgagaatgtgtaaccatttcatatgttttattttgtatacagGCTTGGTTGGCTCATTCGTTTCATTAGCCATTCTGTAATATCTGGGTTCACTACAGCTTCAGCCATTGTTATTGGTTTATCCCAGATAAAGTATTTCTTA
upper sequence: GLYMA02G10590.1 (Glycine max), 3'ss of exon 3
lower sequence: AT5G13550.1 (Arabidopsis thaliana), 3'ss of exon 3
---------------------------------------------------------------tatatgattctgctggctcagcactcagcatc----aaacctgaattttttatgaaagggattttaaggataacctacatatacttgttttttggt--catttcagGCTTGGATGGCTTATTCGTTTCATTAGCCATTCAGTGATATCTGGCTTTACAACCGCTTCAGCTATTGTCATTGGTTTATCTCAAGCAAAATACTTCTTG
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gtaatactactatttttggttagaattcagataaggaaaacgtttattatcttgactgctacttatatagct-tgcctgtgtagtaactgttatccgttaaagcagaagtcttct----aattattgttgtgtcatgttgcgtctcccttgtttgtgatttcaatccagGCTTGGATGGCTTATTCGTTTCATTAGTCACTCAGTCATATCTGGATTTACAAGTGCTTCGGCCATTGTGATTGGGTTATCTCAAATAAAATATTTCCTG
upper sequence: GLYMA02G10590.1 (Glycine max), 3'ss of exon 3
lower sequence: AT3G12520.1 (Arabidopsis thaliana), 3'ss of exon 3
-tatatgattctgctggctcagcactcagcatcaaacctgaattttttatgaaagggattttaaggataacctacatatacttgttttttggtcatttcagGCTTGGATGGCTTATTCGTTTCATTAGCCATTCAGTGATATCTGGCTTTACAACCGCTTCAGCTATTGTCATTGGTTTATCTCAAGCAAAATACTTCTTG
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gtat-ttatagtcttctctttgtttgtgcaaggaatcctgtattttttgtag-------tgttagaacaagttg--ttcgtttgtttttt---caacccagGCTTGGATGGCTTATTCGTTTCATAAGTCACTCAGTCATTTCTGGATTTACAACTGCTTCAGCTGTTGTAATTGGGTTATCCCAACTGAAATACTTCCTA
upper sequence: GLYMA02G10590.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv13s0019g00010.t01 (Vitis vinifera), 3'ss of exon 3
-----ta-tatgattctgctggctcagcactcagcatcaaacctgaattttttatgaaagggattttaaggataacctacatatacttgttttttggtcatttcagGCTTGGATGGCTTATTCGTTTCATTAGCCATTCAGTGATATCTGGCTTTACAACCGCTTCAGCTATTGTCATTGGTTTATCTCAAGCAAAATACTTCTTG
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atttgtactagaaatttgcatattttctatcttttaattattctcaaatttctgtgatgtcatttagaaagaaaatg---atgcacccttttttc---ctttctagGCTTGGATGGCTTATTCGTTTCATCAGTCACTCTGTGATTTCTGGGTTTACGACAGCTTCAGCAATTGTGATTGCCTTATCTCAAGCAAAGTATTTCCTGMapped 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|254320748|gb|GR827197.1|GR827197EST: TTACTGTCCCTTATGGTTGGGATAATGGAGTGCATAATGGGACTCTTGAG GCTTGGATGGCTTATTCGTTTCATTAGCCATTCAGTGATATCTGGCTTTAC
genomic: TTACTGTCCCTTATGGTTGGGATAATGGAGTGCATAATGGGACTCTTGAGgtattttcat ... gtcatttcagGCTTGGATGGCTTATTCGTTTCATTAGCCATTCAGTGATATCTGGCTTTAC
EST:
gi|254333563|gb|GR848481.1|GR848481EST: GTGCATAATGGGACTCTTGAG GCTTGGATGGCTTATTCGTTTCATTAGCCATTCAGTGATATCTGGCTTTAC
genomic: GTGCATAATGGGACTCTTGAGgtattttcat ... gtcatttcagGCTTGGATGGCTTATTCGTTTCATTAGCCATTCAGTGATATCTGGCTTTAC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttatgaaagggattttaaggataacctacatatacttgttttttggtcatttcagGCTTGGATGGCTTATTCGTTTCATTAGCCATTCAGTGATATCTGGCTTTACAACCGCTTCAGCTATTGTCATTGGTTTATCTCAAGCAAAATACTTCTTG
ggataac putative branch site (score: 3)
tcatttc putative PPT
atatacttgtttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tatatgattctgctggctcagcactcagcatcaaacctgaattttttatgaaagggattttaaggataacctacatatacttgttttttggtcatttcagGCTTGGATGGCTTATTCGTTTCATTAGCCATTCAGTGATATCTGGCTTTACAACCGCTTCAGCTATTGTCATTGGTTTATCTCAAGCAAAATACTTCTTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA