Sequence
atgc intronic sequence ATGC exonic sequencegtaagttgtttcaatgcagccatagcttcattgaataattgtttatatcatatttaagcagcacaaatatgctccatgggaagtctattggctgttgcacacacacatagcaaaactcactagctcataaatatggttttctcttatgtttagGTCTGGTTCTGTTTGCTTAGATGTTATTAGCCAGACTTGGAGTCCAATGTTTG
Basic information
species | Glycine max |
transcript | GLYMA08G01940.4 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G01940.3 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os10g31000.1 (Oryza sativa), 3'ss of exon 3
gtaagttgtttcaatgcagccatagcttcattgaataattgtttatatcatatttaagcagcacaaatatgctccatgggaagtctattggctgttgcacacacacatagcaaaactcactagctcataaatatggttttctcttatgtttagGTCTGGTTCTGTTTGCTTAGATGTTATTAGCCAGACTTGGAGTCCAATGTTTG
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-------------------------------------------------gtgaggatttgatgtccatacccttttctggaa--tgattgaagcttgtgtaatcaattgttg---ctgacctgct------tttgttggacttgaaaatgtagGTCTGGTTCTGTGTGTTTGGATGTCATTAACCAGACGTGGAGCCCAATGTTTG
upper sequence: GLYMA08G01940.3 (Glycine max), 3'ss of exon 3
lower sequence: AT1G63800.1 (Arabidopsis thaliana), 3'ss of exon 3
gtaagttgtttcaatgcagccatagcttcattgaataattgtttatatcatatttaagcagcacaa-atatgctccatgggaagtctattggctgttgcacacacacatagcaaaactcactagctcataaatatggttttctcttatgtttagGTCTGGTTCTGTTTGCTTAGATGTTATTAGCCAGACTTGGAGTCCAATGTTTG
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-----------------------------------------------gtgagttcaatcgaatcagtagatcttttggaggagtgattatgttccttctccaaatcttgagtggtgcttatttgttatccctctttgtatgtggttatg--cagGTCAGGTTCTGTTTGTCTAGATGTTATTAACCAGACCTGGAGCCCGATGTTCG
upper sequence: GLYMA08G01940.3 (Glycine max), 3'ss of exon 3
lower sequence: AT5G41340.1 (Arabidopsis thaliana), 3'ss of exon 3
gtaagttgtttcaatgcagccatagcttcattgaataattgtttatatcatatttaagcagcacaaatatgctccatgggaagtctattggctgttgcacacacacatagcaaaactcactagctcataaatatggttttctct-tatgtttagGTCTGGTTCTGTTTGCTTAGATGTTATTAGCCAGACTTGGAGTCCAATGTTTG
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--------------------------------------------------------------gtaagtct-ttttaaattcaatccactagatgttttggatcaatttat-----ttcaatctttttcatctttggtctcctttgtttatgcagGTCGGGTTCTGTTTGTTTAGATGTGATTAACCAAACTTGGAGTCCTATGTTCGMapped 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|192294461|gb|FG987390.1|FG987390EST: CCATCTATTGGCCTTGTCAACAAAATTTTCCATCCTAATGTGGATGAGAT GTCTGGTTCTGTTTGCTTAGATGTTATTAGCCAGACTTGGAGTCCAATGTT
genomic: CCATCTATTGGCTTTGTCAACAAAATTTTCCATCCTAATGTGGATGAGATgtaagttgtt ... ttatgtttagGTCTGGTTCTGTTTGCTTAGATGTTATTAGCCAGACTTGGAGTCCAATGTT
EST:
gi|298163300|gb|HO012033.1|HO012033EST: CCATCTATTGGCTTTGTCAACAAAATTTTCCATCCTAATGTGGATGAGAT GTCTGGTTCTGTTTGCTTAGATGTTATTAGCCAGACTTGGAGTCCAATGTT
genomic: CCATCTATTGGCTTTGTCAACAAAATTTTCCATCCTAATGTGGATGAGATgtaagttgtt ... ttatgtttagGTCTGGTTCTGTTTGCTTAGATGTTATTAGCCAGACTTGGAGTCCAATGTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acacacacatagcaaaactcactagctcataaatatggttttctcttatgtttagGTCTGGTTCTGTTTGCTTAGATGTTATTAGCCAGACTTGGAGTCCAATGTTTG
aactcac putative branch site (score: 2)
ttttctcttatgttt putative PPT
ataaatatggtttt 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 |
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagttgtttcaatgcagccatagcttcattgaataattgtttatatcatatttaagcagcacaaatatgctccatgggaagtctattggctgttgcacacacacatagcaaaactcactagctcataaatatggttttctcttatgtttagGTCTGGTTCTGTTTGCTTAGATGTTATTAGCCAGACTTGGAGTCCAATGTTTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG