Sequence
atgc intronic sequence ATGC exonic sequence...acttctctcattgtctgtattggtagatacaatacaattttttttctcttgatttgccctctttttcctttctttcctttttcacttcttcattttgcagATTGAACCATATCCAAGTGGAAATTTGCCTCCTGGTTTTGATCCAAGTACTTGCCGCAGTGT
Basic information
species | Glycine max |
transcript | GLYMA07G04640.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA07G04640.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os07g42380.1 (Oryza sativa), 3'ss of exon 1
acttctctcattgtctgtattggtagatacaatacaattttttttctcttgatttgccctctttttcctttctttcctttttcacttcttcatttt-gcagATTGAACCATATCCAAGTGGAAATTTGCCTCCTGGTTTTGATCCAAGTACTTGCCGCAGTGT
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-tagtttgcatgtaccaggcttctttttgctaaggcgtttcctattatttgtagatttttatttcttctttctttgtttttttacatttttatttttgcagATAGAGCCAATCCTTACTGGAAATCTGCCTCCTGGCTTTGATACGAGTACATGCCGCAGTGT
upper sequence: GLYMA07G04640.1 (Glycine max), 3'ss of exon 1
lower sequence: AT1G17370.2 (Arabidopsis thaliana), 3'ss of exon 1
acttctctcattgtctgtattggtagatacaatacaattttttttctcttgatttgccctctttttcctttctttcctttttcacttctt--cattttgcagATTGAACCATATCCAAGTGGAAATTTGCCTCCTGGTTTTGATCCAAGTACTTGCCGCAGTGT
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--ttatcgtagcttagttgctgagactttaggaagtaaagttttttcctttatttctttctttttcattttctttggcttcctatttttttcctttttgcagATAGAACCAATCCCAAGTGGAAATCTCCCCCCTGGTTTTGATCCAAGTACTTGCCGCAGTGT
upper sequence: GLYMA07G04640.1 (Glycine max), 3'ss of exon 1
lower sequence: AT3G14100.1 (Arabidopsis thaliana), 3'ss of exon 1
acttctctcattgtctgtattggtagatacaatacaattttttttctcttgatttgccctctttttcctttctttcctttttcacttcttcattttgcagATTGAACCATATCCAAGTGGAAATTTGCCTCCTGGTTTTGATCCAAGTACTTGCCGCAGTGT
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aattgagctgatatttaccttctcgtgcttttctaatggggatagaaaagaaattgcaatccttttcattttctttctttcttacttttggcaattgcagTTAGAGCCTGTTCCAAGTGGAAACCTTCCTCCTGGTTTTGATCCCAGTACTTGCCGTAGCGT
upper sequence: GLYMA07G04640.1 (Glycine max), 3'ss of exon 1
lower sequence: AT1G54080.2 (Arabidopsis thaliana), 3'ss of exon 1
acttctctcattgtctgtattggtagatacaatacaattttttttctcttgatt-tgccctctttttcctttctttcctttttcacttc---ttcattttgcagATTGAACCATATCCAAGTGGAAATTTGCCTCCTGGTTTTGATCCAAGTACTTGCCGCAGTGT
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----tggtaatggtagatgttcgtgtagaaaaggagtggttttggtacttgtttctgcaatcatctcttaatgttttgtttatggttttgcatttttgttgcagATGGAGCCTTTACCAAGTGGAAACCTTCCTCCTGGTTTTGATCCAACTACTTGCCGTAGTGT
upper sequence: GLYMA07G04640.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv09s0002g00880.t01 (Vitis vinifera), 3'ss of exon 1
acttctctcattgtctgtattggtagatacaatacaattttttttctcttgatttgccctctttttcctttctttcctttttcacttcttcattttgcagATTGAACCATATCCAAGTGGAAATTTGCCTCCTGGTTTTGATCCAAGTACTTGCCGCAGTGT
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cttgatgtgggtagatgatttaggggcttgtctttttatattatttttgttctttttctttcttttattttcttttcttttttacatttttattttgcagATAGAGCCAATACCAAGTGGAAATCTGCCTCCTGGTTTTGATTCAAGTACATGCCGCAGTGTMapped 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|7146716|gb|AW508638.1|AW508638EST: CCACCCTGGCCTCCTTGCTCCTCCTCAG ATTGAACCATATCCAAGTGGAAATTTGCCTCCTGGTTTTGATCCAAGTACT
genomic: CCACCCTGGCCTCCTTGCTCCTCCTCAGgttcggaccc ... cattttgcagATTGAACCATATCCAAGTGGAAATTTGCCTCCTGGTTTTGATCCAAGTACT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctcttgatttgccctctttttcctttctttcctttttcacttcttcattttgcagATTGAACCATATCCAAGTGGAAATTTGCCTCCTGGTTTTGATCCAAGTACTTGCCGCAGTGT
tcttgat putative branch site (score: 4)
tttgccctctttttcc CT-rich tract
ttcatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
acttctctcattgtctgtattggtagatacaatacaattttttttctcttgatttgccctctttttcctttctttcctttttcacttcttcattttgcagATTGAACCATATCCAAGTGGAAATTTGCCTCCTGGTTTTGATCCAAGTACTTGCCGCAGTGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - ttgtctg
- - - - - - - - - - - - - - -caataca