Sequence
atgc intronic sequence ATGC exonic sequence...ggcataaaaaaaggtcttctgggtctgttcattatccaatttcattatccagtgtcgtaaaccgtcccatagttgagcgattggtctgattgtaatgcagGTACTGTGGTAGATTCTAAGATCTGTCATCCTTCGGAATTCGACTTCTACTTGTGCAGTCATGCAGGAATTCAG
Basic information
species | Glycine max |
transcript | GLYMA06G23920.1 |
intron # | 18 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA06G23920.1 (Glycine max), 3'ss of exon 18
lower sequence: PP1S173_134V6.1 (Physcomitrella patens), 3'ss of exon 16
ggcataaaaaaaggtcttctgggtctg---ttca-ttatccaatttcattatcc-agtgtcgtaaacc-gtcccatagttgagcgattggtctgattgtaatgcagGTACTGTGGTAGATTCTAAGATCTGTCATCCTTCGGAATTCGACTTCTACTTGTGCAGTCATGCAGGAATTCAG
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---accaggaattatttctttaatgtggggtgcagtttttttttttcaacattctaatcttatgcatttaatctaaatgtatgtgacaaactt---tgcatactagGTACGGTTGTGGACTCTACAATCTGTCACCCTACGGAATTCGACTTCTATCTTTGCAGTCACGCTGGAATTCAG
upper sequence: GLYMA06G23920.1 (Glycine max), 3'ss of exon 18
lower sequence: EFJ15357 (Selaginella moellendorffii), 3'ss of exon 19
ggcataaaaaaaggtcttctgggtctgttcattatccaatttcattatccagtgtcgtaaaccgtcccata-gttgagcgattggtctgattgtaatgcagGTACTGTGGTAGATTCTAAGATCTGTCATCCTTCGGAATTCGACTTCTACTTGTGCAGTCATGCAGGAATTCAG
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-----------------------------------------------gtttgtaggaaagtttgttcaatgtgcttcacaactaaaacgcttttgct--agGTACTGTGGTGGATACGAAGATCTGTCATCCCACGGAATTTGATTTCTACCTCTGCAGTCACGCTGGAATACAG
upper sequence: GLYMA06G23920.1 (Glycine max), 3'ss of exon 18
lower sequence: EFJ24991 (Selaginella moellendorffii), 3'ss of exon 19
ggcataaaaaaaggtcttctgggtctgttcattatccaatttcattatccagtgtcgtaaaccgtcccata-gttgagcgattggtctgattgtaatgcagGTACTGTGGTAGATTCTAAGATCTGTCATCCTTCGGAATTCGACTTCTACTTGTGCAGTCATGCAGGAATTCAG
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-----------------------------------------------gtttgtagcaaagtttgttcaatgtgcttgacaactaaaacgcttttgct--agGTACTGTGGTGGATACGAAGATCTGTCATCCCACGGAATTTGATTTCTACCTCTGCAGTCACGCTGGAATACAGMapped 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|208092068|gb|GD890967.1|GD890967EST: CAATCATGATGACAGAAATAGCACTGATAAGAGTGGGAATATCTTACCTG GTACTGTGGTAGATTCTAAGATCTGTCATCCTTCGGAATTCGACTTCTACT
genomic: CAATCATGATGACAGAAATAGCACTGATAAGAGTGGGAATATCTTACCTGgtaaggtttt ... tgtaatgcagGTACTGTGGTAGATTCTAAGATCTGTCATCCTTCGGAATTCGACTTCTACT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatccagtgtcgtaaaccgtcccatagttgagcgattggtctgattgtaatgcagGTACTGTGGTAGATTCTAAGATCTGTCATCCTTCGGAATTCGACTTCTACTTGTGCAGTCATGCAGGAATTCAG
gtctgat putative branch site (score: 4)
attgtaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ggcataaaaaaaggtcttctgggtctgttcattatccaatttcattatccagtgtcgtaaaccgtcccatagttgagcgattggtctgattgtaatgcagGTACTGTGGTAGATTCTAAGATCTGTCATCCTTCGGAATTCGACTTCTACTTGTGCAGTCATGCAGGAATTCAG
- - -aaaaaaa
- - - - - - - tcttctg
- - - - - - - - - - - gtctgtt
- - - - - - - - - - - - - - - - - - - - - - - - ccagtgt