Sequence
atgc intronic sequence ATGC exonic sequence...ctatagttaggagaattcaaatttttcatttgtgcaataccagtatataaactttgatctgtagggtgtgaaatgaatcgatgtgtatttttctttgcagTTTGCTATCATGGCTGGGTCGGCACCCGAAGGATCACAATTCGATGCTCGTCAATATGATGCTAAGATGAATGAGTT
Basic information
species | Glycine max |
transcript | GLYMA06G05580.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA06G05580.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S383_1V6.3 (Physcomitrella patens), 3'ss of exon 1
ctatagttaggagaattcaaattttt-catttgtgcaataccagtatataaactttgatctgtagggtgtgaaatgaatcgatgtgtatttttctttg--------cagTTTGCTATCATGGCTGGGTCGGCACCCGAAGGATCACAATTCGATGCTCGTCAATATGATGCTAAGATGAATGAGTT
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----ggttctga---cgcaggttgtcacattcttgtaataggtgttattcagcgtt--ttaccagggtgtcggagctgaccatgcttttgtttctttgaaatacagcagCGAAGTAGTATGGCTGGATCTGCACCCGAAGGGTCTCAGTTCGATGCTCGCCAATATGACGCCAAGATGGAGAATAT
upper sequence: GLYMA06G05580.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S383_1V6.1 (Physcomitrella patens), 3'ss of exon 1
ctatagttaggagaattcaaattttt-catttgtgcaataccagtatataaactttgatctgtagggtgtgaaatgaatcgatgtgtatttttctttg--------cagTTTGCTATCATGGCTGGGTCGGCACCCGAAGGATCACAATTCGATGCTCGTCAATATGATGCTAAGATGAATGAGTT
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-catggttctga---cgcaggttgtcacattcttgtaataggtgttattcagcgtt--ttaccagggtgtcggagctgaccatgcttttgtttctttgaaatacagCAGCGAAGTAGTATGGCTGGATCTGCACCCGAAGGGTCTCAGTTCGATGCTCGCCAATATGACGCCAAGATGGAGAATATMapped 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|254324362|gb|GR833787.1|GR833787EST: CACTATTTTTCATCATTCGATAATTCGAACTTCCACCATCTTCCCCAAAG TTTGCTATCATGGCTGGGTCGGCACCCGAAGGATCACAATTCGATGCTCGT
genomic: CACTATTTTTCATCATTCGATAATTCGAACTTCCACCATCTTCCCCAAAGgtttgatttc ... ttctttgcagTTTGCTATCATGGCTGGGTCGGCACCCGAAGGATCACAATTCGATGCTCGT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tataaactttgatctgtagggtgtgaaatgaatcgatgtgtatttttctttgcagTTTGCTATCATGGCTGGGTCGGCACCCGAAGGATCACAATTCGATGCTCGTCAATATGATGCTAAGATGAATGAGTT
ctttgat putative branch site (score: 5)
tatttttcttt putative PPT
tatttttcttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctatagttaggagaattcaaatttttcatttgtgcaataccagtatataaactttgatctgtagggtgtgaaatgaatcgatgtgtatttttctttgcagTTTGCTATCATGGCTGGGTCGGCACCCGAAGGATCACAATTCGATGCTCGTCAATATGATGCTAAGATGAATGAGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - tttgtgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gggtgtg