Sequence
atgc intronic sequence ATGC exonic sequencegtatctaactttgacttctctttttcagattaataagctcttcctatttctaattttctatgtctagtaatcaatgaatcttcttttgcagATAATTGCCATTAGGGATATCATACGACCTCCCAGAAAGGATGCCTTCAATGATGTTTACATTGTTTATGAATTGATGGACACTGATCTTCATCAGATTA
Basic information
species | Glycine max |
transcript | GLYMA01G43100.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA01G43100.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os10g38950.1 (Oryza sativa), 3'ss of exon 2
--gtatctaactttgacttctctttttcagattaataagctcttcctatttctaattttctat------gtctagtaatcaatg-aatcttcttttgcagATAATTGCCATTAGGGATATCATACGACCTCCCAGAAAGGATGCCTTCAATGATGTTTACATTGTTTATGAATTGATGGACACTGATCTTCATCAGATTA
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ttccttttttttttgttgggcggtcaagagcgtgtgatacatttttgactcacacatttatatcatatagtctgatggtgattttaacactggatcacagATTATTGCCATAAAGGACATAATTCGCCCCCCAAGAAGAGACAACTTTAATGATGTTTACATTGTTTCTGAGTTGATGGATACTGATCTCCATCAGATCA
upper sequence: GLYMA01G43100.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os08g06060.1 (Oryza sativa), 3'ss of exon 2
gtatctaactttgacttctct-----ttttcagattaataagctcttcctatttctaattttctatgt--ctagtaatcaa--tgaatcttcttttgcagATAATTGCCATTAGGGATATCATACGACCTCCCAGAAAGGATGCCTTCAATGATGTTTACATTGTTTATGAATTGATGGACACTGATCTTCATCAGATTA
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gtcttttatcttggcaatactagggattgttagatgattagatagtaacaagaaacaattttttttgtgacttgtgacaaaatctagccatttttcacagGTCATCTCAATAAAGGACATCATACGGCCACCAAGGAGGGAGAACTTCAATGATGTCTACATTGTCTATGAGCTCATGGACACTGATCTTCACCACCTTC
upper sequence: GLYMA01G43100.1 (Glycine max), 3'ss of exon 2
lower sequence: AT4G11330.1 (Arabidopsis thaliana), 3'ss of exon 2
gtatctaactttgacttctctttttcagattaataagctcttcctatttctaattttctatgtctagtaatcaatg-aatctt--cttttgcagATAATTGCCATTAGGGATATCATACGACCTCCCAGAAAGGATGCCTTCAATGATGTTTACATTGTTTATGAATTGATGGACACTGATCTTCATCAGATTA
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-----------------------gtaagttttgtactctattttcgcggtaaacgattagagtttc-tagctaatgtggtcttgacttgtacagGTTGTTGTTATAAAAGATATCATTAGACCACCAAAGAAGGAAGATTTCGTTGATGTTTATATAGTTTTTGAGTTAATGGATACTGATCTTCATCAGATTA
upper sequence: GLYMA01G43100.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv02s0025g00270.t01 (Vitis vinifera), 3'ss of exon 2
---------gtatctaactttgacttctctttttcagat-taataagctcttcctatttctaattttctatgtctagtaatcaatgaatcttcttttgcagATAATTGCCATTAGGGATATCATACGACCTCCCAGAAAGGATGCCTTCAATGATGTTTACATTGTTTATGAATTGATGGACACTGATCTTCATCAGATTA
||| | | || | | ||| | | || | || || | || | || | | || | | | ||| | |||||||| | ||| || |||||||| || | ||||| | ||||||||||| ||||||||||||||||||||||||||||||||||||||||| |
tttgccttgttatgtttgtctgggagtgtgtgtacagttatcatgacctattttttcgcctgaaacatggaatc-attgcccagttctttccttgccacagGTTATTGCCATCAAGGACATTATACGACCACCAAAGAAGGAAACTTTCAATGATGTCTACATTGTTTATGAATTGATGGACACTGATCTTCATCAGATCAMapped 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|151408614|gb|EV278422.1|EV278422EST: AACGAACTTTGAGGGAAATCAAGCTCCTTCGCCACATGGACCATGAAAAT ATAATTGCCATTAGGGATATCATACGACCTCCCAGAAAGGATGCCTTCAAT
genomic: AACGAACTTTGAGGGAAATCAAGCTCCTTCGCCACATGGACCATGAAAATgtatctaact ... tcttttgcagATAATTGCCATTAGGGATATCATACGACCTCCCAGAAAGGATGCCTTCAAT
EST:
gi|18712582|gb|BM522669.1|BM522669EST: AACGAACTTTGAGGGAAATCAAGCTCCTTCGCCACATGGACCATGAAAAT ATAATTGCCATTAGGGATATCATACGACCTCCCAGAAAGGATGCCTTCAAT
genomic: AACGAACTTTGAGGGAAATCAAGCTCCTTCGCCACATGGACCATGAAAATgtatctaact ... tcttttgcagATAATTGCCATTAGGGATATCATACGACCTCCCAGAAAGGATGCCTTCAAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gctcttcctatttctaattttctatgtctagtaatcaatgaatcttcttttgcagATAATTGCCATTAGGGATATCATACGACCTCCCAGAAAGGATGCCTTCAATGATGTTTACATTGTTTATGAATTGATGGACACTGATCTTCATCAGATTA
ttctaat putative branch site (score: 2)
tcttcttttgc putative PPT
tatttctaattttcta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatctaactttgacttctctttttcagattaataagctcttcctatttctaattttctatgtctagtaatcaatgaatcttcttttgcagATAATTGCCATTAGGGATATCATACGACCTCCCAGAAAGGATGCCTTCAATGATGTTTACATTGTTTATGAATTGATGGACACTGATCTTCATCAGATTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA