Sequence
atgc intronic sequence ATGC exonic sequence...ccttttgatggtttggtttagtatttccagaccttagtatcatttttttgttgcaattgtatattgtggttacattaatttctgtgaatttcaactgcagACAATGACAACTTTCATGCCACCTCCACCAGCTGCGACATTTCTTGCATTTCATCCTCAAGACAATAATATTATTGCTATTGGCATGGAGGACTCTTCCA
Basic information
species | Glycine max |
transcript | GLYMA17G12110.1 |
intron # | 21 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA17G12110.2 (Glycine max), 3'ss of exon 21
lower sequence: Vv11s0016g05620.t01 (Vitis vinifera), 3'ss of exon 21
ccttttgatggtttggtttagtatttccagaccttagtatcatttttttgttgcaattgtatattgtggttacattaatttctgtgaatttcaactgcagACAATGACAACTTTCATGCCACCTCCACCAGCTGCGACATTTCTTGCATTTCATCCTCAAGACAATAATATTATTGCTATTGGCATGGAGGACTCTTCCA
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nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnagACCATGACAACATTTATGCCCCCACCACCAGCAGCAACATTTTTGGCATTCCATCCTCAAGACAATAATATCATTGCCATAGGCATGGAGGACTCTTCTA
upper sequence: GLYMA17G12110.2 (Glycine max), 3'ss of exon 21
lower sequence: PP1S99_260V6.1 (Physcomitrella patens), 3'ss of exon 20
-------------------------ccttttgatggtttggtttagtatttcca-gaccttagtatcattttt-----ttgttgcaattgtatattgtggttacattaattt-ctgtgaatttcaactgcagACAATGACAACTTTCATGCCACCTCCACCAGCTGCGACATTTCTTGCATTTCATCCTCAAGACAATAATATTATTGCTATTGGCATGGAGGACTCTTCCA
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gtaaagtccgcgaatcatgaggagtctattttattctttgttctaataatatggtgagaagcgttttgtttttggtaattttgacagttgtcaatttttattctgacgcttttcttcggattttgact-cagGTCATGACGACATTCATGCCACCACCTCCAGCAGCTACTTTTCTTGCATTTCATCCACAAGACAACAATATCATTGCTATCGGAATGGAAGATTCGACAA
upper sequence: GLYMA17G12110.2 (Glycine max), 3'ss of exon 21
lower sequence: EFJ17248 (Selaginella moellendorffii), 3'ss of exon 20
ccttttgatggtttggtttagtatttccagaccttagtatcatttttttgttgcaattgtatattgtggttacattaatttctgtgaatttcaactgcagACAATGACAACTTTCATGCCACCTCCACCAGCTGCGACATTTCTTGCATTTCATCCTCAAGACAATAATATTATTGCTATTGGCATGGAGGACTCTTCCA
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------------------------------------gtat-gccgatttgttgct-ttttctccagtgatgaaaccattgtc---gaa--------acagATTATGACACAATTCATGCCGCCTCCGCCAGCAGCAACATTCCTCGCTTTTCATCCTCAGGATAATAATTTTATTGCTATCGGTATGGAGGATTCGGCTA
upper sequence: GLYMA17G12110.2 (Glycine max), 3'ss of exon 21
lower sequence: EFJ30926 (Selaginella moellendorffii), 3'ss of exon 20
ccttttgatggtttggtttagtatttccagaccttagtatcatttttttgttgcaattgtatattgtggttacattaatttctgtgaatttcaactgcagACAATGACAACTTTCATGCCACCTCCACCAGCTGCGACATTTCTTGCATTTCATCCTCAAGACAATAATATTATTGCTATTGGCATGGAGGACTCTTCCA
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------------------------------------gtat-gccgatttgttgctctt-tctccagtgatgaaaccattgtc---gaa--------acagATTATGACACAATTCATGCCGCCTCCGCCAGCAGCAACATTCCTCGCTTTTCATCCTCAGGATAATAATTTTATTGCTATCGGTATGGAGGATTCGGTTA
upper sequence: GLYMA17G12110.2 (Glycine max), 3'ss of exon 21
lower sequence: EFJ32018 (Selaginella moellendorffii), 3'ss of exon 20
ccttttgatggtttggtttagtatttccagaccttagtatcatttttttgttgcaattgtatattgtggttacattaatttctgt--gaattt--caactgcagACAATGACAACTTTCATGCCACCTCCACCAGCTGCGACATTTCTTGCATTTCATCCTCAAGACAATAATATTATTGCTATTGGCATGGAGGACTCTTCCA
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------------------------------------------------------gtatgcacatttttccttc-ttgaccggtgtaagaacttgccatgtccagGTGATGACAGCATTCATGCCACCGCCACCAGCAGCAACGTTCCTGGCTTTTCACCCTCAAGACAACAATATCATAGCGATTGGAATGGAAGATTCTACAAMapped 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|208162409|gb|GD963140.1|GD963140EST: AAAATTTCTCTATTCAATATGATGACATTTAAG ACAATGACAACTTTCATGCCACCTCCACCAGCTGCTACATTTCTTGCATTT
genomic: AAAATTTCTCTATTCAATATGATGACATTTAAGgtatgtcgtg ... tcaactgcagACAATGACAACTTTCATGCCACCTCCACCAGCTGCGACATTTCTTGCATTT
EST:
gi|302141350|gb|HO212226.1|HO212226EST: AAATTTCTCTATTCAATATGATGACATTTAAG ACAATGACAACTTTCATGCCACCTCCACCAGCTGTGACATTTCTTGCATTT
genomic: AAATTTCTCTATTCAATATGATGACATTTAAGgtatgtcgtg ... tcaactgcagACAATGACAACTTTCATGCCACCTCCACCAGCTGCGACATTTCTTGCATTT
EST:
gi|254332906|gb|GR850156.1|GR850156EST: TGTCTGCTTCAGGGGGGAAAATTTCTCTATTCAATATGATGACATTTAAG ACAATGACAACTTTCATGCCACCTCCACCAGCTGCGACATTTCTTGCATTT
genomic: TGTCTGCTTCAGGGGGGAAAATTTCTCTATTCAATATGATGACATTTAAGgtatgtcgtg ... tcaactgcagACAATGACAACTTTCATGCCACCTCCACCAGCTGCGACATTTCTTGCATTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttgttgcaattgtatattgtggttacattaatttctgtgaatttcaactgcagACAATGACAACTTTCATGCCACCTCCACCAGCTGCGACATTTCTTGCATTTCATCCTCAAGACAATAATATTATTGCTATTGGCATGGAGGACTCTTCCA
cattaat putative branch site (score: 3)
ttacattaatttct 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ccttttgatggtttggtttagtatttccagaccttagtatcatttttttgttgcaattgtatattgtggttacattaatttctgtgaatttcaactgcagACAATGACAACTTTCATGCCACCTCCACCAGCTGCGACATTTCTTGCATTTCATCCTCAAGACAATAATATTATTGCTATTGGCATGGAGGACTCTTCCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA