Sequence
atgc intronic sequence ATGC exonic sequence...gaaatgcgatttgtttgattagattagttgagaggagggtggataattttacttttaggaactctttttttttctgtcttcttacatttttattttgcagATAGAGCCTATCTTGAGTGGAAATCTGCCACCTGGCTTTGATTCGAGTTCATGCCGCAGTGT
Basic information
species | Glycine max |
transcript | GLYMA17G05530.4 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA17G05530.4 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os07g42380.1 (Oryza sativa), 3'ss of exon 1
gaaatgcgatttgtttg-attagattagttgagaggagggtggataattttacttttagga----actctttttttttctgtcttcttacatttttatttt-gcagATAGAGCCTATCTTGAGTGGAAATCTGCCACCTGGCTTTGATTCGAGTTCATGCCGCAGTGT
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------tagtttgcatgtaccaggcttctttttgctaaggcgtttcctattatttgtagatttttatttcttctttctttgtttttttacatttttatttttgcagATAGAGCCAATCCTTACTGGAAATCTGCCTCCTGGCTTTGATACGAGTACATGCCGCAGTGT
upper sequence: GLYMA17G05530.4 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G008611_T01 (Zea mays), 3'ss of exon 2
gaaatgcgatttgtttgattagattagttgagaggag-ggtggataattttacttttaggaactcttttttttt---ctgtcttcttacatttttat---tttgcagATAGAGCCTATCTTGAGTGGAAATCTGCCACCTGGCTTTGATTCGAGTTCATGCCGCAGTGT
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-------tttttctttatttaagtcaaatgcgaactgcgatatgaaatcatagatgttatctctgttcttcatagaaccttttgcttacacttgtatgtctttgcagATAGAGCCCATAGTCAGTGGAAACCTGCCTCCTGGGTTTGATTCAAGTACATGCCGCAGCGT
upper sequence: GLYMA17G05530.4 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM5G835213_T02 (Zea mays), 3'ss of exon 1
gaaatgcgatttgtttgattagattagttgagaggagggtggataattttacttttaggaactcttttttttt-----ctgtcttcttacatttttat---tttgcagATAGAGCCTATCTTGAGTGGAAATCTGCCACCTGGCTTTGATTCGAGTTCATGCCGCAGTGT
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-------gttttcttcatttaagacaaatgcgaactgcgtt-atgaaatcatagatgttatctctgttcttcatagaaccttttgcttacacttgtatgtctttgcagATAGAGCCCATAGTCAGTGGAAACCTGCCTCCTGGGTTTGATTCAAGTACATGCCGCAGCGT
upper sequence: GLYMA17G05530.4 (Glycine max), 3'ss of exon 2
lower sequence: Vv11s0016g00700.t01 (Vitis vinifera), 3'ss of exon 1
gaaatgcgatttgtttgattagattagttgagaggagggtggataattttacttttaggaactctttttttt---tctgtcttcttacatttttattttgcagATAGAGCCTATCTTGAGTGGAAATCTGCCACCTGGCTTTGATTCGAGTTCATGCCGCAGTGT
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gtgtctttatatatcta--tgaaatgctctcagtgagtgttgata-ttttatttctaggatttttttttcttctttctattttttcacatttttattttgcagATAGAGCCTATCTTGAGTGGAAATCTGCCTCCTGGGTTTGATTCAAGTACATGCCGCAGTGTMapped 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|11274392|gb|BF324745.1|BF324745EST: TGATGCAACCATCTCTCTACCACCACCCTGCTCTACTTACTCCTCCTCAG ATAGAGCCTATCTTGAGTGGAAATCTGCCACCTGGCTTTGATTCGAGTTCA
genomic: TGATGCAACCATCTCTCTACCACCACCCTGCTCTACTTACTCCTCCTCAGgttcctcttt ... tattttgcagATAGAGCCTATCTTGAGTGGAAATCTGCCACCTGGCTTTGATTCGAGTTCA
EST:
gi|14126550|gb|BG790988.1|BG790988EST: TGATGCAACCATCTCTCTACCACCACCCTGCTCTACTTACTCCTCCTCAG ATAGAGCCTATCTTGAGTGGAAATCTGCCACCTGGCTTTGATTCGAGTTCA
genomic: TGATGCAACCATCTCTCTACCACCACCCTGCTCTACTTACTCCTCCTCAGgttcctcttt ... tattttgcagATAGAGCCTATCTTGAGTGGAAATCTGCCACCTGGCTTTGATTCGAGTTCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attttacttttaggaactctttttttttctgtcttcttacatttttattttgcagATAGAGCCTATCTTGAGTGGAAATCTGCCACCTGGCTTTGATTCGAGTTCATGCCGCAGTGT
ttcttac putative branch site (score: 2)
ctctttttttttctgt CT-rich tract
ttcttacatttttatt 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 |
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gaaatgcgatttgtttgattagattagttgagaggagggtggataattttacttttaggaactctttttttttctgtcttcttacatttttattttgcagATAGAGCCTATCTTGAGTGGAAATCTGCCACCTGGCTTTGATTCGAGTTCATGCCGCAGTGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA