Sequence
atgc intronic sequence ATGC exonic sequence...ttgcaaagcagaattttgtaattcttctgtatgtcgttttcaactttcaagcaattttttgtgcaatttgagggattttgctgataacatgccccggcagGGATATTGGCTTCCTGTATTGGGTGGCTGATGCAAGCAGATGCAAGAGGTTGCTGGGGAGCGCGGAGGTTACCTTCATGGACGAGGCG
Basic information
species | Glycine max |
transcript | GLYMA09G28980.2 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G28980.2 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os02g42540.1 (Oryza sativa), 3'ss of exon 2
ttgcaaagcagaattttgtaattcttctgtatgtcgttttcaactttcaagcaattttt-tgtgcaatttgagggattttgctgataacatgccccggcagGGATATTGGCTTCCTGTATTGGGTGGCTGATGCAAGCAGATGCAAGAGGTTGCTGGGGAGCGCGGAGGTTACCTTCATGGACGAGGCG
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------------------------------------ctttc--ttatcgggtgcttcccacgggcatctatgtgcaatgttctgataacatgccctgacagggattttggctctct--acttggcggttgatgacgacagATGCAGGAGGTTGCTGGTGAACGGGGAGGTTACCTTCATGGGCGAGGAG
upper sequence: GLYMA09G28980.2 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G146786_T01 (Zea mays), 3'ss of exon 2
ttgcaaagcagaattttgtaattcttctgtatgtcgttttcaactttcaagcaattttttgtgcaatttgag-ggattttgctgataacatgccccggcagGGATATTGGCTTCCTGTATTGGGTGGCTGATGCAAGCAGATGCAAGAGGTTGCTGGGGAGCGCGGAGGTTACCTTCATGGACGAGGCG
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--------------------------------------tcaaatgactaagcatttccaataggtatcagtgtacaatgttcttataacatgccctgacagggattttggttctct--actcggtggttgataccaacagATGCAAGAGGTTGCTGGTGATAGGGGAGGCTACCTTCACGGACGAGGAG
upper sequence: GLYMA09G28980.2 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G146786_T02 (Zea mays), 3'ss of exon 2
ttgcaaagcagaattttgtaattcttctgtatgtcgttttcaactttcaagcaattttttgtgcaatttgagggattttg--ctgataacatgccccggcagGGATATTGGCTTCCTGTATTGGGTGGCTGATGCAAGCAGATGCAAGAGGTTGCTGGGGAGCGCGGAGGTTACCTTCATGGACGAGGCG
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--tcacacgaggatgccttgcttttacttaaatgcttgatcaaatgactaagcatttccaataggtatcagtgtacaatgttcttataacatgccctgacagGGATTTTGGTTCTCT--ACTCGGTGGTTGATACCAACAGATGCAAGAGGTTGCTGGTGATAGGGGAGGCTACCTTCACGGACGAGGAG
upper sequence: GLYMA09G28980.2 (Glycine max), 3'ss of exon 2
lower sequence: AT1G73350.2 (Arabidopsis thaliana), 3'ss of exon 2
ttgcaaagcagaattttgtaattcttctgtatgtcgttttcaactttcaagcaattttttgtgcaatttgagggattttgctgataacatgccccggcagGGATATTGGCTTC-CTGTATTGGGTGGCTGATGCAAGCAGATGCAAGAGGTTGCTGGGGAGCGCGGAGGTTACCTTCATGGACGAGGCG
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--------------------------------gtgattcttatgtttgactctatatt----gggactcga----cttttctgataacttgccccggcagggataacggccccgccacattttctggttattgcatatagATGCAAGAGGTTGCTGGTGAACGTGGAGGCTATCTTCATGGACGAGGCG
upper sequence: GLYMA09G28980.2 (Glycine max), 3'ss of exon 2
lower sequence: AT1G73350.3 (Arabidopsis thaliana), 3'ss of exon 2
--ttgcaaagcagaattttgtaattcttc-tgtatgtcgttttcaactttcaagcaattttttgtgcaatttgagggattttgctgataacatgccccggcagGGATATTGGCTTC-CTGTATTGGGTGGCTGATGCAAGCAGATGCAAGAGGTTGCTGGGGAGCGCGGAGGTTACCTTCATGGACGAGGCG
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tatatctttgttagcattagtggttattgatgtgtgtgaagtgattcttatgtttgactctatattgggactc---gacttttctgataacttgccccggcagGGATAACGGCCCCGCCACATTTTCTGGTTATTGCATATAGATGCAAGAGGTTGCTGGTGAACGTGGAGGCTATCTTCATGGACGAGGCG
upper sequence: GLYMA09G28980.2 (Glycine max), 3'ss of exon 2
lower sequence: Vv16s0039g00280.t01 (Vitis vinifera), 3'ss of exon 2
ttgcaaagcagaattttgtaattcttctgtatgtcgttttcaactttcaagcaattttttgtgcaatttgagggattttgctgataacatgccccggcagGGATATTGGCTTCCTGTATTGGGTGGCTGATGCAAGCAGATGCAAGAGGTTGCTGGGGAGCGCGGAGGTTACCTTCATGGACGAGGCG
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------------------------------acatc-tcttctctttttatatgacattctgtg--------gagagttttctgataacatgccccggcagggatcttggcattgcctaccgggtggttgatgtgagcagATGCAAGAGGTTGCAGGGGAACGTGGAGGTTACCTTCATGGACGAGGCGMapped 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|51335221|gb|CO979087.1|CO979087EST: AAGATAAGATTGACGATGAAGACATTACTTTCCAACGCATGGTTGCAAAG GGATATTGGCTTCCTGTATTGGGTGGCTGATGCAAGCAGATGCAAGAGGTT
genomic: AAGATAAGATTGACGATGAAGACATTACTTTCCAACGCATGGTTGCAAAGgttagcgcat ... gccccggcagGGATATTGGCTTCCTGTATTGGGTGGCTGATGCAAGCAGATGCAAGAGGTT
EST:
gi|18040197|gb|BM308491.1|BM308491EST: AAGATAAGATTGACGATGAAGACATTACTTTCCAACGCATGGTTGCAAAG GGATATTGGCTTCCTGTATTGGGTGGCTGATGCAAGCAGATGCAAGAGGTT
genomic: AAGATAAGATTGACGATGAAGACATTACTTTCCAACGCATGGTTGCAAAGgttagcgcat ... gccccggcagGGATATTGGCTTCCTGTATTGGGTGGCTGATGCAAGCAGATGCAAGAGGTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttcaagcaattttttgtgcaatttgagggattttgctgataacatgccccggcagGGATATTGGCTTCCTGTATTGGGTGGCTGATGCAAGCAGATGCAAGAGGTTGCTGGGGAGCGCGGAGGTTACCTTCATGGACGAGGCG
tgataac putative branch site (score: 2)
aattttttgt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttgcaaagcagaattttgtaattcttctgtatgtcgttttcaactttcaagcaattttttgtgcaatttgagggattttgctgataacatgccccggcagGGATATTGGCTTCCTGTATTGGGTGGCTGATGCAAGCAGATGCAAGAGGTTGCTGGGGAGCGCGGAGGTTACCTTCATGGACGAGGCG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- -caaagca
- - - - - - - - - - - - - -tgtatgt
- - - - - - - - - - - - - - - - - - - - - - -ttcaagc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgaggga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgctgat