Sequence
atgc intronic sequence ATGC exonic sequence...ttttctctcttggttatgtactgcctgtttttgctgttttcaactttcaagcaattttttgtgcaatttgagggattttgctgataacatgccccggcagGGATATTGGCTTCCTGTATTGGGTGGCTGATGCAAGCAGATGCAAGAGGTTGCTGGGGAGCGTGGAGGTTACCTTCATGGACGAGGCG
Basic information
species | Glycine max |
transcript | GLYMA16G33570.2 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA16G33570.2 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os02g42540.1 (Oryza sativa), 3'ss of exon 2
ttttctctcttggttatgtactgcctgtttttgctgttttcaactttcaagcaattttt-tgtgcaatttgagggattttgctgataacatgccccggcagGGATATTGGCTTCCTGTATTGGGTGGCTGATGCAAGCAGATGCAAGAGGTTGCTGGGGAGCGTGGAGGTTACCTTCATGGACGAGGCG
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------------------------------------ctttc--ttatcgggtgcttcccacgggcatctatgtgcaatgttctgataacatgccctgacagggattttggctctct--acttggcggttgatgacgacagATGCAGGAGGTTGCTGGTGAACGGGGAGGTTACCTTCATGGGCGAGGAG
upper sequence: GLYMA16G33570.2 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G146786_T01 (Zea mays), 3'ss of exon 2
ttttctctcttggttatgtactgcctgtttttgctgttttcaactttcaagcaattttttgtgcaatttgag-ggattttgctgataacatgccccggcagGGATATTGGCTTCCTGTATTGGGTGGCTGATGCAAGCAGATGCAAGAGGTTGCTGGGGAGCGTGGAGGTTACCTTCATGGACGAGGCG
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--------------------------------------tcaaatgactaagcatttccaataggtatcagtgtacaatgttcttataacatgccctgacagggattttggttctct--actcggtggttgataccaacagATGCAAGAGGTTGCTGGTGATAGGGGAGGCTACCTTCACGGACGAGGAG
upper sequence: GLYMA16G33570.2 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G146786_T02 (Zea mays), 3'ss of exon 2
ttttctctcttggttatgtactgcctgtttttgc-tgttt--tcaactttcaagcaattttttgtgcaatttgagggattttg--ctgataacatgccccggcagGGATATTGGCTTCCTGTATTGGGTGGCTGATGCAAGCAGATGCAAGAGGTTGCTGGGGAGCGTGGAGGTTACCTTCATGGACGAGGCG
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-----tcacacgaggatgccttgcttttacttaaatgcttgatcaaatgactaagcatttccaataggtatcagtgtacaatgttcttataacatgccctgacagGGATTTTGGTTCTCT--ACTCGGTGGTTGATACCAACAGATGCAAGAGGTTGCTGGTGATAGGGGAGGCTACCTTCACGGACGAGGAG
upper sequence: GLYMA16G33570.2 (Glycine max), 3'ss of exon 2
lower sequence: AT1G73350.2 (Arabidopsis thaliana), 3'ss of exon 2
ttttctctcttggttatgtactgcctgtttttgctgttttcaactttcaagcaattttttgtgcaatttgagggattttgctgataacatgccccggcagGGATATTGGCTTC-CTGTATTGGGTGGCTGATGCAAGCAGATGCAAGAGGTTGCTGGGGAGCGTGGAGGTTACCTTCATGGACGAGGCG
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--------------------------------gtgattcttatgtttgactctatatt----gggactcga----cttttctgataacttgccccggcagggataacggccccgccacattttctggttattgcatatagATGCAAGAGGTTGCTGGTGAACGTGGAGGCTATCTTCATGGACGAGGCG
upper sequence: GLYMA16G33570.2 (Glycine max), 3'ss of exon 2
lower sequence: AT1G73350.3 (Arabidopsis thaliana), 3'ss of exon 2
ttttctctcttggttatgtactgcctgtttttgctgttttcaactttcaagcaattttttgtgcaatttgagg----gattttgctgataacatgccccggcagGGATATTGGCTTC-CTGTATTGGGTGGCTGATGCAAGCAGATGCAAGAGGTTGCTGGGGAGCGTGGAGGTTACCTTCATGGACGAGGCG
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---tatatctttgtta-gcattagtggttattgatgtgtgtgaagtgattcttatgtttgactctatattgggactcgacttttctgataacttgccccggcagGGATAACGGCCCCGCCACATTTTCTGGTTATTGCATATAGATGCAAGAGGTTGCTGGTGAACGTGGAGGCTATCTTCATGGACGAGGCG
upper sequence: GLYMA16G33570.2 (Glycine max), 3'ss of exon 2
lower sequence: Vv16s0039g00280.t01 (Vitis vinifera), 3'ss of exon 2
ttttctctcttggttatgtactgcctgtttttgctgttttcaactttcaagcaattttttgtgcaatttgagggattttgctgataacatgccccggcagGGATATTGGCTTCCTGTATTGGGTGGCTGATGCAAGCAGATGCAAGAGGTTGCTGGGGAGCGTGGAGGTTACCTTCATGGACGAGGCG
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-------------------------------acatctcttctctttttatatgacattctgtg--------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|192298082|gb|FG991362.1|FG991362EST: AAGATAAGATTGACGATGAAGACATTACTTTCCAACGCATGGTTGCAAAG GGATATTGGCTTCCTGTATTGGGTGGCTGATGCAAGCAGATGCAAGAGGTT
genomic: AAGATAAGATTGACGATGAAGACATTACTTTCCAACGCATGGTTGCAAAGgttagcgcat ... gccccggcagGGATATTGGCTTCCTGTATTGGGTGGCTGATGCAAGCAGATGCAAGAGGTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttcaagcaattttttgtgcaatttgagggattttgctgataacatgccccggcagGGATATTGGCTTCCTGTATTGGGTGGCTGATGCAAGCAGATGCAAGAGGTTGCTGGGGAGCGTGGAGGTTACCTTCATGGACGAGGCG
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttttctctcttggttatgtactgcctgtttttgctgttttcaactttcaagcaattttttgtgcaatttgagggattttgctgataacatgccccggcagGGATATTGGCTTCCTGTATTGGGTGGCTGATGCAAGCAGATGCAAGAGGTTGCTGGGGAGCGTGGAGGTTACCTTCATGGACGAGGCG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - -ggttatg
- - - - - - - - - tactgcc
- - - - - - - - - - - - - - - -tgctgtt
- - - - - - - - - - - - - - - - - - - - - - -ttcaagc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgaggga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgctgat