Sequence
atgc intronic sequence ATGC exonic sequencegttcataatttcatgatttttcatccttgcttcctagttattttctgctatacttttttttatatgtatattttttctgtctactttattggccgtagtttcttgtaatgtattcttgtgataacatggtacatagGTGAGAAAAGAAAGAAATTAGAGGAAGAGAAGGGCATTATCATCCGATTTGTAATTGGTCATAG
Basic information
species | Glycine max |
transcript | GLYMA13G38500.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G38500.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os03g38050.1 (Oryza sativa), 3'ss of exon 4
gttcataatttcatgatttttcatccttgcttcctagttattttctgctatacttttttttatatgtatattttttctgtctactttattggccgtagtttcttgtaatgtattcttgtgataacatggtacatagGTGAGAAAAGAAAGAAATTAGAGGAAGAGAAGGGCATTATCATCCGATTTGTAATTGGTCATAG
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----------------------------------------------gttgtacattcttttgcatggagaattttttttcccacagta--aaacatgttacctgatattgt--ttctgtgtttgcg------acagGTGAAAAAAGAAGGAAGCTTGAGGAAGAAAAGGGAATTATCATCCGATTCGTCATTGGTCATAG
upper sequence: GLYMA13G38500.1 (Glycine max), 3'ss of exon 4
lower sequence: AT1G05170.2 (Arabidopsis thaliana), 3'ss of exon 4
gttcataatttcatgatttttcatccttgcttcctagttattttctgctatacttttttttatatgtatattttttctgtctactttattggccgtagtttcttgtaatgtattcttgtgataacatggtacatagGTGAGAAAAGAAAGAAATTAGAGGAAGAGAAGGGCATTATCATCCGATTTGTAATTGGTCATAG
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----------------------------------------------------gtttttattacacttttatctttg--atcaactatgtt--ccttgatg----gttgtatctgattgaaatgttgttgttttcagGTGAAAAAAGGAAGAGACTAGAAGAGGAGAAGGGGATTATCATCCGGTTTGTCATTGGTCACAG
upper sequence: GLYMA13G38500.1 (Glycine max), 3'ss of exon 4
lower sequence: AT2G32430.1 (Arabidopsis thaliana), 3'ss of exon 4
gttcataatttcatgatttttcatccttgcttcctagttattttctgctatacttttttttatatgtatattttttctgtctactttattggc-cgtagtttcttgtaatgtattcttgtgataacatggtacatagGTGAGAAAAGAAAGAAATTAGAGGAAGAGAAGGGCATTATCATCCGATTTGTAATTGGTCATAG
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-----------------------------------------gttctaatat-caccttctaggttctttatcttcaagattgctgatatcgatatgttacttgatg-gatgt-ttctaatgaaaatattgcttgtagGTGAGAAAAGAAAGAAGTTGGAAGAAGAGAAGGGAATTATTATACGGTTTGTGATTGGTCATAG
upper sequence: GLYMA13G38500.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv12s0059g00640.t01 (Vitis vinifera), 3'ss of exon 4
gttcataatttcatgatttttcatccttgcttcctagttattttctgctatacttttttttatatgtatattttttctgtctactttattggccgtagtttcttgtaatgtattcttgtgata-acatggtacatagGTGAGAAAAGAAAGAAATTAGAGGAAGAGAAGGGCATTATCATCCGATTTGTAATTGGTCATAG
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--------gttcatggatgtt--tctttgctttcta-----ttcctggagttcttttttct-tattcatatcttattttagcttcttattgg--atgatgtcttacgattgtttcttctggaacacatggaaaatagGTGAAAAAAGGAAGAAGCTGGAGGAAGAGAAGGGCATTATCATTCGCTTTGTCATTGGTCATAGMapped 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|298196082|gb|HO044473.1|HO044473EST: CAGCAGCAGAAAAAGAAGAGACTCAGTTCGAGAGACATGGATGCCACAAG GTGAGAAAAGAAAGAAATTAGAGGAAGAGAAGGGCATTATCATCCGATTTG
genomic: CAGCAGCAGAAAAAGAAGAGACTCAGTTCGAGAGACATGGATGCCACAAGgttcataatt ... tggtacatagGTGAGAAAAGAAAGAAATTAGAGGAAGAGAAGGGCATTATCATCCGATTTG
EST:
gi|209721988|gb|BW659283.1|BW659283EST: CAGCAGCAGAAAAAGAAGAGACTCAGTTCGAGAGACATGGATGCCACAAG GTGAGAAAAGAAAGAAATTAGAGGAAGAGAAGGGCATTATCATCCGATTTG
genomic: CAGCAGCAGAAAAAGAAGAGACTCAGTTCGAGAGACATGGATGCCACAAGgttcataatt ... tggtacatagGTGAGAAAAGAAAGAAATTAGAGGAAGAGAAGGGCATTATCATCCGATTTG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tactttattggccgtagtttcttgtaatgtattcttgtgataacatggtacatagGTGAGAAAAGAAAGAAATTAGAGGAAGAGAAGGGCATTATCATCCGATTTGTAATTGGTCATAG
tgataac putative branch site (score: 2)
taatgtatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttcataatttcatgatttttcatccttgcttcctagttattttctgctatacttttttttatatgtatattttttctgtctactttattggccgtagtttcttgtaatgtattcttgtgataacatggtacatagGTGAGAAAAGAAAGAAATTAGAGGAAGAGAAGGGCATTATCATCCGATTTGTAATTGGTCATAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA