Sequence
atgc intronic sequence ATGC exonic sequencegtaagtggcatttttttaaaattctattatccttgttttcaaatgagaagctttacatgtgtaattgagtagataaagggagcaaataaaaaggatgacaatagcttgtattttaaattttaaaattcataccagtttttctgctgcaactgttcatttattttttgtgtttatgtgtttcaatatataatagGTTTAAAGAAATCGTTGTTTAATGTATTCCAAAATGGCTTATGCCATCTGAAGATGGCATTGGTAATTGATGATCGCCTGAAAGTGTGGGATGAGAAAGA
Basic information
species | Glycine max |
transcript | GLYMA15G07800.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA15G07800.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os04g44710.2 (Oryza sativa), 3'ss of exon 4
gtaagtg---gcatttttttaaaattctattatccttgttttcaaatgagaagctttacatgtgtaattgagtagataaagggagcaaataaaaaggatgacaatagcttgtattttaaattttaaaattcataccagtttttctgctgcaactgttcatttattttttgtgtttatgtgtttcaatatataatagGTTTAAAGAAATCGTTGTTTAATGTATTCCAAAATGGCTTATGCCATCTGAAGATGGCATTGGTAATTGATGATCGCCTGAAAGTGTGGGATGAGAAAGA
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gtaggtgttagcattactattactttcaaacaacacaactaccaaaggaatatagtgtcatttggtatattttgtacaccgcaatcaatgttttgtgttgtctaatttccttcatacaaatttccatgtgcatga-acataatgtcttggaattttccatct---tttgacgttaatgctacaccac-tcttatagGCTCTCGAAAGTCTCTGCTGAATGTATTCCATGATGGGTCTTGCCACCCAGAAATGGCCCTAGTGATTGATGATCGCTTGAAAGTTTGGGATGAGAAAGA
upper sequence: GLYMA15G07800.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G120373_T01 (Zea mays), 3'ss of exon 3
gtaagtggcatttttttaaaattctattatccttgttttcaaatgagaagctttacatgtgtaattgagtagataaagggagcaaataaaaaggatgacaatagcttgtattttaaattttaaaattcataccagtttttctgctgcaactgttcatttattttttgtgtttatgtgtttcaatatataatagGTTTAAAGAAATCGTTGTTTAATGTATTCCAAAATGGCTTATGCCATCTGAAGATGGCATTGGTAATTGATGATCGCCTGAAAGTGTGGGATGAGAAAGA
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------------------gtatgtaattcatcttgtttttgaacaagta---caaaaagagcattagccta---atgtggcctaaatgttgtcatactcaaaagttgacaaactg---tgaaaaatacaattcaaatttttagtttca----ttctactgaaattaatgccaa---atttcc-tattta-tagGTTTAAAAAAGTCCTTGCTAAATGTCTTCCATGATGGTTCTTGCCATCCTGGTATGGCATTAGTAATTGATGATCGCCTGAAAGTTTGGGATGAGAAGGA
upper sequence: GLYMA15G07800.1 (Glycine max), 3'ss of exon 3
lower sequence: AT4G21670.1 (Arabidopsis thaliana), 3'ss of exon 3
gtaagtggcatttttttaaaattctattatccttgttttcaaatgagaagctttacatgtgtaattgagtagataaagggagcaaataaaaaggatgacaatagcttgtattttaaattttaaaattcataccagtttttctgctgcaactgttcatttattttttgtgtttatgtgtttcaatatataatagGTTTAAAGAAATCGTTGTTTAATGTATTCCAAAATGGCTTATGCCATCTGAAGATGGCATTGGTAATTGATGATCGCCTGAAAGTGTGGGATGAGAAAGA
|||| | ||| | | ||||| | || | | | || | | || || ||| || | | | |||||| || || || |||| ||||| || | |||| ||||||| |||||||||||||||||||||||||| ||||||| ||||||||||| ||
-----------------------------------------------------------------------------------------------------------gtatactt--tttggtatcttatacctgcttatatttcatcatggtaaa---acttcttacaagcttgtaattaaccac--cacagGTTTTAAAAAGTCACTGTTCAATGTGTTTCTCGATGGAACCTGCCATCCAAAGATGGCATTGGTAATTGATGATCGATTGAAAGTTTGGGATGAGAAGGA
upper sequence: GLYMA15G07800.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv00s0370g00040.t01 (Vitis vinifera), 3'ss of exon 3
gtaagtggcatttttttaaaattctattatccttgttttcaaatgagaagctttacatgtgtaattgagtagata-aagggagcaaataaaaaggatgacaata-gcttgtatttta---aattttaaaattcataccagtttttctgctgcaactgttcatttatttt----ttgtgtttatgtgtttcaatatat--aatagGTTTAAAGAAATCGTTGTTTAATGTATTCCAAAATGGCTTATGCCATCTGAAGATGGCATTGGTAATTGATGATCGCCTGAAAGTGTGGGATGAGAAAGA
| | ||||||||| || ||| | | | || | ||| | || | | | ||| | ||| | | | | ||| | || | ||| | | | || | || ||| ||| ||||| || |||| | | | |||| | || | || || ||||| | || || || |||| ||||| || ||| |||| | ||||||| |||||||| || |||||||||||||| |||||||||||||||| |||||
-------gtaagtttttaaaa----gaaatggttgatcttagggatgacttatgccatccacagcagaccaaagacaagctaattaattatatagcttctgatatgattttttttcacccattcttgtagttgttacttgttattctgtaaaccacgtacattatcctcaatatcctacttattttctttattaaatttgatagGCTCAAGAAAGTCACTGTTCAATGTCTTTCAAGATGGAATCTGCCATCCTAAGATGGCTTTAGTAATTGATGATCGTTTGAAAGTGTGGGATGAAAAAGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttctgctgcaactgttcatttattttttgtgtttatgtgtttcaatatataatagGTTTAAAGAAATCGTTGTTTAATGTATTCCAAAATGGCTTATGCCATCTGAAGATGGCATTGGTAATTGATGATCGCCTGAAAGTGTGGGATGAGAAAGA
atttattttttgtgtt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtggcatttttttaaaattctattatccttgttttcaaatgagaagctttacatgtgtaattgagtagataaagggagcaaataaaaaggatgacaatagcttgtattttaaattttaaaattcataccagtttttctgctgcaactgttcatttattttttgtgtttatgtgtttcaatatataatagGTTTAAAGAAATCGTTGTTTAATGTATTCCAAAATGGCTTATGCCATCTGAAGATGGCATTGGTAATTGATGATCGCCTGAAAGTGTGGGATGAGAAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG