Sequence
atgc intronic sequence ATGC exonic sequencegttagtatgattaagctaagcattctcctatctctcttaccaaattataattagttcaagttcctgtatgattgcaatgtgtaagtggtccctaatgtttaaaggtcaaaagatattgattctctccttttttctttttctgtagTTATGTTGCACCAGAATATGCATGCACTGGAATGCTGACTGAGAAGAGTGATATTTATAGCTTTGGGATACTTATCATGGAGATAATCACCGGAAGAAGT
Basic information
species | Glycine max |
transcript | GLYMA09G39160.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G39160.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G014366_T03 (Zea mays), 3'ss of exon 4
gttagtatgattaagctaagcattctcctatctctcttaccaaattataattagttcaagttcctgtatgattgcaatgtgtaagtggtccctaatgtttaaaggtcaaaagatattg--attctctccttttttctttttctgtagTTATGTTGCACCAGAATATGCATGCACTGGAATGCTGACTGAGAAGAGTGATATTTATAGCTTTGGGATACTTATCATGGAGATAATCACCGGAAGAAGT
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----------------------------------------------gttagtagtgagaacccttccatcctcatcgc---tactcagtctactacaaacggagctagatcgatcttgtcgttactgagctattggtgctgttgcagGTACGTGGCGCCTGAATATGCCAGCACCGGAATGCTGAACGAGAGGAGTGATGTATATAGCTTTGGCGTACTCATAATGGAGATCATCACTGGTAGATCT
upper sequence: GLYMA09G39160.1 (Glycine max), 3'ss of exon 4
lower sequence: AT1G01540.1 (Arabidopsis thaliana), 3'ss of exon 4
gttagtatgattaagctaagcattctcctatctctcttaccaaattataattagttcaagttcctgtatgattgcaatgtgtaag-tggtccctaatgtt-taaaggtcaaaagatattgattctctccttttttctttttctgtagTTATGTTGCACCAGAATATGCATGCACTGGAATGCTGACTGAGAAGAGTGATATTTATAGCTTTGGGATACTTATCATGGAGATAATCACCGGAAGAAGT
||| ||| | | ||| || |||||| || ||| ||| || | | || | | | ||| || || | | ||| | ||||||||| ||||||||||| || ||||| |||||| | | |||||||||||||| |||||||| || ||||| ||||||||||||||||| |||||||
---------------------------------------gtaaactatta--aactca--ttaactctctcctgcaatctgcaaggcagtctttaggaatgtgaatattaggaaataact-tttactttgtgggttgatttgtttagTTATGTAGCACCAGAATACGCTTGCACCGGAATGTTAAACGAGAAGAGTGATATCTATAGCTTCGGAATACTAATCATGGAGATAATCACTGGAAGAAAC
upper sequence: GLYMA09G39160.1 (Glycine max), 3'ss of exon 4
lower sequence: AT4G01330.1 (Arabidopsis thaliana), 3'ss of exon 4
gttagtatgattaagctaagcattctcctatctctcttaccaaattataattagttcaagttcctgtatgattgcaatgtgtaagtggtccctaatgtttaaaggtcaaaagatattgattctctccttttttcttt-ttctgtagTTATGTTGCACCAGAATATGCATGCACTGGAATGCTGACTGAGAAGAGTGATATTTATAGCTTTGGGATACTTATCATGGAGATAATCACCGGAAGAAGT
|| || | |||||| | | ||| | | || | | || | ||| || || | | | ||| | || | || ||| || ||||| |||||||| || || ||||| ||||| |||||| |||| || ||||||||||| ||||| ||||||||| | ||||||||||||||||||||||||| |
---------------------------------------gtaagttgtttttagttgg----catatataaatatgattgttggatagtattaaggatttcaaattcttgaaaaac--attttgtcttgattggtttgttatgtagATATGTTGCGCCTGAGTATGCTTGCACCGGAATGTTGACAGAAAAGAGTGATATCTATAGTTTTGGGATATTAATCATGGAGATAATCACCGGAAGAAAT
upper sequence: GLYMA09G39160.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv15s0046g02030.t01 (Vitis vinifera), 3'ss of exon 4
gttagtatgattaagctaagcattctcctatctctcttaccaaattataattagttcaagttcctgtatgattgcaatgtgtaagtggtccc-taatgtttaaaggtcaaaagatattgattctctccttttttctttttctgtagTTATGTTGCACCAGAATATGCATGCACTGGAATGCTGACTGAGAAGAGTGATATTTATAGCTTTGGGATACTTATCATGGAGATAATCACCGGAAGAAGT
||||| || | | | | | |||| | || | ||| | | | | ||||| | | | ||| | |||| || |||||||||||||||||||| |||||||| ||||||| ||| || || ||| ||||||||||||| || ||||| ||||||||||| | || |||| |
-------------------------------------------------gttagtccatttccttttg-----gtaatgaatcgaccttcacataaaatggcatattgagaagatttctgatatttcccaatggctttcc----agGTATGTTGCACCAGAATATGCTTGCACTGGTATGCTGAATGAAAAAAGCGATGTTTATAGCTTTGGAATTCTTATTATGGAGATAATTTCAGGCAGAAAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cctaatgtttaaaggtcaaaagatattgattctctccttttttctttttctgtagTTATGTTGCACCAGAATATGCATGCACTGGAATGCTGACTGAGAAGAGTGATATTTATAGCTTTGGGATACTTATCATGGAGATAATCACCGGAAGAAGT
tattgat putative branch site (score: 3)
tattgattctctcctt CT-rich tract
aaaagatattgatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttagtatgattaagctaagcattctcctatctctcttaccaaattataattagttcaagttcctgtatgattgcaatgtgtaagtggtccctaatgtttaaaggtcaaaagatattgattctctccttttttctttttctgtagTTATGTTGCACCAGAATATGCATGCACTGGAATGCTGACTGAGAAGAGTGATATTTATAGCTTTGGGATACTTATCATGGAGATAATCACCGGAAGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT