Sequence
atgc intronic sequence ATGC exonic sequence...tgttaattcttgttcttctaattacattgaagtatttgttagctttgtggatgtactttctgattatttcatactattataacttatttaatcattgcagCATCATGGGCTATATCTGTGTACTTCGCATACCAACGAACCTGGAAGCCTTTTAACCCTATCCTTGGAGAGACTTATGAGATGGCTAACCATGGTGGAAT
Basic information
species | Glycine max |
transcript | GLYMA15G04210.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA15G04210.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os03g16690.1 (Oryza sativa), 3'ss of exon 4
tgttaattcttgttcttctaattacattgaagtatttgt-tagctttgtggatgtactttctgattatttcatactattataacttatttaatcattgcagCATCATGGGCTATATCTGTGTACTTCGCATACCAACGAACCTGGAAGCCTTTTAACCCTATCCTTGGAGAGACTTATGAGATGGCTAACCATGGTGGAAT
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--------------------------gtaagttttgcaccttcccttgtgagcaatgcctttaatatccttgttgtttgatcttttaacttaacttttcagCTGCATGGGCTGTATCGGTCTACTTTGCATACCAGCGTACCTGGAAGCCTTTCAATCCCATCCTTGGGGAGACATATGAGATGGTTAACCACCAGGGTAT
upper sequence: GLYMA15G04210.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G174644_T01 (Zea mays), 3'ss of exon 4
tgttaattcttgttcttctaattacattgaagtatttgttagctttgtggatgtactttctgattatttcatactattataacttatttaatcattg--cagCATCATGGGCTATATCTGTGTACTTCGCATACCAACGAACCTGGAAGCCTTTTAACCCTATCCTTGGAGAGACTTATGAGATGGCTAACCATGGTGGAAT
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---------------------gtaagttttctgcttcccttcccttgcacac-cattctatg-ccatatcatggttgcctgaactgttaatccatttttcagCTACATGGGCTGTTTCTGTGTACTTTGCATATCAACGCACATGGAAGCCTTTTAATCCGATCCTTGGAGAGACTTATGAGATGGTTAACCACCAGGGCAT
upper sequence: GLYMA15G04210.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G114126_T01 (Zea mays), 3'ss of exon 4
tgttaattcttgttcttctaattacattgaagtatttgttagctttgtggatgtactttctgattatttcatactattataacttatttaatcattgcagCATCATGGGCTATATCTGTGTACTTCGCATACCAACGAACCTGGAAGCCTTTTAACCCTATCCTTGGAGAGACTTATGAGATGGCTAACCATGGTGGAAT
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--------gtgagttttctccttcccttgc----cttgcacaccgttcggtgccatatcatggttgacttg-actgagctg-ttaatcaatttgtttcagCTACATGGGCTGTTTCGGTATACTTCGCGTATCAGCGCACATGGAAGCCTTTTAATCCGATCCTTGGAGAGACTTACGAGATGGTTAACCACCAGGGCAT
upper sequence: GLYMA15G04210.1 (Glycine max), 3'ss of exon 4
lower sequence: AT5G59420.1 (Arabidopsis thaliana), 3'ss of exon 4
-----tgttaattcttgttcttctaattacattgaagtatttgttagctttgtg-gatgtactttctgattatttcatactattataact-tatttaatcatt---gcagCATCATGGGCTATATCTGTGTACTTCGCATACCAACGAACCTGGAAGCCTTTTAACCCTATCCTTGGAGAGACTTATGAGATGGCTAACCATGGTGGAAT
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gtaagtattagtatttacaca--caaaaaactcgtattgacttccgactttgtaagatgtatgttaagagt-tttacttttcttgtggttgtacgtgaatttttatatagCATCATGGGCTATATCTGTTTACTATGCCTTCCAACGAACTTGGAAGCCTTTCAATCCTATTCTTGGGGAGACATATGAGATGGTCAACCATGGTGGGAT
upper sequence: GLYMA15G04210.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv06s0004g04930.t01 (Vitis vinifera), 3'ss of exon 4
tgttaattcttgttcttctaattacattgaagtatttgttagctttgtggatgtactttctgattatttcatactattataacttatttaatcattgcagCATCATGGGCTATATCTGTGTACTTCGCATACCAACGAACCTGGAAGCCTTTTAACCCTATCCTTGGAGAGACTTATGAGATGGCTAACCATGGTGGAAT
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---------gtgagtatattcttgcattaaa-tatttcagggc---atacatgtattatctggttaatg-gtggaactttaatg---ttactaattgcagCATCATGGGCTATATCTGTCTATTATGCCTACCAACGAACTTGGAAGCCTTTTAATCCCATTCTTGGTGAGACTTATGAAATGGCTAATCATGGTGGAAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgtggatgtactttctgattatttcatactattataacttatttaatcattgcagCATCATGGGCTATATCTGTGTACTTCGCATACCAACGAACCTGGAAGCCTTTTAACCCTATCCTTGGAGAGACTTATGAGATGGCTAACCATGGTGGAAT
tttctgattatttcat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgttaattcttgttcttctaattacattgaagtatttgttagctttgtggatgtactttctgattatttcatactattataacttatttaatcattgcagCATCATGGGCTATATCTGTGTACTTCGCATACCAACGAACCTGGAAGCCTTTTAACCCTATCCTTGGAGAGACTTATGAGATGGCTAACCATGGTGGAAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - cttgttc
- - - - - - - - - - - - - - - - - - - - - - - gtggatg