Sequence
atgc intronic sequence ATGC exonic sequence...aagtgctccatgcatttgcttttttattcaatgtagtaattttttttatgtgggggtttatttctgaaaaaattggacaatcaattttctgtgactgcagGAATTGTACCATGAATTACATGCTTTGGATAGATTTGAACAAGATATTCAGCGCAAGGGTGAGGAGGAGGAGGATCAAAGAG
Basic information
species | Glycine max |
transcript | GLYMA06G16680.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA06G16680.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os05g35530.1 (Oryza sativa), 3'ss of exon 5
aagtgctccatgcatt-tgcttttttattcaatgtagtaattttttttatgtgggggtttatttctgaaaaaattggacaatcaattttctgtgactgcagGAATTGTACCATGAATTACATGCTTTGGATAGATTTGAACAAGATATTCAGCGCAAGGGTGAGGAGGAGGA------GGATCAAAGAG
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-agcaccgtttgccttctgtgcactgattcgtgttatttctggacttctggttatagatttcacatcactgactcgcttctctttctttcttttctcctagGAATTATATCATGAATTGCATACTTTGGATAGATTTGAACAAGACTGTCGTCGTAAACAGCAAGAACTGGATGGTTTGGGTTCAAGAG
upper sequence: GLYMA06G16680.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os01g65330.2 (Oryza sativa), 3'ss of exon 4
---aagtgctccatgcatttgcttttttattcaatg-tagtaattttttttatgtgggggtttatttctgaaaaaattggacaatcaattttctgtgactgcagGAATTGTACCATGAATTACATGCTTTGGATAGATTTGAACAAGATATTCAGCGCAAGGGTGAGGAGGAGGAGGATCAAAGAG------------
| || | ||||| | | | || || | | || |||| | | | | | ||| | | |||||||| | | |||||| | ||||||||| | ||||| |||||||||||||||||||| ||||||||| |||| ||||| | | ||| |
atatactgttaactgcatcttactatcaatctgctggcatttatcagttttcttcttttgcatgtcttgttgaaattacaaatttcaatttttt----tttcagGAACTATACCATGAAATGCATGCACTGGATAGATTTGAACAAGATTATCAGCGCAAACAGCAGGAAGAGGATGGTTCAAGTGTACACCAAAGAG
upper sequence: GLYMA06G16680.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G097502_T01 (Zea mays), 3'ss of exon 4
aagtgctccatgcatttgcttttt---tattcaatgtagtaattttttttatgtgggggtttatttctgaaaaaattggacaatcaattttctgtgactgcagGAATTGTACCATGAATTACATGCTTTGGATAGATTTGAACAAGATATTCAGCGCAAGGGTGAGGAGGAGGAGGATCAAAGAG------
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gaat-ttgtatgtttttgtcatctgccaatttggtcttcttattctggttat-tagtttcacattacttgtctattttgttttcctacttttttgcact-cagGAATTATATCATGAATTGCATGCTTTGGATAGATTTGAGCATGATTGTCGTCTTAAACAGAAAGAACAGGATGGCTTGAGTTCAAGAG
upper sequence: GLYMA06G16680.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G077621_T01 (Zea mays), 3'ss of exon 4
aagtgctccatgcatttgcttttttattcaatgtagtaattttttttatgt----gggggtttatttctgaaaaaattggacaatcaattttctgtgactgcagGAATTGTACCATGAATTACATGCTTTGGATAGATTTGAACAAGATATTCAGCGCAAGGGTGAGGAGGAGGAGGATCAAAGAG------
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----aatttgtgtatttttgtcatcggccaatttggccttcttattctggttattagcatcacattacttatttatttttttcttcctacttttttgcactcagGAATTATATCATGAATTGCATGCTTTGGATAGATTGGAACATGATTATCGCCTTAAACAGAAAGAACAGGATGGCTTGAGTTTAAGAG
upper sequence: GLYMA06G16680.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G320615_T01 (Zea mays), 3'ss of exon 4
aagtgctccatgcatttgcttttttattcaatgtagtaatttt-ttttatgtgggggtttatttctgaaaaaattggacaatcaattttctgtgactgcagGAATTGTACCATGAATTACATGCTTTGGATAGATTTGAACAAGATATTCAGCGCAAGGGTGAGGAGGAGGAGGATCAAAGAG------
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-atgaatttgtgtatttttgtcatcggccaatttggccttcttattctgtttattagcgtcacattacttattttttttcttcctacttttttgcacttagGAATTATATCATGAATTGCATGCTTTGGATAGATTGGAACATGATTATCGCCTTAAACAAAAAGAACATGATGGTTTGAGTTTAAGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttatgtgggggtttatttctgaaaaaattggacaatcaattttctgtgactgcagGAATTGTACCATGAATTACATGCTTTGGATAGATTTGAACAAGATATTCAGCGCAAGGGTGAGGAGGAGGAGGATCAAAGAG
ttttctgt CT-rich tract
tttatttctgaaaaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aagtgctccatgcatttgcttttttattcaatgtagtaattttttttatgtgggggtttatttctgaaaaaattggacaatcaattttctgtgactgcagGAATTGTACCATGAATTACATGCTTTGGATAGATTTGAACAAGATATTCAGCGCAAGGGTGAGGAGGAGGAGGATCAAAGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - -ccatgca
- - - - - - - - tgctttt
- - - - - - - - - - - - - - -aatgtag
- - - - - - - - - - - - - - - - - - - - - - - - -gtggggg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaaaat