Sequence
atgc intronic sequence ATGC exonic sequence...tttatgagcttgctagcatgcttttctgtcttgaacatatttggtttactttttttttttcaaaaaaaattgatgccacaatgttcttaaattttaccagGTTGGTCAAGAACTTGGGGAGAAGAACACTTTGGAAATGG
Basic information
species | Glycine max |
transcript | GLYMA04G02020.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA04G02020.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os03g04100.2 (Oryza sativa), 3'ss of exon 8
----tttatgagcttgctagcatgcttttctgtcttgaacatatttggtttactttttttttttcaaaaaaaattgatgccacaatgttcttaaattttaccagGTTGGTCAAGAACTTGGGGAGAAGAACACTTTGGAAATGG------------------------------------------------------------
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cctgtttattgcattgttaaatgtgtgcaccgctcgtagtgtgacttatgacttatctgatttccaattgccatccactt----atctgatttgatactttcagGATGGTCAAGAACTTGGGGAGAAGAGCATTTTGGTAATGGGTATGTTCCATCATGACGCTGGTCTCGCATTTGGTTTGACTGACACTTGACATTAATAAA
upper sequence: GLYMA04G02020.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os03g04100.1 (Oryza sativa), 3'ss of exon 8
----tttatgagcttgctagcatgcttttctgtcttgaacatatttggtttactttttttttttcaaaaaaaattgatgccacaatgttcttaaattttaccagGTTGGTCAAGAACTTGGGGAGAAGAACACTTTGGAAATGG
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cctgtttattgcattgttaaatgtgtgcaccgctcgtagtgtgacttatgacttatctgatttccaattgccatccactt----atctgatttgatactttcagGATGGTCAAGAACTTGGGGAGAAGAGCATTTTGGTAATGG
upper sequence: GLYMA04G02020.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G126812_T01 (Zea mays), 3'ss of exon 8
tttatgagcttgct-agcatgcttttctgtcttgaacatatttggtttactttttttttttca--aaaaaaattgatgccacaatgttcttaaattttaccagGTTGGTCAAGAACTTGGGGAGAAGAACACTTTGGAAATGG
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--tgtgatggcgctgaacccagtactttatgacagagatatgaagcagcttttgcttggaatattatgtaggctgatacttcacttgtgttgaaactt-tcagGTTGGTCAAGAACTTGGGGAGAAGAACACTTTGGTAACGG
upper sequence: GLYMA04G02020.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G110345_T01 (Zea mays), 3'ss of exon 8
tttatgagcttgctagcatgcttttctgtcttgaacatatttggtttactttttttttttcaaaaaaaattgatgcc-acaatgtt-cttaaatt----ttaccagGTTGGTCAAGAACTTGGGGAGAAGAACACTTTGGAAATGG
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------tgctggaccccactactttatgatggagatataaagcagtatcatcttttgcttggaataatatgtaggctgataacttcgctcgtgttgaaactttcagGTTGGTCAAGAACCTGGGGAGAAGAACACTTTGGTAACGG
upper sequence: GLYMA04G02020.1 (Glycine max), 3'ss of exon 8
lower sequence: AT1G42430.1 (Arabidopsis thaliana), 3'ss of exon 8
---------------tttatgagcttgctagcatgcttttctgtcttgaacatatttggtttacttttttt---ttttcaaaaaaaattga-tgccacaatgttcttaaattttaccagGTTGGTCAAGAACTTGGGGAGAAGAACACTTTGGAAATGG
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gtcagttccttcttcttcttcttcttcttcttcttcttcttcttcttcttcttctttaaattcctttgtttgactatgtttgtaatctcgcctaacccgataacctcacgtttt--cagGTTGGTCAAGAACGTGGGGAGAGGAACACTTTGGAAACGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttactttttttttttcaaaaaaaattgatgccacaatgttcttaaattttaccagGTTGGTCAAGAACTTGGGGAGAAGAACACTTTGGAAATGG
aattgat putative branch site (score: 4)
ttttacc putative PPT
ttttttttttcaaaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tttatgagcttgctagcatgcttttctgtcttgaacatatttggtttactttttttttttcaaaaaaaattgatgccacaatgttcttaaattttaccagGTTGGTCAAGAACTTGGGGAGAAGAACACTTTGGAAATGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - -gcttgct
- - - - - - - -gcatgct
- - - - - - - - - - - -ttctgtc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgccaca