Sequence
atgc intronic sequence ATGC exonic sequence...ttcgagtcaattataatactttctttaacctaaaactaagaaatatatatgttgctcatatagtaccaagagtaacactttttccctttttctcttacagGGAACACTTGATGATGGAAGAGTTATCGCTGTGAAACAACTATCTGTACAATCCAATCAAGGAAAGAATCAGTTCATAGCTGAGATTGCCACTATCTCCG
Basic information
species | Glycine max |
transcript | GLYMA09G15200.1 |
intron # | 19 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G15200.1 (Glycine max), 3'ss of exon 19
lower sequence: Vv12s0055g00580.t01 (Vitis vinifera), 3'ss of exon 20
------------------------ttcgagtcaattataatactttctttaacctaaaactaagaaatat----atatgttgctcatatagtaccaagagtaacactttttccctttttctcttacagGGAACACTTGATGATGGAAGAGTTATCGCTGTGAAACAACTATCTGTACAATCCAATCAAGGAAAGAATCAGTTCATAGCTGAGATTGCCACTATCTCCG
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gtaggtcattatcctatcgagcttatatatttttttatgattatgagtatgattacaaacatgggatttttctcaatcattcctttttttttttttttggtaataattttatattcaattcgtt--agGGGACACTTTCTGATGGAAGAGTTGTTGCTGTAAAGCAACTATCTGTATCATCACACCAAGGAAAGAATCAGTTTGTAACAGAGATTGCAACCATATCAG
upper sequence: GLYMA09G15200.1 (Glycine max), 3'ss of exon 19
lower sequence: Vv12s0055g00590.t01 (Vitis vinifera), 3'ss of exon 20
-----------ttcgagtcaa-ttataatactttctttaacctaaaactaagaa-atatatatgttgctcatatagtaccaagagtaacactttttccct-------ttttctctta--cagGGAACACTTGATGATGGAAGAGTTATCGCTGTGAAACAACTATCTGTACAATCCAATCAAGGAAAGAATCAGTTCATAGCTGAGATTGCCACTATCTCCG
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gtaggtcattatcctattgagcttatattttttttttatgattataattatgattacaaacatggtatttttctcattctccttttttttttttttttttgcaataattttatattcgttagGGGACACTTTCTGATGGAAGAGTTGTTGCTGTAAAGCAACTATCTGTAGCATCCCACCAAGGAAAGAAGCAGTTTGTAGCAGAGATTGCAACCATATCAG
upper sequence: GLYMA09G15200.1 (Glycine max), 3'ss of exon 19
lower sequence: Vv12s0055g00590.t01 (Vitis vinifera), 3'ss of exon 45
-----------ttcgagtcaattataatactttctttaacctaaaactaagaaatatatatgttgctcatatagtaccaagagtaacactttttccctttttctcttac-----agGGAACACTTGATGATGGAAGAGTTATCGCTGTGAAACAACTATCTGTACAATCCAATCAAGGAAAGAATCAGTTCATAGCTGAGATTGCCACTATCTCCG
| | | | | ||| ||| || || | || || || | | | | | | | | | ||||| | | | | | |||| |||||| ||||||||||||| | ||||| || |||||||||||| ||| | ||||||||||||||||| || | |||||| || || || |
gtaggtcattatcctgttgagcttatatatttttttatgattatgagtatgat-tacaaacatgggatttttctcaatcattctttttttttttatatatatattcaattcgttagGGGACACTTTCTGATGGAAGAGTTGTTGCTGTAAAGCAACTATCTGTATCATCGCACCAAGGAAAGAATCAGTTTGTAACAGAGATTAAAACCATATCAG
upper sequence: GLYMA09G15200.1 (Glycine max), 3'ss of exon 19
lower sequence: Vv12s0055g00610.t01 (Vitis vinifera), 3'ss of exon 2
----------ttcgagtcaattataatactttctttaacctaaaactaagaa-atatatatgttgctcatatagtaccaagagtaacactttttccctttttctctta--cagGGAACACTTGATGATGGAAGAGTTATCGCTGTGAAACAACTATCTGTACAATCCAATCAAGGAAAGAATCAGTTCATAGCTGAGATTGCCACTATCTCCG
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gtaggtcattatcctattgagca-gatatttttttatgattatgattatgattacgaacatggtatttttctcaatcttctttttttttttgtcataattttatattcgttagGGGACACTCTCTGATGGAAGAGTTGTTGCTGTAAAGCAACTATCTGTATCATCCCACCAAGGAAAGAATCCGTTTGTAACAGAGATTGCAACCATATCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatatgttgctcatatagtaccaagagtaacactttttccctttttctcttacagGGAACACTTGATGATGGAAGAGTTATCGCTGTGAAACAACTATCTGTACAATCCAATCAAGGAAAGAATCAGTTCATAGCTGAGATTGCCACTATCTCCG
gagtaac putative branch site (score: 2)
cactttttcccttttt CT-rich tract
atatagta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttcgagtcaattataatactttctttaacctaaaactaagaaatatatatgttgctcatatagtaccaagagtaacactttttccctttttctcttacagGGAACACTTGATGATGGAAGAGTTATCGCTGTGAAACAACTATCTGTACAATCCAATCAAGGAAAGAATCAGTTCATAGCTGAGATTGCCACTATCTCCG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - -aagaaata
- - - - - - - - - - - - - - - - - - - - - - - - -tgttgct