Sequence
atgc intronic sequence ATGC exonic sequence...gttcacttcaaaatcaatttttgcaaatgttcattcaatggcactaaatcctatgtggtttggttagtacttagtactaacaaattaagttaacaagcagGAGAAGTTGCCACCGACAGATTCAAGACTAAGACCTGATCAAAGGTGTTTGGAGAATGGACAGCATGAAATGGCCAATTCTGAAAAGTTGCGGCTGGAAC
Basic information
species | Glycine max |
transcript | GLYMA04G38330.1 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA04G38330.1 (Glycine max), 3'ss of exon 10
lower sequence: Vv07s0031g02980.t01 (Vitis vinifera), 3'ss of exon 8
gttcacttcaaaatcaatttttgcaaatgttcattca-atggcactaaatcctatgtggtttggttagtacttagtactaacaaattaagttaacaagcagGAGAAGTTGCCACCGACAGATTCAAGACTAAGACCTGATCAAAGGTGTTTGGAGAATGGACAGCATGAAATGGCCAATTCTGAAAAGTTGCGGCTGGAAC
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-----------gtatgtttcttactcatctgcattggtgtggaagtgtaagtggaagccttccttccatgttcagtttgcataaaa-actttgaaacacagGAAAAGCTGCCGCCAACAGACTCAAGGCTCAGACCTGATCAGAGATGTTTAGAGAACGGGCAATATGAAATGGCCAATTCAGAGAAGTTGAGGCTGGAGC
upper sequence: GLYMA04G38330.1 (Glycine max), 3'ss of exon 10
lower sequence: PP1S67_260V6.1 (Physcomitrella patens), 3'ss of exon 8
-------------------------------------------------------------gttcacttcaaaatcaatttttgcaaatgttcattcaatggcactaaatcctatgtggtttggttagtacttag-tactaacaaatt-aagttaacaagcagGAGAAGTTGCCACCGACAGATTCAAGACTAAGACCTGATCAAAGGTGTTTGGAGAATGGACAGCATGAAATGGCCAATTCTGAAAAGTTGCGGCTGGAAC
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gtgagtatctgcaattttcttagacttaaatgcttatactagagatttgacttatatatggctgttttttttctttttttcttttttcctttcagttaataagaaatatgaatcggtagacgagtcaacattcatctacttataaatttaatttattttgtagGAAAAGTTGCCACCTACAGATTCAAGGTTGAGACCTGATCAAAGACATCTGGAGAATGGTGAATATGATGCTGCCAATTCAGAAAAACTGCGACTTGAAC
upper sequence: GLYMA04G38330.1 (Glycine max), 3'ss of exon 10
lower sequence: PP1S40_145V6.1 (Physcomitrella patens), 3'ss of exon 8
-------------------------gttcacttcaaaatc----aatttttgcaaatgttcattcaatggcactaaatcctat--gtggtttggttagtacttagt-actaacaaat-taagttaacaagcagGAGAAGTTGCCACCGACAGATTCAAGACTAAGACCTGATCAAAGGTGTTTGGAGAATGGACAGCATGAAATGGCCAATTCTGAAAAGTTGCGGCTGGAAC
| |||| | || || || || || || || || || | | | | |||||| | ||| ||| | | || | || | |||| ||||||||||| ||||||||||| | |||||||||||||| | | |||||||| | |||| |||||||| ||||| |||| || ||||
gtaagtatctgtagtttattcaggcatacactcgagcttcgcttaacttacgccaacgtaaatcttttgcagcttagtggaaacgatactttggtcgatctttacccacttatagatgttgtttgttttgaagGAAAAGTTGCCACCTACAGATTCAAGGTTGAGACCTGATCAAAGACATCTAGAGAATGGCGAATATGATGCTGCCAATTCAGAAAAACTGCGACTTGAAC
upper sequence: GLYMA04G38330.1 (Glycine max), 3'ss of exon 10
lower sequence: EFJ15167 (Selaginella moellendorffii), 3'ss of exon 8
gttcacttcaaaatcaatttttgcaaatgttcattcaatggcactaaatcctatgtggtttggttagtacttagtactaacaaattaagttaacaagcagGAGAAGTTGCCACCGACAGATTCAAGACTAAGACCTGATCAAAGGTGTTTGGAGAATGGACAGCATGAAATGGCCAATTCTGAAAAGTTGCGGCTGGAAC
|| | | | ||| | | | || ||| | | |||||||||| ||||||| |||||||| |||| |||||||||||| | |||||| || || | | || ||| ||||| |||||| ||||| |||||
-----------------------------------------------gtctttcaaagcat--ttattcgctcaagttctcatggtaaa--agcgtgcagGAGAAGCTGCCACCAACAGATTCCCGACTGAGACCTGATCAACGACATTTGGAAAACGGTGAATACGAGCAGGCTAATTCCGAAAAGCTGCGGTTGGAAG
upper sequence: GLYMA04G38330.1 (Glycine max), 3'ss of exon 10
lower sequence: EFJ08416 (Selaginella moellendorffii), 3'ss of exon 9
gttcacttcaaaatcaatttttgcaaatgttcattcaatggcactaaatcctatgtggtttggttagtacttagtactaacaaattaagttaacaagcagGAGAAGTTGCCACCGACAGATTCAAGACTAAGACCTGATCAAAGGTGTTTGGAGAATGGACAGCATGAAATGGCCAATTCTGAAAAGTTGCGGCTGGAAC
|| | | | ||| | | | || ||| | |||||||||| ||||||| |||||||| |||| |||||||||||| | |||||| || || | | || ||| ||||| |||||| ||||| | |||
-----------------------------------------------gtctttcaaagcat--ttattcgctcaagttctcatggtaaaacg-cgtgcagGAGAAGCTGCCACCAACAGATTCCCGACTGAGACCTGATCAACGACATTTGGAAAACGGTGAATACGAGCAGGCTAATTCCGAAAAGCTGCGGTTAGAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaatcctatgtggtttggttagtacttagtactaacaaattaagttaacaagcagGAGAAGTTGCCACCGACAGATTCAAGACTAAGACCTGATCAAAGGTGTTTGGAGAATGGACAGCATGAAATGGCCAATTCTGAAAAGTTGCGGCTGGAAC
taacaaattaagttaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttcacttcaaaatcaatttttgcaaatgttcattcaatggcactaaatcctatgtggtttggttagtacttagtactaacaaattaagttaacaagcagGAGAAGTTGCCACCGACAGATTCAAGACTAAGACCTGATCAAAGGTGTTTGGAGAATGGACAGCATGAAATGGCCAATTCTGAAAAGTTGCGGCTGGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- -cacttca
- - - - - - - - - ttttgca
- - - - - - - - - - - - - - - -cattcaa
- - - - - - - - - - - - - - - - - - - - - - - - -cctatgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - ggtttgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -actaaca