Sequence
atgc intronic sequence ATGC exonic sequence...cacttcaaaatcaattttgtagaatgaatttcattcaaacacactaaatcctatgtagtttggttagtacttagtactaacaatttaagttaacaaatagGAGAAGTTGCCACCGACAGATTCAAGGCTAAGACCTGATCAAAGGTGTTTGGAGAATGGACAGCATGAAATGGCCAATTCTGAAAAGTTGCGGCTAGAAC
Basic information
species | Glycine max |
transcript | GLYMA06G16720.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA06G16720.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv07s0031g02980.t01 (Vitis vinifera), 3'ss of exon 8
---cacttcaaaatcaattttgtaga-atgaatttcattcaaacacactaaatcctatgtagtttggttagtacttagtactaacaatttaagttaacaaatagGAGAAGTTGCCACCGACAGATTCAAGGCTAAGACCTGATCAAAGGTGTTTGGAGAATGGACAGCATGAAATGGCCAATTCTGAAAAGTTGCGGCTAGAAC
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gtatgtttcttactcatctgcattggtgtgga---agtgtaagtggaagccttccttccatgttcagtttgca--------taaaaactt----tgaaacacagGAAAAGCTGCCGCCAACAGACTCAAGGCTCAGACCTGATCAGAGATGTTTAGAGAACGGGCAATATGAAATGGCCAATTCAGAGAAGTTGAGGCTGGAGC
upper sequence: GLYMA06G16720.1 (Glycine max), 3'ss of exon 9
lower sequence: PP1S67_260V6.1 (Physcomitrella patens), 3'ss of exon 8
-------------------------------------------------------------cacttcaaaatcaattttgtagaatgaatttcattcaaacacactaaatcctatgtagtttggttagtacttag-tactaacaa-tttaagttaacaaatagGAGAAGTTGCCACCGACAGATTCAAGGCTAAGACCTGATCAAAGGTGTTTGGAGAATGGACAGCATGAAATGGCCAATTCTGAAAAGTTGCGGCTAGAAC
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gtgagtatctgcaattttcttagacttaaatgcttatactagagatttgacttatatatggctgttttttttctttttttcttttttcctttcagttaataagaaatatgaatcggtagacgagtcaacattcatctacttataaatttaatttattttgtagGAAAAGTTGCCACCTACAGATTCAAGGTTGAGACCTGATCAAAGACATCTGGAGAATGGTGAATATGATGCTGCCAATTCAGAAAAACTGCGACTTGAAC
upper sequence: GLYMA06G16720.1 (Glycine max), 3'ss of exon 9
lower sequence: PP1S40_145V6.1 (Physcomitrella patens), 3'ss of exon 8
----------------------------cacttcaaaatcaattttgtagaatgaatttcattcaaacaca-ctaaatcctat--gtagtttggttagtacttagt-actaaca-atttaagttaacaaatagGAGAAGTTGCCACCGACAGATTCAAGGCTAAGACCTGATCAAAGGTGTTTGGAGAATGGACAGCATGAAATGGCCAATTCTGAAAAGTTGCGGCTAGAAC
|||| | || || | || | | || || || | | | || |||||| | ||| ||| | | || | || |||| ||||||||||| |||||||||||| | |||||||||||||| | | |||||||| | |||| |||||||| ||||| |||| || ||||
gtaagtatctgtagtttattcaggcatacactcgagcttcgcttaacttacgccaacgtaaatcttttgcagcttagtggaaacgatactttggtcgatctttacccacttatagatgttgtttgttttgaagGAAAAGTTGCCACCTACAGATTCAAGGTTGAGACCTGATCAAAGACATCTAGAGAATGGCGAATATGATGCTGCCAATTCAGAAAAACTGCGACTTGAAC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaatcctatgtagtttggttagtacttagtactaacaatttaagttaacaaatagGAGAAGTTGCCACCGACAGATTCAAGGCTAAGACCTGATCAAAGGTGTTTGGAGAATGGACAGCATGAAATGGCCAATTCTGAAAAGTTGCGGCTAGAAC
taacaatttaagttaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cacttcaaaatcaattttgtagaatgaatttcattcaaacacactaaatcctatgtagtttggttagtacttagtactaacaatttaagttaacaaatagGAGAAGTTGCCACCGACAGATTCAAGGCTAAGACCTGATCAAAGGTGTTTGGAGAATGGACAGCATGAAATGGCCAATTCTGAAAAGTTGCGGCTAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
cacttca
- - - - - - - - - - - - - - - - - -caaacac
- - - - - - - - - - - - - - - - - - - - - - - - -cctatgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -actaaca