Sequence
atgc intronic sequence ATGC exonic sequencegtaatataatttctcaaatcatggcatcagctctgtaatcttgaaatgacatgttttgcttcttccaaatttacaataacgtttaagaaagtattttactgtgcttaattaaaattggccttgatttgtcctagGTCCGCTGGGAATAAATTGCCCTTTGGATTGGGACACTAGAATGAAGATCGCCCTTGATGCTGCAAGAGGACTTGCATACATGCATGAAGATTCACAGCC
Basic information
species | Glycine max |
transcript | GLYMA02G01480.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA02G01480.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os01g14932.1 (Oryza sativa), 3'ss of exon 5
-------------------gtaatataatttctcaaatcatggcatcagctctgtaatcttgaaatgacatgttttgcttctt--ccaaatttac-aataacgtttaagaaagtat--tttactgtgcttaattaaaattgg----ccttgatttgtcctagGTCCGCTGGGAATAAATTGCCCTTTGGATTGGGACACTAGAATGAAGATCGCCCTTGATGCTGCAAGAGGACTTGCATACATGCATGAAGATTCACAGCC
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gtatggccaattgagtcaactatttctccttctgaaattgctgcataagttccactcagttgcagttgaatgtggtccttcattgtttaattaattagtggtgatcatgtaatcatgatacaccttgactcttgagtctctgactacttacatttttttcagGTACATTGGGAGCTAGCCGCCCCTTGGACTGGGACACTAGAATGAGGATAGCACTAGATGCTGCCAGGGGATTGGCATACCTTCATGAGGATTCTCAGCC
upper sequence: GLYMA02G01480.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os01g14932.3 (Oryza sativa), 3'ss of exon 6
-------------------gtaatataatttctcaaatcatggcatcagctctgtaatcttgaaatgacatgttttgcttcttc--caaatttac-aataacgtttaagaaagtat--tttactgtgcttaattaaaattgg----ccttgatttgtcctagGTCCGCTGGGAATAAATTGCCCTTTGGATTGGGACACTAGAATGAAGATCGCCCTTGATGCTGCAAGAGGACTTGCATACATGCATGAAGATTCACAGCC----------------
|| | |||| |||| |||| || || ||| | | |||| | |||| | |||| | | | | | | | || || | || || | | | | | | | |||| | |||| | ||||| | |||| ||||| |||||||||||||||| ||| || || |||||||| || ||| | |||||| | ||||| ||||| |||||
gtatggccaattgagtcaactatttctccttctgaaattgctgcataagttccactcagttgcagttgaatgtggtccttcattgtttaattaattagtggtgatcatgtaatcatgatacaccttgactcttgagtctctgactacttacatttttttcaggtacattgggagctagCCGCCCCTTGGACTGGGACACTAGAATGAGGATAGCACTAGATGCTGCCAGGGGATTGGCATACCTTCATGAGGATTCTCAGCCTTGCGTAATCCACAGG
upper sequence: GLYMA02G01480.1 (Glycine max), 3'ss of exon 4
lower sequence: AT4G02010.1 (Arabidopsis thaliana), 3'ss of exon 5
gtaatataatttctcaaatcatggcatcagctctgtaatcttgaaatgacatgttttgcttcttccaaatttacaataacgt-ttaagaaagtattttactgtgcttaattaaaattggccttgatttgtcctagGTCCGCTGGGAATAAATTGCCCTTTGGATTGGGACACTAGAATGAAGATCGCCCTTGATGCTGCAAGAGGACTTGCATACATGCATGAAGATTCACAGCC
|||| |||| || | || || | || || | | | | | | | || ||| | || | || | | | ||| || ||| || | || || | ||| || || || | || || ||| | ||||||||||| ||||||||||| || ||||||||||||||||||||||||||| | |||||||| || || ||
-----gtaatatctc--ctctttgcttc--ccttgctgcct---atttttagatctgacattgtcaaaagtagttattgtacactgagttcatctacaagagtggtttatttaagtcattgtttat--gcttcagGGCCTCTCGGGTTGAACTGTCCTCTTGATTGGGACACCAGAATGAAGATTGCACTTGATGCTGCAAGAGGACTTGCATACCTTCATGAAGACTCGCAACC
upper sequence: GLYMA02G01480.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv07s0005g01590.t01 (Vitis vinifera), 3'ss of exon 4
--------------------------gtaatataatttctcaaatcatggcatcagctctgtaatcttgaaatgacatgttttgcttcttccaaa----tttacaataacgt--ttaagaaagtattttactgtgcttaattaaaattggccttgatttgtcctagGTCCGCTGGGAATAAATTGCCCTTTGGATTGGGACACTAGAATGAAGATCGCCCTTGATGCTGCAAGAGGACTTGCATACATGCATGAAGATTCACAGCC
|||| || | |||| || | || || | | | | || | || || |||| ||| | || || || || | || ||| | | ||| | | ||| | || | || | ||| || |||||| | || || ||||||||||||||||| |||||||||| || ||||||||||| ||||| ||||||||| ||||||| |||||||| ||
gtagtttgctttcttgaaccacagatttaatg-aaatcctcatatatttatctct-ctttccattgtccctattatggattgtgtatcttggaaaaaaatataaaactctgtacttttgggagattttcaatacatagtattgacaatggtcctgttctgctccagGCCCTCTGGGAGTCAACTGTCCTTTGGATTGGGACACCCGAATGAAGATTGCTCTTGATGCTGCCAGAGGGCTTGCATACCTGCATGAGGATTCACAACC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cgtttaagaaagtattttactgtgcttaattaaaattggccttgatttgtcctagGTCCGCTGGGAATAAATTGCCCTTTGGATTGGGACACTAGAATGAAGATCGCCCTTGATGCTGCAAGAGGACTTGCATACATGCATGAAGATTCACAGCC
tttgtcct CT-rich tract
tgcttaattaaaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatataatttctcaaatcatggcatcagctctgtaatcttgaaatgacatgttttgcttcttccaaatttacaataacgtttaagaaagtattttactgtgcttaattaaaattggccttgatttgtcctagGTCCGCTGGGAATAAATTGCCCTTTGGATTGGGACACTAGAATGAAGATCGCCCTTGATGCTGCAAGAGGACTTGCATACATGCATGAAGATTCACAGCC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA