Sequence
atgc intronic sequence ATGC exonic sequence...gtatttgggtaagtattctcccacactttttgtttgcaatttcaacactcttgctactgtttataattgttacgtggtcaattttgtttttgaactaaagGGGGTTATGATATGGAGGAGAAAGCTGCAAGAGCCTATGATCTCGCGGCCCTTAAGTACTGGGGACCTTCAACGCATATAAACTTTTCG
Basic information
species | Glycine max |
transcript | GLYMA04G05080.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA04G05080.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os03g56050.1 (Oryza sativa), 3'ss of exon 3
--gtatttgggtaagtattctcccacactttttgtttgcaatttcaacactctt--gctactgtt-tataattgttacgtggtcaattttgtttttgaactaaagGGGGTTATGATATGGAGGAGAAAGCTGCAAGAGCCTATGATCTCGCGGCCCTTAAGTACTGGGGACCTTCAACGCATATAAACTTTTCG
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gtgtatcttggtgagtaccagtacacaagtacttgggatgaattgattagtttttggaaacaaagatttgattgtgagattg-caatgtaacctttg--ctagGTGGG--TATGACATGGAGGAGAAGGCTGCCAGGGCGTATGATCTTGCTGCGCTCAAGTACTGGGGCCCTTCCACGCACATCAACTTCCCG
upper sequence: GLYMA04G05080.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os07g03250.1 (Oryza sativa), 3'ss of exon 2
-------gtatttgggtaagtattctcccacactttttgtttgcaatttcaacactcttgctactgtttataattgttacgtggtca---attttgtttttgaactaa-agGGGGTTATGATATGGAGGAGAAAGCTGCAAGAGCCTATGATCTCGCGGCCCTTAAGTACTGGGGACCTTCAACGCATATAAACTTTTCG
|||| | || || | || | ||| | | | | | |||| | | | || | |||| || | | ||| || ||||| |||||||||||||| || ||||| ||||| || ||||| || ||||| ||||| ||||| || || || ||||| ||
gtaagtgttattacattcctcatgtggtaactttacatggtaaaaatgttctcgtggtaaaaagtaaaaataaataaaaaaagttcttttactttggttgggggtgattagGTGGGTATGACATGGAGGAGAAAGCGGCGAGAGCGTATGACCTGGCGGCGCTCAAGTATTGGGGCCCTTCCACACACATCAACTTCCCG
upper sequence: GLYMA04G05080.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G008234_T01 (Zea mays), 3'ss of exon 1
-------------------------------------gtatttgggtaagt-attctcccacactttttgtttgcaatttcaacactcttgctactgtttataattgttacgtg-----gtcaattttgtttttgaactaaagGGGGTTATGATATGGAGGAGAAAGCTGCAAGAGCCTATGATCTCGCGGCCCTTAAGTACTGGGGACCTTCAACGCATATAAACTTTTCG
|| | | | | | || | | || |||| | | | ||| || ||| || | | | | | ||| || || || |||||||||| || || |||||||| || || ||||| || ||||||||||| ||||| ||||| || ||||| ||
gtaagcagagcactcacacattcacgcagatgcagctctactagagggggccggccggccggggtagaaagtaaaaaaaaaaacatggtggtaaagatttccttgcattgtgtgtgtatgtggccgtggccgtgggtgtttagGCGGGTACGACGTGGAGGAGAAGGCGGCGAGAGCCTACGACCTGGCGGCGCTCAAGTACTGGGGCCCTTCCACGCACATCAACTTCCCG
upper sequence: GLYMA04G05080.1 (Glycine max), 3'ss of exon 4
lower sequence: AT4G37750.1 (Arabidopsis thaliana), 3'ss of exon 4
gtatttgggtaagt-attctcccacactttttgtttgcaatttcaacactcttgctactgt--ttata-attgttacgtggtcaattttgttt--ttgaactaa----agGGGGTTATGATATGGAGGAGAAAGCTGCAAGAGCCTATGATCTCGCGGCCCTTAAGTACTGGGGACCTTCAACGCATATAAACTTTTCG
||| | | | | ||| | || || || | |||| ||| | | | | || ||| | || | | | |||||||| || || ||| |||||||||||||||||||||||||| |||| |||||||| || || || ||||||||||| || || || || | || || ||
gtaagtacacacttcaatcttcatggattcatgatttccccctcaaatttctcgggaaaataatgatggattttgacttctttatttttgtttgattaaatctttattagGAGGTTATGATATGGAGGAGAAAGCTGCTCGAGCATATGATCTTGCTGCACTCAAGTACTGGGGTCCCTCTACTCACACCAATTTCTCT
upper sequence: GLYMA04G05080.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv18s0001g08610.t01 (Vitis vinifera), 3'ss of exon 4
gtatttgggtaagtattctcccacactttttgtttgcaatttcaacactct-tgctactgt-ttataattgt-----tacgtggtcaattttgtttttgaactaaagGGGGTTATGATATGGAGGAGAAAGCTGCAAGAGCCTATGATCTCGCGGCCCTTAAGTACTGGGGACCTTCAACGCATATAAACTTTTCG
||||| | || ||||||| | | ||| | || | | | | | || | | || || | | ||| | || | |||||| ||||||||||| ||||||||||||||||| || ||||| |||||||| || |||||||||||||| || ||||| ||||| ||
--------gtaagc---ccccttttctttttggtcgaaatgaagaaaccatgtatgagtatattctgttcgtgtttatatttaattgattctacccatgtctttcagGGGGGTATGATATGGAAGAGAAAGCTGCAAGAGCTTACGATCTGGCGGCCCTCAAATACTGGGGACCTTCTACTCATATCAACTTCCCG
upper sequence: GLYMA04G05080.1 (Glycine max), 3'ss of exon 4
lower sequence: EFJ21317 (Selaginella moellendorffii), 3'ss of exon 3
----------gtatttgggtaagtattctcccacactttttgtttgcaatttcaacactcttgctactgtttataattgttacgtggtcaattttgtttttgaactaaagGGGGTTATGATATGGAGGAGAAAGCTGCAAGAGCCTATGATCTCGCGGCCCTTAAGTACTGGGGACCTTCAACGCATATAAACTTTTCG
|| ||||| ||| | | || ||||| | || | | || | | | | |||| | || | | | |||||||||||| | ||| |||||||| || |||| |||||||| ||||| || ||||| ||||||||| | || || |||||| |
aatgcgcagtttacctgggtgagtgtcactct----ttgttgttcgtgcttgaagtgttttttcgttcctcatttaatgtttcttg------ccgggaatgaatgcgcagGGGGTTATGACAAGGAAGAGAAAGCAGCGCGAGCGTATGATCTGGCGGCGCTCAAGTATTGGGGACCTACGACCACCATCAACTTTCCT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cactcttgctactgtttataattgttacgtggtcaattttgtttttgaactaaagGGGGTTATGATATGGAGGAGAAAGCTGCAAGAGCCTATGATCTCGCGGCCCTTAAGTACTGGGGACCTTCAACGCATATAAACTTTTCG
ttttgttttt CT-rich tract
tgtttataattgtta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatttgggtaagtattctcccacactttttgtttgcaatttcaacactcttgctactgtttataattgttacgtggtcaattttgtttttgaactaaagGGGGTTATGATATGGAGGAGAAAGCTGCAAGAGCCTATGATCTCGCGGCCCTTAAGTACTGGGGACCTTCAACGCATATAAACTTTTCG
- - - - - - - - -ctcccac
- - - - - - - - - - - - - - - tgtttgc
- - - - - - - - - - - - - - - - - - - - - - - -ctcttgc