Sequence
atgc intronic sequence ATGC exonic sequencegctagcatttacacagtatatgcattgtaatttaatgtaacaagatttacacctagagaagaattaactttgttctaaactcagttgattctgattaacttggtagcagGCACCACCAACATGGAAGGTGGCAAGCTCGAATTGGAAGGGTAGCCGGAAACAAAGATCTATATCTTGGAACCTTTA
Basic information
species | Glycine max |
transcript | GLYMA01G40380.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA01G40380.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os03g12950.1 (Oryza sativa), 3'ss of exon 7
--gctagcatttacacagtatatgcattgtaatttaatgtaacaagatttacacctagagaagaatta-actttgttctaaactcagttgattctg-attaacttggtagcagGCACCACCAACATGGAAGGTGGCAAGCTCGAATTGGAAGGGTAGCCGGAAACAAAGATCTATATCTTGGAACCTTTA
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gtgtttcattttgtgctgaacaagcatatgcatttttcttgataa---ttatttcaagaacacattcgcatcaagatacaatctcactgtgttaaatgttaactgcattgcagGCATCACCAGCATGGAAGATGGCAAGCTCGGATTGGCAGGGTTGCTGGCAACAAGGACTTGTATCTCGGCACTTTCA
upper sequence: GLYMA01G40380.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G063994_T01 (Zea mays), 3'ss of exon 3
gctagcatttacacagtatatgcattgtaatttaatgtaacaagatttacacctagagaagaattaactttgttctaaactcagttgatt--ctgattaacttggtagcagGCACCACCAACATGGAAGGTGGCAAGCTCGAATTGGAAGGGTAGCCGGAAACAAAGATCTATATCTTGGAACCTTTA----------
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------------------------------gttcgtttgcccagactactatgcc-accgcattttgcttccttagagatcgtctcaatgtacacgctaactgcattgcagGCACCACCAGCAAGGAAGATGGCAGTCTCGGATTGGAAGGGTCGCTGGAAACAAGGATCTATACCTCGACACTTTTAGTAAGAAAGA
upper sequence: GLYMA01G40380.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G021573_T02 (Zea mays), 3'ss of exon 6
gctagcatttacacagtatatgcattgtaatttaatgtaacaagatttacacctagagaagaattaacttt-gttctaaactcagttgattctgattaacttggtagcagGCACCACCAACATGGAAGGTGGCAAGCTCGAATTGGAAGGGTAGCCGGAAACAAAGATCTATATCTTGGAACCTTTA
| | | | | || | | || || | | | || | | | | ||| | | | |||| | | | ||||| | ||||||||||||| || ||||| ||||| |||| |||||||| || || |||||||| |||||||| || || || || |
gttcgtctgtgcagggattgcgccaccgcatctcgcttccttattattgtgcggacaactaacgtaagtgaagagatcgtctcaatgcacac--gctaactgcattgcagGCACCACCAGCAAGGAAGATGGCAGTCTCGGATTGGAAGAGTCGCTGGAAACAAGGATCTATACCTCGGCACTTTCA
upper sequence: GLYMA01G40380.1 (Glycine max), 3'ss of exon 6
lower sequence: AT4G37750.1 (Arabidopsis thaliana), 3'ss of exon 6
gctagcatttacacagtatatgcattgtaatttaatgtaacaagatttacacctagagaagaattaactttgttctaaactcagttgattctgattaacttggtagcagGCACCACCAACATGGAAGGTGGCAAGCTCGAATTGGAAGGGTAGCCGGAAACAAAGATCTATATCTTGGAACCTTTA
| || | | || || || ||| || || ||| | | | | | ||| ||||||| || || | | ||| || || ||||| ||||||||||||||||| || ||||| || || || |||||||||||||| || |||||||| |||
----gtccttttaaattacatttat-ataactttatataatacatagtttaataatgtgaatattgactttgt----------gtgagtttt--------ttgtactagACATCACCAGCATGGAAGGTGGCAAGCACGGATTGGTAGAGTCGCTGGAAACAAAGATCTCTACCTTGGAACTTTTG
upper sequence: GLYMA01G40380.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv07s0151g00440.t01 (Vitis vinifera), 3'ss of exon 6
-----gctagcatttacacagtatat---gcattgtaatt-taatgtaacaagatttacacctagagaagaattaactttgttctaaactcagttgattctgattaacttggtagcagGCACCACCAACATGGAAGGTGGCAAGCTCGAATTGGAAGGGTAGCCGGAAACAAAGATCTATATCTTGGAACCTTTA
||| |||| | ||| | |||||||| || ||| | | | | || ||| || | || || || || | ||| || || |||||| || |||||||||||| ||||||||||||||||||| || || || || ||||| || || |||||||| || || |
gtcttactattattttctgcttatgtctcatcttgtaattgtattgtcatgttctctgagagaaaaggcgaaaaaaaatc-ccctgaaatctctt--tcctgcttcgattcttagcagACATCACCAACATGGACGGTGGCAAGCTCGAATTGGCAGAGTTGCAGGGAACAAGGACCTTTATCTTGGGACATTCA
upper sequence: GLYMA01G40380.1 (Glycine max), 3'ss of exon 6
lower sequence: EFJ26861 (Selaginella moellendorffii), 3'ss of exon 6
gctagcatttacacagtatatgcattgtaatttaatgtaacaagatttacacctagagaagaattaactttgttctaaactcagttgattctgattaacttggtagcagGCACCACCAACATGGAAGGTGGCAAGCTCGAATTGGAAGGGTAGCCGGAAACAAAGATCTATATCTTGGAACCTTTA
|| | | | | | || || | | | | ||| | |||| ||||| ||||| ||| | |||||||| || |||||||| |||||||| ||||||||||| || || ||||| || |
----------------------------------------------gtaagcgtgccgtaaatccttctcctttgcgattcctaacaagctt---taaatcat--gcagACACCATCAACAAGGACGCTGGCAAGCCCGGATTGGAAGAGTAGCCGGCAACAAAGATCTTTACCTCGGAACTTTCA
upper sequence: GLYMA01G40380.1 (Glycine max), 3'ss of exon 6
lower sequence: EFJ21317 (Selaginella moellendorffii), 3'ss of exon 6
gctagcatttacacagtatatgcattgtaatttaatgtaacaagatttacacctagagaagaattaactttgttctaaactcagttgattctgattaacttggta----gcagGCACCACCAACATGGAAGGTGGCAAGCTCGAATTGGAAGGGTAGCCGGAAACAAAGATCTATATCTTGGAACCTTTA
|| | | | || | | ||| | | || | | ||| | |||| ||||| ||||| ||| | |||||||| || |||||||| |||||||| ||||||||||| || || ||||| || |
---------------------------------------------------gtaagcgtggcgtgaatccttct----acttcgcgattcctaacaagctttaaatcatgcagACACCATCAACAAGGACGCTGGCAAGCCCGGATTGGAAGAGTAGCCGGCAACAAAGATCTTTACCTCGGAACTTTCA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agagaagaattaactttgttctaaactcagttgattctgattaacttggtagcagGCACCACCAACATGGAAGGTGGCAAGCTCGAATTGGAAGGGTAGCCGGAAACAAAGATCTATATCTTGGAACCTTTA
gattaac putative branch site (score: 2)
aattaacttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gctagcatttacacagtatatgcattgtaatttaatgtaacaagatttacacctagagaagaattaactttgttctaaactcagttgattctgattaacttggtagcagGCACCACCAACATGGAAGGTGGCAAGCTCGAATTGGAAGGGTAGCCGGAAACAAAGATCTATATCTTGGAACCTTTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG