Sequence
atgc intronic sequence ATGC exonic sequence...aagtcaatggtcatattgattagttgttggattgatatggtcctgttttcattattttacaatgcttaaatttaagcatcattgcctgctttttatacagAGGAACTGATATGACAAGTCCTCATGGCATACCTGTTGACCTGTTGGATCGGTTGGTGATCATTCGAACGCAAACATATGGTCCTGCTGAAATGATACAG
Basic information
species | Glycine max |
transcript | GLYMA08G21830.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G21830.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os01g62040.1 (Oryza sativa), 3'ss of exon 8
------------------------aagtcaatggtcatattgattagttgttggattgata-tggtcctgt---tttcattatt-ttacaatgcttaaatttaagca--tcattgcctgctttt-------tatacagAGGAACTGATATGACAAGTCCTCATGGCATACCTGTTGACCTGTTGGATCGGTTGGTGATCATTCGAACGCAAACATATGGTCCTGCTGAAATGATACAG
||| |||| |||| ||| || | ||| || || | ||| |||| || | |||||| |||| | || | ||| | | | |||||||||||||||||||||||| ||||| ||||| ||||| || | ||||| |||||||| |||||||| ||||||| ||||| |||| ||||| |||
gtaaacggtttgatttaccgctcgaagcactctgtcacattg--cagt-accagagtaatactgcgtctatcagtttgtctattactatgctccttaaagttaacaagtcttttatatacttgtgtgaatgtgtccagAGGAACTGATATGACAAGTCCGCATGGTATACCAGTTGATCTTCTAGATCGATTGGTGATTATTCGAACAGAAACATACGGTCCCACTGAGATGATCCAG
upper sequence: GLYMA08G21830.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os07g08170.1 (Oryza sativa), 3'ss of exon 8
-----------------------aagtcaatggtcatattgattagttgttggattgat-atggtcctgtt------ttcattattttacaatgcttaaa-tttaagcatcattgcctgctttttatacagAGGAACTGATATGACAAGTCCTCATGGCATACCTGTTGACCTGTTGGATCGGTTGGTGATCATTCGAACGCAAACATATGGTCCTGCTGAAATGATACAG
| || | | | | || | || ||| ||| || |||| || | |||||| |||| | ||| || | | |||||||||||||||||||||||| ||||| ||||| ||||| || | || | |||||||| |||||||| ||||||||||||| |||| ||||| |||
gtaaacagtttgatttaccagtcgaagcactctgcgctacattataataccagactaatcatgtgtttgtcagtttgtttattaccatatgctccttaaagtttacaaagtcttgttatgcttgtgtccagAGGAACTGATATGACAAGTCCACATGGTATACCAGTTGATCTTCTAGACAGATTGGTGATTATTCGAACAGAAACATATGGTCCCACTGAGATGATCCAG
upper sequence: GLYMA08G21830.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G018697_T04 (Zea mays), 3'ss of exon 2
------------------------------------aagtcaatggtcatattgattagttgttggattgatatggtcctgttttcattattttacaatgcttaaatttaagcatcattgcctgctttttatacagAGGAACTGATATGACAAGTCCTCATGGCATACCTGTTGACCTGTTGGATCGGTTGGTGATCATTCGAACGCAAACATATGGTCCTGCTGAAATGATACAG
| ||||| || | | | | | | | || || | ||| || | | | ||| | | ||| | || |||| |||||||||||||||||||||||||| ||||| ||||| || || || | ||| || ||||||| ||||| || | |||||||| ||| |||| |||||||||
gtaggcagtttatttgccagactactcttgcagctaagttcaatacccagcataaatctgtacttgtctacta-agttgcaccatgattgattgattacttt---attaatgaatcgtgtaatgatttt-gtacagAGGAACTGATATGACAAGTCCACATGGTATACCGGTGGATCTTCTAGATAGGCTGGTGATTATTCGGACAGAGACATATGGCCCTACTGAGATGATACAG
upper sequence: GLYMA08G21830.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv06s0004g02910.t01 (Vitis vinifera), 3'ss of exon 8
---aagtcaatggtcatattgattagttgttggattgatatggtcctgttttcattattttacaatgcttaaatttaagcatcattgcctgctttttatacagAGGAACTGATATGACAAGTCCTCATGGCATACCTGTTGACCTGTTGGATCGGTTGGTGATCATTCGAACGCAAACATATGGTCCTGCTGAAATGATACAG
| | || | ||| ||| | | | | | || || | ||| | ||| | | | ||| ||| || || | ||||||||||||||||| |||||||||||||||||||||||| |||| || ||||||||||| | || ||| |||| |||||||||||||| ||||| |||
agtactccgatttttatagaagttaacatctaggc-gttgcctggattccttgatcacctta-agctcttgtttctgaacatggcc-ccttctcattttgcagAGGAACTGATATGAGTAGTCCTCATGGCATACCTGTTGACTTGTTAGACCGGTTGGTGATTGTACGGACGGAAACTTATGGTCCTGCTGATATGATTCAGMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|22930082|gb|BU547221.1|BU547221EST: CTATCTCCAATAGTAATCTTTGCTACTAATAGAGGAATATGCAATGTAAG AGGAACTGATATGACAAGTCCTCATGGCATACCTGTTGACCTGTTGGATCG
genomic: CTATCTCCAATAGTAATCTTTGCTACTAATAGAGGAATATGCAATGTAAGgtatgaataa ... ttttatacagAGGAACTGATATGACAAGTCCTCATGGCATACCTGTTGACCTGTTGGATCG
EST:
gi|151406331|gb|EV276146.1|EV276146EST: CTATCTCCAATAGTAATCTTTGCTACTAATAGAGGAATATGCAATGTAAG AGGAACTGATATGACAAGTCCTCATGGCATACCTGTTGACCTGTTGGATCG
genomic: CTATCTCCAATAGTAATCTTTGCTACTAATAGAGGAATATGCAATGTAAGgtatgaataa ... ttttatacagAGGAACTGATATGACAAGTCCTCATGGCATACCTGTTGACCTGTTGGATCG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttcattattttacaatgcttaaatttaagcatcattgcctgctttttatacagAGGAACTGATATGACAAGTCCTCATGGCATACCTGTTGACCTGTTGGATCGGTTGGTGATCATTCGAACGCAAACATATGGTCCTGCTGAAATGATACAG
cctgcttttt CT-rich tract
attattttacaatgct 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aagtcaatggtcatattgattagttgttggattgatatggtcctgttttcattattttacaatgcttaaatttaagcatcattgcctgctttttatacagAGGAACTGATATGACAAGTCCTCATGGCATACCTGTTGACCTGTTGGATCGGTTGGTGATCATTCGAACGCAAACATATGGTCCTGCTGAAATGATACAG
- - - - - - - - - - - gttgttg
- - - - - - - - - - - - - - - - tgatatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -caatgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cattgcc