Sequence
atgc intronic sequence ATGC exonic sequence...catttggcattattacatcacaggcattatacttttttggattgaagtcagattgtatacttaatcagttagctgattcaatggaatttgccctttgcagTGAAATGGGTGCTCATTTTTCACCATGTGGTAGATTTTTAGCTGCCTGTGTTGCATGTGTGCTTCCTCATATAGAAGCAGATCCAGGATTACAAACTCCA
Basic information
species | Glycine max |
transcript | GLYMA03G32620.2 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA03G32620.2 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G353548_T05 (Zea mays), 3'ss of exon 9
-catttggcattattacatcacaggcattatactttt-ttggat-tgaagtcagattgtatacttaatcagttagctgattcaatggaatttgcc--ctttgcagTGAAATGGGTGCTCATTTTTCACCATGTGGTAGATTTTTAGCTGCCTGTGTTGCATGTGTGCTTCCTCATATAGAAGCAGATCCAGGATTACAAACTCCA-
||| || | | ||| | | || ||||||| ||| || | | | || | || | | || | || ||| || || ||||||||||||||||||| |||||||| |||||||| ||||| | | ||||| ||||||||| || | ||||| | ||||| | || | | | || | |
tcatatgtgaattgtacct----gtacttgtacttttgttgcatcttatgcttgagcagggaattg-tgatttcattacttactatgaacttaccaattttgcagTGAAATGGGTGCCCATTTTTCCCCATGTGGACGATTTCTTGTAGCCTGCGTTGCATGTTTGTTGCCTCAAACAGAAGGTGG-CCGTGGTAGCCAATTGCCT
upper sequence: GLYMA03G32620.2 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G167886_T02 (Zea mays), 3'ss of exon 9
catttggcattattacatcacaggcattata-cttttttggattgaagtcagattgtatacttaa---tcagttagctga---ttcaatggaatttgccctttgcagTGAAATGGGTGCTCATTTTTCACCATGTGGTAGATTTTTAGCTGCCTGTGTTGCATGTGTGCTTCCTCATATAGAAGCAGATCCAGGATTACAAACTCCA-
|||| | |||| | || || | |||| | |||| || | | || | ||| ||| ||| ||| | ||||| | ||||| ||||||||| | ||| ||||||| ||||| ||||||| | ||| ||||||||||||||||| || || | | | | | ||| || | ||
---ttggtaatattgagtagcacttatatcatctttgctagatttctatcgcacctgaagtttgagactcatttacttgaagtttctgttaaattt----tctgcagCGAAATGGGTACCCATGTTTCACCCTGTGGGCGATTTTTGGTTGCTTGTGTTGCATGTGTGCTGCCACACAGTTATGGTGGCCATGGAAGTCAG-TTGCAT
upper sequence: GLYMA03G32620.2 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G007229_T01 (Zea mays), 3'ss of exon 9
------catttggcattattacatcacaggcattatacttttttggattgaagtcag--attgtatacttaatcagttag-ctgattcaatggaatttgccctttgcagTGAAATGGGTGCTCATTTTTCACCATGTGGTAGATTTTTAGCTGCCTGTGTTGCATGTGTGCTTCCTCATATAGAAGCAGATCCAGGATTACAAACTCCA-
| | || | || | | | | | | || | ||| | || || ||||| |||| || | ||| |||| | |||||| | |||||||||||||| |||||||| |||||||| ||||| | | || |||||||| ||| || | || || | ||||| || || | | | || | |
cgtaaataaattgctctgttgcct-atatgttatgtagcatcttgagcttcagcaaggaattgtg-acttcattacttactctgaacttaccgaatttac-------agTGAAATGGGTGCCCATTTTTCCCCATGTGGACGATTTCTGGTAGCATGTGTTGCGTGTTTGTTGCCACAAACAGAAGACGA-CCGTGGTAGCCAATTGCCT
upper sequence: GLYMA03G32620.2 (Glycine max), 3'ss of exon 8
lower sequence: AT1G04140.2 (Arabidopsis thaliana), 3'ss of exon 8
catttggcattattacatcacagg-cattatacttttttggattgaagtcagattgtata---cttaatcagttagctgattca-atggaatttgccctt-----tgcagTGAAATGGGTGCTCATTTTTCACCATGTGGTAGATTTTTAGCTGCCTGTGTTGCATGTGTGCTTCCTCATATAGAAGCAGATCCAGGATTACAAACTCCA
| | ||| | | | | || ||| | || ||| || | | |||| || | || || | ||| | || || |||||||| ||||| || |||||||| |||||||| |||| |||||| |||||||||||||| || |||||||| || |||||||| | || || || |
------gtaaaatttctccttatatcgttgtacgatcttagatgatcgtgatgctatataatatttctccttttgatggagatacatgatgtgtgtgtttatcgttgcagTGAGATGGGAGCCCATTTTTCTCCATGTGGGAGATATTTAGCAGCCTGTGTTGCATGCGTTATTCCTCATGCTGAGACAGATCCAAGTTTGCAGACACTG
upper sequence: GLYMA03G32620.2 (Glycine max), 3'ss of exon 8
lower sequence: AT5G43930.3 (Arabidopsis thaliana), 3'ss of exon 8
-----------catttggcattattacatcacaggcattatacttttttggat-tgaagtcagattgtatacttaatcagttagctgattcaatggaatttgccctttgcagTGAAATGGGTGCTCATTTTTCACCATGTGGTAGATTTTTAGCTGCCTGTGTTGCATGTGTGCTTCCTCATATAGAAGCAGATCCAGGATTACAAACTCCA
| ||| | | |||| ||| |||| || | ||| | | || || || || || || || | | |||||||||||| ||||||| ||| |||||||| |||| |||||| ||||||||||| ||||| |||||||| || |||||| ||| | || || | |
gcaaagctccttctctgggtccttgatatcattc-tgttacacttgaatgcctatgatgctaagttttactattggatgtatattgatatctctgcttctttttgtgttcagTGAAATGGGAGCTCATTATTCGCCATGTGGGAGATATTTAGCGGCCTGTGTTGCGTGTGTTTTTCCTCATGGTGAGATAGATCCTGGACTGCAGACACAA
upper sequence: GLYMA03G32620.2 (Glycine max), 3'ss of exon 8
lower sequence: Vv07s0005g04630.t01 (Vitis vinifera), 3'ss of exon 8
-catttggcattattacatcacaggcattatacttttttggattgaagtcagattgtatacttaatcagttagctgattcaatggaatttgccctttgcagTGAAATGGGTGCTCATTTTTCACCATGTGGTAGATTTTTAGCTGCCTGTGTTGCATGTGTGCTTCCTCATATAGAAGCAGATCCAGGATTACAAACTCCA
|| | ||| | ||| | || | | | | | | | | | || ||||| ||| | | || ||||||||||||||| ||||| ||||| ||||| ||||||||||||||||||||||||||||||||||||||| | ||||| ||||| ||||| ||||| |
atatcaagtatttgcatttcataaaatttctgcctagcctg-tcatccttgatccttgttacttatggtttagcatatttatgacacaactgtgattccagTGAAATGGGTGCACATTTATCACCTTGTGGGAGATTTTTAGCTGCCTGTGTTGCATGTGTGCTTCCTCATTTGGAAGCTGATCCTGGATTGCAAACACAG
upper sequence: GLYMA03G32620.2 (Glycine max), 3'ss of exon 8
lower sequence: PP1S58_234V6.1 (Physcomitrella patens), 3'ss of exon 9
catttggcattattacatcacaggcattatacttttttggattgaagtcagattgtatacttaatcagttagctgattcaatggaatttgccctttg--cagTGAAATGGGTGCTCATTTTTCACCATGTGGTAGATTTTTAGCTGCCTGTGTTGCATGTGTGCTTCCTCATATAGAAGCAGATCCAGGATTACAAACTCCA
|| || || | | || | | ||||| | | | | | ||| ||| || || || ||| | || || ||||||||||||||| || |||||||| |||||| ||||| ||||||| |||||||| |||||| | || || | ||| || | | | |
caatttacaccctgaaattcctcttgacttgagattttgcaatc--ttttgtgtttatctgtaacatcttcgcgtgttgaatattgtgtggttcgtgagcagTGAAATGGGTGCGCACTTTTCACCTTGTGGTCGATTTCTAGCTGCGTGTGTTGCCTGTGTGTTGCCCATGGCGGATTCTGATTCACGGCGTGGGAATACG
upper sequence: GLYMA03G32620.2 (Glycine max), 3'ss of exon 8
lower sequence: PP1S150_95V6.1 (Physcomitrella patens), 3'ss of exon 8
catttggcattattacatcacaggcattatacttttttgga---ttgaagtcagattgtatacttaatcagttagctgattcaatggaatttgccctttg--cagTGAAATGGGTGCTCATTTTTCACCATGTGGTAGATTTTTAGCTGCCTGTGTTGCATGTGTGCTTCCTCATATAGAAGCAGATCCAGGATTACAAACTCCA
| ||| | | || || | || |||| | | ||| | | | || || || || | || || ||| | || | | ||||||||||||||| || |||||||| |||||| | ||| ||||||| |||||||| || ||| | ||| | || | || || | || | |
----tatcatggtaatcagtcaagcgt-gtatttttgagaaaatttgtgataattcaatctatttgatacctttggtggtttaatattgtgtggtgtgggagcagTGAAATGGGTGCGCACTTTTCACCGTGTGGTCGGTTTCTAGCTGCGTGTGTTGCTTGCGTGTTGCCTATGGTTGATTCTGAGTCACGTCGTGGAAATACGMapped 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|8669853|gb|BE190960.1|BE190960EST: CTTAATGCTGATAGATGTCGTCTAACCATACCACATGCTGTCCTCTGCAG TGAAATGGGTGCTCATTTTTCACCATGTGGTAGATTTTTAGCTGCCTGTGT
genomic: CTTAATGCTGATAGATGTCGTCTAACCATACCACATGCTGTCCTCTGCAGgtaccttctg ... ccctttgcagTGAAATGGGTGCTCATTTTTCACCATGTGGTAGATTTTTAGCTGCCTGTGT
EST:
gi|193641938|gb|FK590692.1|FK590692EST: CTTAATGCTGATAGATGTCGTCTAACCATACCACATGCTGTCCTCTGCAG TGAAATGGGTGCTCATTTTTCACCATGTGGTAGATTTTTAGCTGCCTGTGT
genomic: CTTAATGCTGATAGATGTCGTCTAACCATACCACATGCTGTCCTCTGCAGgtaccttctg ... ccctttgcagTGAAATGGGTGCTCATTTTTCACCATGTGGTAGATTTTTAGCTGCCTGTGT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agtcagattgtatacttaatcagttagctgattcaatggaatttgccctttgcagTGAAATGGGTGCTCATTTTTCACCATGTGGTAGATTTTTAGCTGCCTGTGTTGCATGTGTGCTTCCTCATATAGAAGCAGATCCAGGATTACAAACTCCA
agctgat putative branch site (score: 4)
tttgcccttt putative PPT
attgtatacttaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
catttggcattattacatcacaggcattatacttttttggattgaagtcagattgtatacttaatcagttagctgattcaatggaatttgccctttgcagTGAAATGGGTGCTCATTTTTCACCATGTGGTAGATTTTTAGCTGCCTGTGTTGCATGTGTGCTTCCTCATATAGAAGCAGATCCAGGATTACAAACTCCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT