Sequence
atgc intronic sequence ATGC exonic sequence...tttgaattatcctggagattttatttatattggcctatttgtttagtgtcccaaacaaatttattcataagtgctttaaccttaatttcatttttatcagATCTATGATATATTCCAGTTGCTTCCATCTAAGATTCAAGTGGGAGTTTTCTCTGCTACAATGCCTCCCGAGGCACTTGAGATCACAAGGAAGTTCATGA
Basic information
species | Glycine max |
transcript | GLYMA09G07530.3 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G07530.3 (Glycine max), 3'ss of exon 4
lower sequence: AT1G72730.1 (Arabidopsis thaliana), 3'ss of exon 4
tttgaattatcctggagattttatttatattggcctatttgtttagtgtcccaaacaaatttattcataagtgctttaaccttaatttcatttttatcagATCTATGATATATTCCAGTTGCTTCCATCTAAGATTCAAGTGGGAGTTTTCTCTGCTACAATGCCTCCCGAGGCACTTGAGATCACAAGGAAGTTCATGA
|| ||| | | | | ||| | || ||| ||| | | |||| | |||| || ||| | || ||||| | | |||||| || || || |||||| | ||||| || ||| |||| || || |||||||||||||||||||||||||| || |||||||||||||||||||||||||
gtttaatcttgtttaatctcccattcacat-------tttctttttctctctgataaaatcaagtcatttgttcttataatttgatttc---tctgtcagATATACGACATCTTCCAGCTTCTTCCTTCCAAGGTTCAGGTTGGTGTTTTCTCTGCTACAATGCCTCCCGAAGCCCTTGAGATCACAAGGAAGTTCATGA
upper sequence: GLYMA09G07530.3 (Glycine max), 3'ss of exon 4
lower sequence: AT1G54270.2 (Arabidopsis thaliana), 3'ss of exon 4
-tttgaattatcctggagattttatttatattggcctatttgtttagtgtcccaaacaaatttattcataagtgctttaaccttaatttcatttttatcagATCTATGATATATTCCAGTTGCTTCCATCTAAGATTCAAGTGGGAGTTTTCTCTGCTACAATGCCTCCCGAGGCACTTGAGATCACAAGGAAGTTCATGA
|||| | | || | | ||| | || ||| | || ||| | || | | | || | | || ||| | | || ||||||||||| ||||||||| | || ||| | |||||||| || ||||| |||||||| ||||||||||| || || | ||||||||||| || |||||||
gtttgttatcttcttcaaagtttgaatctac---cctctgtggtta-tctctgatattgacttggttttgtgttgttttctggtgaatttg-------cagATCTATGACATATTCCAGCTTCTCCCACCAAAGATTCAGGTTGGAGTGTTCTCTGCGACAATGCCTCCGGAAGCTTTGGAGATCACAAGAAAATTCATGA
upper sequence: GLYMA09G07530.3 (Glycine max), 3'ss of exon 4
lower sequence: AT3G13920.2 (Arabidopsis thaliana), 3'ss of exon 4
tttgaattatcctggagattttatttatattggcctatttgtttagtgtcccaaacaaatttat-tcataagt--gctttaacctta---atttc--atttttatcagATCTATGATATATTCCAGTTGCTTCCATCTAAGATTCAAGTGGGAGTTTTCTCTGCTACAATGCCTCCCGAGGCACTTGAGATCACAAGGAAGTTCATGA
||| ||||| | ||||| ||| ||| | ||| | ||| || || | |||| |||| |||||||||||| ||||||||| | |||||| | ||||| ||||| || || ||||| || |||||||| || || || |||||||||||||||||||||||||
--------------------------gtatgcaaatattt-ctcagtgtttcaattccattctcgttatagtttaacttgaatctcactggtttctgggttttttcagATCTATGACATATTCCAGCTTCTTCCACCAAAGATCCAAGTTGGTGTGTTCTCCGCAACAATGCCACCAGAAGCTCTTGAGATCACAAGGAAGTTCATGA
upper sequence: GLYMA09G07530.3 (Glycine max), 3'ss of exon 4
lower sequence: Vv11s0016g01920.t01 (Vitis vinifera), 3'ss of exon 3
---tttgaattatcctggagattttatttatattggcctatttgtttagtgtcccaaacaaatttattcataagtgctttaacc--ttaatttcatttttatcagATCTATGATATATTCCAGTTGCTTCCATCTAAGATTCAAGTGGGAGTTTTCTCTGCTACAATGCCTCCCGAGGCACTTGAGATCACAAGGAAGTTCATGA
||| | | ||| || |||| | | | | | || ||||| || | || | ||| ||| |||| | || |||||||||||||| ||||| | || ||||| || ||||||| ||||| |||||||| |||||||| |||||||| |||||||| ||||||||||| ||||
ttatttttttaactctgtg--ttgtattccaagaacctcaacaacctttcaactttaatgcgtttat--atcactgttctaataaattagtttcttccttg-cagATCTATGATATTTTCCAACTCCTGCCATCAAAAGTTCAAGTTGGAGTGTTCTCTGCCACAATGCCACCCGAGGCCCTTGAGATTACAAGGAAGTTTATGA
upper sequence: GLYMA09G07530.3 (Glycine max), 3'ss of exon 4
lower sequence: PP1S31_150V6.5 (Physcomitrella patens), 3'ss of exon 4
--------------------------------------tttgaattatcctggagatt--ttatttatat---tggcctatttgtttagtgtccc-------aaac----aaatttattcataagtgctt-taaccttaattt---catttttatcagATCTATGATATATTCCAGTTGCTTCCATCTAAGATTCAAGTGGGAGTTTTCTCTGCTACAATGCCTCCCGAGGCACTTGAGATCACAAGGAAGTTCATGA
||| | | | | | | | || ||| | | | | || | || | || || | | | |||| | | ||| | || ||| ||| || ||||| ||||| || |||||| | |||||| ||| |||||||||| || || ||||| |||||||| ||||| || ||||||||||| |||||||||||||
gtttgttcggagagtcctggaatggtagaagaaatttgtttttactcccaagaaaactaattgtttgtgtgactatttcagttctctaattatcctccttataagctatgagagatattgctcaacgctaacgaaattgattcgggcatcttctgcagATTTATGACATCTTCCAGCTTCTTCCACAGAAGCTTCAAGTGGGTGTGTTTTCTGCCACAATGCCACCCGAAGCGCTTGAGATCACCAGGAAGTTCATGA
upper sequence: GLYMA09G07530.3 (Glycine max), 3'ss of exon 4
lower sequence: PP1S383_1V6.3 (Physcomitrella patens), 3'ss of exon 3
tttgaattatcctggagattttatttatattggcctatttgtttag---tgtcccaaacaaatttattcataagtgctttaacct----taatttcatttttat-cagATCTATGATATATTCCAGTTGCTTCCATCTAAGATTCAAGTGGGAGTTTTCTCTGCTACAATGCCTCCCGAGGCACTTGAGATCACAAGGAAGTTCATGA
| || | | ||| | | || ||| ||| ||| || | | | ||| | | || | | || || | | ||||| || || || || ||| |||| || ||| |||||||||| |||||||||||||| |||||||| || || || ||||||||||||||||||||||
--------gtgttgagtggtctgagtatgtcgcactgttttgataggggtgttggtgactgttacggtgaaaaggccgcttacttgcagtgatgtccaatacgtgcagATTTACGACATCTTTCAGCTGCTGCCCCAGAAGCTTCAAGTGGGTGTTTTCTCTGCTACCATGCCTCCTGAAGCCCTCGAGATCACAAGGAAGTTCATGAMapped 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|193661034|gb|FK600868.1|FK600868EST: TTGTATTGGATGAGGCTGATGAAATGCTTTCCCGTGGTTTTAAAGATCAG ACCTATGATATATTCCAGTTGCTTCCATCTAAGATTCAAGTGGGAGCTTTC
genomic: TTGTATTGGATGAGGCTGATGAAATGCTTTCCCGTGGTTTTAAAGATCAGgtgcttttta ... tttttatcagATCTATGATATATTCCAGTTGCTTCCATCTAAGATTCAAGTGGGAGTTTTC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtgtcccaaacaaatttattcataagtgctttaaccttaatttcatttttatcagATCTATGATATATTCCAGTTGCTTCCATCTAAGATTCAAGTGGGAGTTTTCTCTGCTACAATGCCTCCCGAGGCACTTGAGATCACAAGGAAGTTCATGA
tttcattttt CT-rich tract
tttaaccttaatttca 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tttgaattatcctggagattttatttatattggcctatttgtttagtgtcccaaacaaatttattcataagtgctttaaccttaatttcatttttatcagATCTATGATATATTCCAGTTGCTTCCATCTAAGATTCAAGTGGGAGTTTTCTCTGCTACAATGCCTCCCGAGGCACTTGAGATCACAAGGAAGTTCATGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - -tcctgga
- - - - - - - - - - - - - - - - - - - - - - - - - ccaaaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcttta