Sequence
atgc intronic sequence ATGC exonic sequenceTCTTCAGTGCTTCATTCACAACCAAAGTCAACTGTGGGAACTCCTGCATATATTGCTCCAGAAGTATTGCTGAAACAAGAGTATGATGGCAAGgtagagtgtttactgtttagtttcatggtattgttctttttctgtagattaattaattattactgtcacaattaaatgaacaattttgtagttaacttgt...
Basic information
species | Glycine max |
transcript | GLYMA17G20610.2 |
intron # | 6 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA17G20610.4 (Glycine max), 5'ss of exon 6
lower sequence: LOC_Os12g39630.1 (Oryza sativa), 5'ss of exon 6
TCTTCAGTGCTTCATTCACAACCAAAGTCAACTGTGGGAACTCCTGCATATATTGCTCCAGAAGTATTGCTGAAACAAGAGTATGATGGCAAGgtagagtgtttactgtttagtttcatggtattgttctttttctgtagattaattaattattactgtca-caattaaatgaacaattttgtagttaacttgt
|| || || ||||||||||||||||| ||||| || |||||||| || ||||||||||||||||| ||||| || |||| || ||||| |||||| | | | | ||| | ||| | | | | | || | | ||| || | || | | | | | |
TCATCGGTTCTTCATTCACAACCAAAATCAACAGTTGGAACTCCAGCTTATATTGCTCCAGAAGTTTTGCTCAAGAAAGAATACGATGGAAAGgtattatctatcccctttgtgctttaaaagttgccatcctgc-atgcaaagatacactgataccagcagctgcccaacttctatgccttttgctcgacaat
upper sequence: GLYMA17G20610.4 (Glycine max), 5'ss of exon 6
lower sequence: LOC_Os03g55600.1 (Oryza sativa), 5'ss of exon 6
TCTTCAGTGCTTCATTCACAACCAAAGTCAACTGTGGGAACTCCTGCATATATTGCTCCAGAAGTATTGCTGAAACAAGAGTATGATGGCAAGgtagagtgtttactgtttagtttcatggtattgttctttttctgtagattaattaattattactgtcacaattaa--atgaacaattttgtagttaacttgt---
|||||||| || |||||||||||||| || ||||| ||||| ||||| |||||||| || ||||| || |||| |||| || |||||||||||| | ||| | || || || | || || | || || | ||| | | || || | | || | ||| |
TCTTCAGTTCTCCATTCACAACCAAAATCCACTGTAGGAACCCCTGCTTATATTGCACCTGAAGTTCTGTTGAAGAAAGAATACGATGGCAAGgtacatgacttatta---agcttgttgat-ttaatccccgagagcagtacctttggg-aggactatagcttttcgtcttgcatcgtattttgacaaacataaaca
upper sequence: GLYMA17G20610.4 (Glycine max), 5'ss of exon 6
lower sequence: GRMZM2G171435_T02 (Zea mays), 5'ss of exon 6
TCTTCAGTGCTTCATTCACAACCAAAGTCAACTGTGGGAACTCCTGCATATATTGCTCCAGAAGTATTGCTGAAACAAGAGTATGATGGCAAGgtagagtgtttactgtttagtttcatggtattgttctttttctgtagattaattaattattactgtcacaattaaatgaacaattttgtagttaacttgt--------
|| || || |||||||| ||||| ||||||||||| ||||| ||||| |||||||| || ||||| || ||||| |||| ||||||||||||||| | | | || || | | ||| | | ||| || | || ||| || || | | || || | | | ||| |||
TCATCTGTTCTTCATTCCCAACCGAAGTCAACTGTTGGAACACCTGCTTATATTGCACCTGAAGTTCTGTTGAAAAAAGAATATGATGGCAAGgta---cttgtgcgactttccttatttatcttgagatgtgtctttaag--agttgtgtat-acctctgca--tcagtgcactgtagttccataaacatgtgccgcgtg
upper sequence: GLYMA17G20610.4 (Glycine max), 5'ss of exon 6
lower sequence: GRMZM2G138861_T01 (Zea mays), 5'ss of exon 7
TCTTCAGTGCTTCATTCACAACCAAAGTCAACTGTGGGAACTCCTGCATATATTGCTCCAGAAGTATTGCTGAAACAAGAGTATGATGGCAAGgtagagtgtttactgtttagtttcatggtattgttctttttctgtagattaattaattattactgtcacaattaaatgaacaattttgtagttaacttgt--------
|| || || |||||||| || || ||||| ||||| ||||| ||||| |||||||| || ||||| ||| ||||| |||| ||||||||||||||| | | || | | ||| | | ||| | | | | || | | | ||| || | | || || || | | || |||
TCATCTGTTCTTCATTCCCAGCCGAAGTCCACTGTTGGAACACCTGCTTATATTGCACCTGAAGTTTTGTTGAAAAAAGAATATGATGGCAAGgta---cttgtgctatc-actttttttatcttgagaaatgtgtcttga--gagttgtgcatacctctgca--tcagtgcactgttgttccatatacatgtgccacatg
upper sequence: GLYMA17G20610.4 (Glycine max), 5'ss of exon 6
lower sequence: AT5G66880.1 (Arabidopsis thaliana), 5'ss of exon 6
TCTTCAGTGCTTCATTCACAACCAAAGTCAACTGTGGGAACTCCTGCATATATTGCTCCAGAAGTATTGCTGAAACAAGAGTATGATGGCAAGgtagagtgtttactgtttagtttcatggtattgttctttttctgtagattaat---taattatt-actgtcacaattaaatgaacaattttgtagttaacttgt
||||| || |||||||||||||||||||||||||| || ||||||||||| || |||||||| ||| |||| || || ||||||||||||||| || | || | | | || || | | ||||| ||| ||| ||| ||| | ||| || ||| |
TCTTCTGTTCTTCATTCACAACCAAAGTCAACTGTTGGTACTCCTGCATACATCGCTCCAGAGGTACTGCTTCGTCAGGAATATGATGGCAAGgtaaag-gcttttagagaattcctctgtaatctctgtatttctaaggatgaatagccaatcattgagtgttacggttaccag----------------------
upper sequence: GLYMA17G20610.4 (Glycine max), 5'ss of exon 6
lower sequence: AT3G50500.1 (Arabidopsis thaliana), 5'ss of exon 6
TCTTCAGTGCTTCATTCACAACCAAAGTCAACTGTGGGAACTCCTGCATATATTGCTCCAGAAGTATTGCTGAAACAAGAGTATGATGGCAAGgtagagtgtttactgtttagtttcatggtattgttctttttct-gtagattaat-taattattactgtcacaattaaa---tgaacaattttgt-agttaacttgt---------------
||||| || |||||||| ||||||||||||||||| || ||||||||||| ||||| ||||| | | || ||| || ||||||||||||||| | | | | | || | || | | | | | || || | | | || | ||||| || ||| | | | | || || ||
TCTTCTGTTCTTCATTCCCAACCAAAGTCAACTGTTGGTACTCCTGCATACATTGCACCAGAGATTCTTCTTCGACAGGAATATGATGGCAAGgtaaggccatga--gaccaattcctctgtctagagttcaaaccagcttatccatatgactgtttataccacaaatattctttgagttgtcctctgaaatagctggtgttacatttttccag
upper sequence: GLYMA17G20610.4 (Glycine max), 5'ss of exon 6
lower sequence: Vv07s0197g00080.t01 (Vitis vinifera), 5'ss of exon 6
TCTTCAGTGCTTCATTCACAACCAAAGTCAACTGTGGGAACTCCTGCATATATTGCTCCAGAAGTATTGCTGAAACAAGAGTATGATGGCAAGgtagagtg-------tttactgtttagtttca--tggtattgttctttttctgtagattaattaattattactgtcacaattaaatgaacaattttgtagttaacttgt
||||| |||||||||||||||||||| |||||||| |||||||||||||| ||||||||||||||||| ||| ||||| || |||||||||||| | ||||| ||| ||||| | |||| | |||| || | || || | ||| | | | || || || |||||| |
TCTTCGGTGCTTCATTCACAACCAAAATCAACTGTTGGAACTCCTGCATACATTGCTCCAGAAGTATTAATGAGGCAAGAATACGATGGCAAGgtaaaaccatttaattttacatcttaatttcaattaagcttgtgcatttttctaagttctatccatgaa-acttt---agctttatcaataaagatgtagtaag-----
upper sequence: GLYMA17G20610.4 (Glycine max), 5'ss of exon 6
lower sequence: PP1S116_98V6.1 (Physcomitrella patens), 5'ss of exon 6
TCTTCAGTGCTTCATTCACAACCAAAGTCAACTGTGGGAACTCCTGCATATATTGCTCCAGAAGTATTGCTGAAACAAGAGTATGATGGCAAGgtagagtgtttactgtttagtttcatggtattgttctttttctgtagattaattaattattactgtcacaattaaatgaacaattttgtagttaacttgt------------------------------------------------
|| || || | || || ||||| ||||| ||||||||||| ||||| || ||||||||||| || ||| || ||||||| |||||||||||| |||| | |||| || | | | || || | | || || ||| || || | | | || | || ||
TCGTCTTTGTTGCACTCGCAACCGAAGTCGACTGTGGGAACACCTGCCTACATTGCTCCAGAGGTCCTGCAAAAGAAAGAGTACGATGGCAAGgtacgtggtttgcacaagggtttttgaccgcaaggattggggtttcgcttcatgatgtctttctactg-aatcaagtgtgttagtgtttactaaagttcaaggcaccttatcggggaactgaaggaacccacttgcttcgagatgcagMapped 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|17152867|gb|BM142800.1|BM142800EST: CTGCATATATTGCTCCAGAAGTATTGCTGAAACAAGAGTATGATGGCAAG CTTGCAGATGTCTGGTCATGTGGAGTAACCTTATATGTGATGCTAGTGGGA
genomic: CTGCATATATTGCTCCAGAAGTATTGCTGAAACAAGAGTATGATGGCAAGgtagagtgtt ... ttaatattagCTTGCAGATGTCTGGTCATGTGGAGTAACCTTATATGTGATGCTAGTGGGA
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
TCTTCAGTGCTTCATTCACAACCAAAGTCAACTGTGGGAACTCCTGCATATATTGCTCCAGAAGTATTGCTGAAACAAGAGTATGATGGCAAGgtagagtgtttactgtttagtttcatggtattgttctttttctgtagattaattaattattactgtcacaattaaatgaacaattttgtagttaacttgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT