Sequence
atgc intronic sequence ATGC exonic sequence...ggacaaaaacatatttttgcctttaactaatgaagaaattgcgtattgctgaagttttatattcttcggagaaattttgaaacgaggaagtggtttgcagGGTTTGAAAACGGCCATTGTTGAGGGAGACGTGGTTGGAGGGACATGTGTGAACAGAGGATGTGTTCCTTCTAAGGCTCTTTTGGCTGTGAGTGGTCGAA
Basic information
species | Glycine max |
transcript | GLYMA15G15310.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA15G15310.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os01g23610.2 (Oryza sativa), 3'ss of exon 1
ggacaaaaacatatttttgcctttaactaatgaagaaattgcgtattgctgaagttttatattcttcggagaaattttgaaacgaggaagtgg---------tttgcagGGTTTGAAAACGGCCATTGTTGAGGGAGACGTGGTTGGAGGGACATGTGTGAACAGAGGATGTGTTCCTTCTAAGGCTCTTTTGGCTGTGAGTGGTCGAA
|||||||| | | | | | ||| | |||| | || | ||| | ||| ||| || || | ||| |||||||| ||||||| ||||| ||||||| || || || || ||||| |||||||||||||| |||||||| || ||||| ||| | ||||| || ||||| |
--------ccatattttggatactgagctttttctggactgcaaacaattgaactattgaagatttcag-gaagcattgtaatgaatatgtgaaaatgtactcatgcagGGTCTGAAAACTGCCATAATTGAGGGGGATGTTGTAGGTGGGACTTGTGTGAACAGAGGTTGTGTTCCGTCGAAGGCACTTCTTGCTGTCAGCGGTCGGA
upper sequence: GLYMA15G15310.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os05g06460.1 (Oryza sativa), 3'ss of exon 1
ggacaaaaacatatttttgcctttaactaatgaa--gaaattgcgtattgctgaagttttatattcttcggagaaattttgaaacgaggaagtggtttgcagGGTTTGAAAACGGCCATTGTTGAGGGAGACGTGGTTGGAGGGACATGTGTGAACAGAGGATGTGTTCCTTCTAAGGCTCTTTTGGCTGTGAGTGGTCGAA
| | || | || | | ||| | | ||| | || | | | | | | | | | || | || | | || | | |||||||||||||||| || ||| |||||||||| || || || ||||| ||||| |||||||| ||||| || || || || ||| | ||||| || ||||| |
ataagattgcagagttataaatgtaataacctgttcgttattac-tagtccactactgctgtctcaatgtgttaagtgttaactggcccaaatt-tgtgcagGGTTTGAAAACTGCAATTATTGAGGGAGATGTTGTAGGTGGGACTTGTGTAAACAGAGGTTGTGTCCCATCAAAAGCACTTCTTGCTGTCAGCGGTCGCA
upper sequence: GLYMA15G15310.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G145595_T02 (Zea mays), 3'ss of exon 1
ggacaaaaacatatttttgcctttaactaatgaagaaattgcgtattgctgaagttttatattcttcggagaaattttgaaac----gaggaagtggtt--tgcagGGTTTGAAAACGGCCATTGTTGAGGGAGACGTGGTTGGAGGGACATGTGTGAACAGAGGATGTGTTCCTTCTAAGGCTCTTTTGGCTGTGAGTGGTCGAA
| | |||| | | || | | ||| |||| | |||||| ||| | || || || | || ||||||||||||| ||||| ||||||||||||| || || || || ||||| |||||||| |||||||| || |||||||| | ||||| |||||| | |
------ccatgtgttttgaacatggacctttatctatgctgccagcaattgaactcacatattcaataagtttttttaatgatttttgaaaaaatgtctcatgtagGGTTTGAAAACTGCCATAATTGAGGGAGACGTCGTGGGTGGAACTTGTGTCAACAGAGGCTGTGTTCCGTCAAAGGCTCTCCTTGCTGTAAGTGGTAGGA
upper sequence: GLYMA15G15310.1 (Glycine max), 3'ss of exon 1
lower sequence: AT3G16950.1 (Arabidopsis thaliana), 3'ss of exon 1
ggacaaaaacatatttttgcctttaactaatgaagaaattgcgtattgctgaagttttatattcttcggagaaattttgaaacgaggaagtggtttgcagGGTTTGAAAACGGCCATTGTTGAGGGAGACGTGGTTGGAGGGACATGTGTGAACAGAGGATGTGTTCCTTCTAAGGCTCTTTTGGCTGTGAGTGGTCGAA
| || | | | | | | | ||||| | | | | | | | | ||| | ||| || || | |||| | ||||| |||||| |||| ||||| || ||||||||||| ||||| |||||||||||||| |||||||| |||||| | ||||| ||||||||||
gtttgaagtttcttatataacctgatttgatgaaagtaaaagattt-------gctctgcttattatggaaacatt----ggtgattttgtttgtgttagGGACTTAAAACAGCCATTATTGAAGGAGATGTTGTTGGAGGGACTTGTGTTAACAGAGGATGTGTGCCTTCTAAAGCTCTTCTTGCTGTTAGTGGTCGAA
upper sequence: GLYMA15G15310.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S352_68V6.1 (Physcomitrella patens), 3'ss of exon 1
-ggacaaaaacatatttttgcctttaactaatga---agaaattgcgtattgctgaagtt-ttatattcttcggagaaattttgaaacgaggaagtggtttgcagGGTTTGAAAACGGCCATTGTTGAGGGAGACGTGGTTGGAGGGACATGTGTGAACAGAGGATGTGTTCCTTCTAAGGCTCTTTTGGCTGTGAGTGGTCGAA
| || | | || | || |||| | |||||| | ||| || | | | || ||| || | | ||| ||| || |||||||| || || || ||||| ||||||||||| ||||| || |||||||| || |||||||| ||||| || ||||| ||| | ||||| ||||| || |
ttgcttaatctacttcttcctgtacaattaattagctagaaatccctctctgccccgcttgccagactttt-----aaaattgaacattgtgaattgggttacagGGTTTAAAGACAGCAATTGTCGAGGGAGACGTTGTTGGGGGTACATGTGTTAATAGAGGATGCGTTCCGTCCAAGGCGCTTCTCGCTGTAAGTGGACGTA
upper sequence: GLYMA15G15310.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S112_186V6.1 (Physcomitrella patens), 3'ss of exon 1
-------ggacaaaaacatatttttgcctttaactaatgaag--aaattgcgtattgc---tgaagttttatattct--------tcggagaaat------tttgaaacgagga--agtggttt-------gcagGGTTTGAAAACGGCCATTGTTGAGGGAGACGTGGTTGGAGGGACATGTGTGAACAGAGGATGTGTTCCTTCTAAGGCTCTTTTGGCTGTGAGTGGTCGAA
|| | |||||||| | | | | | | ||| | | | | ||| | || | ||| || ||||| || ||| |||| | |||||| ||||| ||||| || | ||||| ||||| ||||| || || ||||| ||| |||| ||||| ||||| || ||||| |||||||||||||| || |
gtaggacggctggatccatattttgctccgtttgtgagtacgtcgtgttgagcgacgtccttcgtggtttctgctcaaccgggcgttggatgtatcgtgggtttgatgcgtggattggtggcattggcaacgcagGGGTTGAAGACGGCGATCATCGAGGGGGACGTTGTTGGCGGTACTTGTGTCAACCGAGGGTGTGTGCCTTCGAAAGCTCTCTTGGCTGTGAGTGGGCGTA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgctgaagttttatattcttcggagaaattttgaaacgaggaagtggtttgcagGGTTTGAAAACGGCCATTGTTGAGGGAGACGTGGTTGGAGGGACATGTGTGAACAGAGGATGTGTTCCTTCTAAGGCTCTTTTGGCTGTGAGTGGTCGAA
aagttttatattctt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ggacaaaaacatatttttgcctttaactaatgaagaaattgcgtattgctgaagttttatattcttcggagaaattttgaaacgaggaagtggtttgcagGGTTTGAAAACGGCCATTGTTGAGGGAGACGTGGTTGGAGGGACATGTGTGAACAGAGGATGTGTTCCTTCTAAGGCTCTTTTGGCTGTGAGTGGTCGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - aaaaaca
- - - - - - - ttttgcc
- - - - - - - - - - - - - - aatgaag
- - - - - - - - - - - - - - - - - - - - - - - tgctgaa