Sequence
atgc intronic sequence ATGC exonic sequence...ccctacatgtacacattaaaggatcttatgcttaattttctttccacaagggaaaacatatgtttctaattttcctcctttcatttatgtgtgggtttagAAATGCATACAACATGGTGCTTCACAAATTTGGTGAGAAGCTCTACTCAGGGCTGGTTGCAACCATGACTGGACATCTCAAAGATATAGCTCAATCTGTT
Basic information
species | Glycine max |
transcript | GLYMA18G15240.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA18G15240.1 (Glycine max), 3'ss of exon 1
lower sequence: AT1G26830.1 (Arabidopsis thaliana), 3'ss of exon 2
-----------ccctacatgtacacattaaaggatcttatgcttaattttctttccacaagggaaaacatatgtttctaatt--ttcctcctttcatttatgtgtgggtttagAAATGCATACAACATGGTGCTTCACAAATTTGGTGAGAAGCTCTACTCAGGGCTGGTTGCAACCATGACTGGACATCTCAAAGATATAGCTCAATCTGTT
| | | | | | | ||| | | | | | | | | | || ||||| || | || | ||| | || | |||||||| ||||||||||| || ||||| |||||||||||||| || | ||| | |||| || |||||| ||||||||||| | | | | | |
gtcaatttctttcattctcttgcctttctttgaatcctgtagaaactggtaatgtttctggaacttagctaggtttcgtgttaatggaattatttgtgtatattgtggctcagAAATGCGTACAACATGGTCCTGCACAAGTTTGGTGAGAAGCTATATACTGGGTTTATTGCTACTATGACTTCTCATCTCAAAGAAAAATCCAAGCTTATC
upper sequence: GLYMA18G15240.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv01s0026g02230.t01 (Vitis vinifera), 3'ss of exon 1
ccctacatgtacacattaaaggatcttatgcttaattttctttccacaagggaaaacatatgtttctaat-tttcctcctttcatttatgtgtgggtttagAAATGCATACAACATGGTGCTTCACAAATTTGGTGAGAAGCTCTACTCAGGGCTGGTTGCAACCATGACTGGACATCTCAAAGATATAGCTCAATCTGTT
|| | | | || | | ||||| ||| | || | | | | | | | ||| | || || || || || ||||| ||||| ||||| || |||||||||||||||||| | ||||||||||||||| |||| |||||| |||||||||||| ||| | | | | |
tactgtctctttcactctcttctctttgttcaggattttgtttttgatatcctaattttgaatcttttttacctgatgttttaacttcggtatgt-ttcagGAATGCTTACAATATGGTACTGCACAAATTTGGTGAGAAGTTGTACTCAGGGCTGGTTTCAACTATGACTTCACATCTCAAAGACATATCAAAGTTTATA
upper sequence: GLYMA18G15240.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S311_38V6.1 (Physcomitrella patens), 3'ss of exon 1
ccctacatgtacacattaaaggatcttatgcttaattttctttccacaagggaaaacatatgtttctaattttcctc---ctttcatttatgtgtgggtttagAAATGCATACAACATGGTGCTTCACAAATTTGGTGAGAAGCTCTACTCAGGGCTGGTTGCAACCATGACTGGACATCTCAAAGATATAGCTCAATCTGTT
| || || | |||| || | || | | || | | | | |||| || | ||| || || |||| | || |||||| || || |||||||||||||||||||||| || ||||| ||||| ||||| | ||| ||| ||||| ||| | || ||||| || |
--ttggataatcatctgttaggacctagttct-actattaaatattctatgttaaactaatttagtaaatgttgatcatgctttggtgaatcgccatgtttagGAACGCGTACAACATGGTGCTTCACAAATACGGAGAGAAACTCTATTCAGGAGTTGTTCAAACAATGACGCAGCATTTGCGGGAGATAGCAAAAATAATC
upper sequence: GLYMA18G15240.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S31_336V6.1 (Physcomitrella patens), 3'ss of exon 2
ccctacatgtacacattaaaggatcttatgcttaattttctttccacaagggaaaacatatgtttctaattt-tcctcctttcatttatgtgtgggtttagAAATGCATACAACATGGTGCTTCACAAATTTGGTGAGAAGCTCTACTCAGGGCTGGTTGCAACCATGACTGGACATCTCAAAGATATAGCTCAATCTGTT
| | || | || || || || || | | || | || | | || || || || | || | | ||| || ||||| |||||||||||||| ||||| | ||| ||||| ||||||||||| | || | || ||||| ||| | || ||||||| | ||||
catttggtg-atgatctatgaaattaattgtatatattcgatacttcacgtgactaatttagtatcccatcaatcatgaattgggatttcaaaatgttcagGAATGCGTACAACATGGTGCTCCACAAGTATGGAGAGAAACTCTACTCAGGAGTTGTGACGACAATGACGCAGCATTTGCGGGAGATAGCTCGAATTGTT
upper sequence: GLYMA18G15240.1 (Glycine max), 3'ss of exon 1
lower sequence: EFJ05563 (Selaginella moellendorffii), 3'ss of exon 1
------------------------------ccctacatgtacacattaaaggatcttatgctt---aattttctttccacaagggaaaacatatgtttctaattttcctcctttcatttatgtgtgggttt---agAAATGCATACAACATGGTGCTTCACAAATTTGGTGAGAAGCTCTACTCAGGGCTGGTTGCAACCATGACTGGACATCTCAAAGATATAGCTCAATCTGTT
|| | | | || || | | | | || ||||| | ||| | | | | | | || || || | || || ||| ||| || || ||||| ||||||||||| |||||||| | ||| |||||||||||| | ||||||| | || ||||| ||| | |||| | ||| |
gttcgtgctttactttcctttgccgcgattccattccattccattttctttgctttgctcctcgtgaatttgcattctttagagtagatccattcttcctccttgtgctaaagtcttttttgttcttcctttctagGAATGCCTACAACATGGTTCTTCACAAGTATGGAGAGAAGCTCTACGCGGGGCTGGAAACCACGATGACGCAGCATTTGCAAGAGTTTTCTCGGGTGATC
upper sequence: GLYMA18G15240.1 (Glycine max), 3'ss of exon 1
lower sequence: EFJ26179 (Selaginella moellendorffii), 3'ss of exon 1
------------------------------ccctacatgtacacattaaaggatcttatgctt---aattttctttccacaagggaaaacatatgtttctaattttcctcc----tttcatttatgtgtgggtttagAAATGCATACAACATGGTGCTTCACAAATTTGGTGAGAAGCTCTACTCAGGGCTGGTTGCAACCATGACTGGACATCTCAAAGATATAGCTCAATCTGTT
|| | | | || || | | | | || ||||| | ||| | | | | | | || || || | ||| || || | | | ||| ||||| ||||||||||| |||||||| | ||| |||||||||||| | ||||||| | || ||||| ||| | |||| | ||| |
gttcgtgctttactttcctttgccgcgattccattccattccattttctttgctttgctcctcgtgaatttgcattctttagagtagatccattcttcctccttgtgctctaagtcttttttcttcttcctttctagGAATGCCTACAACATGGTTCTTCACAAGTATGGAGAGAAGCTCTACGCGGGGCTGGAAACCACGATGACGCAGCATTTGCAAGAGTTTTCTCGGGTGATC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acaagggaaaacatatgtttctaattttcctcctttcatttatgtgtgggtttagAAATGCATACAACATGGTGCTTCACAAATTTGGTGAGAAGCTCTACTCAGGGCTGGTTGCAACCATGACTGGACATCTCAAAGATATAGCTCAATCTGTT
ttctaat putative branch site (score: 2)
aaaacatatgtttcta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ccctacatgtacacattaaaggatcttatgcttaattttctttccacaagggaaaacatatgtttctaattttcctcctttcatttatgtgtgggtttagAAATGCATACAACATGGTGCTTCACAAATTTGGTGAGAAGCTCTACTCAGGGCTGGTTGCAACCATGACTGGACATCTCAAAGATATAGCTCAATCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
ccctaca
- - - -tgtacac
- - - - - - - - - - - - cttatgc
- - - - - - - - - - - - - - - - - - - - - -ccacaag
- - - - - - - - - - - - - - - - - - - - - - - - - ggaaaac