Sequence
atgc intronic sequence ATGC exonic sequence...ctttcttgtgatatatggataatatatacgtgctatatataataatttgaatgtatatattctcatcaataaattattctataattttttcatgaaatagGGAAGGCAAAGATGGGAGAAAAAGAATGGTACTTCTTCAGTCTGAGAGACCGTAAATACCCAACGGGTGTGAGAACAAATCGAGCAACTAACGCCGGGTA
Basic information
species | Glycine max |
transcript | GLYMA06G08440.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA06G08440.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os09g32260.2 (Oryza sativa), 3'ss of exon 2
-------ctttcttgtgatatatggata-atatatacgtgctatatataataatttgaatgtatatattctcatcaataaattattctataattttttcatgaaatagGGAAGGCAAAGATGGGAGAAAAAGAATGGTACTTCTTCAGTCTGAGAGACCGTAAATACCCAACGGGTGTGAGAACAAATCGAGCAACTAACGCCGGGTA
| || |||| ||| | || | | | || || | | | | ||| ||||| |||| || || |||| |||| |||| | || || ||||||||| |||||||| || |||||||||||||| || || || || || || |||||||| || ||| | ||||| ||||||||||| || || ||
aggttctgaatgttcaaatatgtggtcacattttttcacact-tacacattcac---aatctatatgttct-atgtattaatt-ttctctaataaat--gtgctccagAGAAGGCAAAAATGGGAGAGAAGGAATGGTACTTCTTTAGCCTAAGGGATCGAAAGTACCCAACTGGCGTGCGCACAAACCGAGCAACTAATGCTGGTTA
upper sequence: GLYMA06G08440.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G386163_T02 (Zea mays), 3'ss of exon 1
ctttcttgtgatatatggataatatatacgtgctatatataataatttgaatgtatatattctcat-caataaattattctataattttttcatgaaat-------agGGAAGGCAAAGATGGGAGAAAAAGAATGGTACTTCTTCAGTCTGAGAGACCGTAAATACCCAACGGGTGTGAGAACAAATCGAGCAACTAACGCCGGGTA
||||| | || | || | | || || ||| | || ||| | || || |||| | || |||| || | ||| || ||| || ||| ||||||||||||| ||||| |||||||| ||||| ||||| || ||||||||||||||| ||||||| || || |||||||| || ||
-------aatgtatataaccggt-taaaagttagctttgaaaaaagttgcgttcatttatgcacacataaaaaatgaaacttggatttatttgttgaattgttgccagAGAAAGCGAAGCTGGGAGAAAAAGAGTGGTATTTCTTCAGCCTGAGGGACCGCAAGTACCCAACGGGTGTGCGAACAAACCGTGCCACTAACGCTGGTTA
upper sequence: GLYMA06G08440.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv04s0008g02710.t01 (Vitis vinifera), 3'ss of exon 1
-ctttcttgtgatatatggataatatatacgtgctatatataataatttgaatgtatatattctcatcaataaattattctataattttttcatgaaatagGGAAGGCAAAGATGGGAGAAAAAGAATGGTACTTCTTCAGTCTGAGAGACCGTAAATACCCAACGGGTGTGAGAACAAATCGAGCAACTAACGCCGGGTA
||||||||||| | || | |||| | | | | || || | || | | | | | || | || || || | | |||||||||| || ||||||||||| || ||||| |||||||| || || ||||| ||||||||||| || || |||||||| ||||| || ||| | || ||
aatttcttgtgatgaa-agagagcatattcttcattttccaaacaaacttggaaaatttcctatatcttctgatctagttaatctttgttctctcgattagGGAAGGCGAAAATGGGAGAAAAGGAGTGGTATTTCTTCAGCCTCAGGGACCGGAAATACCCAACTGGAGTAAGAACAAACCGAGCCACAAACACTGGTTA
upper sequence: GLYMA06G08440.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S279_85V6.1 (Physcomitrella patens), 3'ss of exon 1
----------------------------------------------ctttc--ttgtgatatatggataatat-atacgtgctatatataataatttga-atgtatatattctcatcaataaattattc------tataattttttc------atgaaat---agGGAAGGCAAAGATGGGAGAAAAAGAATGGTACTTCTTCAGTCTGAGAGACCGTAAATACCCAACGGGTGTGAGAACAAATCGAGCAACTAACGCCGGGTA
|| | ||||| ||| | || || | || || || | || | | | || || ||| ||| ||||| || | | | | |||| | || ||||| ||| | ||||| || ||||||||||||||||||||| | ||||| ||||||||||| || | |||| || |||| ||| | || ||
gtatttttttcttttcgcattatccttcagaacatttggtgtagacctaacaattgtgttattcgtgtagtaggaaacctgatacgaaatttagtgtaagattcgcatgatctacagaatgctttatttgtgggataaagctgctccgtctcgatgattttgcagATAAGGCCAAGGTTGGAGAGAAGGAATGGTACTTCTTCAGTCTGCGTGACCGAAAATACCCAACCGGCCAGCGAACTAACAGAGCCACTGATAAGGGATA
upper sequence: GLYMA06G08440.1 (Glycine max), 3'ss of exon 1
lower sequence: EFJ11746 (Selaginella moellendorffii), 3'ss of exon 1
-------------------------------------------------------------------------------------------ctttcttgtgatatatggataatatatacgtgctatatataataatttgaatgtatatattctcatcaataaattattctataattttttcatga----aatagGGAAGGCAAAGATGGGAGAAAAAGAATGGTACTTCTTCAGTCTGAGAGACCGTAAATACCCAACGGGTGTGAGAACAAATCGAGCAACTAACGCCGGGTA
| ||| || || | | | | | | | ||| || | | | | || || | | || | | |||| || ||| ||||| |||||||| || |||||||||||||| || |||| |||||||| ||||| ||||| || | || ||||| ||||| | ||||| ||
gtaaggaggaactctctcatcttctctcgcattcgcttctatcatttcctctcactctctcgacgttcttgggcttgaatttgctgcattgcattcatggcattccaaggaacttggaatcgatcacttgggtcgagttgcctggacgaaattcctctaaaaatctctcctttgttcttttttctttcccggcagAGAAAGCAAACATGGGAGAGAAGGAATGGTACTTCTTTAGCTTGAGGGACCGTAAGTACCCGACGGGGATGCGTACGAATCGGGCAACCGAGGCCGGCTA
upper sequence: GLYMA06G08440.1 (Glycine max), 3'ss of exon 1
lower sequence: EFJ37734 (Selaginella moellendorffii), 3'ss of exon 1
ctttcttgtgatatatgg-ataatatatacgtgcta-tatataataatttgaatgtatatattctcatcaataaattattctataattttttcatgaaatagGGAAGGCAAAGATGGGAGAAAAAGAATGGTACTTCTTCAGTCTGAGAGACCGTAAATACCCAACGGGTGTGAGAACAAATCGAGCAACTAACGCCGGGTA
|| || | | ||||| | | | | ||| || | || || | | || | || | || | | | | || | | | || ||||| ||||||||||| || |||||||||||||||| ||| ||||||| || || || ||||| || | ||||| ||||| || | ||||| ||
-ttctatgcatcgtttctcataatcttggctagatgctatctatttcttggagtccgtgagcact-actaacactttcgtttttggctcttgctccacacagACAAGGCCAAGATGGGAGAGAAGGAATGGTACTTCTTCACGCTGCGAGACCGAAAGTATCCTACGGGAATGCGCACAAACCGAGCCACCGAGGCCGGATA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttgaatgtatatattctcatcaataaattattctataattttttcatgaaatagGGAAGGCAAAGATGGGAGAAAAAGAATGGTACTTCTTCAGTCTGAGAGACCGTAAATACCCAACGGGTGTGAGAACAAATCGAGCAACTAACGCCGGGTA
ttttttcat CT-rich tract
atgtatatattctcat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctttcttgtgatatatggataatatatacgtgctatatataataatttgaatgtatatattctcatcaataaattattctataattttttcatgaaatagGGAAGGCAAAGATGGGAGAAAAAGAATGGTACTTCTTCAGTCTGAGAGACCGTAAATACCCAACGGGTGTGAGAACAAATCGAGCAACTAACGCCGGGTA
- -tcttgtg
- - - - - - - - - - - - - tacgtgc
- - - - - - - - - - - - - - - - - - - - - - - - gaatgta