Sequence
atgc intronic sequence ATGC exonic sequencegtattgtgcatttacttttataagattttctgccttggtgttcgtctctatatcatgttgatcaatgctttgctggatatagGGTGCCAACATTCTAGTTGATAACAAAGGGTGCATTAAACTCACAGACTTTGGGGCATCCAAGAAAGTTGTTGAACTG
Basic information
species | Glycine max |
transcript | GLYMA20G28090.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G28090.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os09g21510.1 (Oryza sativa), 3'ss of exon 5
-------------gtattgtgcatttacttttataagattttctgccttggtgttcgtc-tctatatcatgttgatcaatgct--ttgctggatat-agGGTGCCAACATTCTAGTTGATAACAAAGGGTGCATTAAACTCACAGACTTTGGGGCATCCAAGAAAGTTGTTGAACTG
| ||| || | || | ||| | | | | || | || | || ||| | || || | ||| || |||| || |||||||| |||||||||||||| ||||||||||| | || ||||||||||| ||| |||| | | ||
gtactcaaaatctgaattctgaacacacaataatatg--tatttattttaccacttgttgtgctcattatgattattcctgttatttgtcaaattccagGGAGCGAACATTCTTGTTGATAACAAAGGATGCATTAAACTTGCTGATTTTGGGGCATCTAAGCAAGTGGCAAAGTTG
upper sequence: GLYMA20G28090.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G098828_T01 (Zea mays), 3'ss of exon 5
-----------------gtattgtgca-tttacttttataagattttctgccttggtgttcgtctctatatcatgttgatcaatgctttgctggatat-agGGTGCCAACATTCTAGTTGATAACAAAGGGTGCATTAAACTCACAGACTTTGGGGCATCCAAGAAAGTTGTTGAACTG
|| | | | | | | | | || | || || || || | | ||| | || ||||| || | ||||||| |||||||| |||||||| ||||||||||| ||||| | || ||||||||||| ||| |||||| | ||
gtatgcacgttgaagtcttaatatataatgcagatatttggccttgtttgttctgttgcaatgcttattctaatgaacttgaaaattttgccaaatttcagGGTGCAAACATTCTTGTTGATAATAAAGGGTGCATCAAACTTGCTGATTTTGGGGCATCTAAGCAAGTTGCAAAGTTG
upper sequence: GLYMA20G28090.1 (Glycine max), 3'ss of exon 5
lower sequence: AC197029.3_FGT003 (Zea mays), 3'ss of exon 5
------gtattgt-gcatttacttttata---agattttctgccttggt-gttcgtctctata-tcatgttga---tcaatgctttgctggatatagGGTGCCAACATTCTAGTTGATAACAAAGGGTGCATTAAACTCACAGACTTTGGGGCATCCAAGAAAGTTGTTGAACTG
| || || || || | || |||| || || ||| | |||| | || | | ||| | | ||| | | ||||||| |||||||| || ||||| ||||||||||| ||||| | || ||||||||||| ||| |||| | | ||
gtatgaacactgaagccttaacatataatggcagatctttggctttgcttgttctgttgaatgcttctaatgaaccttgaaattttccaaatttcagGGTGCAAACATTCTTGTAGATAATAAAGGGTGCATCAAACTTGCTGATTTTGGGGCATCTAAGCAAGTGGCAAAGTTG
upper sequence: GLYMA20G28090.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G064613_T03 (Zea mays), 3'ss of exon 5
gtattgtgcatttactt-ttata-agattttctgc-cttggtgttcgtctctatatcatgttgatcaatgctttgctggatat-agGGTGCCAACATTCTAGTTGATAACAAAGGGTGCATTAAACTCACAGACTTTGGGGCATCCAAGAAAGTTGTTGAACTG
| | || | | ||||| | ||| | | | | || | || || | | | || | | |||| || |||| || || || || |||||||||||||| |||||||| || |||| ||||||||||| ||| |||| | | ||
gcacaaaaatttctcatgttatacaaattgtgtacgcaaaatggttgtgatgatgtg--gataattattattttgtcatattccagGGCGCAAATATACTTGTTGATAACAAAGGTTGCATTAAGCTAGCAGATTTTGGGGCATCTAAGCAAGTAGAAAAGTTG
upper sequence: GLYMA20G28090.1 (Glycine max), 3'ss of exon 5
lower sequence: AT3G06030.1 (Arabidopsis thaliana), 3'ss of exon 5
gtattgtgcatttacttttataagattttctgc-cttggtgttcgtctctatatcatgttgatcaatgctttgctggatatagGGTGCCAACATTCTAGTTGATAACAAAGGGTGCATTAAACTCACAGACTTTGGGGCATCCAAGAAAGTTGTTGAACTG
|| | || ||| || || | | |||| ||| || || | | | || | | ||||| || || ||| | || ||||||||||| ||||| | |||| |||| ||||| || |||||||||||||| || ||
-----gtactttcctctttccaacatgtgatatgcttgtggtttctcaaaattccgctataactcttgtcatattct-cctagGGGGCAAATATTTTGGTCGATAACAAAGGTTGCATCAGACTCGCAGATTTTGGTGCTTCCAAGAAAGTTGTAGAGCTA
upper sequence: GLYMA20G28090.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv05s0020g02910.t01 (Vitis vinifera), 3'ss of exon 5
---------------------------gtattgtgcat-----ttacttttataagattttctgccttggtgttcgtctctatatcatgttgatcaatg-ctttgctggatatagGGTGCCAACATTCTAGTTGATAACAAAGGGTGCATTAAACTCACAGACTTTGGGGCATCCAAGAAAGTTGTTGAACTG
|||| || | |||||| |||| | ||| | || ||| || || | |||| | ||| || |||| || || || || |||||||| || || ||||||||||| |||||||||| ||||| |||||||||||||| |||
gtatctccttttttcttgcaaatggtattattatggaactccattacttgtatatgtgcgcatgcttatgttttctacttgtgtctatatctcataatggccgtgcatcattcagGGGGCAAATATCCTGGTTGATAATAAGGGATGCATTAAACTTGCAGACTTTGGTGCATCTAAGAAAGTTGTTGAGCTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttctgccttggtgttcgtctctatatcatgttgatcaatgctttgctggatatagGGTGCCAACATTCTAGTTGATAACAAAGGGTGCATTAAACTCACAGACTTTGGGGCATCCAAGAAAGTTGTTGAACTG
tgttgat putative branch site (score: 4)
ctttgct putative PPT
tatatcat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtattgtgcatttacttttataagattttctgccttggtgttcgtctctatatcatgttgatcaatgctttgctggatatagGGTGCCAACATTCTAGTTGATAACAAAGGGTGCATTAAACTCACAGACTTTGGGGCATCCAAGAAAGTTGTTGAACTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA