Sequence
atgc intronic sequence ATGC exonic sequence...tccattattaaggttgaagacatatttaagtatgaaagaagttctactttccaacttagtttgagtaagattgtttatgtgtatcaattggctttggcagATCATTTTGGTCAGGAGCAGCTTCAAATGCTGTGGTGGTTGAGGCAGATGCTTTCAAGGAGAGTGACGTCATATATAGAGCCCTTAGCTCCAGAGGTCAC
Basic information
species | Glycine max |
transcript | GLYMA20G34750.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G34750.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os05g43300.1 (Oryza sativa), 3'ss of exon 4
tccattattaagg--ttgaagacatatttaagtatgaaagaagttctactttccaacttagtttgagtaagattgtt-tatgtgtatcaattggct--ttggcagATCATTTTGGTCAGGAGCAGCTTCAAATGCTGTGGTGGTTGAGGCAGATGCTTTCAAGGAGAGTGACGTCATATATAGAGCCCTTAGCTCCAGAGGTCAC
|||| | | || | || | | | | | | || | | ||| || || ||| || | | || | || | | ||||| |||| ||||| ||||||||| ||||||| || || || ||||||||||| |||||||| | ||| || || ||| |||| | ||||| ||||| |||
--cattgcttggactttttaatcaaagccagagcagctaaagaatataaaatacgcctt---ttcagaaagcttatcgtgctgctacctgtttcttgatctgcagAGCATTCTGGTCCGGAGCAGCTGCAAATGCAGTAGTTGTAGAGGCAGATGCATTCAAGGAAACTGATGTAATCTATCGAGCTATCAGCTCAAGAGGCCAC
upper sequence: GLYMA20G34750.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os03g43010.1 (Oryza sativa), 3'ss of exon 5
---------------------------tccattattaaggttgaagacatattta-agtatgaaagaagttctactttccaact---tagtttgagtaagattgtttatgtgtatcaattggctttggcagATCATTTTGGTCAGGAGCAGCTTCAAATGCTGTGGTGGTTGAGGCAGATGCTTTCAAGGAGAGTGACGTCATATATAGAGCCCTTAGCTCCAGAGGTCAC
|| || || || || | | || || || | || || || | || ||||| | |||| | || | || | || ||| || | ||||| | | | ||||| |||||||||||||| ||||| |||||||||| ||||| || || | ||| ||||||||| || |||
gtaagcaaattaagctagcgagagagctctgtttttttaaaaaaaattatttgcacagcatttaaattgca-taggttataattgaataatttgaa-acgattttaaatataaattctataatgtt--cagGCCACTGTGGTCCAAGGACGAGGCGAATGCGGTGGTGGTTGAGGCGGATGCGTTCAAGGAGACGGACGTGATCTACCGTGCCATTAGCTCCATGGGCCAC
upper sequence: GLYMA20G34750.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv05s0020g04820.t01 (Vitis vinifera), 3'ss of exon 5
tccattattaaggttgaagacatatttaagtatgaaagaagttctactttccaacttagtttgagtaagattgtttatgtgtatcaattggct------ttggcagATCATTTTGGTCAGGAGCAGCTTCAAATGCTGTGGTGGTTGAGGCAGATGCTTTCAAGGAGAGTGACGTCATATATAGAGCCCTTAGCTCCAGAGGTCAC
|| | | | || || | | || ||||| | | || | || | | ||||| | ||||||| |||| ||||||||||||| |||| |||||| || ||||||||||||||||| |||| || ||||| || |||||||||||||| | ||
---------------------gtactctcacttccact--cttttattatatt-ctcagttttacaacaatgatccctgagcttatattggatgtatgattggcagCGCATTCTGGTCAGGAGCAGAAGCAAACTGTGTGGTAGTGGAGGCAGATGCTTTCAAAGAGACCGATGTCATTTACAGAGCCCTTAGCTCTCATCGCCAT
upper sequence: GLYMA20G34750.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv05s0020g04840.t01 (Vitis vinifera), 3'ss of exon 5
tccattattaaggttgaagacatatttaagtatgaaagaagttctactttccaacttagtttgagtaagattgtttatgtgtatcaattggct------ttggcagATCATTTTGGTCAGGAGCAGCTTCAAATGCTGTGGTGGTTGAGGCAGATGCTTTCAAGGAGAGTGACGTCATATATAGAGCCCTTAGCTCCAGAGGTCAC
|| | | | || || | | || ||||| | | || | || | | ||||| | ||||||| |||| ||||||||||||| |||| |||||| || ||||||||||||||||| |||| || ||| | || |||||||||||||| ||
---------------------gtactctcacttccact--cttttattatatt-ctcagttttacaataatgatccctgagcttatattggatgtatgattggcagCGCATTCTGGTCAGGAGCAGAAGCAAACTGTGTGGTAGTGGAGGCAGATGCTTTCAAAGAGACCGATGTCGTTTACAGAGCCCTTAGCTCTCATCACCAT
upper sequence: GLYMA20G34750.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv05s0020g04850.t01 (Vitis vinifera), 3'ss of exon 5
tccattattaaggttgaagacatatttaagtatgaaagaagttctactttccaacttagtttgagtaagattgtttatgtgtatc----aattggctttggcagATCATTTTGGTCAGGAGCAGCTTCAAATGCTGTGGTGGTTGAGGCAGATGCTTTCAAGGAGAGTGACGTCATATATAGAGCCCTTAGCTCCAGAGGTCAC
| | || | || | | || |||| ||| | | ||| | | | |||| | | ||||||| |||| ||||||| ||||| |||| |||||||| || ||||||||||||||||| |||| || ||||| || |||||||||||||| ||
---------------gtacactcacttccactctttttatttattattttctcactctacattaataatgatccctgagcttatcttggatacgtggctggcagAGCATTCTGGTCAGAGGCAGCAGCAAACGCTGTGGTAGTGGAGGCAGATGCTTTCAAAGAGACCGATGTCATTTACAGAGCCCTTAGCTCTCATCACCAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.actttccaacttagtttgagtaagattgtttatgtgtatcaattggctttggcagATCATTTTGGTCAGGAGCAGCTTCAAATGCTGTGGTGGTTGAGGCAGATGCTTTCAAGGAGAGTGACGTCATATATAGAGCCCTTAGCTCCAGAGGTCAC
attgtttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tccattattaaggttgaagacatatttaagtatgaaagaagttctactttccaacttagtttgagtaagattgtttatgtgtatcaattggctttggcagATCATTTTGGTCAGGAGCAGCTTCAAATGCTGTGGTGGTTGAGGCAGATGCTTTCAAGGAGAGTGACGTCATATATAGAGCCCTTAGCTCCAGAGGTCAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA