Sequence
atgc intronic sequence ATGC exonic sequence...caatcgtagaatttacatttgcatttgctaatgtatccctactttgttttcctatcattcgtttactatttcactgacaatggcttggattcttgatgagTATTCAAAGTTTCATGGACATTCACCAGCAGTTGTGACTGGGAAGCCTTTT
Basic information
species | Glycine max |
transcript | GLYMA11G04090.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA11G04090.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os04g45970.1 (Oryza sativa), 3'ss of exon 3
caatcgtagaatttacatttgcatttgctaatgtatccctactttgttttcctatcat------tcgtttactattt---cactgacaatggcttggattcttgatgagTATTCAAAGTTTCATGGACATTCACCAGCAGTTGTGACTGGGAAGCCTTTT----
| || | ||| || ||| | | | ||||| | ||||| || | |||| ||| ||| |||||||||||| | |||||||| || || || ||||| |||||||| |||||||| ||||||||||| |
----------gtatat-tctgctttctctagtatttttctactacttcccttcatcatgtaacatcccctgtaattttgacacagACCATGGCTTGGATTTTGGATGAGTACTCGAAATTCCATGGTCATTCACCGGCAGTTGTCACTGGGAAGCCAATAGTAA
upper sequence: GLYMA11G04090.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os04g45970.2 (Oryza sativa), 3'ss of exon 3
caatcgtagaatttacatttgcatttgctaatgtatccctactttgttttcctatcat------tcgtttactattt---cactgacaatggcttggattcttgatgagTATTCAAAGTTTCATGGACATTCACCAGCAGTTGTGACTGGGAAGCCTTTT
| || | ||| || ||| | | | ||||| | ||||| || | |||| ||| ||| |||||||||||| | |||||||| || || || ||||| |||||||| |||||||| ||||||||||| |
----------gtatat-tctgctttctctagtatttttctactacttcccttcatcatgtaacatcccctgtaattttgacacagACCATGGCTTGGATTTTGGATGAGTACTCGAAATTCCATGGTCATTCACCGGCAGTTGTCACTGGGAAGCCAATA
upper sequence: GLYMA11G04090.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv00s1491g00010.t01 (Vitis vinifera), 3'ss of exon 1
----------------------------------caatcgtagaatttacatttgcatttgctaatgtatccctactttg--ttttcctatcattcgtttactatttcactgacaatggcttggattcttgatgagTATTCAAAGTTTCATGGACATTCACCAGCAGTTGTGACTGGGAAGCCTTTT
| || ||| | || | | | | | | || || ||| |||| || || || | | || || ||| ||||| |||||||| ||||| || |||||||||||||| |||||||| |||||||| || || ||||| ||
gttttccattcctgaatctaatatgtagtgtgtcctttccaggaaaaaaaatattgactctttgacctttctttaacttgaattttactttccttactctcgatttggacagACGATGGCATGGATTCTGGATGAATACTCAAAGTTTCATGGGCATTCACCTGCAGTTGTTACAGGAAAGCCAATT
upper sequence: GLYMA11G04090.1 (Glycine max), 3'ss of exon 3
lower sequence: EFJ36430 (Selaginella moellendorffii), 3'ss of exon 3
-------------------caatcgtagaatttacatttgcatttgctaatgtatccctactttgttttcctatcattcgtttactat-ttcactgacaatggcttggattcttgatgagTATTCAAAGTTTCATGGACATTCACCAGCAGTTGTGACTGGGAAGCCTTTT
| | |||| ||| ||||| | | | | ||| ||| | | ||| ||| | | ||||| ||| |||||||||||||| |||||||| || ||||||||||| | || |||||||| || ||||| ||||| ||
gtttttttttcacttttttttgttctttcttttat-ttttcatttttttgtttcttt-tacaaagttggatttttatttttttggtttcttcacagACCATGGCTTGGATTCTGGATGAGTACTCCAAGTTTCATGGGTACTCTCCAGCAGTAGTCACTGGAAAGCCACTT
upper sequence: GLYMA11G04090.1 (Glycine max), 3'ss of exon 3
lower sequence: EFJ06181 (Selaginella moellendorffii), 3'ss of exon 3
caatcgtagaatttacatttgcatttgctaatgtatccctacttt----gttttcctatcattcgttt-actatttcactgacaatggcttggattcttgatgagTATTCAAAGTTTCATGGACATTCACCAGCAGTTGTGACTGGGAAGCCTTTT
| | ||| | |||| || || | || | || ||| | ||||| ||| | ||||| ||| |||||||||||||| |||||||| || ||||||||||| | || |||||||| || ||||| ||||| ||
-gtttttttctttttcttttgttctttctttcttttctttttttgcaaagttggattttcattttttttgtttcttcacagACCATGGCTTGGATTCTGGATGAGTACTCCAAGTTTCATGGGTACTCTCCAGCAGTAGTCACTGGAAAGCCACTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gttttcctatcattcgtttactatttcactgacaatggcttggattcttgatgagTATTCAAAGTTTCATGGACATTCACCAGCAGTTGTGACTGGGAAGCCTTTT
cactgac putative branch site (score: 2)
ttctt putative PPT
tttactattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
caatcgtagaatttacatttgcatttgctaatgtatccctactttgttttcctatcattcgtttactatttcactgacaatggcttggattcttgatgagTATTCAAAGTTTCATGGACATTCACCAGCAGTTGTGACTGGGAAGCCTTTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - -tgcattt
- - - - - - - - - - - - - gctaatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - actgaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tggcttg