Sequence
atgc intronic sequence ATGC exonic sequencegtaagcttgattcattatgtgcttttcctgaatttgctagaatttttgtgtttcattggttttgcctgtggtgtaagcaatgacttaatgcttatttattttgtgatggctatgcattaactgatagttttagttactcttatttcaatttttcttaatattcctttccttctcagAACTTGAAAGGGATACATTCAGCTAGAGAGTTTGTTTGGTGGTATAATGGGCACCCATATGGACAAAATCTTGAGCCAGACCTAAAGAGCACTGATACAG
Basic information
species | Glycine max |
transcript | GLYMA08G04100.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G04100.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os02g17700.1 (Oryza sativa), 3'ss of exon 4
gtaagcttgattcattatgtgcttttcctgaatttgctagaatttttgtgtttcattggttttgcctgtggtgtaagcaatgacttaatgcttatttattttgtgatggctatgcattaactgatagttttagttactcttatttcaatttttcttaatattcctttccttctcagAACTTGAAAGGGATACATTCAGCTAGAGAGTTTGTTTGGTGGTATAATGGGCACCCATATGGACAAAATCTTGAGCCAGACCTAAAGAGCACTGATACAG
||| | || | | |||||| || |||| | | || | | | | | | | || |||| | | | || || | || | ||| || |||||||| ||| |||||||||| |||||||||||||| || ||| | || | | || ||| | | ||||| ||| | |
--------------------------------------------------------------------tggca-agattgtgtagtgctatcaatttatcttatgat--tttcgttttgttttttcatcatgcgtg----tgagttgtttattctcagtgtcatctttgttat-agGATCTGAGGGGAATACATTCGGCTCGAGAGTTTGTGTGGTGGTATAATGGACATCCAGACATGTGCAACTTGGCACCTGACTTGCAAAGCACAGATTCTG
upper sequence: GLYMA08G04100.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv11s0016g03550.t01 (Vitis vinifera), 3'ss of exon 4
---------gtaagcttgattcattatgtgcttttcctgaatttgctagaatttttgtgtttcattggttttgcctgtggtgtaagcaatgacttaatgcttatttattttgtgatggctatgcattaactgatagttttagttactcttatttcaatttttcttaat-attcctttccttctcagAACTTGAAAGGGATACATTCAGCTAGAGAGTTTGTTTGGTGGTATAATGGGCACCCATATGGACAAAATCTTGAGCCAGACCTAAAGAGCACTGATACAG
||| | || || || |||| | |||| | | | | ||| | | ||| || | | | | ||| ||| ||| || | ||| ||| || |||| | | | | | | | | | ||| | || | || |||| || ||| | || ||| ||||| ||||||||||| ||||||||||||||||||||||| ||| | | |||| || || || || | ||||||||||||||||
gtacgttttataaaaataatgttttgtgc-ctttgtttaaattatccattagtcttgcatattatt--ttctatcacaagggatttcaaatactgaat---taatggtttcaggattttgataatttaatttcaaaatgttataagcgtagatgtagtttctgttgtttatgtatttcttttccagGATTTTGCAGGAATACACTCAGCTAGAGAATTTGTTTGGTGGTATAATGGGCATCCAGACTGCAAAAACCTGGATCCTGATTTGAAGAGCACTGATACAG
upper sequence: GLYMA08G04100.1 (Glycine max), 3'ss of exon 4
lower sequence: PP1S302_37V6.1 (Physcomitrella patens), 3'ss of exon 5
gtaagcttgattcattatgtgcttttcctgaatttgctagaatttttgtgtttcattggttttgcctgtggtgtaagcaatgacttaatgcttatttattttgtgatggctatgcattaactgatagttttagttactcttatttcaatttttcttaatattcctttcctt-----ctcagAACTTGAAAGGGATACATTCAGCTAGAGAGTTTGTTTGGTGGTATAATGGGCACCCATATGGACAAAATCTTGAGCCAGACCTAAAGAGCACTGATACAG
|| |||| || ||| | || | ||| | | | | ||||| | || ||| || | | ||||| | || ||| | || ||| ||||| |||| ||||||||||| |||||||||||||| || || || | || | | ||||| || | | ||||| |
-------------------------------------------------------------------------------at-actttatccttgtgagcatttgtttagctcttggaatattcgcatcattagt-gcctgtagcacaacttgtgctgatattttccgcgttgagtctgcagGAGCTGGTAGGCGTACATGCAGCAAGAGAGTTTGTCTGGTGGTATAATGGTCATCCTGATCAAGTCAACTTGCAACCAGATCTTCAATCTTCAGATACTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgatagttttagttactcttatttcaatttttcttaatattcctttccttctcagAACTTGAAAGGGATACATTCAGCTAGAGAGTTTGTTTGGTGGTATAATGGGCACCCATATGGACAAAATCTTGAGCCAGACCTAAAGAGCACTGATACAG
tcttaat putative branch site (score: 3)
tttttcttaatattcc CT-rich tract
ttttagttactcttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagcttgattcattatgtgcttttcctgaatttgctagaatttttgtgtttcattggttttgcctgtggtgtaagcaatgacttaatgcttatttattttgtgatggctatgcattaactgatagttttagttactcttatttcaatttttcttaatattcctttccttctcagAACTTGAAAGGGATACATTCAGCTAGAGAGTTTGTTTGGTGGTATAATGGGCACCCATATGGACAAAATCTTGAGCCAGACCTAAAGAGCACTGATACAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA