Sequence
atgc intronic sequence ATGC exonic sequence...ttagacaggttcaatggtactaaatttggatatcgtattatcacaacataagacctatgttgttcttatttatttgtttattattattattattttgcagAAGTTAGTAATCAAATGTTAGAGCTGTATGAACAAAATCGAATGCCACCTTCCAACGATGTCGAAGGAGGTGGGACTTCCAATCAGACCACTGCAAAAGC
Basic information
species | Glycine max |
transcript | GLYMA08G17960.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G17960.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os12g30020.2 (Oryza sativa), 3'ss of exon 6
ttagacaggttcaatggtactaaatttggatatcgtattatcacaacataagacctatgttgttcttatttatttgtttattatta------ttattattttgcagAAGTTAGTAATCAAATGTTAGAGCTGTATGAACAAAATCGAATGCCACCTTC-CAACGATGTCGAAGGAGGTGGGACTTCCAATCAGACCACTGCAAAAGC---
|| || || || | | || ||| | | |||| ||| | | | |||||| || | | || || | | | ||||||||||||| ||||||||||| ||||||||||| ||||| | ||| | |||| | | | ||| || || | || | |||| | |
-tatacttatttaac--tttttgat---aatacaatttgatcatgacacattcctttctgggttcttgttaaatcagataataatgcatgtctcccttgattgcagAAGTTAGCAATCAAATGTTGGAGCTGTATGAGCAAAACTGTGCAGCACAGGCACAACCGTCCC-ATGGAAATGAAGCT---GAAGGGAGCTCTGCTAGTGTTCC
upper sequence: GLYMA08G17960.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv19s0027g01670.t01 (Vitis vinifera), 3'ss of exon 5
---ttagacaggttcaatggtactaaatttggatatcgtattatcacaacataagacctatgttgttcttatttatttgtttattattattattattttgcagAAGTTAGTAATCAAATGTTAGAGCTGTATGAACAAAATCGAATGCCACCTTCCAACGATGTCGAAGGAGGTGGGACTTCCAATCAGACCACTGCAAAAGC
|| | | || | | | | | | || || || || || | | || || | | | ||| | | | ||| | | || ||| || |||||||||||||| ||||| || |||||||||||| |||||||||| | | |||| | || | | |||| |
aagggagggtgatgaaaagatcccacagtgattaattgttttggaactactttatga--atatttatatcaccc-tttaatggtggtcatttgtttcttttagAGGTCAGTAATCAAATGTTGGAGCTCTACGAACAAAATCGAGTGCCACCTTCTCAAGGCAGTGAAGTTGAAGGAAGTGTTGGAGGTGGGGCTGCTCATCG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acataagacctatgttgttcttatttatttgtttattattattattattttgcagAAGTTAGTAATCAAATGTTAGAGCTGTATGAACAAAATCGAATGCCACCTTCCAACGATGTCGAAGGAGGTGGGACTTCCAATCAGACCACTGCAAAAGC
ttatttt CT-rich tract
tatgttgttcttattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttagacaggttcaatggtactaaatttggatatcgtattatcacaacataagacctatgttgttcttatttatttgtttattattattattattttgcagAAGTTAGTAATCAAATGTTAGAGCTGTATGAACAAAATCGAATGCCACCTTCCAACGATGTCGAAGGAGGTGGGACTTCCAATCAGACCACTGCAAAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - -cacaaca
- - - - - - - - - - - - - - - - - - - - - - - - - - -cctatgt