Sequence
atgc intronic sequence ATGC exonic sequencegtgaggactctcatgaacttcatcttttccttatagatgttggcttgctttcaagaatattttgccccttactatttctgccgaatgtatatttgacagatctttactggtagtgccctttaaacattttgacttccactattgcagCGTGATGTTGTTGTATCACATTTAGATAGTGGAAGACCTGTAGATGATGAAGGTGTTGAAGATGCTTTTGAGCTCTTACATGAAATGAATGAACGTGTCA
Basic information
species | Glycine max |
transcript | GLYMA13G43680.2 |
intron # | 14 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G43680.2 (Glycine max), 3'ss of exon 14
lower sequence: LOC_Os06g05180.1 (Oryza sativa), 3'ss of exon 14
gtgaggactctcatgaacttcatcttttccttatagatgttggcttgctttcaagaatattttgccccttactatttctgccgaatgtatatttgacagatctttactggtagtgccctttaaacat---tttgacttccactattgcagCGTGATGTTGTTGTATCACATTTAGATAGTGGAAGACCTGTAGATGATGAAGGTGTTGAAGATGCTTTTGAGCTCTTACATGAAATGAATGAACGTGTCA
| |||| | | || || | | | || || | | || | | | | | ||| || ||||| | || | | | || | | | || | | ||| | ||||| |||| || || |||| ||||| |||||| ||||| ||||| |||||||||||||||||||| | ||||| | ||||| || ||
-------------------------gtaagttattg-tattatctaaatgttcattatgttatttcttttctcctcttgaatgtgttattgcgtgaaagttctttttttaccatggcatgaagttatgtttgtaatttgtgttcctacagAGAGATGTCGTTGCGTCTTATCTAGAATCTGGAAAACCTGTGGATGAGGAAGGCGTTGAAGATGCTTTTGAGCTGCTTCATGAGGTTAATGAGCGAGTGC
upper sequence: GLYMA13G43680.2 (Glycine max), 3'ss of exon 14
lower sequence: GRMZM2G095348_T03 (Zea mays), 3'ss of exon 14
gtgaggactctcatgaacttcatcttttccttatagatgttggcttgctt--tcaagaatattttgccccttactatttctgccgaatgtatatttgacagatctttactggtagtgccctttaaacattttgacttccactattgcagCGTGATGTTGTTGTATCACATTTAGATAGTGGAAGACCTGTAGATGATGAAGGTGTTGAAGATGCTTTTGAGCTCTTACATGAAATGAATGAACGTGTCA---
|| |||| ||| | | | | | ||| ||| ||| | || | || | | | | | | | ||| | || | | ||| | || || || | |||||||||| || || |||| |||||| ||||| ||||| |||||| ||||||||||||||||| | || || | ||||| || || |
------------------------------gta-agatattgtatcgtcaaatgattattatcttgtttctttttccttttacccaccttgtgatgcatgg--cgttataaacaa--------aatgactatgatatgtgctttt-tagAGAGATGTTGTTGCTTCTTATCTAGAAGGTGGAAAGCCTGTGGATGA---AGGTGTCGAAGATGCTTTTGAGCTGCTTCACGAGGTCAATGAGCGAGTGAGAA
upper sequence: GLYMA13G43680.2 (Glycine max), 3'ss of exon 14
lower sequence: AT1G52360.2 (Arabidopsis thaliana), 3'ss of exon 14
gtgaggactctcatgaacttcatcttttccttatagatgttggcttgctttcaagaatattttgccccttactatttctgccgaatgtatatttgacagatctttactggtagtgccctttaaacattttgacttccactattgcagCGTGATGTTGTTGTATCACATTTAGATAGTGGAAGACCTGTAGATGATGAAGGTGTTGAAGATGCTTTTGAGCTCTTACATGAAATGAATGAACGTGTCA
|| | | | || | | | || |||||| || | || | ||| | ||||| ||||| || ||| | | ||||| || | ||| |||||||| ||||| ||||||||| || || ||||||||||| |||||||||||| | | ||||||| |||||||||| |
------------------------------------gtgaggatcctgtccaacaaacactcttatgctgtgaatttct-----atatgcgattcatggattgtcca----agtgct-----aacatggtg--ttcttgttatacagCGCGACTTAGTTACCTCACATTTTGATAGCGGAAGACCTACTGAGGAAGAAGGTGTTGAGGATGCTTTTGAGGTTCTCCATGAAAATGATGAACGTGTTA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgacagatctttactggtagtgccctttaaacattttgacttccactattgcagCGTGATGTTGTTGTATCACATTTAGATAGTGGAAGACCTGTAGATGATGAAGGTGTTGAAGATGCTTTTGAGCTCTTACATGAAATGAATGAACGTGTCA
ttttgac putative branch site (score: 3)
cttccact CT-rich tract
tttaaacattttga 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgaggactctcatgaacttcatcttttccttatagatgttggcttgctttcaagaatattttgccccttactatttctgccgaatgtatatttgacagatctttactggtagtgccctttaaacattttgacttccactattgcagCGTGATGTTGTTGTATCACATTTAGATAGTGGAAGACCTGTAGATGATGAAGGTGTTGAAGATGCTTTTGAGCTCTTACATGAAATGAATGAACGTGTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG