Sequence
atgc intronic sequence ATGC exonic sequencegtatgttttagcatatgatcacctgtcctctcttaactcctctctgttcacccaggccctgagttctgtttatcttctcttgacagTGGTGATAGAACCCCCAAGCAGAAAGTGAAACTAAAAGTTACAGAGGAGAAACTGTTAAACCTGATGTTGAAGTACAATGGAGGAAAACCAAGAGCTGAG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G15070.2 |
intron # | 13 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G15070.2 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: LOC_Os03g48300.1 (Oryza sativa), 3'ss of exon 12
gtatgttttagcatatgatcacctgtcctctcttaactcctctctgttcacccaggccctgagttctg-tttatcttctcttgacagTGGTGATAGAACCCCCAAGCAGAAAGTGAAACTAAAAGTTACAGAGGAGAAACTGTTAAACCTGATGTTGAAGTACAATGGAGGAAAACCAAGAGCTGAG
||| | ||| | | || | | | | || || || || | | | ||| ||||| ||| | || || ||||||||||||||| | |||||||| ||||| ||||| | || |||||||||| |||||||| ||||| ||||||||||||
gtaaggattactgcctctatgctggt--taagctggtattgaatgataaatattggtgttgtgtcttgacatctaatatctgtttagTGGCGATCGGACACCAAAGCAGAAAGTGAAATTGAAAGTTACTGAGGAAAAACTCCTGAATTTGATGTTGAAATACAATGGTGGAAAGCCAAGAGCTGAG
upper sequence: AT5G15070.2 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GLYMA09G37610.1 (Glycine max), 3'ss of exon 10
gtatgttttagcatatgatcacctgtcctctcttaactcctctctgtt---cacccaggccctgagttctgtttatcttctcttgacagTGGTGATAGAACCCCCAAGCAGAAAGTGAAACTAAAAGTTACAGAGGAGAAACTGTTAAACCTGATGTTGAAGTACAATGGAGGAAAACCAAGAGCTGAG
|||| || | |||| | |||||| | ||| || | | | | | | | | | | ||| ||||||||||||||| ||||| ||||| ||||| ||||||||||| ||||| |||||| ||||||| |||||||| ||||||||||| ||| |||||||||
------------gtatgttc--ttttccttttttaacttaaattagttaagcatcttgttctttgctatttactcttctgttttggcagTGGTGATAGAACTCCCAAACAGAAGGTGAAGCTAAAAGTTACTGAGGAAAAACTGCTAAACCTAATGTTGAAATACAATGGAGGCCGACCTAGAGCTGAG
upper sequence: AT5G15070.2 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GLYMA18G49000.1 (Glycine max), 3'ss of exon 12
gtatgttttagcatatgatcacctgtcctctcttaactcctctctgtt---cacccaggccctgagttctgtttatcttctcttgacagTGGTGATAGAACCCCCAAGCAGAAAGTGAAACTAAAAGTTACAGAGGAGAAACTGTTAAACCTGATGTTGAAGTACAATGGAGGAAAACCAAGAGCTGAG
|||| || | ||| | |||||| | ||| || | | | || | | | |||| | | | ||||||||||||||| ||||| ||||| ||||| ||||||||||| ||||| || ||| ||||||| |||||||| ||||||||||| ||| |||||||||
------------gtatgttc--ttttccctttttaacttaaattagttaagcatcttgttcttgccatttactc-tcttgtttcggcagTGGTGATAGAACTCCCAAACAGAAGGTGAAGCTAAAAGTTACTGAGGAAAAGCTGCTAAACCTAATGTTGAAATACAATGGAGGCCGACCTAGAGCTGAG
upper sequence: AT5G15070.2 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GLYMA19G02260.1 (Glycine max), 3'ss of exon 10
gtatgttttagcatatgatcacctgtcctctcttaactcctctctgttcacccaggccctgagttctgttta---tcttctcttgacagTGGTGATAGAACCCCCAAGCAGAAAGTGAAACTAAAAGTTACAGAGGAGAAACTGTTAAACCTGATGTTGAAGTACAATGGAGGAAAACCAAGAGCTGAG
|||| || | | | | || || | |||| | | | | || || | || | ||| ||| ||||||||||||||| || || ||||| ||||| ||||| ||||| ||||| || ||| | ||| | |||||||| |||||||| || || ||| |||||
------------gtatgttctattccctttttttttatctggtttgttaa---atgtcttgttccctatatactcttctcttttggcagTGGTGATAGAACTCCAAAACAGAAGGTGAAGCTAAAGGTTACTGAGGAAAAGCTGCTGAACTTAATGTTGAAATACAATGGTGGCCGGCCGAGATCTGAG
upper sequence: AT5G15070.2 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: Vv14s0066g02540.t01 (Vitis vinifera), 3'ss of exon 12
gtatgttttagcatatgatcacctgtcctctcttaactcctctctgttcacccaggccctgagttctgtt-tatcttctcttgacagTGGTGATAGAACCCCCAAGCAGAAAGTGAAACTAAAAGTTACAGAGGAGAAACTGTTAAACCTGATGTTGAAGTACAATGGAGGAAAACCAAGAGCTGAG
||| | | || | | ||| | | || | ||||| | ||| | | | || | ||| | | || | | | |||||||||||| || ||||| ||||| |||||| | ||||| ||||||||||| || || || ||||||| || |||||||| || | || ||| |||||
gtaagatcta---tgtcatcccatttctttacttaaattaaga-tgtaacctttctctcccagcttagttgtgttttatttgggcagTGGTGATAGGACTCCCAAACAGAAGGTGAAATTGAAAGTCACAGAGGAGAAGCTATTGAATTTGATGTTAAAATACAATGGGGGGAGGCCTAGATCTGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttaactcctctctgttcacccaggccctgagttctgtttatcttctcttgacagTGGTGATAGAACCCCCAAGCAGAAAGTGAAACTAAAAGTTACAGAGGAGAAACTGTTAAACCTGATGTTGAAGTACAATGGAGGAAAACCAAGAGCTGAG
tcttaac putative branch site (score: 2)
ttctgtttatcttctc putative PPT
tttatctt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgttttagcatatgatcacctgtcctctcttaactcctctctgttcacccaggccctgagttctgtttatcttctcttgacagTGGTGATAGAACCCCCAAGCAGAAAGTGAAACTAAAAGTTACAGAGGAGAAACTGTTAAACCTGATGTTGAAGTACAATGGAGGAAAACCAAGAGCTGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA