Sequence
atgc intronic sequence ATGC exonic sequencegtaattctctctttcagttagatactttcttcctcctcttctctactcatttcagacctttatttttctgtttattgatttaaaagtttctgttgttgcagGAAGCTCTGGACATTGTGCATGTTAGTAAAGAAGATCAAGAAAGTGTATTTGCAATGCTTGCTGCAGTTTTATGGCTGGGAAACGTTTCCTTCACCGTTA
Basic information
species | Arabidopsis thaliana |
transcript | AT3G19960.2 |
intron # | 12 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G19960.2 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA20G00320.1 (Glycine max), 3'ss of exon 11
------------------------gtaattctctctttcag----ttagatactttcttcctcctcttctct-------actcatttcagacctttatttttctgttta-ttgatttaaaagtttctgttgttgcagGAAGCTCTGGACATTGTGCATGTTAGTAAAGAAGATCAAGAAAGTGTATTTGCAATGCTTGCTGCAGTTTTATGGCTGGGAAACGTTTCCTTCACCGTTA
| || | | || ||| || || ||| || || | | | | |||| | || ||| | |||| | | || | || |||||||| || || |||| || ||||||||||||| || || | |||||||||||||||||||||||| |||||| | |||||| | || || || || |
gtacactatctttgtagtttaaagatgatctgccttcatagactcttaaatgattacttacttctgcttgattggactgattgattttgaaatgatagtttgacacaaaattgaatatactattgccaac-ttccagGAAGCCCTTGATGTTGTCCACATTAGTAAAGAAGACCAGGAGAATGTATTTGCAATGCTTGCTGCAGTATTATGGTTAGGAAACATATCATTTACTGTGA
upper sequence: AT3G19960.2 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA10G43230.1 (Glycine max), 3'ss of exon 9
-------------------------------------------------gtaattctctctttcagttag-atactttcttcctcctcttctctactcatttcagacctttatttttctgtttattgatttaaaagtttctgttgttg-----cagGAAGCTCTGGACATTGTGCATGTTAGTAAAGAAGATCAAGAAAGTGTATTTGCAATGCTTGCTGCAGTTTTATGGCTGGGAAACGTTTCCTTCACCGTTA
|| | | | | | | || | | |||| | |||| | | | | | || || | || ||| | || || || |||||||||||||| |||| || |||| |||| ||| || || | |||||||||||||||||||||||| |||||| | |||||| | || || || ||
gtacacattatttttcatcactttttgcttatgaatgatctgcattcacataggtttatatatgattttttacaatttccattttgtcttatggtttgagtctgaaataatagcttgacatacatgagtttttttcatgctatttttaatttccagGAAGCTCTGGATGTTGTCCACATTAGCAAAGGAGACCAGGAGAATGTATTTGCAATGCTTGCTGCAGTATTATGGTTAGGAAACATATCATTTACTGTGG
upper sequence: AT3G19960.2 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA20G23660.1 (Glycine max), 3'ss of exon 11
-------------------------------------------------gtaattctctctttcagttag-atactttcttcctcctcttctctactcatttcagacctttatttttctgtttattgatttaa--aagtttctgttg--ttgcagGAAGCTCTGGACATTGTGCATGTTAGTAAAGAAGATCAAGAAAGTGTATTTGCAATGCTTGCTGCAGTTTTATGGCTGGGAAACGTTTCCTTCACCGTTA
||| | | | | | | || | | |||| | ||| | | | | | || || | || ||| | | | | || || |||||||||||||| |||| || |||| |||| ||| || || | |||||||||||||||||||||||| |||||| | |||||| | || || || ||
gtatacattatttttcatcgcttgttgcttatgaatgatctgcattcacataagtttatatatgatttcttacaatttccattttgacttgtggtttgagtctgaaataatagcttgacatacatgagttttttcatgctatttttaatttccagGAAGCTCTGGATGTTGTCCACATTAGCAAAGGAGACCAGGAGAATGTATTTGCAATGCTTGCTGCAGTATTATGGTTAGGAAACATATCATTTACTGTGG
upper sequence: AT3G19960.2 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA09G42180.1 (Glycine max), 3'ss of exon 9
------------------------gtaattctctctttcag----ttagatactttcttcctcctcttc--tctactcatt--tcagacctttatttttctgtttattgatttaaaagtttctgttg--ttgcagGAAGCTCTGGACATTGTGCATGTTAGTAAAGAAGATCAAGAAAGTGTATTTGCAATGCTTGCTGCAGTTTTATGGCTGGGAAACGTTTCCTTCACCGTTA
| || || | || ||| || |||||| || || | | ||| ||| | | || || | | || | | | || || ||||||||||| || |||| || | || |||||||| || || | |||||||||||||||||||||||| |||||| | |||||| | || || || || |
gtacactatctttgtagtttaaagatgatctgctttcatagactcttaaatgatttcttacttctgcttgattgactgattgattttgaaatgatagtttgatacaaaaatgaatatactattgccaacttccagGAAGCTCTAGATGTTGTCCACATCAGAAAAGAAGACCAGGAGAATGTATTTGCAATGCTTGCTGCAGTATTATGGTTAGGAAACATATCATTTACTGTGA
upper sequence: AT3G19960.2 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: Vv10s0071g00210.t01 (Vitis vinifera), 3'ss of exon 10
-----------------------gtaattctctctt--tcagttagatactttcttcctcctcttctctactcatttcagacctttatttttctgttta-ttgatttaaaagtttctgttgttgcagGAAGCTCTGGACATTGTGCATGTTAGTAAAGAAGATCAAGAAAGTGTATTTGCAATGCTTGCTGCAGTTTTATGGCTGGGAAACGTTTCCTTCACCGTTA
|| | | || ||| || ||| | || || |||| || || | | || | | | || ||||||| || ||| || ||||||||| |||| ||||| ||||| || ||||| || ||||| ||||||||||| ||||||||||||||||| ||| ||||||| || || || || || |
gtattttttcccttcttgatgactaaacccaatattaatcatttttgtacctattttcttctctatgatatggataaagggtggtgatgtgtgcatgtacttgattttaattttt------tttcagGAAGCTTTGGATATTGTTCATGTCAGCAAAGAGGACCAAGAGAGTGTATTTGCCATGCTTGCTGCAGTTTTGTGGATGGGAAATGTCTCGTTTACTGTGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcatttcagacctttatttttctgtttattgatttaaaagtttctgttgttgcagGAAGCTCTGGACATTGTGCATGTTAGTAAAGAAGATCAAGAAAGTGTATTTGCAATGCTTGCTGCAGTTTTATGGCTGGGAAACGTTTCCTTCACCGTTA
tattgat putative branch site (score: 3)
tttctgtt putative PPT
tttatttttctgttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaattctctctttcagttagatactttcttcctcctcttctctactcatttcagacctttatttttctgtttattgatttaaaagtttctgttgttgcagGAAGCTCTGGACATTGTGCATGTTAGTAAAGAAGATCAAGAAAGTGTATTTGCAATGCTTGCTGCAGTTTTATGGCTGGGAAACGTTTCCTTCACCGTTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG