Sequence
atgc intronic sequence ATGC exonic sequencegtgagtgcattaatatcttacattaattctccattaatatccaattgtttgttgctctaaaaccctatgtatttagGTTCATTTGGCACCTGGTATGAAGTTTGATTTTCAAAAGTACATCAAAAGATCTTTGGAAGACGACTTCAAGGTGGTTGTAGGAATAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G42560.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G42560.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G000376_T01 (Zea mays), 3'ss of exon 4
------gtgagtgcattaatatcttacattaattctccattaatatccaattgtttgttgctctaaaaccc-tat-gtatttagGTTCATTTGGCACCTGGTATGAAGTTTGATTTTCAAAAGTACATCAAAAGATCTTTGGAAGACGACTTCAAGGTGGTTGTAGGAATAAG-----------
| | | | || || ||| || || |||| | | || ||| |||| |||| ||| |||| ||||| | ||||||||||| |||||||||||||| | ||| |||| ||||||||||||||| | || || || ||
gtatgtagggccacgccagcttgtt-tgttcgttccttcttcattggcaatcagcagcaacaacaatgtatgtatcgtatgcagGTCCATCTGGCCCCTGGCACCAAGTTTGATTTCCAAAAGTACATCAAGCGGTCTCTGGAGGACGACTTCAAGGTGATCGTGGGGATCAGCCCTCCTTTGT
upper sequence: AT1G42560.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA06G01800.1 (Glycine max), 3'ss of exon 7
------------------gtgagtgcattaatat-cttacattaatt--ctccattaatatccaattgtttgttgctctaaaaccctatgtatttagGTTCATTTGGCACCTGGTATGAAGTTTGATTTTCAAAAGTACATCAAAAGATCTTTGGAAGACGACTTCAAGGTGGTTGTAGGAATAAG
| | | || |||||| ||| | | || || | | || | ||| || ||| | | | | | ||||||||||| ||||| || | ||||||||||||||||| || ||||| || || || ||||| ||||| ||||| ||||||||||| ||
gttagtagttttgacaatgcaacttcagtaatatgcttgcgctgtttgtctttttcattaactaatg--ttaatgcccc----cttcacttttgtagGTTCATTTAGCACCGGGAAGTAAGTTTGATTTTCAAAAATATATCAAGAGGTCATTAGAAGATGACTTTAAGGTAGTTGTAGGAATCAG
upper sequence: AT1G42560.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA04G01710.1 (Glycine max), 3'ss of exon 8
------------------gtgagtgcattaatat-cttacattaatt--ctccattaatatccaattgtttgttgctctaaaaccctatgtatttagGTTCATTTGGCACCTGGTATGAAGTTTGATTTTCAAAAGTACATCAAAAGATCTTTGGAAGACGACTTCAAGGTGGTTGTAGGAATAAG
| | | || |||||| ||| || | || || || | || | || | || ||| | | || | | |||||||||| ||||| || | ||||||||||||||||| || ||||| || || || ||||| ||||| ||||| ||||||||||| ||
gttagtagttttggcaatgcaacttcagtaatatgcttgcactgtttgtctttatcattaactaa--ggttaatgcccc----cttcatttttgcagGTTCATTTAGCACCGGGAAGTAAGTTTGATTTTCAAAAATATATCAAGAGGTCATTAGAAGATGACTTTAAGGTAGTTGTAGGAATCAG
upper sequence: AT1G42560.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv18s0122g00910.t01 (Vitis vinifera), 3'ss of exon 7
gtgagtgcattaatatcttacattaattctccattaatatccaattgtttgttgctctaaaaccctatgt-atttagGTTCATTTGGCACCTGGTATGAAGTTTGATTTTCAAAAGTACATCAAAAGATCTTTGGAAGACGACTTCAAGGTGGTTGTAGGAATAAG
||| || | | | |||| |||| || | | || | || || | || ||| | ||||| ||||| || ||||| | ||||| | || |||||||||||||||||||| |||||||| ||||||||||| ||||| ||||| ||
----gtgagtttcttcactgaa--aattttccaatattgtgtt-ttaaatcttactattaattaagttgttgtatagGTACATTTAGCCCCTGGAAGTAAGTTCAACTTCCAAAAGTACATCAAAAGATCCTTGGAAGATGACTTCAAGGTAGTTGTGGGAATCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attaattctccattaatatccaattgtttgttgctctaaaaccctatgtatttagGTTCATTTGGCACCTGGTATGAAGTTTGATTTTCAAAAGTACATCAAAAGATCTTTGGAAGACGACTTCAAGGTGGTTGTAGGAATAAG
ctctaaa putative branch site (score: 3)
attaatatccaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagtgcattaatatcttacattaattctccattaatatccaattgtttgttgctctaaaaccctatgtatttagGTTCATTTGGCACCTGGTATGAAGTTTGATTTTCAAAAGTACATCAAAAGATCTTTGGAAGACGACTTCAAGGTGGTTGTAGGAATAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA