Sequence
atgc intronic sequence ATGC exonic sequence...accctaattttgttattatgctttttaggttaaaacagagaaactaagttacatattttcttggaaagcctaatttgtgtgaattggtttaattttgtagGTGGATTTGGTGGGAGGATACTACGATGCAGGGGACAATATGAAGTTTGGATTCCCAATGGCATTCACAACCACAATGCTCTCATGGAGTTTAATTGAGT
Basic information
species | Arabidopsis thaliana |
transcript | AT1G02800.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G02800.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os01g21070.1 (Oryza sativa), 3'ss of exon 1
---------------accctaattttgttattatgctttttaggttaaaacagagaaactaagttacatattttct-----------tggaaagcctaatttgtgtgaattggt---ttaattttgtagGTGGATTTGGTGGGAGGATACTACGATGCAGGGGACAATATGAAGTTTGGATTCCCAATGGCATTCACAACCACAATGCTCTCATGGAGTTTAATTGAGT
||| | | | || | || | | || | | | ||| | ||| | || ||| | || | | ||||||| ||||||||||| |||||||| || || ||||| |||||||| || ||||| |||| |||| | || ||||| | ||||| | | ||||
gcaagaaactctccgctcctccgcgtttcaccatttcgtcggcattggcgccgtctctctctctctctctctctctctctctctctctctctcgccatggtctcatggcttgatgcgtttgtctctcagGTGGACTTGGTGGGAGGGTACTACGACGCCGGCGACAACATGAAGTTCGGGTTCCCGCTGGCGTTCAGCATGACGATGCTGGCGTGGAGCGTGGTGGAGT
upper sequence: AT1G02800.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA02G01990.1 (Glycine max), 3'ss of exon 1
accctaattttgttattatgctttttaggttaaaacagagaaactaagttacatattttcttggaaagcctaatt-tgtgtgaattggtttaattttgtagGTGGATTTGGTGGGAGGATACTACGATGCAGGGGACAATATGAAGTTTGGATTCCCAATGGCATTCACAACCACAATGCTCTCATGGAGTTTAATTGAGT
|| | || | | | | | | | | ||| | | |||| |||| || || || ||||||||| || ||| | |||| |||||||| ||||| ||||| ||||| ||||||||| |||| ||||| || || ||||||||||| ||||| ||||| |||||||| | |||||||
----gtatgtatataccaagttaccaactctcacattaccatgcta---tttgtgtttttttggtttgcttatttatgtgtgaat--gtgcaat---gcagGTTGATTTGGTTGGAGGGTACTATGATGCTGGGGACAATGTGAAATTTGGTTTTCCCATGGCATTCACCACCACCATGCTTTCATGGAGCGTTATTGAGT
upper sequence: AT1G02800.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv07s0005g00740.t01 (Vitis vinifera), 3'ss of exon 1
accctaattttgttattatgctttttaggttaaaacagagaaactaagttacatattttcttggaa-agcctaatttgtgtgaa--ttggtttaattttgtagGTGGATTTGGTGGGAGGATACTACGATGCAGGGGACAATATGAAGTTTGGATTCCCAATGGCATTCACAACCACAATGCTCTCATGGAGTTTAATTGAGT
| | | |||||| | | || || | || || || || | | | || | || | | | || ||||||||||||| ||||| ||||| || |||||||||||| |||||||||| ||||||||||| ||||| ||||| ||||| ||||||||| | || ||||
-gtatgtgtaaatgtgtatgctctgtttcttcaattacttgttttagatttttcatcttttgaagttggttttgttaatttgggcgtggaaatggaaatgcagGTGGATTTGGTTGGAGGGTACTATGACGCAGGGGACAATGTGAAGTTTGGGTTCCCAATGGCCTTCACCACCACCATGCTTTCATGGAGTGTGATCGAGT
upper sequence: AT1G02800.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: EFJ21535 (Selaginella moellendorffii), 3'ss of exon 1
accctaattttgttattatgctttttaggttaaaacagagaaactaagttacatattttcttggaa--agcctaatttgtgtgaattggtt-taattttgtagGTGGATTTGGTGGGAGGATACTACGATGCAGGGGACAATATGAAGTTTGGATTCCCAATGGCATTCACAACCACAATGCTCTCATGGAGTTTAATTGAGT
| | ||||| | | | | ||| || ||| | ||| |||||| | | || |||||| | | ||||| ||| ||| | || ||||| | |||||||||||||| ||||||||||| | ||| ||||| |||||||| | || || |
---------------------------------gtatgcgtttctaagatcctgctcgttttgtaacaagctctacttgatctctttggttgttctcttcaagGTGGTTCTCCGAGGAGGCTACATCGACTCTGGAGACAACGTAAAGTTTGGATTCCCCATGGCATTCACGATCACCATGCTTTCATGGAGCGTGATAGAAT
upper sequence: AT1G02800.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: EFJ23913 (Selaginella moellendorffii), 3'ss of exon 1
accctaattttgttattatgctttttaggttaaaacagagaaactaagttacatattttcttggaaagcctaatttgtgtgaattggtttaattttgtagGTGGATTTGGTGGGAGGATACTACGATGCAGGGGACAATATGAAGTTTGGATTCCCAATGGCATTCACAACCACAATGCTCTCATGGAGTTTAATTGAGT
| | || | | | |||| | ||| ||| || | | | | | | | || |||||| | | ||||| ||| ||| | || ||||| | |||||||||||||| ||||||||||| | ||| ||||| |||||||| | || || |
---------------------------gtatgcgtttctgagatc---ctgctcgttttataagaagctctacttgatctctttggttgttctcttcaagGTGGTTCTCCGAGGAGGCTACGTCGACTCTGGAGACAACGTAAAGTTTGGATTCCCCATGGCATTCACGATCACCATGCTTTCATGGAGCGTGATAGAAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aagttacatattttcttggaaagcctaatttgtgtgaattggtttaattttgtagGTGGATTTGGTGGGAGGATACTACGATGCAGGGGACAATATGAAGTTTGGATTCCCAATGGCATTCACAACCACAATGCTCTCATGGAGTTTAATTGAGT
aattggtttaatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
accctaattttgttattatgctttttaggttaaaacagagaaactaagttacatattttcttggaaagcctaatttgtgtgaattggtttaattttgtagGTGGATTTGGTGGGAGGATACTACGATGCAGGGGACAATATGAAGTTTGGATTCCCAATGGCATTCACAACCACAATGCTCTCATGGAGTTTAATTGAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
accctaa
- - - - - - - - - - - - - - - - aaacaga
- - - - - - - - - - - - - - - - - - - - aaactaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - agcctaa