Sequence
atgc intronic sequence ATGC exonic sequencegtaagttttgaggagagcttcgtggagttgataacaaggatttgtcttgcctgttctcgtgttgctaagtttgtttcaacctctttctcttgcttaatagGGTGGTGATCTCACGGAGATTGGAGAAAGAGGTGTTAATATCAGTGGAGGACAGAAGCAGAGGGTTTCCATGGCTAGGGCCGTTTACTCAAATTCAGATG
Basic information
species | Arabidopsis thaliana |
transcript | AT2G34660.1 |
intron # | 18 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G34660.1 (Arabidopsis thaliana), 3'ss of exon 18
lower sequence: LOC_Os04g52900.2 (Oryza sativa), 3'ss of exon 18
gtaagttttgaggagagcttcgtggagttgataacaaggatttgtcttgcctgttctcgtgttgctaagtttgtttcaacctct---ttctcttgcttaat---agGGTGGTGATCTCACGGAGATTGGAGAAAGAGGTGTTAATATCAGTGGAGGACAGAAGCAGAGGGTTTCCATGGCTAGGGCCGTTTACTCAAATTCAGATG
|| || || | | | | || || | || |||| | | |||| || || || || | | |||| ||||| | |||||||||| || || ||||||||||||||||| ||||| || ||||| ||||| || ||||| || || ||||| || || ||||| || |||||||||
--aaattatgttgccaatacctt----tttctatcttggttttgcgctttatattcttgtacctgcaaattgacaagaaaatatatcttcttatgcttgttgtcagGGTGGTGACCTAACAGAGATTGGAGAAAGAGGAGTTAACATTAGTGGGGGACAAAAACAGAGAGTCTCAATGGCAAGAGCTGTTTATTCTGATTCAGATG
upper sequence: AT2G34660.1 (Arabidopsis thaliana), 3'ss of exon 18
lower sequence: GLYMA13G29180.1 (Glycine max), 3'ss of exon 18
----gtaagttttgaggagagcttcgtggagttgataacaaggatttgtcttgcctg-ttctcgtgttgctaagt-ttgtttcaacctctttctc--ttgcttaat----agGGTGGTGATCTCACGGAGATTGGAGAAAGAGGTGTTAATATCAGTGGAGGACAGAAGCAGAGGGTTTCCATGGCTAGGGCCGTTTACTCAAATTCAGATG
|| | | | ||| | | | || | | || ||| | || | ||| | | ||| ||| || | |||| | |||||| |||||||||||| || || ||||| |||||||| || || |||||||| || || |||||||| || ||||||||||| || || ||||||||||| ||||
gtgagtgtatactagttatagcgtttaagtgcatccaatgaacaatttaattgttagatttttaagtttgtgggccttgcttccttctttctctcacatacttaatgactagGGTGGTGATCATACTGAAATTGGTGAAAGAGGGGTAAACATCAGTGGTGGCCAAAAGCAGAGAGTATCCATGGCTAGAGCTGTCTACTCAAATTCTGATG
upper sequence: AT2G34660.1 (Arabidopsis thaliana), 3'ss of exon 18
lower sequence: GLYMA15G09900.1 (Glycine max), 3'ss of exon 18
gtaagt-tttgagg-agagcttcgtggagttgataacaaggatttgtcttgcctgtt-----ctcgtgttgctaagtttgtttcaacctctttctcttgcttaatagGGTGGTGATCTCACGGAGATTGGAGAAAGAGGTGTTAATATCAGTGGAGGACAGAAGCAGAGGGTTTCCATGGCTAGGGCCGTTTACTCAAATTCAGATG
|| ||| | |||| | ||| | | | | || | || || | || | |||| || | | | | | |||||||||| | | |||||||||||||| || || ||||| |||||||| || || ||||| || || || |||||||| || ||||||||||| || || ||||| ||||| ||||
gtgagtgtatgagttatagcatttaagtgcatacaatgaatgttcaatttaattattagatttttaagttggtaggcctttcttc-cttctttctcttaatgactagGGTGGTGATCTTACTGAAATTGGTGAAAGAGGGGTAAACATCAGCGGTGGCCAAAAGCAGAGAGTATCCATGGCTAGAGCTGTCTACTCCAATTCTGATG
upper sequence: AT2G34660.1 (Arabidopsis thaliana), 3'ss of exon 18
lower sequence: Vv10s0003g04390.t01 (Vitis vinifera), 3'ss of exon 18
----gtaagttttgaggaga-gcttcgtggagttgataacaaggatttg-----tcttgc-ctgttctcg---tgttgctaagtttgtttcaacctcttt---ctcttgcttaatagGGTGGTGATCTCACGGAGATTGGAGAAAGAGGTGTTAATATCAGTGGAGGACAGAAGCAGAGGGTTTCCATGGCTAGGGCCGTTTACTCAAATTCAGATG
|| ||| | | ||| | || || | | | | | ||||| || || | || ||| || | | ||| | || |||| || |||||||||||||| || |||||||| ||||| || || ||||| ||||| || || ||||| | ||||||||||||||||| || || || ||||||||||
gtaagtttgttctcaagagttgtatcatgttgcagttctcttgaatttgcaaattcctgtattactcatagtttgtggccgtatattttttggtcatcttacattcttatttgttagGGTGGTGATCTTACTGAGATTGGTGAAAGGGGGGTGAATATTAGTGGTGGTCAAAAGCAACGAGTTTCCATGGCTAGGGCAGTATATTCCAATTCAGATG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttgcctgttctcgtgttgctaagtttgtttcaacctctttctcttgcttaatagGGTGGTGATCTCACGGAGATTGGAGAAAGAGGTGTTAATATCAGTGGAGGACAGAAGCAGAGGGTTTCCATGGCTAGGGCCGTTTACTCAAATTCAGATG
tttgtttcaacctctt CT-rich tract
ttaata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagttttgaggagagcttcgtggagttgataacaaggatttgtcttgcctgttctcgtgttgctaagtttgtttcaacctctttctcttgcttaatagGGTGGTGATCTCACGGAGATTGGAGAAAGAGGTGTTAATATCAGTGGAGGACAGAAGCAGAGGGTTTCCATGGCTAGGGCCGTTTACTCAAATTCAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG