Sequence
atgc intronic sequence ATGC exonic sequenceAAGAGATCTTTGATGCCTTGAAGAATCAGACTGTGGATCTGGTTTTGACTGCTCATCCTACTCAGTCTGTGCGTAGATCATTGCTTCAGAAGCATGGGAGgttagtttttgacttagttgttttctggagagagtgagaaaactctgtttgcttgtgtgttgacctgacattaaatgttttctcag
Basic information
species | Arabidopsis thaliana |
transcript | AT3G14940.1 |
intron # | 3 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G14940.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: LOC_Os08g27840.1 (Oryza sativa), 5'ss of exon 2
AAGAGATCTTTGATGCCTTGAAGAATCAGACTGTGGATCTGGTTTTGACTGCTCATCCTACTCAGTCTGTGCGTAGATCATTGCTTCAGAAGCATGGGAGgttagtttttgacttagttgttttctggagagagtgagaaaactctgtttgcttgtgtgttgacc-tgacatt--aaatgttttctcag
|||| ||||||||||| | |||| ||||||||| || |||||||||||||| ||||| || ||||| ||| | || ||| ||||||| || || |||| |||| || | | | | || | | | || || || ||| | | | ||| ||| |||| | | |
CAGAGGTCTTTGATGCCCTTAAGAGTCAGACTGTTGACCTGGTTTTGACTGCACATCCAACACAGTCAGTGAGGAGGTCACTGCTTCAAAAACACTCAAGgtgagttacagaaacaatactat------gatatcaaacatcctatggtttcttatcatctaattgtgaaatttcaaatataatttag-
upper sequence: AT3G14940.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: LOC_Os09g14670.1 (Oryza sativa), 5'ss of exon 2
AAGAGATCTTTGATGCCTTGAAGAATCAGACTGTGGATCTGGTTTTGACTGCTCATCCTACTCAGTCTGTGCGTAGATCATTGCTTCAGAAGCATGGGAGgttagtttttgacttagttgttttctggagagagtgagaaaactctgtttgcttgtgtgttgacctgacattaa--atgttttctcag
||| ||||||||||| | |||| ||||||||| || || ||||||||||| ||||| || ||||||||| | || ||| |||| ||||| || |||||||| || || | | || | | | | | || || || | | | || ||| | || | ||||
CTGAGGTCTTTGATGCCCTCAAGAGTCAGACTGTTGACCTTGTTTTGACTGCACATCCAACACAGTCTGTGAGGAGGTCACTGCTCCAGAAACACTCCAGgttagtcggcgaaacagc-gcgatttgctcacaccacatga--tgtagtttctagtctctaatctcgattgtaacattcttatttcag
upper sequence: AT3G14940.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GRMZM2G110714_T01 (Zea mays), 5'ss of exon 2
AAGAGATCTTTGATGCCTTGAAGAATCAGACTGTGGATCTGGTTTTGACTGCTCATCCTACTCAGTCTGTGCGTAGATCATTGCTTCAGAAGCATGGGAGgttagt---------ttttgacttagttgttttctgga-gagagtga---gaaaactctgtttgcttg-tgtgttga---cctgacattaaatgttttctcag
||| | |||||||| | |||||||| ||||| || || || ||||||| ||||| |||||||| || || |||||||||||||| |||||||| |||||||| || ||| || | | | | ||| |||| | | || || || | ||| | || || | || || |||| | |
TGGAGGTATTTGATGCTCTCAAGAATCAAACTGTTGACCTCGTCCTGACTGCACATCCAACTCAGTCAGTCCGGAGATCATTGCTTCAAAAGCATGGCAGgttagtctcgaagctttctgaattgttagatcccaggatgagatttacttgatgacattgaatatttgctatgcagaaatcttggttctatttgttcttt---
upper sequence: AT3G14940.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GRMZM2G473001_T02 (Zea mays), 5'ss of exon 2
AAGAGATCTTTGATGCCTTGAAGAATCAGACTGTGGATCTGGTTTTGACTGCTCATCCTACTCAGTCTGTGCGTAGATCATTGCTTCAGAAGCATGGGAGgttagtttttgacttagttgttttctggagagagtgagaaaactctgtttgcttgtgtgttgacctgacattaaatgttttctcag
||| | ||||||||| | |||| |||||||| ||||||||||||||||| ||||| || ||||||||| | || ||| |||| ||||| || ||||||||||| | ||| | || | | || | |||| ||| | | | | ||| || | || ||||
CTGAGGTATTTGATGCCCTCAAGAGCCAGACTGTTGATCTGGTTTTGACTGCACATCCAACACAGTCTGTGAGGAGGTCACTGCTCCAGAAACACTCGAGgttagtttgccaaccagt-gcattgtagttgacatgc-acaacttcgttca---gcctttaatcttgatcccaatattcttatcag
upper sequence: AT3G14940.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: Vv12s0028g02180.t01 (Vitis vinifera), 5'ss of exon 2
AAGAGATCTTTGATGCCTTGAAGAATCAGACTGTGGATCTGGTTTTGACTGCTCATCCTACTCAGTCTGTGCGTAGATCATTGCTTCAGAAGCATGGGAGgttagtttttgacttag--------ttgttttctggagagagtgaga-------aaactctgtttgctt---gtgtgttgac-ctgacattaaatgttttctcag--------
|||| | |||||||| |||||||| |||||||| ||| |||| | || || ||||||||||| ||||| || ||||| |||||||| ||||||| ||||| ||| | | ||| || | |||| | | || ||| || | ||||||| | | | ||| | | ||| ||
AAGAAGTTTTTGATGCTTTGAAGAACCAGACTGTAGATTTGGTCCTTACAGCACATCCTACTCAATCTGTCCGGAGATCTTTGCTTCAAAAGCATGCAAGgtttgttctccagttaccgtaatatttttattcttgtaaacgtaagagagggaaaagggttatttgcttcacataggctcttgttgatgctttgtttttccttcccttttcagMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|86073317|gb|DR369074.1|DR369074EST: GCTCATCCTACTCAGTCTGTGCGTAGATCATTGCTTCAGAAGCATGGGAG GATAAGGGACTGTCTTGCTCAACTCTATGCAAAGGACATTACTCCTGATGA
genomic: GCTCATCCTACTCAGTCTGTGCGTAGATCATTGCTTCAGAAGCATGGGAGgttagttttt ... gttttctcagGATAAGGGACTGTCTTGCTCAACTCTATGCAAAGGACATTACTCCTGATGA
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
AAGAGATCTTTGATGCCTTGAAGAATCAGACTGTGGATCTGGTTTTGACTGCTCATCCTACTCAGTCTGTGCGTAGATCATTGCTTCAGAAGCATGGGAGgttagtttttgacttagttgttttctggagagagtgagaaaactctgtttgcttgtgtgttgacctgacattaaatgttttctcag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC