Sequence
atgc intronic sequence ATGC exonic sequencegtttcaatttcatatctactccaatcttaaactgtgaaagatgatgcataattttgaactattcatctgttttgttagATCCTTGGGACTGGAATGGATACACAGGATACGTCACCTTCTGTATTACTCTTCTTTGACAAACAAAGATTCATCTTTAATGCTGGAGAG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G16260.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G16260.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os01g13150.1 (Oryza sativa), 3'ss of exon 3
---gtt--tcaatttcat-atctactccaatctt---aaactgtgaaagatg---atgc--ataattttgaactattcatctg----ttttgtt----agATCCTTGGGACTGGAATGGATACACAGGATACGTCACCTTCTGTATTACTCTTCTTTGACAAACAAAGATTCATCTTTAATGCTGGAGAG
||| |||| | | | || ||| ||| | || | ||| ||| | || || | | ||| | ||| | |||| ||||| || |||||||| ||||| ||||| |||||||| | |||||||||||||||||||| || || || ||||||||||| |||
tcagttaatcaaccccctcacttagatcaactcatgggaacagggacaaatgcctttgccagtgatcttaccccttcgttcttggcttcttgctgtgcagATACTTGGTACAGGAATGGACACACAAGATACTTCACCTTCCATTTTACTCTTCTTTGACAAACAGAGGTTTATATTTAATGCTGGCGAG
upper sequence: AT3G16260.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G379286_T01 (Zea mays), 3'ss of exon 1
----gtttcaatttcatatct-actccaatcttaaactgtgaaagatgatgca----taattttgaactattc---atctgttttgtta----------gATCCTTGGGACTGGAATGGATACACAGGATACGTCACCTTCTGTATTACTCTTCTTTGACAAACAAAGATTCATCTTTAATGCTGGAGAG
| ||||||| | || | | | | || | || || | |||| | | || || ||||||| ||| ||||| || |||||||| |||||||| || ||||||||| | |||| ||||||||||||||||| || || |||||||| || |||
tgtgggggcaatttcttcccttgaactagttcatgagtgcaggaactgttgttcttttggttttcattcaatctcactcccctttgttattcctgcgcagATACTTGGTACAGGAATGGACACACAGGACACTTCACCTTCTATTCTACTATTCTTTGACAAACAAAGGTTTATTTTTAATGCGGGCGAG
upper sequence: AT3G16260.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv09s0002g04000.t01 (Vitis vinifera), 3'ss of exon 1
-----gtttc----aatttcatatctactccaatcttaaactgtgaaagatgatgcataattttgaa----------ctattcatctgttttgtt---agATCCTTGGGACTGGAATGGATACACAGGATACGTCACCTTCTGTATTACTCTTCTTTGACAAACAAAGATTCATCTTTAATGCTGGAGAG
||| || | || | || || || | | |||||| | || || || | | || | || | |||| || |||||||| ||||||||||| ||||| || ||||||| || || |||||||| ||||||||||| || || ||||||||||||
tcaaaattttggggaacccaacatagcttaaaagtttgaagtatccaagatgtcttgtggttaaaaatatttgatatcttcttacttgctatgattgcagATTCTGGGGACTGGGATGGATACACAAGATACTTCGTCTTCTGTCTTGCTTTTCTTTGATAAACAAAGATTTATTTTCAATGCTGGAGAGMapped 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|19877303|gb|AU238134.1|AU238134EST: AGAGGAATACTCGCACCCTTAACCCTACCAATACCATCGCCTATGTTCAG ATCCTTGGGACTGGAATGGATACACAGGATACGTCACCTTCTGTATTACTC
genomic: AGAGGAATACTCGCACCCTTAACCCTACCAATACCATCGCCTATGTTCAGgtttcaattt ... gttttgttagATCCTTGGGACTGGAATGGATACACAGGATACGTCACCTTCTGTATTACTC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atcttaaactgtgaaagatgatgcataattttgaactattcatctgttttgttagATCCTTGGGACTGGAATGGATACACAGGATACGTCACCTTCTGTATTACTCTTCTTTGACAAACAAAGATTCATCTTTAATGCTGGAGAG
tctgtttt CT-rich tract
ataattttgaactatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttcaatttcatatctactccaatcttaaactgtgaaagatgatgcataattttgaactattcatctgttttgttagATCCTTGGGACTGGAATGGATACACAGGATACGTCACCTTCTGTATTACTCTTCTTTGACAAACAAAGATTCATCTTTAATGCTGGAGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA