Sequence
atgc intronic sequence ATGC exonic sequence...tcacaaatcttattatcaatgcttaaactttggatttgggttattgcagatcatctcgcaagtttgatccttttttatatatttttctgaatctctgcagTTAAGGTGGACAGAGCTGTGAGCACAAGTATCTACTTCTTGCTTCCATCTGGGAGCGTTTCTCGTCTTCATCGCATACCAATGGCTGAAACCTGGCACTT
Basic information
species | Arabidopsis thaliana |
transcript | AT1G19130.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G19130.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: EFJ31212 (Selaginella moellendorffii), 3'ss of exon 1
tcacaaatcttattatcaatgcttaaactttggatttgggttattgcagatcatctcgcaagtttgatccttttttatatatttttctgaatctctgcagTTAAGGTGGACAGAGCTGTGAGCACAAGTATCTACTTCTTGCTTCCATCTGGGAGCGTTTCTCGTCTTCATCGCATACCAATGGCTGAAACCTGGCACTT
| |||| || |||| || | | |||||| ||||||||||| | ||||||||| |||||||||||||||||||| || || || | |||||||| || ||| ||||| ||
------------------------------------------------------gtgagtagttctttctttttccatctctcacaggactgtcttgcagTCAAGGTGGACAGGCCCGTGAGCACAGCCATCTACTTCTTGCTTCCATCCGGCTCGGTCTCCAAATTGCATCGCATCCCTTCTAGCGAAGTGTGGCATTT
upper sequence: AT1G19130.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: EFJ17135 (Selaginella moellendorffii), 3'ss of exon 1
tcacaaatcttattatcaatgcttaaactttggatttgggttattgcagatcatctcgcaagtttgatccttttttatatatttttctgaatc--tctgcagTTAAGGTGGACAGAGCTGTGAGCACAAGTATCTACTTCTTGCTTCCATCTGGGAGCGTTTCTCGTCTTCATCGCATACCAATGGCTGAAACCTGGCACTT
|| || | ||||||| || | | | | | |||||| ||||||||||| | ||||||||| |||||||||||||||||||| ||| || || | |||||||| || ||| ||||| ||
-------------------------------------------------------gtgcgtagttctttctttttt-catctctcacaggactgtcttgcagTCAAGGTGGACAGGCCCGTGAGCACAGCCATCTACTTCTTGCTTCCATCCGGGTCGGTCTCCAAATTGCATCGCATCCCTTCTAGCGAAGTGTGGCATTTMapped 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|19877300|gb|AU238131.1|AU238131EST: TTTCAGAGATTCTTCTGTTTTCCTCTCCACCTCTCAGCTCCCTCCAACCT TTAAGGTGGACAGAGCTGTGAGCACAAGTATCTACTTCTTGCTTCCATCTG
genomic: TTTCAGAGATTCTTCTGTTTTCCTCTCCACCTCTCAGCTCCCTCCAACCTgtagctctct ... atctctgcagTTAAGGTGGACAGAGCTGTGAGCACAAGTATCTACTTCTTGCTTCCATCTG
EST:
gi|125015824|gb|EL088093.1|EL088093EST: CTCCCTCCAACCT TTAAGGTGGACAGAGCTGTGAGCACAAGTATCTACTTCTTGCTTCCATCTG
genomic: CTCCCTCCAACCTgtagctctct ... atctctgcagTTAAGGTGGACAGAGCTGTGAGCACAAGTATCTACTTCTTGCTTCCATCTG
EST:
gi|116462142|gb|EG504734.1|EG504734EST: TTTCAGAGATTCTTCTGTTTTCCTCTCCACCTCTCAGCTCCCTCCAACCT TTAAGGTGGACAGAGCTGTGAGCACAAGTATCTACTTCTTGCTTCCATCTG
genomic: TTTCAGAGATTCTTCTGTTTTCCTCTCCACCTCTCAGCTCCCTCCAACCTgtagctctct ... atctctgcagTTAAGGTGGACAGAGCTGTGAGCACAAGTATCTACTTCTTGCTTCCATCTG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gcagatcatctcgcaagtttgatccttttttatatatttttctgaatctctgcagTTAAGGTGGACAGAGCTGTGAGCACAAGTATCTACTTCTTGCTTCCATCTGGGAGCGTTTCTCGTCTTCATCGCATACCAATGGCTGAAACCTGGCACTT
gtttgat putative branch site (score: 5)
tctctgc putative PPT
aagtttgatccttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tcacaaatcttattatcaatgcttaaactttggatttgggttattgcagatcatctcgcaagtttgatccttttttatatatttttctgaatctctgcagTTAAGGTGGACAGAGCTGTGAGCACAAGTATCTACTTCTTGCTTCCATCTGGGAGCGTTTCTCGTCTTCATCGCATACCAATGGCTGAAACCTGGCACTT
tcacaaa
- - - - - - - - - - -cttaaac
- - - - - - - - - - - - - - - - gatttgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - agtttga