Sequence
atgc intronic sequence ATGC exonic sequencegtacactgctttatttctcttccactttgttttcctttgttcatgtctgacgctcaattctgatccacctctctcccaatttgtccagATCCGATTCATATTATTGCAGAACAGACAAGGTAAGACTCGTCTAGCCAAATACTATGTCCCTCTCGAAGAATCCGAGAAACACAAAGTCGAATACGAG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G47830.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G47830.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA17G37730.1 (Glycine max), 3'ss of exon 1
----------------------------gtacactgctttatttctcttccactttgtt--ttcctttgttcatgtctgacgctc-aattctgatccacctctctcccaatttgtccagATCCGATTCATATTATTGCAGAACAGACAAGGTAAGACTCGTCTAGCCAAATACTATGTCCCTCTCGAAGAATCCGAGAAACACAAAGTCGAATACGAG-
| | || | | ||| | | | | | || |||| | || | | | | || || | | ||||| | || || |||||||||||||| | ||||||||||| || || ||||| ||||| ||||||||||| || |||||||| || |||||||| ||||| ||||||||||||
gttccttcgttcatcattctattccctctttcgctccataattacaataataatctcttcgttccaatatttcttttttccattctaaaattcgttttcctcttttccgcatt-cgcagATCCGATTCATTCTGTTGCAGAACAGGCAGGGCAAGACCCGTCTTGCCAAATACTACGTTCCTCTCGAGGACTCCGAGAAGCACAAGGTCGAATACGAGG
upper sequence: AT1G47830.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA14G40430.2 (Glycine max), 3'ss of exon 1
----gtacactgctttatttc-tcttccactttgttttcctttgttcatgtctgacgctcaattctgatccacctctctcccaatttgtccagATCCGATTCATATTATTGCAGAACAGACAAGGTAAGACTCGTCTAGCCAAATACTATGTCCCTCTCGAAGAATCCGAGAAACACAAAGTCGAATACGAG
|| || | |||| | |||| | | |||| ||| |||| | ||| ||| | ||| ||| | ||| ||| | |||||||||||||| | ||||||||||| || || ||||| ||||| ||||||||||| || |||||||| || |||||||| ||||| || |||||||||
gttcgttcataattctattccctctttcgttccattttttttt--tcatttttgaa---tgattgttttcc-cctttttccgcattcg--cagATCCGATTCATTCTGTTGCAGAACAGGCAGGGCAAGACCCGTCTTGCCAAATACTACGTTCCTCTCGAGGATTCCGAGAAGCACAAGGTGGAATACGAG
upper sequence: AT1G47830.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv18s0001g14240.t01 (Vitis vinifera), 3'ss of exon 2
gtacactgctttatttctcttccactttgttttcctttgttcatgtctgacgctcaattctgatccacctctctcccaatttgtccagATCCGATTCATATTATTGCAGAACAGACAAGGTAAGACTCGTCTAGCCAAATACTATGTCCCTCTCGAAGAATCCGAGAAACACAAAGTCGAATACGAG
||| | || | | || | | ||| | | | || | || ||| | || | ||||||||||||||| | | |||||||| || || ||||| || || ||||| |||||||| ||||| |||||||||||||| ||||| ||||||||||||
--gtactctctcgattatgat--gattcaatcttgattgcgaggagattgagttgctgactcgttcattaatctttgatttgg--cagATCCGATTCATAATTCTACAGAACAGGCAGGGCAAGACCCGCCTCGCCAAGTACTATGTTCCTCTTGAAGAATCCGAGAAGCACAAGGTCGAATACGAG
upper sequence: AT1G47830.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv04s0023g03340.t01 (Vitis vinifera), 3'ss of exon 1
gtacactgctttatttctcttccactttgttttcctttgt-----tcatgtc---tgacgctc--aattctgatccacctctctcc-caatttgtc-cagATCCGATTCATATTATTGCAGAACAGACAAGGTAAGACTCGTCTAGCCAAATACTATGTCCCTCTCGAAGAATCCGAGAAACACAAAGTCGAATACGAG
||| | | || ||| | ||| || ||||||||| | | |||| || | ||||||||| || | || ||| |||| ||||||||||||||||| ||||||||||| || || |||||||| ||||||| ||||| || ||| |||| ||||| ||||||||||| ||||||||||||
gtaaattttcttcttttttttctttctttttttcctttttggatttgatgttgagtggaacctgaaattctgatttttcttttcccacaaattgtggcagATCCGATTCATATTGTTGCAGAACAGGCAGGGAAAGACTCGATTAGCCAAGTACTACGTTCCTTTCGAGGAATCTGAGAAACACAAGGTCGAATACGAG
upper sequence: AT1G47830.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: EFJ11600 (Selaginella moellendorffii), 3'ss of exon 1
gtacactgctttatttctcttccactttgttttcctttgttcatgtctgacgctcaattctgatccacctctctcccaatt---tgtccagATCCGATTCATATTATTGCAGAACAGACAAGGTAAGACTCGTCTAGCCAAATACTATGTCCCTCTCGAAGAATCCGAGAAACACAAAGTCGAATACGAG
| | || | || | || | |||| || | || || || || ||||| ||||||| | ||||| || | || || ||||||||||| ||||| ||||||||||| |||||||| |||||||| || || || | || |||
------------------------------gtgagtggattttcgcttg--gatccgtgctgagacatcgatcgccgtgttggatgcgcagATTAGATTCATCCTCTTGCAAAATCGCCAGGGGAAGACTCGTCTCGCCAAGTACTATGTCCCGCTCGAAGACTCCGAGAAGCAAAAGCTCCAGTATGAG
upper sequence: AT1G47830.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: EFJ09792 (Selaginella moellendorffii), 3'ss of exon 1
gtacactgctttatttctcttccactttgttttcctttgttcatgtctgacgctcaattctgatccacctctctcccaatttgtccagATCCGATTCATATTATTGCAGAACAGACAAGGTAAGACTCGTCTAGCCAAATACTATGTCCCTCTCGAAGAATCCGAGAAACACAAAGTCGAATACGAG
| || || | | || | | | |||| | | | || ||||| ||||||| | ||||| || | || || ||||||||||| ||||| ||||||||||| |||||||| |||||||| || || || | || |||
------------------------gtgagtggattttcgcttggatccgtgccgagacatcgatcgccgtgtt-----ggatgcgcagATTAGATTCATCCTCTTGCAAAATCGCCAGGGGAAGACTCGTCTCGCCAAGTACTATGTCCCGCTCGAAGACTCCGAGAAGCAAAAGCTCCAGTATGAGMapped 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|164091763|gb|ES070511.1|ES070511EST: GAATTCTCCATTAGATTTTGCAGAGAAAATG ATCCGATTCATATTATTGCAGAACAGACAAGGTAAGAC
genomic: GAATTCTCCATTAGATTTTGCAGAGAAAATGgtacactgct ... atttgtccagATCCGATTCATATTATTGCAGAACAGACAAGGTAAGAC
EST:
gi|116464176|gb|EG506768.1|EG506768EST: ATCGCTCACGATTTCTCCTGAATTCTCCATTAGATTTTGCAGAGAAAATG ATCCGATTCATATTATTGCAGAACAGACAAGGTAAGACTCGTCTAGCCAAA
genomic: ATCGCTCACGATTTCTCCTGAATTCTCCATTAGATTTTGCAGAGAAAATGgtacactgct ... atttgtccagATCCGATTCATATTATTGCAGAACAGACAAGGTAAGACTCGTCTAGCCAAA
EST:
gi|116464171|gb|EG506763.1|EG506763EST: ATCGCTCACGATTTCTCCTGAATTCTCCATTAGATTTTGCAGAGAAAATG ATCCGATTCATATTATTGCAGAACAGACAAGGTAAGACTCGTCTAGCCAAA
genomic: ATCGCTCACGATTTCTCCTGAATTCTCCATTAGATTTTGCAGAGAAAATGgtacactgct ... atttgtccagATCCGATTCATATTATTGCAGAACAGACAAGGTAAGACTCGTCTAGCCAAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cctttgttcatgtctgacgctcaattctgatccacctctctcccaatttgtccagATCCGATTCATATTATTGCAGAACAGACAAGGTAAGACTCGTCTAGCCAAATACTATGTCCCTCTCGAAGAATCCGAGAAACACAAAGTCGAATACGAG
ttctgat putative branch site (score: 3)
cctctctcccaattt putative PPT
aatttgt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacactgctttatttctcttccactttgttttcctttgttcatgtctgacgctcaattctgatccacctctctcccaatttgtccagATCCGATTCATATTATTGCAGAACAGACAAGGTAAGACTCGTCTAGCCAAATACTATGTCCCTCTCGAAGAATCCGAGAAACACAAAGTCGAATACGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA