Sequence
atgc intronic sequence ATGC exonic sequencegtgatttgctactgtatctctaggagctacatctctacagattctagtttgttttcttatgctgaccaatatatttttctcagGCCTCATCAGCTTACTGGAAGGGTGACAAAGACCGTGAGAGCTTGCAGAGAGTTTATGGGATATCTTATCCTGATCAGAAGCAGCTGAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G26830.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G26830.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA01G03930.1 (Glycine max), 3'ss of exon 5
----------------gtgatttgctactgtatct--ctaggagctacatctctacagattc----tagtttgttttcttatgctgaccaatatatttt---tctcagGCCTCATCAGCTTACTGGAAGGGTGACAAAGACCGTGAGAGCTTGCAGAGAGTTTATGGGATATCTTATCCTGATCAGAAGCAGCTGAAG
| ||| || | ||| | || || | ||| || | | ||| || || | | ||| | |||||| |||||||| || |||| ||| |||||||| || || || || || ||||||||||| |||||||||||||||||||| ||||||
gtatgcttaaactatcttatcatgcaaccatttctacttttgatttatccattaacatatcaatgacaagtactttggtttaattggttatcgtgtttggaatttcagGCTTCATCAGCATATTGGAGGGGGGACAAAGATCGGGAAAGTTTACAAAGAGTTTATGGCATATCTTATCCTGATCAGAAAAGTCTGAAG
upper sequence: AT5G26830.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA02G03750.1 (Glycine max), 3'ss of exon 5
-----------------------------gtgatttgctactgtatctctaggagctacatctctacagattctagtttgttttcttatgctgaccaatatatttttctcagGCCTCATCAGCTTACTGGAAGGGTGACAAAGACCGTGAGAGCTTGCAGAGAGTTTATGGGATATCTTATCCTGATCAGAAGCAGCTGAAG
| | | | | | || | | || || || | | || |||| |||| | | | || | ||| ||||| |||||||| || |||| ||| |||||||| || || || || || ||||||||||| |||||||||||||||||||| || |||
gtacgtataaactattttatcagtctaccatttctagttttgatttatccattaact-tatgtcaatggcaagtactttggtttcattggttattgtatttggaattc-cagGCTTCATCAGCATATTGGAGGGGGGACAAAGATCGGGAAAGTTTACAAAGAGTTTATGGCATATCTTATCCTGATCAGAAAAGTCTAAAG
upper sequence: AT5G26830.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv19s0015g00470.t01 (Vitis vinifera), 3'ss of exon 6
-------gtgatttgc-tactgtatctctag----gagctacatctctacagatt--ctagtttgttttct--tatgctgaccaatatatt-tttctcagGCCTCATCAGCTTACTGGAAGGGTGACAAAGACCGTGAGAGCTTGCAGAGAGTTTATGGGATATCTTATCCTGATCAGAAGCAGCTGAAG
|| |||| || | | || ||| ||| || | | | || | | | | |||||| | | |||| | | | ||| |||||| |||||||||||||||| || | | ||| ||||| || ||||| ||||||||||||||||| ||||||||| || | |||||
gtgatgtgttcgttgcataaaggacctgtagttgggaggtaattttatgtgtgtttgcaaatctattttctgttttactgaggtgtttgtaatttttcagGCTTCATCAGCTTACTGGAGAGGAAATAGAGATCGTGAAAGTTTGCAAAGAGTTTATGGGATATCGTATCCTGATTCAAAACGATTGAAG
upper sequence: AT5G26830.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv01s0026g00340.t01 (Vitis vinifera), 3'ss of exon 6
gtgatttgctac-tgtatctctaggagctacatc--tctacagattctagtttgttttct--tatgctgaccaatatatttttctcagGCCTCATCAGCTTACTGGAAGGGTGACAAAGACCGTGAGAGCTTGCAGAGAGTTTATGGGATATCTTATCCTGATCAGAAGCAGCTGAAG
|||| | | | | | | |||| | | | | | | | | | |||||| | | || | | | | || ||||| |||||||||||||||| || | ||||| |||||||| ||||| ||||||||||||||||||||||||||| || | |||||
---gtttgttgcgtatgtagttgggagttgatttcatttgtgcttgcaaatctattttctgttttacttaggcgtctgtaatttccagGCTTCATCAGCTTACTGGAGAGGAAATAAAGATCGTGAGAGTTTGCAAAGAGTTTATGGGATATCTTATCCTGATTCAAAACGATTGAAGMapped 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|164111701|gb|ES161302.1|ES161302EST: GACCGCACATACCAAATACTTCCTTTGTGAAAGCGTTCAAGTGTTTGAGG GCCTCATCAGCTTACTGGAAGGGTGACAAAGACCGTGAGAGCTTACAGAGA
genomic: GACCGCACATACCAAATACTTCCTTTGTGAAAGCGTTCAAGTGTTTGAGGgtgatttgct ... tttttctcagGCCTCATCAGCTTACTGGAAGGGTGACAAAGACCGTGAGAGCTTGCAGAGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acatctctacagattctagtttgttttcttatgctgaccaatatatttttctcagGCCTCATCAGCTTACTGGAAGGGTGACAAAGACCGTGAGAGCTTGCAGAGAGTTTATGGGATATCTTATCCTGATCAGAAGCAGCTGAAG
tgctgac putative branch site (score: 2)
tatttttctc putative PPT
aatatatttttctca 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgatttgctactgtatctctaggagctacatctctacagattctagtttgttttcttatgctgaccaatatatttttctcagGCCTCATCAGCTTACTGGAAGGGTGACAAAGACCGTGAGAGCTTGCAGAGAGTTTATGGGATATCTTATCCTGATCAGAAGCAGCTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG