Sequence
atgc intronic sequence ATGC exonic sequencegtgggtatgtgacacaacttcgtatctgtgagttttgataaaaaaaggtttggaattttaagtcctaatttgttttggctattgttgtgtagtagGTGGTTGGAGAAGAGCTAGGAGTACTTCCAGGGATGGATTCCATCTTTTCAATGCTTGAACTCGAGAGGCTTGTTGGTTTCTTTAGGCAAGCAACCCGAA
Basic information
species | Arabidopsis thaliana |
transcript | AT1G26090.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G26090.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv01s0011g02870.t01 (Vitis vinifera), 3'ss of exon 2
gtgggtatgtgacacaacttcgtatctgtgagttttgataaaaaaaggtttggaattttaagtcctaa---------tttgttttggctattgttgtgtagtagGTGGTTGGAGAAGAGCTAGGAGTACTTCCAGGGATGGATTCCATCTTTTCAATGCTTGAACTCGAGAGGCTTGTTGGTTTCTTTAGGCAAGCAACCCGAA
||| || || || |||||| || | | || || | ||| | | || | || || | | || ||||||||||||| ||||||||||| ||||| ||||| ||||||||||| | ||| || |||| | ||| |||||||| || || ||||| || | ||||
--aattatctggttgaatgtc--atctgtaagggatagtgggctgagtgtttcactttcatctgtgaaggaatttcttatgcatttgtcttcattatgtagtagGTGGTGGGAGAAGAGCTTGGAGTGCTTCCTGGGATGGATTCTGTGTTTACATTGCTCGCACTTGAGAGGCTGGTGGGATTCTTAGGGAATTTGGGTCGAA
upper sequence: AT1G26090.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv10s0003g05110.t01 (Vitis vinifera), 3'ss of exon 3
----------------------------------gtgggtatgtgacacaacttcgtatctgtgagttttgataaaaaaaggtttggaattttaagtcctaa---------tttgttttggctattgttgtgtagtagGTGGTTGGAGAAGAGCTAGGAGTACTTCCAGGGATGGATTCCATCTTTTCAATGCTTGAACTCGAGAGGCTTGTTGGTTTCTTTAGGCAAGCAACCCGAA
| ||| || || ||| |||| | || | | | || || | ||| | | || | || || | | || ||||||||||||| ||||||||||| ||||| ||||| ||||||||||| | ||| || |||||| ||| |||||||| || || ||||| || | ||||
gtgggtatgtaataaatacataggtctcttgatcttaattatctggttgaatttc--atctataagggatagtggactgagtatttcactttcatctgtgaaggaatttcttatgcatttgtcttaattatgtagtagGTGGTGGGAGAAGAGCTTGGAGTGCTTCCTGGGATGGATTCTGTGTTTACATTGCTTGCACTTGAGAGGCTGGTGGGATTCTTAGGGAATTTGGGTCGAA
upper sequence: AT1G26090.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv14s0006g02920.t01 (Vitis vinifera), 3'ss of exon 3
------------------------------gtgggtatgtgacacaacttcgtatctgtgagttttgataaaaaaaggtttggaattttaagtcctaa----tttgttttg-----gctattgttgtgtagtagGTGGTTGGAGAAGAGCTAGGAGTACTTCCAGGGATGGATTCCATCTTTTCAATGCTTGAACTCGAGAGGCTTGTTGGTTTCTTTAGGCAAGCAACCCGAA
|| ||| ||| || | |||| || || | | | || || | ||| | | || ||| || || | | || ||||||||||||| ||||||||||| |||| ||||| ||||||||||| || ||| || |||||| ||| |||||||| || || ||||| || | |
gtatataatagatacataggtttcttgatagtaattatctgattgaatgt--tatcagtaagggatagtggactgagtgtttcactttcatctgtgaaggaatttcttatgcacttgtcttcattatgtagTAGGTGGTGGGAGAAGAGCTTAGAGTGCTTCCTGGGATGGATTCTATGTTTACATTGCTTGCACTTGAGAGGCTGGTGGGATTCTTAGGGAATTTGGGTC---Mapped 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|116387063|gb|EG429655.1|EG429655EST: TGAAGCAAGCAGATGCTCGACTTAATATGACCCAAGGGGTTCTTGAAGGG GTGGTTGGAGAAGAGCTAGGAGTACTTCCAGGGATGGATTCCATCTTTTCA
genomic: TGAAGCAAGCAGATGCTCGACTTAATATGACCCAAGGGGTTCTTGAAGGGgtgggtatgt ... tgtgtagtagGTGGTTGGAGAAGAGCTAGGAGTACTTCCAGGGATGGATTCCATCTTTTCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaaaaaggtttggaattttaagtcctaatttgttttggctattgttgtgtagtagGTGGTTGGAGAAGAGCTAGGAGTACTTCCAGGGATGGATTCCATCTTTTCAATGCTTGAACTCGAGAGGCTTGTTGGTTTCTTTAGGCAAGCAACCCGAA
tcctaat putative branch site (score: 2)
taatttgtttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgggtatgtgacacaacttcgtatctgtgagttttgataaaaaaaggtttggaattttaagtcctaatttgttttggctattgttgtgtagtagGTGGTTGGAGAAGAGCTAGGAGTACTTCCAGGGATGGATTCCATCTTTTCAATGCTTGAACTCGAGAGGCTTGTTGGTTTCTTTAGGCAAGCAACCCGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA