Sequence
atgc intronic sequence ATGC exonic sequencegttgtattctgagcttctaactttataaaagtgtatctgaccgtcttgttatgtgttagagagtccagggattgtttttgatggatttaagtttgttacttgaatcagGCAAGTGAATGTAATACCTATGCTGATATAGATGCAGCATATACTTGCCTCAAGGAACATTATGGTGTAAAAGATGATCAACTGATATTATATGGTCAGT
Basic information
species | Arabidopsis thaliana |
transcript | AT5G38220.3 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G38220.3 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA13G07810.2 (Glycine max), 3'ss of exon 2
gttgtattctgagcttctaactttataaaagtgtatctgaccgtcttgttatgtgttagagagtccagggattgtttttgatggatttaagtttgttacttgaatcagGCAAGTGAATGTAATACCTATGCTGATATAGATGCAGCATATACTTGCCTCAAGGAACATTATGGTGTAAAAGATGATCAACTGATATTATATGGTCAGT
| ||| | | ||||| ||||| ||| ||| |||||||||||| || || ||||| ||||| ||||||| ||||| || || || || || || |||||||| ||| ||||||| |||||||| |
---------------------------------------------------------------------gtaagttaacagtcatcctt--tttgtatgttgaaacagCCAACTGAATGTAATACATACGCAGATATTGATGCTGCATATAAATGCCTAAAAGAGCAATACGGGGTGAAAGATGAACAATTGATATTGTATGGTCAAT
upper sequence: AT5G38220.3 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv14s0006g02620.t01 (Vitis vinifera), 3'ss of exon 2
gttgtattctgagcttctaactttataaaagtgtatctgaccgtct-tgttatgtgttagagagtccagggattgtttttgatggatttaagtttgttacttgaatcagGCAAGTGAATGTAATACCTATGCTGATATAGATGCAGCATATACTTGCCTCAAGGAACATTATGGTGTAAAAGATGATCAACTGATATTATATGGTCAGT
|| | | ||| | | | || | | | || | | | | | | |||||| | | || | || || || || || ||| | ||| || ||||||||||| ||||| || || ||||||| ||||| ||||| ||||| || || || || |||||||| ||| | ||||||||||||||||
--tgaactttgacatgtttagttgcttaggg---atataatcatttctattatgtaccattt-gcacataatataacattcatccatcc---ctttttctttggaacagCCATCAGAATGTAATACATATGCAGACATTGATGCAGTATATAAATGCCTTAAGGAGCAGTACGGGGTTAAAGATGAGCAATTAATATTATATGGTCAGTMapped 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|19875872|gb|AU236703.1|AU236703EST: GTATGATTACTCTGGTTATGGTCAGTCTACTGGAAAG GCAAGTGAATGTAATACCTATGCTGATATAGATGCAGCATATACTTGCCTC
genomic: GTATGATTACTCTGGTTATGGTCAGTCTACTGGAAAGgttgtattct ... cttgaatcagGCAAGTGAATGTAATACCTATGCTGATATAGATGCAGCATATACTTGCCTC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgttagagagtccagggattgtttttgatggatttaagtttgttacttgaatcagGCAAGTGAATGTAATACCTATGCTGATATAGATGCAGCATATACTTGCCTCAAGGAACATTATGGTGTAAAAGATGATCAACTGATATTATATGGTCAGT
ttttgat putative branch site (score: 4)
atttaagtttgtta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttgtattctgagcttctaactttataaaagtgtatctgaccgtcttgttatgtgttagagagtccagggattgtttttgatggatttaagtttgttacttgaatcagGCAAGTGAATGTAATACCTATGCTGATATAGATGCAGCATATACTTGCCTCAAGGAACATTATGGTGTAAAAGATGATCAACTGATATTATATGGTCAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG