Sequence
atgc intronic sequence ATGC exonic sequencegtacttgagagttttaaacaaacaagtctgaatgatgtagttaggtttctcttgttggtttatcgaggaatcagcatgctctatgatttggatgcagGTTGTGTACTTTGTGAATTCTGGCTCAGAAGCTAATGAGCTAGCAATGATGATGGCTAGGCTTTACACTGGTAGCCTTGAGATGATTTCCTTGAGAAATG
Basic information
species | Arabidopsis thaliana |
transcript | AT4G39660.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G39660.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G124353_T01 (Zea mays), 3'ss of exon 2
gtacttgagagttttaaacaaacaagtctgaatgatgtagttaggtttctcttgttg-gtttatcgaggaatcagcatgctctatgatttgga----tgcagGTTGTGTACTTTGTGAATTCTGGCTCAGAAGCTAATGAGCTAGCAATGATGATGGCTAGGCTTTACACTGGTAGCCTTGAGATGATTTCCTTGAGAAATG
| ||| | || | ||| | || | || | | | |||| ||| | ||||||||| ||| |||||||||||||| | ||||| |||||| | |||||| ||||||| |||| || | ||| | || ||| || | | |||||||
---------------------------------gtaaaagtaatgtctgtctgggtgcagtcataacacgcaccatttcatttatgtttttggatcctgcagGTTGCGTATTTTGTGAATTCTGGGACCGAAGCGAATGAGTTGGCAATGTTGATGGCCCGGCTGTATAGTGGGAATCTCAGTATGGTTGCGCTCAGAAATG
upper sequence: AT4G39660.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA08G14850.2 (Glycine max), 3'ss of exon 2
gtacttgagagttttaaacaaacaagtctgaatgatgtagttaggtttctcttgttggtttatcgaggaatcagcatgctc-----------tatgatttgga--tgcagGTTGTGTACTTTGTGAATTCTGGCTCAGAAGCTAATGAGCTAGCAATGATGATGGCTAGGCTTTACACTGGTAGCCTTGAGATGATTTCCTTGAGAAATG
||| | ||| || | | | || | | ||| |||| ||| ||| |||| | || | ||||||| | |||||||||| || ||||| |||||||| |||||||| ||||| |||||||||||||||| | | || |||||||| |||| |||||||| ||||||||||
-------agaaatgtaa-tgttcagttttt--taatctggctagaattcttttgacaaggaatcaaggatcctaattgatgacagttaaaaacatgattttaaattgcagGTTGTTTATTTTGTAAATTCTGGTTCAGAAGCAAATGAATTAGCAATGATGATGGCCCGTTTATATACTGGTAGTCTTGGTATGATTTCTTTGAGAAATG
upper sequence: AT4G39660.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA05G31630.1 (Glycine max), 3'ss of exon 2
gtacttgagagttttaaacaaacaagtctgaatgatgtagttaggtttctcttgttggtttatcgaggaatcagcatgctc-----------tatgatttgga--tgcagGTTGTGTACTTTGTGAATTCTGGCTCAGAAGCTAATGAGCTAGCAATGATGATGGCTAGGCTTTACACTGGTAGCCTTGAGATGATTTCCTTGAGAAATG
| | | | || | | | |||| | ||| ||||| ||| | | |||| | || | ||||||| | |||||||||| || ||||| |||||||| |||||||| ||||| |||||||||||||||| | | || ||||||| || | |||||||| ||||||||||
--------ttgctcttagtgttcagttttt--taatgtggctagatttcttttgacaaggaaaccaggatcctaattgatgacagttaaaaacatgattttaaattgcagGTTGTTTATTTTGTAAATTCTGGTTCAGAAGCAAATGAATTAGCAATGATGATGGCCCGTTTATATACTGGTAATCTCGGTATGATTTCTTTGAGAAATG
upper sequence: AT4G39660.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv07s0031g01330.t01 (Vitis vinifera), 3'ss of exon 2
--------gtacttgagagttt-taaacaaacaagtctgaatgatgtagttaggtttctcttgttggtttatcgaggaatcagcatgctctatgatttggatgcagGTTGTGTACTTTGTGAATTCTGGCTCAGAAGCTAATGAGCTAGCAATGATGATGGCTAGGCTTTACACTGGTAGCCTTGAGATGATTTCCTTGAGAAATG
| | | || | | | | ||| | | | | || | || | | | | | | | | | || | |||||||||||||| |||||||| ||||| |||||||| ||||| |||||||| ||||||| | || || | ||||| |||| ||||||||||| |||||||
atgggatgacatcgaaaaattcctggtttgttgaatataaatc-tctggcaaaaatttccatgaggatatctggtgactttaac-----tcattgtcaaaatgcagGTTGTGTATTTTGTGAACTCTGGATCAGAAGCCAATGAATTAGCAATGCTGATGGCACGACTATATAGTGGTAATCTTGGTATGATTTCCTTAAGAAATGMapped 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|116444401|gb|EG486993.1|EG486993EST: TTGGTGATTTTGCTGAAGCATTGGCTGCCAAGATGCCCGGAAATCTTAAG GTTGTGTACTTTGTGAATTCTGGCTCAGAAGCTAATGAGCTAGCAATGATG
genomic: TTGGTGATTTTGCTGAAGCATTGGCTGCCAAGATGCCCGGAAATCTTAAGgtacttgaga ... ttggatgcagGTTGTGTACTTTGTGAATTCTGGCTCAGAAGCTAATGAGCTAGCAATGATG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aggtttctcttgttggtttatcgaggaatcagcatgctctatgatttggatgcagGTTGTGTACTTTGTGAATTCTGGCTCAGAAGCTAATGAGCTAGCAATGATGATGGCTAGGCTTTACACTGGTAGCCTTGAGATGATTTCCTTGAGAAATG
tatgattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacttgagagttttaaacaaacaagtctgaatgatgtagttaggtttctcttgttggtttatcgaggaatcagcatgctctatgatttggatgcagGTTGTGTACTTTGTGAATTCTGGCTCAGAAGCTAATGAGCTAGCAATGATGATGGCTAGGCTTTACACTGGTAGCCTTGAGATGATTTCCTTGAGAAATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG