Sequence
atgc intronic sequence ATGC exonic sequencegtacgtttcttgttttggacgtagagttgttaagggagcatgcagacttgattattccttgaatgtttacattttggcgctgcagGAAAGACTGTGATCACCAGTGACCATGCTTTGAAATTAGAGTCTGTCCCTGAGTGGATTGCAATTGTAGGAAGTGGTTATATTGGTCTTGAGTTCAGTGA
Basic information
species | Arabidopsis thaliana |
transcript | AT3G16950.2 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G16950.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os05g06460.1 (Oryza sativa), 3'ss of exon 4
-------gtacgtttcttgttttggacgtagagttgtt----aagggagcatgcagacttgattattcct-tgaatgtttacattttggcgct---gcagGAAAGACTGTGATCACCAGTGACCATGCTTTGAAATTAGAGTCTGTCCCTGAGTGGATTGCAATTGTAGGAAGTGGTTATATTGGTCTTGAGTTCAGTGA
| || || || ||| | | |||| | | || ||| ||| | | | | | | | ||||| || ||||| | |||||||| ||||| | ||| | ||||||||||| || ||||| ||||| || |||||||| || ||||| ||||| ||||||||
aagattagcacaattgggtttgcagacccaaatgtgttgcctaccatttcttgttatacctattgttcttacagaagcctgctgggcaacttttgtgcagGGAAAACTGTTTTTACCAGTGATCATGCACTAAAACTTGAGTCTGTCCCGGACTGGATAGCAATCGTTGGAAGTGGATACATTGGGCTTGAATTCAGTGA
upper sequence: AT3G16950.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G145595_T02 (Zea mays), 3'ss of exon 3
---------gtacgtttcttgttttgg---acgtagagttgttaagggagcatgcagacttgattattcctt-gaatgtttacattttggcgct--gcagGAAAGACTGTGATCACCAGTGACCATGCTTTGAAATTAGAGTCTGTCCCTGAGTGGATTGCAATTGTAGGAAGTGGTTATATTGGTCTTGAGTTCAGTGA
|| ||| | | | | | | | ||||| | | | | || |||| || | || || ||| | ||||| || ||||| | || ||||| ||||| | ||| | ||||| |||||||| |||||||| ||||| ||||||||||| ||||| ||||| ||||||||
ccttatcatatatgttgcatactacagcttaaatgcatttgttgccattcctatttcattctagcatccctttaaaagcttgcaccatggttttatgcagGTAAAACTGTATTTACTAGTGATCATGCACTAAAACTTGAGTCAGTCCCTGAATGGATTGCTATTGTTGGAAGTGGTTACATTGGACTTGAATTCAGTGA
upper sequence: AT3G16950.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G073774_T01 (Zea mays), 3'ss of exon 4
---gtacgtttcttgttttgg-acgtagagttgttaagggagcatgcagactt---------gattattccttgaatgtttacattttggcgct--gcagGAAAGACTGTGATCACCAGTGACCATGCTTTGAAATTAGAGTCTGTCCCTGAGTGGATTGCAATTGTAGGAAGTGGTTATATTGGTCTTGAGTTCAGTGA
|| | ||| || || || | || | | ||| | || |||| || | | || | ||| || | ||||| || ||||| | || ||||| ||||| ||||| | ||||| || || || ||||| || ||||| ||||||||||| ||||| ||||||||||||||
tgggtgcattttttattgtgacatgtgtattagttgacattttttgtgtactttccttgttgtatgttctcacaaaattctactggatgattatatgcagGGAAAACTGTATTTACTAGTGATCATGCACTGAAACTTGAGTCAGTTCCAGACTGGATAGCTATTGTTGGAAGTGGTTACATTGGACTTGAGTTCAGTGA
upper sequence: AT3G16950.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA15G15310.1 (Glycine max), 3'ss of exon 4
----------gtacgtt--tcttgttttggacgtagagttgttaagggagcatgcagacttg--attattccttgaatgtttacattttggcgc-tgcagGAAAGACTGTGATCACCAGTGACCATGCTTTGAAATTAGAGTCTGTCCCTGAGTGGATTGCAATTGTAGGAAGTGGTTATATTGGTCTTGAGTTCAGTGA
|| | | | ||| || |||| | | |||| || ||| | || | || | || | |||||||||||||||| |||||||||||||| | ||| | ||| |||| ||||| ||||| |||||||||||||||||||||||||| ||||| ||||||||
ggggatctttgttcactgatactgtccctcttgtttttctgttttgttatttcttcttcttggtatcattaatgaaagctcaccaagtaaatgcattcagGAAAGACTGTGATTACCAGTGACCATGCACTCAAACTGGAGACTGTTCCTGATTGGATAGCAATTGTAGGAAGTGGTTATATTGGCCTTGAATTCAGTGA
upper sequence: AT3G16950.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA17G03560.1 (Glycine max), 3'ss of exon 4
---------gtacgtttcttgttttggacgtagagttgttaagggagcatgcagact-tgattattcctt---gaatgtttacattttggc--gctgcagGAAAGACTGTGATCACCAGTGACCATGCTTTGAAATTAGAGTCTGTCCCTGAGTGGATTGCAATTGTAGGAAGTGGTTATATTGGTCTTGAGTTCAGTGA
| | | || || | | ||| | || || | |||||| | || ||| ||| | | || |||| ||||||||||| ||||||||||| || | ||| | |||||||| ||||| ||||| ||||||||||||||||| |||||||||||||| ||||||||
aaaccttgtttctttatgtttttcccatctctggattgcttcaaagtattgttgagtatgattactttttagtgaaaattttcctaaaaattaccttcagGGAAGACTGTGATTACCAGTGACCACGCACTCAAACTGGAGTCTGTTCCTGATTGGATAGCAATTGTAGGAAGTGGATATATTGGTCTTGAATTCAGTGA
upper sequence: AT3G16950.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA07G37050.2 (Glycine max), 3'ss of exon 4
------gtacgttt---cttgttttggacgtagagttgttaagggagcatgc-agacttgattattcctt---gaatgtttacattttggc--gctgcagGAAAGACTGTGATCACCAGTGACCATGCTTTGAAATTAGAGTCTGTCCCTGAGTGGATTGCAATTGTAGGAAGTGGTTATATTGGTCTTGAGTTCAGTGA
||| ||| || ||| | ||| | || | | |||| | || ||| || | | || |||| ||||||||||| |||||||| || || | ||| | || ||||| ||||| ||||| ||||||||||||||||| |||||||||||||| ||||||||
acctttgtatctttatgtttttttccatctcttgattgcttctaagttttgttgggtataattactttttagtgaaaactttcctaaaaatcatcttcagGGAAGACTGTGATTACCAGTGATCACGCACTCAAACTGGAATCTGTTCCTGATTGGATAGCAATTGTAGGAAGTGGATATATTGGTCTTGAATTCAGTGA
upper sequence: AT3G16950.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: PP1S112_186V6.1 (Physcomitrella patens), 3'ss of exon 4
------------gtacgtttcttgttttggacg----tagagttgttaagggagcat-gcagacttgattattccttgaatgtttacattttggcgctgcagGAAAGACTGTGATCACCAGTGACCATGCTTTGAAATTAGAGTCTGTCCCTGAGTGGATTGCAATTGTAGGAAGTGGTTATATTGGTCTTGAGTTCAGTGA
| |||| | | || | | || |||| | || || | | | ||||||| ||||| | | | | | | |||||||||| ||| ||||||| || ||||| |||| | |||| |||| || |||||||| ||||| ||||||||||| ||||||||||||||||| ||
gtaagaagtcatggtcgttggtggattaaaatgcttttaaagtttatgctggtcgattgtaaaaatgattatctcttga----tcaaactgcgtgtatccagGAAAGACGGTGTTCACCAGCGATCATGCGCTGAAGCTGGAGTGGATCCCAGACTGGATTGCCATTGTTGGAAGTGGTTACATTGGTCTTGAGTTCAGCGA
upper sequence: AT3G16950.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: PP1S35_94V6.1 (Physcomitrella patens), 3'ss of exon 4
-----gtacgtttcttgttttggacgtagagttgttaagggagcatgcagacttgattattccttgaatgtttacattttggcgctgc--agGAAAGACTGTGATCACCAGTGACCATGCTTTGAAATTAGAGTCTGTCCCTGAGTGGATTGCAATTGTAGGAAGTGGTTATATTGGTCTTGAGTTCAGTGA
|| | | ||| |||| || | | | | ||| | | | | ||| | | | ||| ||||||||| ||| |||| ||||||||||| ||||| | |||| | || || ||||| | ||||| ||||||||||| ||||||||||||||||||||
gtaagaaactatcatcgttgatactttagatgctttcaaatcttgtattgccgcgataagaacaaaatctgattcatatggaggatgctcagGAAAGACGGTGTTCACGAGTGACCATGCGTTGAAGCTGGAGTGGATTCCCGACTGGATCACTATTGTCGGAAGTGGTTACATTGGTCTTGAGTTCAGTGAMapped 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|125277206|gb|EL291291.1|EL291291EST: CATTGCCACTGGATCTGTGCCGTTTGTCCCTAAAGGAATTGAAGTTGATG GAAAGACTGTGATCACCAGTGACCATGCTTTGAAATTAGAGTCTGT
genomic: CATTGCCACTGGATCTGTGCCGTTTGTCCCTAAAGGAATTGAAGTTGATGgtacgtttct ... ggcgctgcagGAAAGACTGTGATCACCAGTGACCATGCTTTGAAATTAGAGTCTGT
EST:
gi|47831000|gb|CK120684.1|CK120684EST: CATTGCCACTGGATCTGTGCCGTTTGTCCCTAAAGGAATTGAAGTTGATG GAAAGACTGTGATCACCAGTGACCATGCTTTGAAATTAGAGTCTGTCCCTG
genomic: CATTGCCACTGGATCTGTGCCGTTTGTCCCTAAAGGAATTGAAGTTGATGgtacgtttct ... ggcgctgcagGAAAGACTGTGATCACCAGTGACCATGCTTTGAAATTAGAGTCTGTCCCTG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.taagggagcatgcagacttgattattccttgaatgtttacattttggcgctgcagGAAAGACTGTGATCACCAGTGACCATGCTTTGAAATTAGAGTCTGTCCCTGAGTGGATTGCAATTGTAGGAAGTGGTTATATTGGTCTTGAGTTCAGTGA
acttgat putative branch site (score: 5)
aatgtttacatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacgtttcttgttttggacgtagagttgttaagggagcatgcagacttgattattccttgaatgtttacattttggcgctgcagGAAAGACTGTGATCACCAGTGACCATGCTTTGAAATTAGAGTCTGTCCCTGAGTGGATTGCAATTGTAGGAAGTGGTTATATTGGTCTTGAGTTCAGTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA