Sequence
atgc intronic sequence ATGC exonic sequencegtcattataattaacacaaatcttgttttgattattataagatatagacatatagtcctggttattgttgtttaatatatttatttttcatataaaaaagGCTGAGGATGTGAAACACTCTGGTCCAACCACAATGGTGCTTTACTTCACCGGAGCCACCAACATTCTCTACACCTTTGGTGGCCACGCCGTCACAGT
Basic information
species | Arabidopsis thaliana |
transcript | AT1G77690.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G77690.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os03g14080.1 (Oryza sativa), 3'ss of exon 4
---------------gtcattata-attaacacaaatcttgttttgattatt--ataagatatagacatatagtcctggttattgttgttt----------------aatatatttatttttcatataaaaa--agGCTGAGGATGTGAAACACTCTGGTCCAACCACAATGGTGCTTTACTTCACCGGAGCCACCAACATTCTCTACACCTTTGGTGGCCACGCCGTCACAGT
|| || ||| || | | || || ||| | ||| || | |||| ||| || | || | | | ||||| ||| || | ||| || | ||||| ||||| || || || | ||||| || ||||||||||| ||||| ||||||||||||||||| ||||| ||||| || || ||
gtagtacaacacaaaagcaccatctgttagcatgcagcatgcttgcatttctcgtctgaatagcgaggcgcatgcctgaacattattacattgcgttgtgctgaaaaaacacttgtgttttttgtatgaatatcagGTCGATGGAGTGAAGCACTCGGGCCCTACAAAGATGGTCCTCTACTTCACCGGGGCCACAAACATTCTCTACACCTTCGGTGGGCACGCTGTTACTGT
upper sequence: AT1G77690.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os10g05690.1 (Oryza sativa), 3'ss of exon 2
--gtcattataattaacacaaatcttgttttgattattataagatatagacatatagtcctggttattgttgtttaatatatttatttttcatataaaaaagGCTGAGGATGTGAAACACTCTGGTCCAACCACAATGGTGCTTTACTTCACCGGAGCCACCAACATTCTCTACACCTTTGGTGGCCACGCCGTCACAGT
|| | | | || | || | || || || | || || | ||||| | | || | | | | | ||| || |||| ||| |||| |||| |||||||| || || | || ||||| |||||||| || ||||||||||| ||||||||||| || |||||||| ||||| ||
ataagatcaaagtcc-caaacgtcacttatttatgataacaaaatgatagta-atagtgatagatagtaattgtaatagtgcatatattgggaataatgcagGTGGAGGGTGTGGCGCACTCTGGGCCCACAAGCATCGTGCTCTACTTCACGGGGGCCACCAACATCCTCTACACCTTCGGGGGCCACGCTGTCACCGT
upper sequence: AT1G77690.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G045057_T02 (Zea mays), 3'ss of exon 4
----------------gtcattataattaacacaaatcttgttttgattattataagatatagacatatagtcctggttattgttgtttaatatatttatttttcat-----ataaaaaagGCTGAGGATGTGAAACACTCTGGTCCAACCACAATGGTGCTTTACTTCACCGGAGCCACCAACATTCTCTACACCTTTGGTGGCCACGCCGTCACAGT
| ||| ||| | || | | | | ||| || || || ||| | || | | ||| ||| | ||| | ||| || | ||||| ||||| || |||| || |||||||| ||||||||||| ||||||||||| |||||||||||||| ||||| || ||||| ||
gtatatatgcgctgagcgtgtgatatgatgcactagtcgattgatcgcctgcttgcgctatgtccagcagatcgtgtatatggccgtaccaaacattaattgatggacgacaatattatagGTGGAAGGTGTGACGCACTCGGGCCCAAGCAAGATGGTGCTCTACTTCACCGGTGCCACCAACATCCTCTACACCTTTGGAGGCCATGCTGTCACTGT
upper sequence: AT1G77690.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G149481_T03 (Zea mays), 3'ss of exon 5
------------gtcattataat-taacacaaatcttgt---tttgattattataagatatagacatatagtcctggttattgttgtttaatatatttatttttcatataaaaaagGCTGAGGATGTGAAACACTCTGGTCCAACCACAATGGTGCTTTACTTCACCGGAGCCACCAACATTCTCTACACCTTTGGTGGCCACGCCGTCACAGT--
| || | ||| | || ||| || | | | | | | | | || ||| | | | | | | | | | || ||| | ||||| ||||| || || |||| |||||||| ||||||||||| ||||| |||||||||||||| || || || ||||| || || ||
gtacgcaagcgtagcgttgaagcataatatgcattctgtgggcctgtggcctgtggcctgtgggtgaccggccgagacgatg--tgtgtgcttctgctgctctacttgttgca--gGTTGATGGCGTGAAGCACTCCGGGCCGACCAAGATGGTGCTCTACTTCACCGGGGCCACAAACATTCTCTACACTTTCGGAGGGCACGCTGTTACCGTGT
upper sequence: AT1G77690.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G149481_T02 (Zea mays), 3'ss of exon 4
------------gtcattataat-taacacaaatcttgt---tttgattattataagatatagacatatagtcctggttattgttgtttaatatatttatttttcatataaaaaagGCTGAGGATGTGAAACACTCTGGTCCAACCACAATGGTGCTTTACTTCACCGGAGCCACCAACATTCTCTACACCTTTGGTGGCCACGCCGTCACAGT
| || | ||| | || ||| || | | | | | | | | || ||| | | | | | | | | | || ||| | ||||| ||||| || || |||| |||||||| ||||||||||| ||||| |||||||||||||| || || || ||||| || || ||
gtacgcaagcgtagcgttgaagcataatatgcattctgtgggcctgtggcctgtggcctgtgggtgaccggccgagacgatg--tgtgtgcttctgctgctctacttgttgca--gGTTGATGGCGTGAAGCACTCCGGGCCGACCAAGATGGTGCTCTACTTCACCGGGGCCACAAACATTCTCTACACTTTCGGAGGGCACGCTGTTACCGT
upper sequence: AT1G77690.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv18s0001g03540.t01 (Vitis vinifera), 3'ss of exon 4
-------gtcattataattaacacaaatcttgttttgattattataagatataga-catatagtcctggtta----ttgttgt-ttaatatatttatt------tttcatataaa-----------aaagGCTGAGGATGTGAAACACTCTGGTCCAACCACAATGGTGCTTTACTTCACCGGAGCCACCAACATTCTCTACACCTTTGGTGGCCACGCCGTCACAGT
| | |||||| | | || | || || | || | ||| | ||| ||| ||| | || || |||||||| | ||| | |||| ||||| ||||| |||||||| ||||||| |||||| || |||||||| || || |||||||||||||||||||||||||| || || ||||||||
gtatgtatttaccttaattagctgtattcatcacttagttttaatttcaaataattcccataatcccatcccccctttgatacattgatttatttattaagtaatcccatgctgatttgcttgtttgaagGTTGAGGGGGTGAAGCACTCTGGCCCAACCAAAATGGTTCTCTACTTCACTGGGGCTACCAACATTCTCTACACCTTTGGTGGTCATGCTGTCACAGT
upper sequence: AT1G77690.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: PP1S213_89V6.1 (Physcomitrella patens), 3'ss of exon 4
-------------gtcattataattaacacaaatcttgttttgattattataagatatagacatatagtcctggttatt-gttgtttaatatatttattttt-catataaaaa----------agGCTGAGGATGTGAAACACTCTGGTCCAACCACAATGGTGCTTTACTTCACCGGAGCCACCAACATTCTCTACACCTTTGGTGGCCACGCCGTCACAGT
| ||| || || | ||| | || | ||| | || | | | ||| ||| | | || ||| ||| || | ||| || || | | || | ||| ||| || | | ||| | |||||||| ||||| ||||||||||||||||||||||| ||||||| || |||||
gtaaaaccattcaaactttagaaccgactcgcatcctcaaccactttct-taacttgcagttgaactggtcgggtgatttatagattgatagattccttcctgcattcctgaatatgttttccagACCTCTGGCGTAACGCACAATGGCCCCGTGTCGAGGGTTTTATACTTCACGGGAGCAACCAACATTCTCTACACCTTTGGAAGCCACGCTGTGACAGT
upper sequence: AT1G77690.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: PP1S90_46V6.1 (Physcomitrella patens), 3'ss of exon 4
------------------------------------gtcattataattaacacaaatcttgttttgattattataagatatagacatatagtc--ctggttattgttgtttaatatattta------tttt----tcatataaaaa-agGCTGAGGATGTGAAACACTCTGGTCCAACCACAATGGTGCTTTACTTCACCGGAGCCACCAACATTCTCTACACCTTTGGTGGCCACGCCGTCACAGT
| ||| | || || | || | || | | || | | |||||| ||| | || || | | || | || || | | ||| | ||| || |||| || |||| |||||| || | ||| | |||||||| ||||| ||||| ||||| |||||||||||||| ||||| || || ||
gtaatggacttcaacgacgtgaattgctacgggttttttatttacaggaagacgagtcat-ttctattcatctttatatatagccatcaatctaatcaatttctgctttccaacactcctaacgaggttctggacttttatggagccagGTTGCCAATGTTGTTCATTCTGCTCCAACGACCAAGGTCTTGTACTTCACAGGAGCAACCAATATTCTGTACACCTTTGGTGGTCACGCTGTTACTGT
upper sequence: AT1G77690.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: EFJ18760 (Selaginella moellendorffii), 3'ss of exon 4
--------------------------------------------------------------gtcattataattaacacaaatcttgttttgat---------tattataagat--------atagacatatagtcctggttat---tgttgtttaatatatttatttttcata---------taaaaaagGCTGAGGATGTGAAACACTCTGGTCCAACCACAATGGTGCTTTACTTCACCGGAGCCACCAACATTCTCTACACCTTTGGTGGCCACGCCGTCACAGT
| || ||||| | || || ||||| | || || |||| ||||| | | ||| || || ||| || || || ||| | | ||| | ||| || || || | |||| | | || | || ||||| |||||||||||||| | ||||||||||||||||| |||||||| ||
gtgagagaagcatctaaaaaagctccactggatgataagcttgtctcgtcaaagtttgctgtagaactagaattatctttcattttcttttgctgctttgctacatcatgagatgatagaggatagattttaaacttcttgtataggcgtggtctaacatgaataattctcacacttcttcacttttgcagGACCCAGGTGTAAAGCATTCGGCCCCAAATAATCTCGTCCAATATTTCACTGGAGCCACCAACATCTTGTACACCTTTGGTGGCCATGCCGTCACTGT
upper sequence: AT1G77690.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: EFJ36050 (Selaginella moellendorffii), 3'ss of exon 4
------------------------------------------------------gtcattataattaacacaaatcttgttttgattattataagata-----tagac-----atatagtcctggt-tattgttgtttaatatatttatttttcatataaaaaagGCTGAGGATGTGAAACACTCTGGTCCAACCACAATGGTGCTTTACTTCACCGGAGCCACCAACATTCTCTACACCTTTGGTGGCCACGCCGTCACAGT
| | || ||| ||| | ||| |||| || |||| || || | |||| | |||| || | | | | | || |||| | | | | ||| ||| || || || | |||| | | || | || ||||| |||||||||||||| | |||||||||||||| || |||||||| ||
gtgagagaagcatctaaaaaagctccactggatgataagcttgtctcgtcaaagtttgctgtag--aactagaattatctttcatttatcatgggatagattttaaacttcttacataggcgtggtctaacatcaataattctcacacttcttcacttttgcagGACCCAGG-TGTAAAGCATTCGGCCCCAAATAATCTCGTCCAATATTTCACTGGAGCCACCAACATCTTGTACACCTTTGGTGGTCATGCCGTCACTGTMapped 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|125234529|gb|EL248614.1|EL248614EST: CCACTTACACTTCTTGGTATCTCACCATTGCTTCACTCCTTCATGGCCAG GCTGAGGATGTG
genomic: CCACTTACACTTCTTGGTATCTCACCATTGCTTCACTCCTTCATGGCCAGgtcattataa ... tataaaaaagGCTGAGGATGTG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agacatatagtcctggttattgttgtttaatatatttatttttcatataaaaaagGCTGAGGATGTGAAACACTCTGGTCCAACCACAATGGTGCTTTACTTCACCGGAGCCACCAACATTCTCTACACCTTTGGTGGCCACGCCGTCACAGT
gtttaat putative branch site (score: 4)
tttttcat putative PPT
ttattgttgtttaata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtcattataattaacacaaatcttgttttgattattataagatatagacatatagtcctggttattgttgtttaatatatttatttttcatataaaaaagGCTGAGGATGTGAAACACTCTGGTCCAACCACAATGGTGCTTTACTTCACCGGAGCCACCAACATTCTCTACACCTTTGGTGGCCACGCCGTCACAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG