Sequence
atgc intronic sequence ATGC exonic sequencegtgcgaacccttttagcatcttgaatttcgttcatatgtatgctattttgttctttaggctctaatatgtatatgtcttctcagAAATCGACTCCGTCTCCTCACTCAGTTCTTGGAGCATCTAGTTAGTGAGGGAAGCCAAGATGTGCATGTCCATAATGCCTTGGGTAAAATTATCATAGAC
Basic information
species | Arabidopsis thaliana |
transcript | AT3G11130.1 |
intron # | 22 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 22
lower sequence: GRMZM2G057576_T01 (Zea mays), 3'ss of exon 21
gtgcgaacccttttagcatcttgaattt---cgttcatatgtatgctattttgttctttag--gctctaatatgtatatgtct---tctcagAAATCGACTCCGTCTCCTCACTCAGTTCTTGGAGCATCTAGTTAGTGAGGGAAGCCAAGATGTGCATGTCCATAATGCCTTGGGTAAAATTATCATAGAC
|| ||| |||| || | | | | | | || | ||| || || || | || || ||| | | | | |||| || || || || | || ||||| ||||||||||||||||| ||||| || |||||||||||||||||||| ||||| | || ||||| ||||| |||
gtttgaattcttt--attcctggggtctgcaaagtgacaagtttcacattccctttttaagtggatcacatctgtttgaatatgtgtatcagGAACCGCCTACGGTTGCTTACTCAATTCTTGGAGCATCTAGTGAGTGAAGGTAGCCAAGATGTGCATGTCCACAATGCTCTTGGGAAAATCATCATCGAC
upper sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 22
lower sequence: GRMZM2G111355_T02 (Zea mays), 3'ss of exon 2
gtgcgaacccttttagcatcttga-atttcgttcatatgtatgctattttgttctttaggctctaatatgtata-tgtcttctcagAAATCGACTCCGTCTCCTCACTCAGTTCTTGGAGCATCTAGTTAGTGAGGGAAGCCAAGATGTGCATGTCCATAATGCCTTGGGTAAA-ATTATCATAGAC-----------------------
| |||| ||| | | || | || ||| || || || | ||| || | ||||| | | | | || | || |||||| | ||| | || ||| | | | | | || |||||||| ||| | | | |
----gtttgtttttcatatcctcccagtttacttattcacatgagtgaaggtagccaagatgtgcatgtccataatgctcttggtaaaatcatcattgacagCAACAACAATCCT--GAGCATTTCCTTACTACC--AACCCAT----TTTACGACTCTCGTGTTGTGGGTAAATATTGTGAAAAGCGGGATCCTACACTTGCTGTTGTT
upper sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 22
lower sequence: GLYMA02G42560.1 (Glycine max), 3'ss of exon 22
gtgcgaacccttttagcatcttgaatttcgttcatatgtatgc-tattttgttctttaggctctaatatgtatatgtcttctcagAAATCGACTCCGTCTCCTCACTCAGTTCTTGGAGCATCTAGTTAGTGAGGGAAGCCAAGATGTGCATGTCCATAATGCCTTGGGTAAAATTATCATAGAC
||| |||||| | || | | | | || | || | | | ||| | |||| || | | | || | ||| ||||| || ||| | ||||| ||||||||||| ||||| || |||||||||||||| ||||| ||||| || ||||| |||||||||||||||| ||
gtgtttgccctttga---tcctaagtgttattgctttgcgttcgtgtttcttattttatcctgtggctttttgatatg----cagGAATCGGCTTCGTTTGCTCACACAGTTCTTGGAACATCTTGTAAGTGAGGGAAGCCAGGATGTACATGTTCACAATGCACTGGGTAAAATTATCATTGAT
upper sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 22
lower sequence: GLYMA14G06340.1 (Glycine max), 3'ss of exon 22
gtgcgaacccttttagcatcttgaatttcgttcatatgtatgctattttgttctttaggctctaatatgtatatgtcttct-cagAAATCGACTCCGTCTCCTCACTCAGTTCTTGGAGCATCTAGTTAGTGAGGGAAGCCAAGATGTGCATGTCCATAATGCCTTGGGTAAAATTATCATAGAC
||| | ||| | | | || | || || | ||||| ||| | | | ||| | | | | | ||| |||||||| ||| | ||||| ||||||||||| || || || |||||||||||||| ||||| ||||| || ||||| |||||||||||||||| ||
gtggtgttttccctttgatcctatgtgttattgctttgcat----tcttgtttcttattttatcctgtgtctttttgatatgcagGAATCGACTTCGTATGCTCACACAGTTCTTGGAACACCTTGTAAGTGAGGGAAGCCAGGATGTACATGTTCACAATGCACTGGGTAAAATTATCATTGAT
upper sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 22
lower sequence: GLYMA14G06340.2 (Glycine max), 3'ss of exon 22
gtgcgaacccttttagcatcttgaatttcgttcatatgtatgctattttgttctttaggctctaatatgtatatgtcttct-cagAAATCGACTCCGTCTCCTCACTCAGTTCTTGGAGCATCTAGTTAGTGAGGGAAGCCAAGATGTGCATGTCCATAATGCCTTGGGTAAAATTATCATAGAC
||| |||||| | || | | | || | || || | ||||| ||| | | | ||| | | | | | ||| |||||||| ||| | ||||| ||||||||||| || || || |||||||||||||| ||||| ||||| || ||||| |||||||||||||||| ||
gtgttttccctttga---tcctatgtgttattgctttgcat----tcttgtttcttattttatcctgtgtctttttgatatgcagGAATCGACTTCGTATGCTCACACAGTTCTTGGAACACCTTGTAAGTGAGGGAAGCCAGGATGTACATGTTCACAATGCACTGGGTAAAATTATCATTGAT
upper sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 22
lower sequence: GLYMA11G35460.1 (Glycine max), 3'ss of exon 21
gtgcgaacccttttagcatcttgaatttcgttcatatgtatgctattttgttctttaggctctaatatgtatatgtcttctcagAAATCGACTCCGTCTCCTCACTCAGTTCTTGGAGCATCTAGTTAGTGAGGGAAGCCAAGATGTGCATGTCCATAATGCCTTGGGTAAAATTATCATAGAC
|| | | || | ||| | ||| | || | || | || || | || || | || | | | | ||| ||||| || ||| | ||||| ||||| ||||| ||||| || |||||||||||||| ||||| ||||| || ||||| |||||||||| ||||| ||
gtagtatctgttctctaatccttcattactttt-tgtgctcacatttctgattatt---ctgtggtacttttcttggtatgcagGAATCGGCTTCGTTTGCTCACACAGTTTTTGGAACATCTTGTAAGTGAGGGAAGCCAGGATGTACATGTTCACAATGCACTGGGTAAAATCATCATTGAT
upper sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 22
lower sequence: GLYMA18G02960.1 (Glycine max), 3'ss of exon 21
gtgcgaacccttttagcatcttgaatttcgttcatatgtatgctattttgttctttaggctctaatatgtatatgtcttctcagAAATCGACTCCGTCTCCTCACTCAGTTCTTGGAGCATCTAGTTAGTGAGGGAAGCCAAGATGTGCATGTCCATAATGCCTTGGGTAAAATTATCATAGAC
|| | | || | ||| | ||||| || | || || || || | || | || | | || ||| ||||| || ||| | || || ||||| ||||| ||||| || |||||||||||||| ||||| ||||| || ||||| |||||||||| ||||| ||
gtagtatcttttctctaatcctacatttctttt-tgtgctcgcatttctgattattccgtggtacttggcatg--------cagGAATCGGCTTCGTTTGCTTACACAGTTTTTGGAACATCTTGTAAGTGAGGGAAGCCAGGATGTACATGTTCACAATGCACTGGGTAAAATCATCATTGAT
upper sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 22
lower sequence: Vv13s0067g01290.t01 (Vitis vinifera), 3'ss of exon 22
gtgcgaacccttttagcatcttgaatttcgttcatatgtatgctattttgttctttaggctctaata-tgtatatgtc-ttctcagAAATCGACTCCGTCTCCTCACTCAGTTCTTGGAGCATCTAGTTAGTGAGGGAAGCCAAGATGTGCATGTCCATAATGCCTTGGGTAAAATTATCATAGAC
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----gtgatgtgtccctaccatatgccctgttcgggttcactttctttt-tacttcaattgcttatgctttgcatgtggttttcagAAATCGACTCCGTTTACTCACTCAGTTCTTGGAGCATCTTGTGAGTGAGGGAAGCCAAGATGTGCATGTCCATAATGCTCTGGGTAAAATCATTATAGAC
upper sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 22
lower sequence: EFJ24508 (Selaginella moellendorffii), 3'ss of exon 22
gtgcgaacccttttagcatcttgaatttcgttcatatgtatgctattttgttctttaggctctaatatgtatatgtcttctcagAAATCGACTCCGTCTCCTCACTCAGTTCTTGGAGCATCTAGTTAGTGAGGGAAGCCAAGATGTGCATGTCCATAATGCCTTGGGTAAAATTATCATAGAC
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--------------------gtctgtttcgttttttcatg---tatctcattattgagctt--------aattttcttttccagTAATCGGCTGAGACTTCTCACTCAGTTTTTGGAGCACCTGGTTAGCGAAGGTAGCCAAGACGTGCATGTGCACAATGCGCTCGGAAAAATTATCATCGATMapped 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|86063114|gb|DR358871.1|DR358871EST: TGTTGAACCCCTTGTTGCAGAATGTGAAAAGAG AAATCGACTCCGTCTCCTCACTCAGTTCTTGGAGCATCTAGTTAGTGAGGG
genomic: TGTTGAACCCCTTGTTGCAGAATGTGAAAAGAGgtgcgaaccc ... gtcttctcagAAATCGACTCCGTCTCCTCACTCAGTTCTTGGAGCATCTAGTTAGTGAGGG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gttcatatgtatgctattttgttctttaggctctaatatgtatatgtcttctcagAAATCGACTCCGTCTCCTCACTCAGTTCTTGGAGCATCTAGTTAGTGAGGGAAGCCAAGATGTGCATGTCCATAATGCCTTGGGTAAAATTATCATAGAC
ctctaat putative branch site (score: 3)
tgtcttctc putative PPT
tattttgttcttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgcgaacccttttagcatcttgaatttcgttcatatgtatgctattttgttctttaggctctaatatgtatatgtcttctcagAAATCGACTCCGTCTCCTCACTCAGTTCTTGGAGCATCTAGTTAGTGAGGGAAGCCAAGATGTGCATGTCCATAATGCCTTGGGTAAAATTATCATAGAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG