Sequence
atgc intronic sequence ATGC exonic sequence...agatattgttggcgtaactatttctgttcttatctggtataacttttcctctaagctctcaacatgattgtatttctgatttatctccccttcttgatagATATGTTGTCATAGATTTGTCTGCGGGGCCTTGTACATATGGGAAGATTGAAACTGAAGAGGGCAGTGTTAGTCCCAGAACAGTGCCAAGGATACGAAAC
Basic information
species | Arabidopsis thaliana |
transcript | AT4G16180.2 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G16180.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os03g19690.2 (Oryza sativa), 3'ss of exon 5
agatattgttggcgtaactatttctgttcttatctggtataacttttcctctaagctctcaacatgattgtat-ttctgatttatctcccctt----cttgatagATATGTTGTCATAGATTTGTCTGCGGGGCCTTGTACATATGGGAAGATTGAAACTGAAGAGGGCAGTGTTAGTCCCAGAACAGTGCCAAGGATACGAAAC
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attttttccccctttatgctatactggaattatttga-gcaactgtaacc--aagctct--gtatgctgatatgctctaaaccaccactgcattggtccttgcagATTTGTTGTAATAGATCTGTCAGCAGGCCCTTGTACGTATGGAAAAATAGAAACTGAAGAGGGCAGTGTGAGTTATAGGTCATTGCCACGGCTATTAAAT
upper sequence: AT4G16180.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G135968_T01 (Zea mays), 3'ss of exon 5
-agatattgttggcgtaactatttctgttcttatctggtataacttttcctctaagctctcaacatgattgtatttctgatttatctcccctt---cttgatagATATGTTGTCATAGATTTGTCTGCGGGGCCTTGTACATATGGGAAGATTGAAACTGAAGAGGGCAGTGTTAGTCCCAGAACAGTGCCAAGGATACGAAAC
| | |||| || | | | | | | || | || | ||| | ||| | || | |||| | | | || || |||| |||||| |||||| | || ||||| ||||||||||||||||| || ||||||||||| |||||||| || || || ||||| || | | |
tttgcact-ttggagttgttttcttt-taatgatgcacttcaattgttcaagca-gctttaaat-tatttgtgctctaaactcccacttgattggcctctgcagATTTGTTGTAATAGATCTTTCAGCGGGCCCTTGTACATATGGGAAAATAGAAACTGAAGAAGGCAGTGTCAGCTATAGGTCAATGCCACGGCTGTCACAA
upper sequence: AT4G16180.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv05s0077g00820.t01 (Vitis vinifera), 3'ss of exon 5
---agatattgttggcgtaactatttctgttcttatctggtataacttttcctctaagctctcaacatgattgtatttctgatttatctccccttcttgatagATATGTTGTCATAGATTTGTCTGCGGGGCCTTGTACATATGGGAAGATTGAAACTGAAGAGGGCAGTGTTAGTCCCAGAACAGTGCCAAGGATACGAAAC
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tttagaggttttttgccgcttgaattttgaggacaat--gtacttttagtcctccaca-tctctctctctctctcaatctaatttcctgcctgtactattcagATTTGTTGTCATCGACCTCTCAGCAGGGCCTTGCACATATGGAAAGATTGAAACTGAAGAAGGAAGTGTCAGTTCAAAAACACTCCCACGGTTGCGGAATMapped 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|116426968|gb|EG469560.1|EG469560EST: TATAGATACAATGGTGGAGGAGCATCCCAAGTTTGGCTTGCATCAGGCAG ATATGTTGTCATAGATTTGTCTGCGGGGCCTTGTACATATGGGAAGATTGA
genomic: TATAGATACAATGGTGGAGGAGCATCCCAAGTTTGGCTTGCATCAGGCAGgtaaactcat ... ttcttgatagATATGTTGTCATAGATTTGTCTGCGGGGCCTTGTACATATGGGAAGATTGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttcctctaagctctcaacatgattgtatttctgatttatctccccttcttgatagATATGTTGTCATAGATTTGTCTGCGGGGCCTTGTACATATGGGAAGATTGAAACTGAAGAGGGCAGTGTTAGTCCCAGAACAGTGCCAAGGATACGAAAC
ttctgat putative branch site (score: 3)
tttctgatttatctcc CT-rich tract
tatttctgatttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
agatattgttggcgtaactatttctgttcttatctggtataacttttcctctaagctctcaacatgattgtatttctgatttatctccccttcttgatagATATGTTGTCATAGATTTGTCTGCGGGGCCTTGTACATATGGGAAGATTGAAACTGAAGAGGGCAGTGTTAGTCCCAGAACAGTGCCAAGGATACGAAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - -ctgttct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctcaaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tatctcc