Sequence
atgc intronic sequence ATGC exonic sequence...acgagaacttatttcctgtttaatggttatagagtttttgttttctcttgctcagtatgtactcaaggttcactaattgtttgttctcctactcgatcagCTGTGGCTGCCGAGGTTACCGTGGTACCACCTTCACGGTTAATGGCTTTGATAGGTCAGGCTTTAAAGTGGCAACAACATCAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G73720.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G73720.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os01g21940.1 (Oryza sativa), 3'ss of exon 3
------acgagaacttatttcctgtttaatggttatagagtttttgttttctcttgctcagtatgtactcaaggt-------tcactaattgt--------ttgttctcctact----cgat--cagCTGTGGCTGCCGAGGTTACCGTGGTACCACCTTCACGGTTAATGGCTTTGATAGGTCAGGCTTTAAAGTGGCAACAACATCAAG
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gtgagcttgctgatcatttttcttcttccttactaaaaggttctcttaactccatataatacaggagctggagctattcttatttctaatcctaataatagttgtccctctgccatgccaatttcagCTATTGCTTCTGAAGTTTCAGTAGTTCCACCTTCTCGGTTAATGGCACTGATTGGTCAGGCTTTGAAATGGCAACAGCACCAAG
upper sequence: AT1G73720.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA08G13560.1 (Glycine max), 3'ss of exon 4
----------------------------------------------------------------------------------------------acgagaacttatttcctgttta---atggttatagagtttttgttttctcttgctcagtatgtactcaaggtt-cactaattgtttgttctcc--tactcgatcagCTGTGGCTGCCGAGGTTACCGTGGTACCACCTTCACGGTTAATGGCTTTGATAGGTCAGGCTTTAAAGTGGCAACAACATCAAG
| || | || ||| | | | || | ||| | |||| | ||| || | | | || | ||| || | | | | | |||||| | || || || ||||| || || ||||| || || || |||||||| || |||||||||||||||||||| || |||||||
gtttctgtcttttacttttgtattagttactatctagttttgatactaattttttgttttttaattgtaatgaacaactgtttcttgattggaaatgaaagttttcttcttccattgctagggatccagacatacagtttgttattgatctatttttggggggttttactttaagaacttctctttcattgcattttcagCTCTTGCAGCAGAAGTTACTGTAGTGCCACCATCCCGATTGATGGCTTTAATTGGTCAGGCTTTAAAGTGGCAGCAGCATCAAG
upper sequence: AT1G73720.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: PP1S31_68V6.1 (Physcomitrella patens), 3'ss of exon 4
-----------------------------------------acgagaacttatttcctgtttaatgg---ttatagagtttttgttttc----tcttgctcagtatgtactcaaggttcactaattgtttgttctcctactcgatcagCTGTGGCTGCCGAGGTTACCGTGGTACCACCTTCACGGTTAATGGCTTTGATAGGTCAGGCTTTAAAGTGGCAACAACATCAAG
| | | || ||| | | || | | | |||||| | ||| | || | | | ||||| | || | | ||||| | ||| |||||| || || ||||| || || || | ||||||||||| |||||||| ||||| ||||||||||||||||
gtgtagacatagttttcttctcgagctctctctagcatcgctcaaaacttttccgtctgcgtggctgagttttttaatatcatgttttaaaaattttgattgttaaaattttagtatcgttaaattgaagtatgctttatttg--cagCTCTATCTGTCGAGGTCACTGTTGTACCTCCCTCTAGGCTGATGGCTTTGATTGGTCAGGCATTAAAATGGCAACAACATCAAG
upper sequence: AT1G73720.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: PP1S136_176V6.1 (Physcomitrella patens), 3'ss of exon 4
---------------acgagaacttatttcctgtttaatggttatagagtttttgt--tttctcttgctcagtatgtactcaaggttcactaattgtttgttctcctactcgatcagCTGTGGCTGCCGAGGTTACCGTGGTACCACCTTCACGGTTAATGGCTTTGATAGGTCAGGCTTTAAAGTGGCAACAACATCAAG
| | | | | || || | |||| | | || || | ||| | ||||| | | |||| || | | | | | ||||| | ||| |||||| ||||| ||||| || || | | ||||||||||| |||||||| || |||||||||||||||||||
gtctgcatccccccctccctgctgtgtgtgtttgtttttgtgtgtagatctgtggtggttaatgttgtctattatgttatgat--ttcaatacat-taaaataagaattttgtgcagCTCTCTCTGTCGAGGTCACCGTTGTACCCCCATCCAGACTGATGGCTTTGATCGGTCAGGCATTGAAGTGGCAACAACATCAAGMapped 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|86068517|gb|DR364274.1|DR364274EST: GCTTATGGAGACTCAACTAAAGAAAGAAAACGGGCACAGATTGCTCAAG CTGTGGCTGCCGAGGTTACCGTGGTACCACCTTCACGGTTAATGGCTTTGA
genomic: GCTTATGGAGACTCAACTAAAGAAAGAAAACGGGCACAGATTGCTCAAGgttggccatt ... actcgatcagCTGTGGCTGCCGAGGTTACCGTGGTACCACCTTCACGGTTAATGGCTTTGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcttgctcagtatgtactcaaggttcactaattgtttgttctcctactcgatcagCTGTGGCTGCCGAGGTTACCGTGGTACCACCTTCACGGTTAATGGCTTTGATAGGTCAGGCTTTAAAGTGGCAACAACATCAAG
cactaat putative branch site (score: 2)
tttgttctcctactc putative PPT
taattgttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
acgagaacttatttcctgtttaatggttatagagtttttgttttctcttgctcagtatgtactcaaggttcactaattgtttgttctcctactcgatcagCTGTGGCTGCCGAGGTTACCGTGGTACCACCTTCACGGTTAATGGCTTTGATAGGTCAGGCTTTAAAGTGGCAACAACATCAAG
acgagaa
- - - - - - - - - - - - - - - - -gtttttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - actcaag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tcactaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtttgt