Sequence
atgc intronic sequence ATGC exonic sequencegtaacatcactctctgtaccccattctcttttactgttttccgtttttcaaagttgtatgatttccttaaccgagaatcttcaattttacagCTTGAAATGGAAGATGGAGATGAGATCGATGCAATGCTTCATCAGACTGGTGGTGGTGCTAAAAATGGCCTGAAGCTCTTCTGCTTTTAGTGGCGGTTAT
Basic information
species | Arabidopsis thaliana |
transcript | AT5G55160.2 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G55160.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: PP1S317_15V6.1 (Physcomitrella patens), 3'ss of exon 2
------------------------------------------------------------------------------------------gtaacatcactctctgtaccccatt--ctcttttac-tgttttccgtttttcaaagttgtatgatttccttaaccgagaatcttcaatttt------acagCTTGAAATGGAAGATGGAGATGAGATCGATGCAATGCTTCATCAGACTGGTGGTGGTGCTAA--AAATGGCCTGAAGCTCTTCTGCTTTTAGTGGCGGTTAT
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gtatgcatttcaagttactgtatatttatcttgttctcagtagtagaattttagcatcccgtggctttgtttttctgtcgagatggacggttcacttgattcaactttctcgatttactcacttacctgtctaattttgtttccaaatgttttgtgttttaacataagaattttccacgttgatgtgacagCTTGAAATGGAAGATGGAGATGAGATCGATGCCATGCTTCATCAAACTGGTGGAAATGCTTGCTGACTTGAATGCCGATGCAGGAGTTCGAACATCGTGT--
upper sequence: AT5G55160.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: EFJ36475 (Selaginella moellendorffii), 3'ss of exon 2
gtaacatcactctctgtaccccattctcttttactgttttccgtttttcaaagttgtatgatttccttaaccgagaatcttcaattttacagCTTGAAATGGAAGATGGAGATGAGATCGATGCAATGCTTCATCAGACTGGTGG--TGGTGCTAAAAATGGCCTGAAGCTCTTCTGCTTTTAGTGGCGGTTAT
| ||||| | | | | ||| || | || | ||| ||| || | |||||||||||||| ||||| || ||||| |||||||| |||||||| || || | | | |
-------------------------------------gtagcgtttcttcttttccttttcttttttttttcttgattgttc---tttgtagTTGGAAATGGAAGATGGCGATGAAATAGATGCCATGCTTCACCAGACTGGAGGAATGCCGTTGTTATAG---------------------------------
upper sequence: AT5G55160.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: EFJ18574 (Selaginella moellendorffii), 3'ss of exon 2
gtaacatcactctctgtaccccattctcttttactgttttccgtttttcaaagttgtatgatttccttaaccgagaatcttcaattttacagCTTGAAATGGAAGATGGAGATGAGATCGATGCAATGCTTCATCAGACTGGTGG--TGGTGCTAAAAATGGCCTGAAGCTCTTCTGCTTTTAGTGGCGGTTAT
| ||||| | | | | ||| || | || | ||| ||| || | |||||||||||||| ||||| || ||||| |||||||| |||||||| || || | | |
-------------------------------------gtagcgtttcttcttttccttttcttttttttttcttgattgttc---tttgtagTTGGAAATGGAAGATGGCGATGAAATAGATGCCATGCTTCACCAGACTGGAGGAATGCCGTTGTAG------------------------------------Mapped 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|163966477|gb|ES185369.1|ES185369EST: CTTTCTTGTTTGATGGTCGTCGTCTTCGTGCCGAGCAGACTCCAGATGAG CTTGAAATGGAAGATGGAGATGAGATCGATGCAAT
genomic: CTTTCTTGTTTGATGGTCGTCGTCTTCGTGCCGAGCAGACTCCAGATGAGgtaacatcac ... aattttacagCTTGAAATGGAAGATGGAGATGAGATCGATGCAAT
EST:
gi|164126265|gb|ES092834.1|ES092834EST: ATGGTCGTCGTCTTCGTGCCGAGCAGACTCCAGATGAG CTTGAAATGGAAGATGGAGATGAGATCGATGCAATGCTTCATCA
genomic: ATGGTCGTCGTCTTCGTGCCGAGCAGACTCCAGATGAGgtaacatcac ... aattttacagCTTGAAATGGAAGATGGAGATGAGATCGATGCAATGCTTCATCA
EST:
gi|163979819|gb|ES135192.1|ES135192EST: CGTCGTCTTCGTGCCGAGCAGACTCCAGATGAG CTTGAAATGGAAGATGGAGATGAGATCGATGCAATGCTTCATCAGACTGG
genomic: CGTCGTCTTCGTGCCGAGCAGACTCCAGATGAGgtaacatcac ... aattttacagCTTGAAATGGAAGATGGAGATGAGATCGATGCAATGCTTCATCAGACTGG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttccgtttttcaaagttgtatgatttccttaaccgagaatcttcaattttacagCTTGAAATGGAAGATGGAGATGAGATCGATGCAATGCTTCATCAGACTGGTGGTGGTGCTAAAAATGGCCTGAAGCTCTTCTGCTTTTAGTGGCGGTTAT
ccttaac putative branch site (score: 3)
aatcttcaatttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaacatcactctctgtaccccattctcttttactgttttccgtttttcaaagttgtatgatttccttaaccgagaatcttcaattttacagCTTGAAATGGAAGATGGAGATGAGATCGATGCAATGCTTCATCAGACTGGTGGTGGTGCTAAAAATGGCCTGAAGCTCTTCTGCTTTTAGTGGCGGTTAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC