Sequence
atgc intronic sequence ATGC exonic sequencegtaaataaatgtgtgaatatgataaaaaaattctattgatgagctttatgggaaagctgtaaggcagatatgtatgagctgctttatcttgatttttttcgtctttgagcagGATAAGTCCTGGCGTGTGCGTTATATGGTTGCAAATCAGCTCTATGAACTTTGTGAAGCTGTAGGACCGGAGCCAACTAG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G13320.2 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G13320.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G102858_T01 (Zea mays), 3'ss of exon 4
-----------------------------------------------------------------------gtaaataaatgtgtgaatatgata-----aaaaaattctattg---atgagctttatggg--aaagctgtaaggcagatatgtatgagctgctttatcttgatttttttcgtctttgag------cagGATAAGTCCTGGCGTGTGCGTTATATGGTTGCAAATCAGCTCTATGAACTTTGTGAAGCTGTAGGACCGGAGCCAACTAG
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gtatatcttacacacttttggtggcttaataaatgttgggagaaaagataaagttgtcaatactaattctcgtaaa-aattactagagtaagatttccataagatctgctactagacaataatttcatgtgcttaagtttcagcacactaccatacatggttaatgatttcaattgcttatgttttcttaacatctcagGATAAATCTTGGCGTGTGCGCTATATGGTGGCAAATCAACTGTATGAACTATGTGAAGCTGTTGGTACTGAACCCACAAG
upper sequence: AT1G13320.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA02G10790.2 (Glycine max), 3'ss of exon 4
gtaaataaatgtgtgaatatgataaaaaaattctattgatgagctttatgggaaagctgtaaggcagatatgtatgagctgctttatcttgatttttttcgtctttgagcagGATAAGTCCTGGCGTGTGCGTTATATGGTTGCAAATCAGCTCTATGAACTTTGTGAAGCTGTAGGACCGGAGCCAACTAG
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gtgtatatatgtgtgtttgtatgtggaatgtgttttcaccaaact--------aagtccccattttgatttgatta----gttttcctttgacttgatttgatcccaaacagGATAAGTCGTGGCGTGTGCGGTACATGGTTGCAAATCAATTGTATGAGCTTTGTGAAGCTGTAGGCCCTGAACCTACCAG
upper sequence: AT1G13320.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA20G24790.1 (Glycine max), 3'ss of exon 4
gtaaa-taaatgtgtgaatatgataaaaaaattctattgatgagctttatgggaaagctgtaaggcagatatgtatgagctgctttatcttgatttttttcgtctttgagcagGATAAGTCCTGGCGTGTGCGTTATATGGTTGCAAATCAGCTCTATGAACTTTGTGAAGCTGTAGGACCGGAGCCAACTAG
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ttagtctccctgcattcatatgtctgtaaaatgttat--atgcaccataccgaatattttt----------tttttaaatttatttatgtgatttaatttcatcctgga-tagGATAAGTCTTGGCGTGTGCGTTACATGGTTGCAAATCAATTGTATGAGCTTTGCGAAGCTGTAGGCCCTGAACCTACCAG
upper sequence: AT1G13320.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA10G42250.1 (Glycine max), 3'ss of exon 4
gtaaataaatgtgtgaatatgataaaaaaattctattgatgagctttatgggaaagctgtaaggcagatatgtatgagctgctttatcttgatttttttcgtctttgagcagGATAAGTCCTGGCGTGTGCGTTATATGGTTGCAAATCAGCTCTATGAACTTTGTGAAGCTGTAGGACCGGAGCCAACTAG
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---------tatttagtttgcctgcatttatatgtctgtagaatgttatatgca--ccataccaaatattcttttttatttatttatgtgatttaatttcatcctgga-tagGATAAGTCTTGGCGCGTGCGTTACATGGTTGCAAATCAATTGTATGAGCTTTGTGAAGCTGTAGGCCCTGAACCTACCAG
upper sequence: AT1G13320.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: EFJ35758 (Selaginella moellendorffii), 3'ss of exon 3
gtaaataaatgtgtgaatatgataaaaaaattctattgatgagctttatgggaaagctgtaaggcagatatgtatgagctgctttatcttgatttttttcgtctttgagcagGATAAGTCCTGGCGTGTGCGTTATATGGTTGCAAATCAGCTCTATGAACTTTGTGAAGCTGTAGGACCGGAGCCAACTAG
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----------------------------------------------------------gtatgtctcattcttttattgttcctgttgctgatgcggtgcgtgtttctacagGACAAGTCCTGGCGGGTACGTTATATGGTTGCTAATCAACTATATGAACTCTGTGAAACTGTTGGACCGGAATGTACTAG
upper sequence: AT1G13320.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: EFJ10709 (Selaginella moellendorffii), 3'ss of exon 3
gtaaataaatgtgtgaatatgataaaaaaattctattgatgagctttatgggaaagctgtaaggcagatatgtatgagctgctttatcttgatttttttcgtctttga----gcagGATAAGTCCTGGCGTGTGCGTTATATGGTTGCAAATCAGCTCTATGAACTTTGTGAAGCTGTAGGACCGGAGCCAACTAG
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----------------------------------------------------------gtatgtctcattcttttattgttcctgttgctgatgcggtgcgtgtttgtttctacagGACAAGTCCTGGCGGGTACGTTATATGGTTGCTAATCAACTATATGAACTCTGTGAAACTGTTGGACCGGAATGTACTAGMapped 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|116468454|gb|EG511046.1|EG511046EST: CCCAGGACTGTGTTGCACACATTCTTCCTGTGATTGTCAATTTCTCGCAG -ATAAGTCCTGGCGTGTGC
genomic: CCCAGGACTGTGTTGCACACATTCTTCCTGTGATTGTCAATTTCTCGCAGgtaaataaat ... ctttgagcagGATAAGTCCTGGCGTGTGC
EST:
gi|116468455|gb|EG511047.1|EG511047EST: CCCAGGACTGTGTTGCACACATTCTTCCTGTGATTGTCAATTTCTCGCAG GATAAGTCCTGGCGTGTGC
genomic: CCCAGGACTGTGTTGCACACATTCTTCCTGTGATTGTCAATTTCTCGCAGgtaaataaat ... ctttgagcagGATAAGTCCTGGCGTGTGC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgtaaggcagatatgtatgagctgctttatcttgatttttttcgtctttgagcagGATAAGTCCTGGCGTGTGCGTTATATGGTTGCAAATCAGCTCTATGAACTTTGTGAAGCTGTAGGACCGGAGCCAACTAG
tcttgat putative branch site (score: 4)
tttttttcgtcttt CT-rich tract
tttatcttgatttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaataaatgtgtgaatatgataaaaaaattctattgatgagctttatgggaaagctgtaaggcagatatgtatgagctgctttatcttgatttttttcgtctttgagcagGATAAGTCCTGGCGTGTGCGTTATATGGTTGCAAATCAGCTCTATGAACTTTGTGAAGCTGTAGGACCGGAGCCAACTAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG