Sequence
atgc intronic sequence ATGC exonic sequencegtatgaatatgattccagtttcaaattcaaccatcagaattatagaagcatatgatccgaatgtagaaatttgattcacagGGTGGTGGTCAACTATGATTTTCCAAATGGAGTAGAGGATTATGTCCATAGAATTGGAAGAACTGGAAGAGCTGGAGCAACCGGTCTAGCTTACACCTTC
Basic information
species | Arabidopsis thaliana |
transcript | AT5G14610.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G14610.2 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: LOC_Os01g07740.2 (Oryza sativa), 3'ss of exon 9
--------------------------------------------------gtatgaatatgat-tccagtttcaaatt-caaccatcagaattatagaa----gcatatgatccgaatgtagaa---------atttgattcacagGGTGGTGGTCAACTATGATTTTCCAAATGGAGTAGAGGATTATGTCCATAGAATTGGAAGAACTGGAAGAGCTGGAGCAACCGGTCTAGCTTACACCTTC
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gttgggacttctttgcaacttgtagagctgagatctcattgtaggccatagcataaagatgatgtccctgtgcatgttgtaacgactaatgacctgtaattcttcaaatggtattcactgacaattctctcatattcctgttacagAGTTGTGGTCAACTACGATTTCCCAACAGGTGTTGAGGATTACGTCCATAGAATTGGGAGAACAGGACGGGCTGGAGCGACTGGAGTTGCCTATACATTC
upper sequence: AT5G14610.2 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA05G08750.1 (Glycine max), 3'ss of exon 11
-----------------------------------------------gtat-gaatatgattccagtttcaaattcaaccatcagaattatagaagcatatgatccg--aatgtagaaatttgattcacagGGTGGTGGTCAACTATGATTTTCCAAATGGAGTAGAGGATTATGTCCATAGAATTGGAAGAACTGGAAGAGCTGGAGCAACCGGTCTAGCTTACACCTTC
|| | | || | || | | | || | | || || | |||| | | | || ||||||||| ||||| ||||| || || | ||||| || |||||||| ||||| |||||||| ||||||||||||||||| || || ||||||||||| |||
gttgttaattgtttgttttattgtattttttttattctgaggcccatgtgttgggtactttacccactgtagtagaacttgtcttggaaaagtgactattgtatttgacaatgaccataaatattttgcagGGTGGTTGTCAATTATGACTTCCCTACAGGAGTGGAAGATTATGTTCATAGGATTGGAAGGACTGGAAGAGCTGGAGCCACTGGGCTAGCTTACACTTTC
upper sequence: AT5G14610.2 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA19G00260.1 (Glycine max), 3'ss of exon 7
------------------------------------------------gtatgaatatgattc-cagtttcaaattcaaccatcagaattatagaagcatatgatccgaatgtagaaatttgattcacagGGTGGTGGTCAACTATGATTTTCCAAATGGAGTAGAGGATTATGTCCATAGAATTGGAAGAACTGGAAGAGCTGGAGCAACCGGTCTAGCTTACACCTTC
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gttgttaattgtttgttttatcatgttttttttattctgagacccgtgttgggtactttacccactgtagtgaaattagtcttggaaaagtaaccattgtattttac-aatgaccataaatattttgcagGGTGGTTGTCAATTATGACTTCCCTACAGGAGTGGAAGATTATGTTCATAGGATTGGAAGGACTGGAAGAGCTGGAGCCACTGGGCTAGCTTACACTTTC
upper sequence: AT5G14610.2 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv14s0066g01020.t01 (Vitis vinifera), 3'ss of exon 7
----------gtatgaatatgattc----cagtttcaaattcaaccatcagaattataga--agcatatgatcc--gaatgtagaaatttgat-tcacagGGTGGTGGTCAACTATGATTTTCCAAATGGAGTAGAGGATTATGTCCATAGAATTGGAAGAACTGGAAGAGCTGGAGCAACCGGTCTAGCTTACACCTTC
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gtcaaagtgtgtgtatatatgtctcttctccatcctttctttagatttcaaaggtaaaaattaggttataatgctagaatgacctgatcttttatcacagGGTGGTTATCAACTATGATTTCCCAACTGGAGTAGAGGATTATGTGCACAGGATTGGAAGGACTGGTAGGGCAGGTGCCACTGGAGTTGCTTACACATTCMapped 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|124760518|gb|EH850648.1|EH850648EST: CTTGTTGCAACTGATGTAGCTGCTCGTGGACTTGACGTTAAGGACATAAG GGTGGTGGTCAACTATGATTTTCCAAATGGAGTAGAGGATTATGTCCATAG
genomic: CTTGTTGCAACTGATGTAGCTGCTCGTGGACTTGACGTTAAGGACATAAGgtatgaatat ... tgattcacagGGTGGTGGTCAACTATGATTTTCCAAATGGAGTAGAGGATTATGTCCATAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcaaccatcagaattatagaagcatatgatccgaatgtagaaatttgattcacagGGTGGTGGTCAACTATGATTTTCCAAATGGAGTAGAGGATTATGTCCATAGAATTGGAAGAACTGGAAGAGCTGGAGCAACCGGTCTAGCTTACACCTTC
atttgat putative branch site (score: 5)
aattatagaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgaatatgattccagtttcaaattcaaccatcagaattatagaagcatatgatccgaatgtagaaatttgattcacagGGTGGTGGTCAACTATGATTTTCCAAATGGAGTAGAGGATTATGTCCATAGAATTGGAAGAACTGGAAGAGCTGGAGCAACCGGTCTAGCTTACACCTTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA