Sequence
atgc intronic sequence ATGC exonic sequencegtaatataactcagtctgcgtttactgctgtggaggattgtcaccataaatatcattctattagcttagttatgcttacagtgtctcacatcttcactttcttatatagGTTGCTCTAAAGTTTGAGCATAGGAGCAGCAAGGGTTGCAACTATGGTCCTCCACATGAGTGGCAGGTTTACAA
Basic information
species | Arabidopsis thaliana |
transcript | AT3G13670.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G13670.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv06s0004g01090.t01 (Vitis vinifera), 3'ss of exon 2
gtaatataactcagtctgcgtttactgctgtggaggattgt-caccataaatatcattc-tattagcttagttatgcttacagtgtctcacatcttcacttt---cttatat-agGTTGCTCTAAAGTTTGAGCATAGGAGCAGCAAGGGTTGCAACTATGGTCCTCCACATGAGTGGCAGGTTTACAA
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gtaacctagtcccagcttt-cttactgactaataaaattgtgtatccgaattaggattagtgttattaaaagtaatcatattatgacttcattcttcttattgtgtttttatcagGTAGCTTTGAAATTCGAGCACAGAAACAGCAAAGGCTGCAACTATGGCCCTCCATATGAGTGGCAGGTGTACAA
upper sequence: AT3G13670.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: PP1S66_174V6.1 (Physcomitrella patens), 3'ss of exon 2
----------------gtaatataactcagtctgcgtttactgctgtggaggattgtca-ccataaatatcattctattagcttagttatgcttacagtgtctcacatc----ttcactttcttat--atagGTTGCTCTAAAGTTTGAGCATAGGAGCAGCAAGGGTTGCAACTATGGTCCTCCACATGAGTGGCAGGTTTACAA
| | | || | | || | | || || | | | ||| | | || ||| | | || | | || | | |||| | |||| ||| |||||||||| ||| ||||||||||||||||||| ||||||||||| | |||||||| ||||||||
gtactctttactctaattcgttgaggtccggtcgtgtcgtattccgtatagtgccgagggttgtgattatttagcgagtatctttgctttgtgtctggaagtacaaactgagtcttgttttcgtgctcgcagGTAGCTTTAAAGTTTGAACATCGGAGCAGCAAGGGTTGCAATTATGGTCCTCCTTACGAGTGGCAAGTTTACAA
upper sequence: AT3G13670.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: PP1S131_16V6.1 (Physcomitrella patens), 3'ss of exon 2
--------------gtaatataactcagtctgcgtttactgctg---------tggaggattgtcaccataa-atatca---ttctattagcttagttatgcttacagtgtctcacatcttca-ctttcttatatagGTTGCTCTAAAGTTTGAGCATAGGAGCAGCAAGGGTTGCAACTATGGTCCTCCACATGAGTGGCAGGTTTACAA
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gtattcaatttcttacaatttgttctgctctacttctttcgcagcagcatgtttggaagatactctgcatattgcatcgaggtcttgtgatttttaatgtaataagttttgtattcatattgaactcgtttgtgcagGTTGCGTTGAAGTTCGAGCATCGGAGTAGTAAGGGCTGCAATTATGGTCCTCCTTATGAGTGGCAGGTTTACAC
upper sequence: AT3G13670.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: EFJ13521 (Selaginella moellendorffii), 3'ss of exon 2
gtaatataactcagtctgcgtttactgctgtggaggattgtcaccataaatatcattctattagcttagttatgcttacagtgtctcacatcttcactttcttatatagGTTGCTCTAAAGTTTGAGCATAGGAGCAGCAAGGGTTGCAACTATGGTCCTCCACATGAGTGGCAGGTTTACAA
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---------------------------------------gtcggtg-gcgtttcctcttctttttttgcttatgctgattgtgttataa-----cgctcgtttgcgcagGTTGCTCTCAAGTTCGAGCATAGGAGCAGCAAAGGTTGCAACTACGGGCCTCCTTACGAATGGCAGGTTTACGA
upper sequence: AT3G13670.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: EFJ38433 (Selaginella moellendorffii), 3'ss of exon 2
gtaatataactcagtctgcgtttactgctgtggaggattgtcaccataaatatcattctattagcttagttatgcttacagtgtctcacatcttcactttcttatatagGTTGCTCTAAAGTTTGAGCATAGGAGCAGCAAGGGTTGCAACTATGGTCCTCCACATGAGTGGCAGGTTTACAA
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--------------------------------gtagactgtt--cgaagat-ttgctcagttggattggctcttttctcagcggctga----tcaaagatgttgt-cagGTTGCTTTGAAGTTTGAACACAGAAGCAGTAAAGGATGCAACTATGGGCCTCCGTATGAGTGGCAAGTTTACAC
upper sequence: AT3G13670.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: EFJ19085 (Selaginella moellendorffii), 3'ss of exon 2
gtaatataactcagtctgcgtttactgctgtggaggattgtcaccataaatatcattctattagcttagttatgcttacagtgtctcacatcttcactttcttatatagGTTGCTCTAAAGTTTGAGCATAGGAGCAGCAAGGGTTGCAACTATGGTCCTCCACATGAGTGGCAGGTTTACAA
||| | || | | || || ||||||| | |||| | | || || |||||||||| ||||| ||||||||||||||||| |||||||||||||| ||||| | || |||||||||||| |
---------------------------------------gtcggtg-gcgtttcctcttctttttttgcttatgctgattgtgttataa-----cgctcgtttgcgcagGTTGCTCTCAAGTTCGAGCATAGGAGCAGCAAAGGTTGCAACTATGGGCCTCCTTACGAATGGCAGGTTTACGA
upper sequence: AT3G13670.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: EFJ31718 (Selaginella moellendorffii), 3'ss of exon 2
gtaatataactcagtctgcgtttactgctgtggaggattgtcaccataaatatcattctattagcttagttatgcttacagtgtctcacatcttcactttcttatatagGTTGCTCTAAAGTTTGAGCATAGGAGCAGCAAGGGTTGCAACTATGGTCCTCCACATGAGTGGCAGGTTTACAA
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--------------------------------gtagactgtt----cgaagattttctcagttggattgctcttttctcagcggctga----tcaaagatgttgt-cagGTTGCTTTGAAGTTTGAACACAGAAGCAGTAAAGGATGCAACTATGGGCCTCCGTATGAGTGGCAAGTTTACACMapped 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|86068919|gb|DR364676.1|DR364676EST: GTCGTATTAGTGGCGGTAATGATCGAAGTGCAGGAGCTAGCATCTTGGAG GTTGCTCTAAAGTTTGAGCATAGGAGCAGCCNAGGGTTGCA-CTATGGNCC
genomic: GTCGTATTAGTGGCGGTAATGATCGTAGTGCAGGAGCTAGCATCTTGGAGgtaatataac ... tcttatatagGTTGCTCTAAAGTTTGAGCATAGGAGCAGCA-AGGGTTGCAACTATGGTCC
EST:
gi|116444765|gb|EG487357.1|EG487357EST: GTCGTATTAGTGGCGGTAATGATCGTAGTGCAGGAGCTAGCATCTTGGAG GTTGCTCTAAAGTTTGAGCATAGGAGCAGCAAGGGTTGCAACTATGGTCCT
genomic: GTCGTATTAGTGGCGGTAATGATCGTAGTGCAGGAGCTAGCATCTTGGAGgtaatataac ... tcttatatagGTTGCTCTAAAGTTTGAGCATAGGAGCAGCAAGGGTTGCAACTATGGTCCT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attctattagcttagttatgcttacagtgtctcacatcttcactttcttatatagGTTGCTCTAAAGTTTGAGCATAGGAGCAGCAAGGGTTGCAACTATGGTCCTCCACATGAGTGGCAGGTTTACAA
catcttcactttctt CT-rich tract
tttcttatata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatataactcagtctgcgtttactgctgtggaggattgtcaccataaatatcattctattagcttagttatgcttacagtgtctcacatcttcactttcttatatagGTTGCTCTAAAGTTTGAGCATAGGAGCAGCAAGGGTTGCAACTATGGTCCTCCACATGAGTGGCAGGTTTACAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG