Sequence
atgc intronic sequence ATGC exonic sequencegtaagttttgctactttccttgtatgtttataatctcgttctgctcatatttttgtctaaacaacatgaaacatatttagGTTGAGTGGGATGAGATCAATGCTGCTTGGGGCCAAGCCTGTCTTCTCCTCCATACGATGTGTAACTATTTCCGGCCAAAGTTTCA
Basic information
species | Arabidopsis thaliana |
transcript | AT3G61710.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G61710.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os03g44200.2 (Oryza sativa), 3'ss of exon 7
-------------------------------------gtaagttttgctactttccttgtat---gtttataatct---cgttctgctcatatt-----tttgtct-----aaacaac-atgaaacatattt---agGTTGAGTGGGATGAGATCAATGCTGCTTGGGGCCAAGCCTGTCTTCTCCTCCATACGATGTGTAACTATTTCCGGCCAAAGTTTCA
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gtaattatgcaaaatgtgcagatatcacgtccattcactatcttttagtgctttccttgaattctattcaagatgtacatggaatgttcatgttgatcctttgtgttaatgtaacaactgtgttactcttttcttagGTGGAGTGGGATGAGATAAATGCTGCTTGGGGCCAGGCTGCTCTTCTGTTGCATACCATGGCTCAGTACTTCTTCCCAAAATTTGA
upper sequence: AT3G61710.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os01g48920.1 (Oryza sativa), 3'ss of exon 6
gtaagttttgctactttccttgtatgtttataatctcgttctgctcatatttttgtctaaacaacatgaaacatattt---agGTTGAGTGGGATGAGATCAATGCTGCTTGGGGCCAAGCCTGTCTTCTCCTCCATACGATGTGTAACTATTTCCGGCCAAAGTTTCA
|||| || ||| | || | | | || | || | || | ||||| ||| || ||| || ||| ||||||| ||||||||||| |||||||||||||| || || |||||| | ||||| ||| | | || ||| ||||| ||| |
gtaa-ttatgcaaaatt---tacagatataccacatc-tcatgtttgatcctttgt-taataaatctgatacccttttcttagGTTGAATGGGATGAGATAAATGCTGCTTGGGGTCAGGCTGCTCTTCTTTTGCATACCATGGCTCAGTACTTCACCCCAAAATTTGA
upper sequence: AT3G61710.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G092112_T01 (Zea mays), 3'ss of exon 6
gtaagttttgctactttcc--ttgtatgtttataatctcgttctgctcatatttttgtctaaacaacatgaaacatatttagGTTGAGTGGGATGAGATCAATGCTGCTTGGGGCCAAGCCTGTCTTCTCCTCCATACGATGTGTAACTATTTCCGGCCAAAGTTTCA
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gtaa-ttatactgattgcaaaacgcatagatacaactttgtgtcact-atactcggcgcttctgataataa----tgtacagGTTGAGTGGGATGAGATAAATGCTGCATGGGGTCAGGCTGCACTGCTGTTGCATACCATGGCTCAGTATTTCACCCCAAAATTCCA
upper sequence: AT3G61710.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA04G26840.1 (Glycine max), 3'ss of exon 6
------------------------gtaagttttgctactttccttgtatgttt--ataatctcgttctgctcatatttttgtctaaacaacatgaaacatatttagGTTGAGTGGGATGAGATCAATGCTGCTTGGGGCCAAGCCTGTCTTCTCCTCCATACGATGTGTAACTATTTCCGGCCAAAGTTTCA
| | || | ||| ||| |||| ||| | | | || | || | || || |||||| | |||||||||| ||||||||||| |||||||| ||||||||||| || || || || ||||| ||||| | |||||||| || ||||||||
ttatcctagagaattttcttaatcttgaattgaataatttttcttcctagtttgaatatttaagctttgattatgatgttcacttt----tatgaaa--tgtttagGTTGAATGGGATGAGATAAATGCTGCCTGGGGCCAAGCTTGCCTCCTTCTTCATACTATGTGCCAATATTTCCGACCGAAGTTTCA
upper sequence: AT3G61710.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA11G21490.1 (Glycine max), 3'ss of exon 6
------------------gtaagttttgctactttccttgtatgtttataatctcgttct----gctcatatttttgtctaaacaacatgaaacatatttagGTTGAGTGGGATGAGATCAATGCTGCTTGGGGCCAAGCCTGTCTTCTCCTCCATACGATGTGTAACTATTTCCGGCCAAAGTTTCA
| | | ||| | | | | || || | | | | ||| ||| | | | | | |||||| | |||||||||| ||||||||||| |||||||| ||||||||||| || || || || || || ||||| | |||||||| || ||||||||
tttatcctagagaattttcttaatcttgaactgaatcctttttcttcctagtttgaatattgaagctttgattatgatgttactattatgaaa--tgtttagGTTGAATGGGATGAGATAAATGCTGCCTGGGGCCAAGCTTGCCTCCTTCTTCACACTATGTGCCAGTATTTCCGACCGAAGTTTCA
upper sequence: AT3G61710.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv15s0046g00950.t01 (Vitis vinifera), 3'ss of exon 6
-----------------------gtaagttttgctactttccttgtatgtttataatctcgttctg-ctcatatttttgtctaaacaacatgaaacatatttagGTTGAGTGGGATGAGATCAATGCTGCTTGGGGCCAAGCCTGTCTTCTCCTCCATACGATGTGTAACTATTTCCGGCCAAAGTTTCA
|| || ||||||||||| || || | | | | | || | | ||| ||| || |||||||| |||||||| ||||||||||| |||||||| ||||||||||| || ||||| |||||||| ||| | | |||||||| |||||||| ||
tatgtcatcaactagtatacagcttattttagaatactttccttg-atattggaactgaggcaccgactaagaagtttatctgtactgtg-gaaacata--tagGTTGAATGGGATGAGATAAATGCTGCCTGGGGCCAAGCTTGCCTTCTTCTCCATACAATGGTTCAATATTTCCGACCAAAGTTCCAMapped 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|116473301|gb|EG515893.1|EG515893EST: AATTTGGTACAATTAACAATTTTCGACTTGGAAGACTCCCTGCCATAAAA GTTGAGTGGGATGAGATCAATGCTGCTTGGGGCCAAGCCTGTCTTCTCCTC
genomic: AATTTGGTACAATTAACAATTTTCGACTTGGAAGACTCCCTGCCATAAAAgtaagttttg ... acatatttagGTTGAGTGGGATGAGATCAATGCTGCTTGGGGCCAAGCCTGTCTTCTCCTC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtttataatctcgttctgctcatatttttgtctaaacaacatgaaacatatttagGTTGAGTGGGATGAGATCAATGCTGCTTGGGGCCAAGCCTGTCTTCTCCTCCATACGATGTGTAACTATTTCCGGCCAAAGTTTCA
gtctaaa putative branch site (score: 3)
atatttttgtctaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagttttgctactttccttgtatgtttataatctcgttctgctcatatttttgtctaaacaacatgaaacatatttagGTTGAGTGGGATGAGATCAATGCTGCTTGGGGCCAAGCCTGTCTTCTCCTCCATACGATGTGTAACTATTTCCGGCCAAAGTTTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC