Sequence
atgc intronic sequence ATGC exonic sequencegtacttgtctgttgatttgtatttctttctcacatcttgcaatcctttataagtcaaacaactttcgatttcaacttttcagATGAAAGCTCTGGCAATGTTCCAGAACGATGCTGATTGCATGGCACTTTTGATGGATGGAAGTGGGGCCCTTGGTCTTGATTTGAGTTTTGTAACACATG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G54460.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G54460.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA04G28970.2 (Glycine max), 3'ss of exon 5
--gtacttgtctgttgatttgtatttctttctcacatcttgcaatcctttataa---------gtcaaacaactttcgatttcaacttttcagATGAAAGCTCTGGCAATGTTCCAGAACGATGCTGATTGCATGGCACTTTTGATGGATGGAAGTGGGGCCCTTGGTCTTGATTTGAGTTTTGTAACACATG
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gtataatgctcaaattttctattactgtttctgaaaattaaaatttacttttggtttctgaccgttggttaatttgcc-tttccccttttcagAAGAAGTCATTGGCCATGTTCCAGCATGATTCAAATTGTATGGCACTTCTGATGGATGGAAGTGCTGCATTGGGTCTTGATTTGAGTTTTGTTACGCATG
upper sequence: AT3G54460.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA11G21600.1 (Glycine max), 3'ss of exon 5
-----gtacttgtctgttgatttg-tatttctt---tctcacatcttgcaatcctttataa--gtcaaacaactttcgatttcaacttttcagATGAAAGCTCTGGCAATGTTCCAGAACGATGCTGATTGCATGGCACTTTTGATGGATGGAAGTGGGGCCCTTGGTCTTGATTTGAGTTTTGTAACACATG
| || | | || ||| | |||||| | | || | | ||| | | || || || | |||| ||| |||| ||| | | || ||||||||| | ||| | |||| ||||||||| ||||||||||||||| || | |||||||| ||||||||||| || ||||
gtataatgctggaattttcttttactgtttcttaaaattaaaatttacttttggtttctgaccgttggttaatttgccttttcc-ttttccagAAGAAGTCATTAGCCATGTTCCAGCATGATTCAAATTGTATGGCACTTCTGATGGATGGAAGTGCTGCATTGGGTCTTGACTTGAGTTTTGTTACGCATG
upper sequence: AT3G54460.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv13s0067g03330.t01 (Vitis vinifera), 3'ss of exon 6
gtacttgtctgttgatttgtatttctttctcacat-cttgcaatcctttataagtcaaacaactttcgatttcaacttttcagATGAAAGCTCTGGCAATGTTCCAGAACGATGCTGATTGCATGGCACTTTTGATGGATGGAAGTGGGGCCCTTGGTCTTGATTTGAGTTTTGTAACACATG
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gtactaatataatccattttctgtatttccaactttctttaaattatttccaagattaa-----ttcactgtcagtttttcagATGAAGTCGCTATCCACCTTCCAGCATGATGCAGATTGTATGGCTCTTTTGATGGATGGAAGTGCAGCATTAGGCCTTGATTTGAGCTTTGTAACACATGMapped 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|116406001|gb|EG448593.1|EG448593EST: CTGGCATCAAGTTTGGTAAAATGTACAGTCCAATGCAGTCGTATAATAAG ATGAAAGCTCTGGCAATGTTCCAGAACGATGCTGATTGCATGGCACTTTTG
genomic: CTGGCATCAAGTTTGGTAAAATGTACAGTCCAATGCAGTCGTATAATAAGgtacttgtct ... aacttttcagATGAAAGCTCTGGCAATGTTCCAGAACGATGCTGATTGCATGGCACTTTTG
EST:
gi|116471154|gb|EG513746.1|EG513746EST: CTGGCATCAAGTTTGGTAAAATGTACAGTCCAATGCAGTCGTATAATAAG ATGAAAGCTCTGGCAATGTTCCAGAACGATGCTGATTGCATGGCGCTTTTG
genomic: CTGGCATCAAGTTTGGTAAAATGTACAGTCCAATGCAGTCGTATAATAAGgtacttgtct ... aacttttcagATGAAAGCTCTGGCAATGTTCCAGAACGATGCTGATTGCATGGCACTTTTG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctcacatcttgcaatcctttataagtcaaacaactttcgatttcaacttttcagATGAAAGCTCTGGCAATGTTCCAGAACGATGCTGATTGCATGGCACTTTTGATGGATGGAAGTGGGGCCCTTGGTCTTGATTTGAGTTTTGTAACACATG
ttctcac putative branch site (score: 2)
cttttc putative PPT
tttataagt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacttgtctgttgatttgtatttctttctcacatcttgcaatcctttataagtcaaacaactttcgatttcaacttttcagATGAAAGCTCTGGCAATGTTCCAGAACGATGCTGATTGCATGGCACTTTTGATGGATGGAAGTGGGGCCCTTGGTCTTGATTTGAGTTTTGTAACACATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG