Sequence
atgc intronic sequence ATGC exonic sequencegtttttaacaatgctattcactgagaatgattagtttttttatgagacttcctctaactcttagttgaaatgaaacagGTTCATATATCTGAAGCAAGGGTTTCGACTGCTTTAGACAAGTTAGCCCACATGGAAGAATTGGTTAATGATAGGTTGTTACCTGGCAGAGTTGTAACGG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G44446.3 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G44446.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA13G03430.1 (Glycine max), 3'ss of exon 3
---------------------------------------------------gtttttaacaatgcta--ttcactgagaatgattagtttttttatgagacttc-ctctaact-cttagttgaa---atga-aacagGTTCATATATCTGAAGCAAGGGTTTCGACTGCTTTAGACAAGTTAGCCCACATGGAAGAATTGGTTAATGATAGGTTGTTACCTGGCAGAGTTGTAACGG
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gtatttaattttagcagtagcaaaccagtcagcgcaacttgaaaccgagttgtttttaattgatctaacttggcagaaacttgtcaatatgttattaatttgtcactatatttactcaacttaatgaataacaacagGTTCATATATCTGAAGCAAGGGTTACCACTGCTTTAGATAAACTTGCTTACATGGAAGAATTGGTAAATGATAGGCTGTTGCAAGATCGAAGCACGACTG
upper sequence: AT1G44446.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA14G23860.1 (Glycine max), 3'ss of exon 3
---------------------------------------------------gtttttaacaatgctattca--ctgagaatgattagttttt---ttatgagacttcctctaactct-------tagttgaaatgaaacagGTTCATATATCTGAAGCAAGGGTTTCGACTGCTTTAGACAAGTTAGCCCACATGGAAGAATTGGTTAATGATAGGTTGTTACCTGGCAGAGTTGTAACGG
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gtatagaatttttagcagtgaagaccagtcagcacaacttgaaactgagttgtttttaattgatctatctaacttggcagaaatttgtcaataggttattaacctgtcactatatttattcaacttaatgaataacaacagGTTCATATATCTGAAGCAAGGGTTACCACTGCTTTGGATAAACTTGCTTACATGGAAGAATTGGTAAATGATAGGCTGTTGCAAGACAGAAGCACAGCTG
upper sequence: AT1G44446.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA06G11920.1 (Glycine max), 3'ss of exon 3
----------------------------------------------------gtttttaacaatgctattca-ctgagaatgattagtttttttatgagacttc--ctctaactcttagttgaaatgaaacagGTTCATATATCTGAAGCAAGGGTTTCGACTGCTTTAGACAAGTTAGCCCACATGGAAGAATTGGTTAATGATAGGTTGTTACCTGGCAGAGTTGTAACGG
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gtaccaatcattacatgttacgaactaatcagcacaacatgtagctgagattgtcttgatttgtccgacttggctggaacttgttcataaagttatcaatattcaattcatgttacttattgaacaaaaacagGTTCATATATCTGAGGCAAGGGTGTCCACTGCTTTAGATAAACTAGCTTACATGGAAGAATTAGTAAACGATAAGTTGTTGCAAGAAAGAACCACAACCG
upper sequence: AT1G44446.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA04G42840.1 (Glycine max), 3'ss of exon 3
---------------------------------------------------gtttttaacaatgctattcactgagaa-----tgattagtttttt-tatgagacttcctcta-actcttagttgaaatgaaacagGTTCATATATCTGAAGCAAGGGTTTCGACTGCTTTAGACAAGTTAGCCCACATGGAAGAATTGGTTAATGATAGGTTGTTACCTGGCAGAGTTGTAACGG
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gtactgatcattacatgttaataagtaatcagcacaacatgtagctgagatgtcttgattcgtccaacttgcctggaacttgttcataagttatcaatatgagactttattcatgttacttattgaacaaaaacagGTTCATATATCTGAGGCAAGGGTGTCCAGTGCTTTAGATAAACTAGCTTACATGGAAGAATTAGTAAACGATAAGTTGTTGCAAGAAAGAAGCACCACAG
upper sequence: AT1G44446.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv18s0001g02700.t01 (Vitis vinifera), 3'ss of exon 2
------------------gtttttaacaatgctattca--ctgagaatgattagtttttttatgagacttcctctaactcttagttgaaatgaa--acagGTTCATATATCTGAAGCAAGGGTTTCGACTGCTTTAGACAAGTTAGCCCACATGGAAGAATTGGTTAATGATAGGTTGTTACCTGGCAGAGTTGTAACGG
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ctaaatctggattttccggttccaattggttatgtacatgctttgaaactgcaatctcatggccatttttttttttgttccttgtgactgtgaataacagGTTCATATATCTGAAGCAAGGGTTGGCACTGCTTTAGATAAGTTGGCTTACATGGAAGAATTGGTTAATGATAGGCTATTACAAGACAGAAATACAGCAGMapped 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|125287798|gb|EL301883.1|EL301883EST: ATTGCAGGAAGAATTATCGAAAGCACACCAACAG GTTCATATATCTGAAGCAAGGGTTTCGACTGCTTTAGACAAGTTAGCCCAC
genomic: ATTGCAGGAAGAATTATCGAAAGCACACCAACAGgtttttaaca ... aatgaaacagGTTCATATATCTGAAGCAAGGGTTTCGACTGCTTTAGACAAGTTAGCCCAC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agaatgattagtttttttatgagacttcctctaactcttagttgaaatgaaacagGTTCATATATCTGAAGCAAGGGTTTCGACTGCTTTAGACAAGTTAGCCCACATGGAAGAATTGGTTAATGATAGGTTGTTACCTGGCAGAGTTGTAACGG
ctctaac putative branch site (score: 2)
attagtttttttatga 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttttaacaatgctattcactgagaatgattagtttttttatgagacttcctctaactcttagttgaaatgaaacagGTTCATATATCTGAAGCAAGGGTTTCGACTGCTTTAGACAAGTTAGCCCACATGGAAGAATTGGTTAATGATAGGTTGTTACCTGGCAGAGTTGTAACGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA