Sequence
atgc intronic sequence ATGC exonic sequencegtttgtgtagaaatcttaagcatatagtatgttttcaattcaaatcgagcattttagctattggttattggagtatatttacttgttcagGTTCTAGAGATGATTAACAACCCACACTATCTATATCGGATGACGATTCTTCGTGCAGTATCGCTTCTCGCTCCAGTAATGGGATCCGAGATCACATGTT
Basic information
species | Arabidopsis thaliana |
transcript | AT1G13320.2 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G13320.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GRMZM2G164352_T03 (Zea mays), 3'ss of exon 10
----------gtttgtgtagaaatcttaagcatatagtatgttttcaattcaaatcgagcattttagctattggttattgga-gtatatttacttgttcagGTTCTAGAGATGATTAACAACCCACACTATCTATATCGGATGACGATTCTTCGTGCAGTATCGCTTCTCGCTCCAGTAATGGGATCCGAGATCACATGTT
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tctccaaaacaattgtcca-accccccaaagataaattgtcattgttgtgatggcatggggtttctgctagtctttacaacccactcgcttgttttcccagGTGCTGGAGAAGATCAACAACCCACACTATTTATACCGCATGACGATTCTGCAGGCAATCTCCTTGCTAGCTCCTGTCATGGGTGCAGAAATCACCTGTC
upper sequence: AT1G13320.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA10G42250.1 (Glycine max), 3'ss of exon 10
--------------------------------------------------------------------------gtttgtgtagaaatctt-aagcatatagtatgttttcaat-tcaaatcgagcattttagctattg--gttattggagtatatttac--------ttgttcagGTTCTAGAGATGATTAACAACCCACACTATCTATATCGGATGACGATTCTTCGTGCAGTATCGCTTCTCGCTCCAGTAATGGGATCCGAGATCACATGTT
|||| ||| | |||| || |||| | | | | | | | ||| | | | || | | ||||| | || | | |||||| | ||||||| ||||||||||||||| | ||||||||||| ||||||||||| | || || || ||||| || ||||| | || ||||| ||||
gttcatctatttacttaatttattattaacgaaatgatacaccaacatatgtcaacattaattcgtctgtgtgggtttttgtgcatgtcttgaaatatatgtttgctatatgctattaccttttctattctcccaagtgtaacttcagaagtatctatatggaatgtgtggaacagGTTTTGGAGATGAACAACAACCCACACTATTTGTATCGGATGACTATTCTTCGTGCTATCTCTCTGCTTGCTCCTGTGATGGGCCCTGAAATCACTTGTT
upper sequence: AT1G13320.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA20G24790.1 (Glycine max), 3'ss of exon 10
-------------------------------------------------------------------------------------------gtttgtgtagaaatcttaagcatatagtatgttttcaattcaaatcgagcattttagctattggttattggagtatattta-------cttgttcagGTTCTAGAGATGATTAACAACCCACACTATCTATATCGGATGACGATTCTTCGTGCAGTATCGCTTCTCGCTCCAGTAATGGGATCCGAGATCACATGTT
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gttcatctatttgcttaatttattattaacgaaatgacacaccaacatatgtcaacattaattcgtctgtgtaggtttttgtgcatgtctagtggaaattgaaatat-atgcttgttatatgctattacttct--tctattctcctaagtgcaactt-cagaagtatctatatggaatgctggaacagGTTTTGGAGATGAACAACAATCCACACTATTTGTATCGGATGACCATTCTTCGTGCTATCTCTCTGCTTGCTCCTGTGATGGGCCCTGAAATCACTTGTTMapped 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|116425639|gb|EG468231.1|EG468231EST: TTGCTGAAGAGTTTGGTCCTGAATGGGCAATGCAGCATATAGTTCCTCAG GTTCTAGAGATGATTAACAACCCACACTATCTATATCGGATGACGATTCTT
genomic: TTGCTGAAGAGTTTGGTCCTGAATGGGCAATGCAGCATATAGTTCCTCAGgtttgtgtag ... acttgttcagGTTCTAGAGATGATTAACAACCCACACTATCTATATCGGATGACGATTCTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.caattcaaatcgagcattttagctattggttattggagtatatttacttgttcagGTTCTAGAGATGATTAACAACCCACACTATCTATATCGGATGACGATTCTTCGTGCAGTATCGCTTCTCGCTCCAGTAATGGGATCCGAGATCACATGTT
tttactt CT-rich tract
tatatttacttgtt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttgtgtagaaatcttaagcatatagtatgttttcaattcaaatcgagcattttagctattggttattggagtatatttacttgttcagGTTCTAGAGATGATTAACAACCCACACTATCTATATCGGATGACGATTCTTCGTGCAGTATCGCTTCTCGCTCCAGTAATGGGATCCGAGATCACATGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA