Sequence
atgc intronic sequence ATGC exonic sequencegtcctactgtcttaactaaaccagtcctttggttgtttctatttgttccaattgctgatgttgtttgcacttttttattttcaaagGTACGTTGCAACCGCAGTGACATCAGTCCATGAGATGGAGAATGGGTTCACCATATGGTCTTTCAACGGGATTATGCTTTACCGGATATTGAAGGATCAT
Basic information
species | Arabidopsis thaliana |
transcript | AT5G27640.1 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G27640.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA03G00470.1 (Glycine max), 3'ss of exon 9
--------------------------------------------------------------------------------------------------------------gtcctactgtcttaactaaaccagtcctt-tggttgtttc--tatttgttccaattgctgatgttgtttgcacttttttattttcaaagGTACGTTGCAACCGCAGTGACATCAGTCCATGAGATGGAGAATGGGTTCACCATATGGTCTTTCAACGGGATTATGCTTTACCGGATATTGAAGGATCAT
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gtatatggtctatctgaatgagtaatgatattgctaataaaggcagttcataggttaatcttttgtaaaatcagtttaaaattgtatttaccttagtcattaagtgtctgatttttgccactttactgaaaaagtgcttattgttggtttgttaattatcccaa--gcttatattgctttctctttata----tggcagATATGTTGCAACTGCAGTGACTTCAGTTCATGAAATGGAGAATGGTTTCAATATATGGTCTTTCAATGGCAAGCATCTATATCGGATTCTGAAGGATCAT
upper sequence: AT5G27640.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA07G14870.1 (Glycine max), 3'ss of exon 9
--------------------------------------------------------------------------------------------------------------gtcctactgtcttaactaaaccagtcctt-tggttg--tttctatttgttccaattgctgatgttgtttgcacttttttattttcaaagGTACGTTGCAACCGCAGTGACATCAGTCCATGAGATGGAGAATGGGTTCACCATATGGTCTTTCAACGGGATTATGCTTTACCGGATATTGAAGGATCAT
| | || ||| || ||| ||| |||||| || || || | |||| ||| || ||| || | |||| | | | || || |||||||| || ||||| ||||| ||||| ||||||||||| |||| |||||||||||||| || | || || ||||| ||||||||||
gtatatggtctatctgaatgagtaatgatattgctaataaaggcagtttataggttaatcttttgtaaaatcagtttaaaattgtatttacctttgtcatcatgtgtttgataattgcaattttactgaaaaagtgcttatggttggtttcttaattatcccaa--gcttatattgctttctctttatactgt----agATATGTTGCAACTGCGGTGACTTCAGTTCATGAAATGGAGAATGGTTTCAATATATGGTCTTTCAATGGCAAGCATCTATATCGGATTCTGAAGGATCAC
upper sequence: AT5G27640.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA04G06080.1 (Glycine max), 3'ss of exon 13
---------------------------------------------------------------------------------------------------------------gtcctactgtcttaactaaaccagtcctt-tggttgttt-ctatttgttccaattgctgatgttgtttgcacttttttattttcaaagGTACGTTGCAACCGCAGTGACATCAGTCCATGAGATGGAGAATGGGTTCACCATATGGTCTTTCAACGGGATTATGCTTTACCGGATATTGAAGGATCAT--
|| | ||| ||| || ||| ||| | | |||| || || | |||| ||| || ||| || | |||| | | ||||| |||||||| || ||||| ||||| ||||| ||||||||||| |||| ||||||||||||| || | || || ||||| ||||||||||
gtatatggtctatctgaatgaataatgatattgctaataaaggcagctcataggttaatcttttgtaaaatcagtctaaaattgtatttaccttagtcatcaaagtgtttggtatttgccacttcactgaaaaagtacttattatggtttgttaattatcccaa--gcttatattgctttctctttatg----ccgcagGTATGTTGCAACTGCTGTGACTTCAGTTCATGAAATGGAGAATGGTTTCA--GTATGGTCTTTCAATGGCAAACATCTATATCGGATTCTGAAGGATCACTT
upper sequence: AT5G27640.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: Vv04s0008g07070.t01 (Vitis vinifera), 3'ss of exon 9
----------------------------------------------------------------------------------gtcctactgtct-taacta-aaccagtcctttggttgtttctatttgttccaattgctgatgttgtttgcacttttttattttcaaagGTACGTTGCAACCGCAGTGACATCAGTCCATGAGATGGAGAATGGGTTCACCATATGGTCTTTCAACGGGATTATGCTTTACCGGATATTGAAGGATCAT
| | | | || ||| | || | | | || ||||||| | | || | ||| | | | | ||| | ||||| |||||||| |||| || ||||| ||||||||||| ||||| || | ||||||||| |||||||| | | || || |||||| | ||||||||
gtagttttggaagaactattatattgttttgttttctaaatgaaatatcagttatcttacaatatttatcttgtccttaaaaattcgatttcctgtaatcagaaggaatttagtcatttgttctatt-gcttgtatcttggctgtgatatttaactctttgcatctttagGTATGTTGCAACTTCAGTTACTTCAGTTCATGAGATGGAAAATGGCTTTAACATATGGTCCTTCAACGGCAAGCTCCTGTATCGGATACTAAAGGATCACMapped 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|86060060|gb|DR355817.1|DR355817EST: ACAGCTGAACACTTCATGGCCACGGATATCGAATGGGACCCGACTGGAAG GTACGTTGCAACCGCAGTGACATCAGTCCATGAGATGGAGAATGGGTTCAC
genomic: ACAGCTGAACACTTCATGGCCACGGATATCGAATGGGACCCGACTGGAAGgtcctactgt ... attttcaaagGTACGTTGCAACCGCAGTGACATCAGTCCATGAGATGGAGAATGGGTTCAC
EST:
gi|47832098|gb|CK121782.1|CK121782EST: ACAGCTGAACACTTCATGGCCACGGATATCGAATGGGACCCGACTGGAAG GTACGTTGCAACCGCAGTGACATCAGTCCATGAGATGGAGAATGGGTTCAC
genomic: ACAGCTGAACACTTCATGGCCACGGATATCGAATGGGACCCGACTGGAAGgtcctactgt ... attttcaaagGTACGTTGCAACCGCAGTGACATCAGTCCATGAGATGGAGAATGGGTTCAC
EST:
gi|164009351|gb|EL996264.1|EL996264EST: ACAGCTGAACACTTCATGGCCACGGATATCGAATGGGACCCGACTGGAAG GTACGTTGCAACCGCAGTGACA
genomic: ACAGCTGAACACTTCATGGCCACGGATATCGAATGGGACCCGACTGGAAGgtcctactgt ... attttcaaagGTACGTTGCAACCGCAGTGACA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gttgtttctatttgttccaattgctgatgttgtttgcacttttttattttcaaagGTACGTTGCAACCGCAGTGACATCAGTCCATGAGATGGAGAATGGGTTCACCATATGGTCTTTCAACGGGATTATGCTTTACCGGATATTGAAGGATCAT
tgctgat putative branch site (score: 3)
cacttttttattttc putative PPT
acttttttattttcaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtcctactgtcttaactaaaccagtcctttggttgtttctatttgttccaattgctgatgttgtttgcacttttttattttcaaagGTACGTTGCAACCGCAGTGACATCAGTCCATGAGATGGAGAATGGGTTCACCATATGGTCTTTCAACGGGATTATGCTTTACCGGATATTGAAGGATCAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG