Sequence
atgc intronic sequence ATGC exonic sequenceGGAAGAGATAAAACAGCGGAAGAGAGAAGGATTGCTATATGCATTTTTGATGATGTAGCAGAACAATGCCGTGAAGCTGCCTTTAAgtaaggatacgcatccactggatcattttacatttgtaggtttccagttttagagttctgataagacaccttatatttgtttggcag
Basic information
species | Arabidopsis thaliana |
transcript | AT5G19820.1 |
intron # | 14 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G19820.1 (Arabidopsis thaliana), 5'ss of exon 14
lower sequence: LOC_Os03g49420.1 (Oryza sativa), 5'ss of exon 13
GGAAGAGATAAAACAGCGGAAGAGAGAAGGATTGCTATATGCATTTTTGATGATGTAGCAGAACAATGCCGTGAAGCTGCCTTTAAgtaa--ggatacgcatccactggatcattttacatttgtaggtttccagttttagagttctgataagacaccttatatttgtttggcag-------
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GCCAAGGACAAAACAGTAGAGGAACGAAGGATTGCCATATGCATTTTTGATGATGTTGCAGAGCACTGTCGCGAAGCAGCTGTCAGgtaacagtttaatgacccttttaaccttttta--ttggatgaaatgattcttctaacttttgatgaaacgtaatttgtatgatctgtggttctcag
upper sequence: AT5G19820.1 (Arabidopsis thaliana), 5'ss of exon 14
lower sequence: LOC_Os07g38760.1 (Oryza sativa), 5'ss of exon 14
GGAAGAGATAAAACAGCGGAAGAGAGAAGGATTGCTATATGCATTTTTGATGATGTAGCAGAACAATGCCGTGAAGCTGCCTTTAAgtaaggatacgcatccactggatcattttacatttgtaggtttccagttttagagttctgataagacaccttatatttgtttggcag
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GGAAAAGATAAGACTGCTGAAGAGAGAAGGATAGCTATCTGTATATTTGATGATATTGCAGAGCAATGTCGTGAATCTGCTCTCAAgta----tgttcctcaaagctatttggttggatgca-gggcttgta--tttgtaactgaattatgtattttcctatctgattag---
upper sequence: AT5G19820.1 (Arabidopsis thaliana), 5'ss of exon 14
lower sequence: GRMZM2G033619_T01 (Zea mays), 5'ss of exon 13
GGAAGAGATAAAACAGCGGAAGAGAGAAGGATTGCTATATGCATTTTTGATGATGTAGCAGAACAATGCCGTGAAGCTGCCTTTAAgtaa-ggatacgcatccactggat--cattttacatt-tgtaggtttccagttttagagttctgataagacaccttatatttgtttggcag-------------
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GGTAAGAATAAATCACCAGAAGAAAGAAGGATTGCCATATGCATTTTTGATGATGTTGCTGAGCATTGCCGTGAAGCAGCAGTTAGgtaacagttgtacgatccatacatgacactttgcttggtgaaggtgaaagattgttgtgagctgtgatcattttacatgtttttttgtgatatctgattgtcag
upper sequence: AT5G19820.1 (Arabidopsis thaliana), 5'ss of exon 14
lower sequence: GLYMA08G12120.1 (Glycine max), 5'ss of exon 14
GGAAGAGATAAAACAGCGGAAGAGAGAAGGATTGCTATATGCATTTTTGATGATGTAGCAGAACAATGCCGTGAAGCTGCCTTTAAgtaaggatacgc--atccactggatcattttacatttgtaggtttccagttttagagttctgataa-gacaccttatatttgtttggcag--------
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GGAAGGGACAAGACTCCTGAAGAGAGAAGAATTGCAATTTGTATTTTTGATGATGTTGCAGAGCAGTGTCGTGAAGCTGCTATTAAgtaagcactctttgttttgctaggttaccattttattgtgcagtgattattatgaaggcatgtcatcaacttcattcttttatataccaattgagcag
upper sequence: AT5G19820.1 (Arabidopsis thaliana), 5'ss of exon 14
lower sequence: GLYMA05G28950.1 (Glycine max), 5'ss of exon 16
GGAAGAGATAAAACAGCGGAAGAGAGAAGGATTGCTATATGCATTTTTGATGATGTAGCAGAACAATGCCGTGAAGCTGCCTTTAAgtaaggatacgc--atccactggatcattttacatttgtaggtttccagttttagagttctgataa-gacaccttatatttgtttggcag--------
||||| || || || | ||||||||||| ||||| || || |||||||||||||| ||||| || || ||||||||||| ||||||||| | | | || | | | | ||||| | | |||| || | || || | | ||| | | ||
GGAAGGGACAAGACTCCAGAAGAGAGAAGAATTGCAATTTGTATTTTTGATGATGTTGCAGAGCAGTGTCGTGAAGCTGCTGTTAAgtaagcactctttgtttttctaggttaccatttttttgtgcagtgataattttgaaggcattttatcaacttcattcttttatataccaattgagcag
upper sequence: AT5G19820.1 (Arabidopsis thaliana), 5'ss of exon 14
lower sequence: Vv06s0004g00500.t01 (Vitis vinifera), 5'ss of exon 14
GGAAGAGATAAAACAGCGGAAGAGAGAAGGATTGCTATATGCATTTTTGATGATGTAGCAGAACAATGCCGTGAAGCTGCCTTTAAgtaaggatacgcatccactgga---tcattttacatttgtaggtttccagttttagagttct----gataagac-accttatatttgtttggcag--
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GGCAAAGATAAAACAGCCGAAGAGAGAAGGATTGCAATCTGCATCTTTGATGATGTTGCAGAGCAATGTCGTGAAGCGGCTCTTAAgtaagtgaatatacccctaggacttttactttgtaattttgg--ttgcagttttggctgtttatgcgatgtaattgttctaaatgtggttggaacagMapped 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|125003620|gb|EL075889.1|EL075889EST: GCCGTGAAGCTGCCTTTTAA ATATTATGATACCTATCTTCCATTTGTACTGGAAGCTTGCAATGACGAGA
genomic: GCCGTGAAGCTGCC-TTTAAgtaaggatac ... tgtttggcagATATTATGATACCTATCTTCCATTTGTACTGGAAGCTTGCAATGACGAGA
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GGAAGAGATAAAACAGCGGAAGAGAGAAGGATTGCTATATGCATTTTTGATGATGTAGCAGAACAATGCCGTGAAGCTGCCTTTAAgtaaggatacgcatccactggatcattttacatttgtaggtttccagttttagagttctgataagacaccttatatttgtttggcag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC