Sequence
atgc intronic sequence ATGC exonic sequencegtactactccacgtttgatattcaaccttgctgttttcttgacacaatgggcctcttataacatttcaaatgtcaaacgaaaacagGAGCGCGAGAACCCGACATTGACAGACTGGGACCGTTTTGCACATAGAGAGTATATTCGGCTATCAATGGAAGAAGATGTTGAAGATGCATCCAATGGAA
Basic information
species | Arabidopsis thaliana |
transcript | AT5G28850.1 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G28850.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: LOC_Os10g33680.1 (Oryza sativa), 3'ss of exon 11
gtactactccacgtttgatattcaaccttgctgttttcttgacacaatgggcctcttataacatttcaaat-gtcaaacgaaaacagGAGCGCGAGAACCCGACATTGACAGACTGGGACCGTTTTGCACATAGAGAGTATATTCGGCTATCAATGGAAGAAGATGTTGAAGATGCATCCAATGGAA
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gtgatcacaacttcttgccataaagcagtgaattcactgttaatcatctaa------ataacaagttggatcatctttttatttcagGAACGTGAAAATCCAACTTTAACCGAGTGGGATCGGTTCGCACATAGAGAGTATATTAGATTGTCCATGGAAGAAGATGGTGAAGATGCTTCAAATGGAA
upper sequence: AT5G28850.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GRMZM2G148323_T01 (Zea mays), 3'ss of exon 11
gtactactccacgtttgatattcaaccttgctgttttcttgacacaatgggcctcttataacatttcaaatgtcaaacgaaaacagGAGCGCGAGAACCCGACATTGACAGACTGGGACCGTTTTGCACATAGAGAGTATATTCGGCTATCAATGGAAGAAGATGTTGAAGATGCATCCAATGGAA
| | | | || | ||| || || | | | | | |||| | | ||||| || |||| || || || || || | || || |||||||| |||||||||||||| |||||| | | || ||||||||||||| ||| ||||| || |||||||
--gtgattataatcct--taataaactttagatttgctgccaagtattaag--ttaaataat-tggctaatgtttaattg---tagGAACGTGAAAATCCAACTCTAACTGAGTGGGACCGGTTTGCACATAGAGAATATATTAGATTGTCCATGGAAGAAGATGGTGAGGATGCTTCAAATGGAA
upper sequence: AT5G28850.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA10G30930.1 (Glycine max), 3'ss of exon 11
------------------gtactactccacgtttgatattcaaccttgctgttttcttgacacaatgggcctctt--ataac-atttcaaatgtcaaacgaaaacagGAGCGCGAGAACCCGACATTGACAGACTGGGACCGTTTTGCACATAGAGAGTATATTCGGCTATCAATGGAAGAAGATGTTGAAGATGCATCCAATGGAA
| | | || | | | | || || | | | | || | ||| | || || | || |||| || |||||||| ||||||||||| ||||| || ||||| ||| |||| |||||| |||| ||||||||||||||||| |||||||| || |||||||
gtgcatgaaatatttgataaaatttattgcattcttgagttagtatgtatgcttggctactgttagtgacttccttggtaattggtatgcatatcttgtgtgaatagGAACGTGAGAACCCAACATTGACAGAGTGGGATCGATTTGCTCATCGAGAATATATTAGGCTTTCAATGGAAGAAGATGTAGAAGATGCCTCTAATGGAA
upper sequence: AT5G28850.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA03G41180.1 (Glycine max), 3'ss of exon 11
--gtactactccacgtttgatattcaaccttgctgttttcttgacacaatgggc--ctcttataacatttcaa------------atgtcaaacgaaaacagGAGCGCGAGAACCCGACATTGACAGACTGGGACCGTTTTGCACATAGAGAGTATATTCGGCTATCAATGGAAGAAGATGTTGAAGATGCATCCAATGGAA
| | | | | | | | | ||||||| | | || | | | || | ||| | ||||| | ||||||| || ||||| || ||||||||||| ||||| || ||||| |||||||| |||||| |||| || |||||||||||||| || ||||| || || || |
gtgcatgaatatttgataaaagtgttattgtgctgttgagtcagtatgattgactattgttggtaagttttgactgccttggtatatgtcttgtgtgaacagGAACGTGAGAATCCTACATTGACAGAGTGGGATCGCTTTGCTCATAGAGAATATATTAGGCTTTCTATGGAAGAAGATGTAGAGGATGCCTCTAACGGTA
upper sequence: AT5G28850.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA20G36530.1 (Glycine max), 3'ss of exon 11
------------------gtactactccacgtttgatattcaaccttgctgttttcttgacacaatgggcctctt--ataac-atttcaaatgtcaaacgaaaacagGAGCGCGAGAACCCGACATTGACAGACTGGGACCGTTTTGCACATAGAGAGTATATTCGGCTATCAATGGAAGAAGATGTTGAAGATGCATCCAATGGAA
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gtgcatgaaatatttgataaaatttattgcattgttgagttagtatttatgcttggctactgttagtgacttccttggtaattggtatgcatgtcttgtgggaatagGAACGTGAGAACCCAACATTGACAGAGTGGGATCGATTTGCTCATCGAGAATATATTAGGCTTTCAATGGAAGAAGACATAGAAGATGCCTCTAACGGAAMapped 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|125075211|gb|EL138861.1|EL138861EST: TAAACAAATTTATGGCATTTGAAACCCGGGATCCGTTCCTCATTCGTCAG GAGCGCGAGAACCCGACATTGACAGACTGGGACCGTTTTG
genomic: TAAACAAATTTATGGCATTTGAAACCCGGGATCCGTTCCTCATTCGTCAGgtactactcc ... acgaaaacagGAGCGCGAGAACCCGACATTGACAGACTGGGACCGTTTTG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgttttcttgacacaatgggcctcttataacatttcaaatgtcaaacgaaaacagGAGCGCGAGAACCCGACATTGACAGACTGGGACCGTTTTGCACATAGAGAGTATATTCGGCTATCAATGGAAGAAGATGTTGAAGATGCATCCAATGGAA
ttataac putative branch site (score: 2)
ttataacatttcaaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtactactccacgtttgatattcaaccttgctgttttcttgacacaatgggcctcttataacatttcaaatgtcaaacgaaaacagGAGCGCGAGAACCCGACATTGACAGACTGGGACCGTTTTGCACATAGAGAGTATATTCGGCTATCAATGGAAGAAGATGTTGAAGATGCATCCAATGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG