Sequence
atgc intronic sequence ATGC exonic sequencegcaagcatatttaaactaagctttgtgatattcttggatatggaactgcagatgtggttctgctcgtatagtttccactaatatcctatgctaccttttattgtttcagATAAGTTTCCAGGAGTTCAAAAACAAGCTACTCGAGCCTGGTTTAGTTGACCACATAGATGTTTCAAACAAATCAGTAGCAAAAGTCTACGTGAGGAGCA
Basic information
species | Arabidopsis thaliana |
transcript | AT2G29080.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G29080.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os05g38400.2 (Oryza sativa), 3'ss of exon 4
gcaagcatatttaaactaagctttgtgatattcttggatatggaactgcagatgtggttctgctcgtatagtttccactaatatcctatgctaccttttattgtttcagATAAGTTTCCAGGAGTTCAAAAACAAGCTACTCGAGCCTGGTTTAGTTGACCACATAGATGTTTCAAACAAATCAGTAGCAAAAGTCTACGTGAGGAGCA
||| | | | | | || || || | || | | | | | || || | || || | |||| | ||| | |||||||| |||||||| ||||| || |||||||| || |||||||||||||||| ||| | ||||||||| |||||||| ||||| ||||| || |||||
-----tgattttgtggttgcatatttattctttttaaatctatgg-tgaacaattattctcgatcttaaatggaatctcaagatattttgct---tcaaatttctgcagATAAGCTTCCAGGAATTCAAGAATAAGCTACTAGAACCTGGTTTAGTTGACCGCATTGTTGTTTCAAATAAATCAGTGGCAAAGGTCTATGTCAGGAGTT
upper sequence: AT2G29080.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os01g62500.1 (Oryza sativa), 3'ss of exon 4
gcaagcatatttaaactaagctttgtgatattcttggatatggaactgcagatgtggttctgctcgtatagtttccactaatatcctatgctaccttttattgttt-cagATAAGTTTCCAGGAGTTCAAAAACAAGCTACTCGAGCCTGGTTTAGTTGACCACATAGATGTTTCAAACAAATCAGTAGCAAAAGTCTACGTGAGGAGCA
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-------cacttcagttc--cctaccagtttctttttctgtgcgac-acatacattcatttcctagtccattataacttgtgatacccacttaattgtaattcttttcagATAAGCTTCCAAGAATTCAAGAATAAGTTGTTGGAACCTGGTTTAGTTGACCACATTGTTGTTTCAAACAAGTCAATTGCTAAGGTTTACGTCAGGAGTT
upper sequence: AT2G29080.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G038401_T01 (Zea mays), 3'ss of exon 4
gcaagcatatttaaactaagctttgtgatattcttggatatggaactgcagatgtggttctgctcgtatagtttccactaatatcctatgctaccttttattgtttcagATAAGTTTCCAGGAGTTCAAAAACAAGCTACTCGAGCCTGGTTTAGTTGACCACATAGATGTTTCAAACAAATCAGTAGCAAAAGTCTACGTGAGGAGCA
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----gcaaagaaggactgc-ttgcatagcagtcgttgcccc----ttctaagtgtgcgtactatagtataatggttcgttataatgtcttttgtatcaaacatctgcagATAAGCTTCCAAGAGTTCAAGAACAAGTTACTAGAACCTGGTTTAGTTGATCGCATTGTTGTTTCAAATAAATCAGTAGCGAAGGTCTACATCAGGAGTT
upper sequence: AT2G29080.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv06s0004g05030.t01 (Vitis vinifera), 3'ss of exon 4
gcaagcatattta-aactaagctttgtgatattcttggatatggaactgcagatgtggttctgctcgtatagtttccactaatatcctatgctaccttttattgtttcagATAAGTTTCCAGGAGTTCAAAAACAAGCTACTCGAGCCTGGTTTAGTTGACCACATAGATGTTTCAAACAAATCAGTAGCAAAAGTCTACGTGAGGAGCA
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----atatgttgatgacttgtgcctgcca-gtcatttcattt----tttccaatttgcctgtctacatatgatttagctttttaatgttggtttctgaatat-gttgcagATTAGTTTCCAAGAGTTTAAAAACAAGCTTCTGGAACCAGGTTTGGTGGACCACATAGTTGTTTCTAATAAATCAGTTGCAAAGGTGTATGTAAGGGGCT
upper sequence: AT2G29080.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: EFJ17143 (Selaginella moellendorffii), 3'ss of exon 3
gcaagcatatttaaactaagctttgtgatattcttggatatggaactgcagatgtggttctgctcgtatagtttccactaatatcctatgctaccttttattgtttcagATAAGTTTCCAGGAGTTCAAAAACAAGCTACTCGAGCCTGGTTTAGTTGACCACATAGATGTTTCAAACAAATCAGTAGCAAAAGTCTACGTGAGGAGCA
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---------------------------------------gtaaagtttcgattgc--tttcagtcataagga------aaatgttctaactatcaacacttcgcagCAGATCAGCTTCCAGGAGTTCAAAAACAAGCTTCTGGAGACTGGTCTCGTTGATCACATAGAGGTTGTGAATAAGGCGGTCGCAAGAGTATATGTTCGCG---Mapped 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|116477683|gb|EG520275.1|EG520275EST: TTGCTGTATTCTTTTCTACTTTCTCGTTTGGCTCTGGGGAACAACAACAG ATAAGTTTCCAGGAGTTCAAAAACAAGCTACTCGAGCCTGGTTTAGTTGAC
genomic: TTGCTGTATTCTTTTCTACTTTCTCGTTTGGCTCTGGGGAACAACAACAGgcaagcatat ... attgtttcagATAAGTTTCCAGGAGTTCAAAAACAAGCTACTCGAGCCTGGTTTAGTTGAC
EST:
gi|47830890|gb|CK120574.1|CK120574EST: TTGCTGTATTCTTTTCTACTTTCTCGTTTGGCTCTGGGGAACAACAACAG ATAAGTTTCCAGGAGTTCAAAAACAAGCTACTCGAGCCTGGTTTAGTTGAC
genomic: TTGCTGTATTCTTTTCTACTTTCTCGTTTGGCTCTGGGGAACAACAACAGgcaagcatat ... attgtttcagATAAGTTTCCAGGAGTTCAAAAACAAGCTACTCGAGCCTGGTTTAGTTGAC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tggttctgctcgtatagtttccactaatatcctatgctaccttttattgtttcagATAAGTTTCCAGGAGTTCAAAAACAAGCTACTCGAGCCTGGTTTAGTTGACCACATAGATGTTTCAAACAAATCAGTAGCAAAAGTCTACGTGAGGAGCA
cactaat putative branch site (score: 2)
ccttttattgtttc putative PPT
ttttattgttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gcaagcatatttaaactaagctttgtgatattcttggatatggaactgcagatgtggttctgctcgtatagtttccactaatatcctatgctaccttttattgtttcagATAAGTTTCCAGGAGTTCAAAAACAAGCTACTCGAGCCTGGTTTAGTTGACCACATAGATGTTTCAAACAAATCAGTAGCAAAAGTCTACGTGAGGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA