Sequence
atgc intronic sequence ATGC exonic sequence...ttaatcaatcaagtctataagcatcatcagcatctcagtctgtcttatttgactggtagaaaacacatctcatgtgaatcttgttgaatattttctacagGAACCGGTGATCCCAGGATGCTTTCTTCGGGCCAAAGCTATTGGTCTGATGCCAATGATTGATCAG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G53620.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G53620.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA13G19500.2 (Glycine max), 3'ss of exon 5
ttaatcaatcaagtctataagcatcatcagcatctcagtctgtcttatttga--ctggtagaaaacacatctcatgtgaatctt--gttgaatatt-ttctacagGAACCGGTGATCCCAGGATGCTTTCTTCGGGCCAAAGCTATTGGTCTGATGCCAATGATTGATCAG
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---atc--tttagtatattaattaattaatctattaagtacgttttgttttatgcttttactgtttttttgtgatgctaacccttggtcgtacttggttggacagGAGCCAGTTCTTCCGGGTTGCTTTCTTCGGGCCAAAGCTATTGGTCTCATGCCTATGATTGATCAG
upper sequence: AT3G53620.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA19G35710.1 (Glycine max), 3'ss of exon 7
-----ttaatcaatcaagtctataagcatcatcagcatctcagtctgtcttatttgactggtagaaaacacatctcatgtgaatcttgttgaatattttctacagGAACCGGTGATCCCAGGATGCTTTCTTCGGGCCAAAGCTATTGGTCTGATGCCAATGATTGATCAG
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tggatcttgtcgttgtcgtctt--agtattaaatctgtcttaatttatgttatgtatgttttgtaaattgtaag--attcaaaacttaactcatacttga-acagGAGCCGGTTCTTCCAGGTTGCTTTCTTCGGGCCAAAGCAATTGGTCTCATGCCCATGATTGATCAG
upper sequence: AT3G53620.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA03G33000.4 (Glycine max), 3'ss of exon 7
ttaatcaatcaagtctataagcatcatc--agcatctcagtctgtcttatttgactggtagaaaacacatctcatgtgaatcttgttgaatattttctacagGAACCGGTGATCCCAGGATGCTTTCTTCGGGCCAAAGCTATTGGTCTGATGCCAATGATTGATCAG
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acaatta-tggatcttattattatcatcttagtattaaatttttcttaatttatgttatgtatgcttcgtaagattcaaaactttactcatacttga-acagGAGCCGGTTCTTCCAGGTTGCTTTCTTCGGGCCAAAGCAATTGGTCTCATGCCCATGATTGATCAG
upper sequence: AT3G53620.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA10G05130.1 (Glycine max), 3'ss of exon 5
ttaatcaatcaagtctataagcat--catcagcatctcag-tctgtcttatttgac-tggtagaaaacacatctcatgtgaatcttgttgaatattttct---acagGAACCGGTGATCCCAGGATGCTTTCTTCGGGCCAAAGCTATTGGTCTGATGCCAATGATTGATCAG
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-------attatcttcagtagtatgttattaatctattaggtacttcttgttttatgtttttagtgttttgtgtgatgctaacccttcgtcttacttggttggacagGAGCCAGTTCTTCCAGGTTGCTTTCTACGGGCCAAAGCTATTGGACTCATGCCTATGATTGATCAG
upper sequence: AT3G53620.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv08s0040g02470.t01 (Vitis vinifera), 3'ss of exon 5
-------ttaatcaatcaagtctataagcatcatcagcatctcagtctgtcttatttgactggtagaaaacacatctcatgtgaatcttgttgaatattttctacagGAACCGGTGATCCCAGGATGCTTTCTTCGGGCCAAAGCTATTGGTCTGATGCCAATGATTGATCAG
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aattttttggatgtgcttggtttctgaatat--tccatattacaaagcaatggttataaatggaaactctcatattccttatgg--cttttcaaacattt---acagGAACCAGTTCTTCCAGGATGCTTTCTCCGGGCTAAAGCTATTGGTCTCATGCCTATGATTGATCAGMapped 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|125160838|gb|EL188236.1|EL188236EST: GTACCCTTTGTGAGGACAGTGACCCTATTGATGTTCTTGTCATTATGCNG GA-CCGGTGATCCCAGGATGCTTTCTTCGGGCCAAA
genomic: GTACCCTTTGTGAGGACAGTGACCCTATTGATGTTCTTGTCATTATGCAGgtaacatatt ... ttttctacagGAACCGGTGATCCCAGGATGCTTTCTTCGGGCCAAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatttgactggtagaaaacacatctcatgtgaatcttgttgaatattttctacagGAACCGGTGATCCCAGGATGCTTTCTTCGGGCCAAAGCTATTGGTCTGATGCCAATGATTGATCAG
atttgac putative branch site (score: 4)
tattttct putative PPT
ttgttgaatatttt 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 |
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ttaatcaatcaagtctataagcatcatcagcatctcagtctgtcttatttgactggtagaaaacacatctcatgtgaatcttgttgaatattttctacagGAACCGGTGATCCCAGGATGCTTTCTTCGGGCCAAAGCTATTGGTCTGATGCCAATGATTGATCAG
- - -caatcaa
- - - - - - - - - - - - - - - catctca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaacaca