Sequence
atgc intronic sequence ATGC exonic sequencegtgtgtctgtgttagttttttttcgcttatgttttcatgctggtgattgtattttttctctctaagattgtagacatttcgattttgttttgcagGCTATAGCTGCCATGGCCTGGGGGACAGATTCTTGTCCAAAGGTTGAGAAGATTTTTGGTCCTGGGAACCAGTATGTCACAGCTGCTAAGATGATTCTTC
Basic information
species | Arabidopsis thaliana |
transcript | AT5G63890.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G63890.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G058584_T01 (Zea mays), 3'ss of exon 10
gtgtgtctgtgttagttttttttcgcttatgttttcatgctggtgattgtattttttctctctaagattgtagacatttcgattttgttttgcagGCTATAGCTGCCATGGCCTGGGGGACAGATTCTTGTCCAAAGGTTGAGAAGATTTTTGGTCCTGGGAACCAGTATGTCACAGCTGCTAAGATGATTCTTC--
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-------------------------------tcaccaagttctacagcatttttttatgatttcctgt-attggctgtgcactctcattcaacca--cataacttttgctaacttcattacaatgtcca---tacagGCTGAGAAGATTTTTGGACCTGGTAACCAGTATGTAACAGCTGCCAAAATGATTCTTCAG
upper sequence: AT5G63890.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA09G02960.1 (Glycine max), 3'ss of exon 8
gtgtgtctgtgttagttttttttcgcttatgttttcatgctggtgattgtattttttct-ctctaagattgtagacat-ttcgattttgttttgcagGCTATAGCTGCCATGGCCTGGGGGACAGATTCTTGTCCAAAGGTTGAGAAGATTTTTGGTCCTGGGAACCAGTATGTCACAGCTGCTAAGATGATTCTTC--
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--------------------------ttgtgattaaaccgtacttaagatgtaacttcaacaagaaaacttcatacttatttgatcattttt----aattttaattg---tgaatttgtgatgaaactagt------agGTTGAAAAGATTTTTGGCCCTGGAAACCAATATGTCACTGCTGCAAAAATGATACTTCAA
upper sequence: AT5G63890.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA15G13910.1 (Glycine max), 3'ss of exon 8
gtgtgtctgtgttagttttttttcgcttatgttttcatgctggtgattgtattttttctctctaagattgtagacatttcgattttgttttgcagGCTATAGCTGCCATGGCCTGGGGGACAG-ATTCTTGTCCAAAGGTTGAGAAGATTTTTGGTCCTGGGAACCAGTATGTCACAGCTGCTAAGATGATTCTTC--
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--------------------------------------tcttgtgaatgaatcgtacttaagatgtaacttcaacaaaaccttcatacttagttgatcatttttaatttaaattgtgaatttgtggtgaaacttgtagGTTGAAAAGATTTTTGGCCCTGGAAACCAATATGTCACTGCTGCAAAAATGATACTTCAA
upper sequence: AT5G63890.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA08G08630.1 (Glycine max), 3'ss of exon 7
gtgtgtctgtgttagttttttttcgcttatgttttcatgctggtgattgtattttttctctcta-agattgtagacatttcgattttgttttgcagGCTATAGCTGCCATGGCCTGGGGGACAGATTCTTGTCCAAAGGTTGAGAAGATTTTTGGTCCTGGGAACCAGTATGTCACAGCTGCTAAGATGATTCTTC--
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--------------------------acatagtgacataacattatttgaaatttaggttaacataaaatttaaatacttca---tagttcttaaattttttgc-ataatttcttgtaatac----ttttgt----agGTTGAGAAAATTTTTGGCCCAGGAAACCAATATGTCACAGCTGCAAAAATGATACTACAA
upper sequence: AT5G63890.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv18s0166g00300.t01 (Vitis vinifera), 3'ss of exon 10
gtgtgtctgtgttagttttttttcgcttatgttttcatgctggtgattgtattttttctctctaagattgtagacatttcgattttgttttgcagGCTATAGCTGCCATGGCCTGGGGGACAGATTCTTG-TCCAAAGGTTGAGAAGATTTTTGGTCCTGGGAACCAGTATGTCACAGCTGCTAAGATGATTCTTC--
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--------------------------------------ctttgagttacttcatcaaagatgtagtattttaattagttttgcttggctgcatcagaaatgacatccagttctaagtgtatttagtcataatttgcagGTGGAAAAGATTTTTGGCCCTGGAAATCAGTATGTCACGGCTGCAAAAATGATTCTCCAAMapped 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|124955145|gb|EL030181.1|EL030181EST: GCGCCAAGAGGGCTGGTGTTACTCACATACTCAAAGCTGGTGGAGCGCAG GCTATAGCTGCCATGGCCTGGGGGGACAGATT
genomic: GCGCCAAGAGGGCTGGTGTTACTCACATACTCAAAGCTGGTGGAGCGCAGgtgtgtctgt ... tgttttgcagGCTATAGCTGCCATGGCCTGGGGG-ACAGATT
EST:
gi|124730155|gb|EH821557.1|EH821557EST: GCGCCAAGAGGGCTGGTGTTACTCACATACTCAAAGCTGGTGGAGCGCAG GCTATAGCTGCCATGGCC
genomic: GCGCCAAGAGGGCTGGTGTTACTCACATACTCAAAGCTGGTGGAGCGCAGgtgtgtctgt ... tgttttgcagGCTATAGCTGCCATGGCC
EST:
gi|125011540|gb|EL083809.1|EL083809EST: GCGCCAAGAGGGCTGGTGTTACTCACATACTCAAAGCTGGTGGAGCGCAG GCTATAGCTGCCATGGCCTGGGGGAC
genomic: GCGCCAAGAGGGCTGGTGTTACTCACATACTCAAAGCTGGTGGAGCGCAGgtgtgtctgt ... tgttttgcagGCTATAGCTGCCATGGCCTGGGGGAC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tggtgattgtattttttctctctaagattgtagacatttcgattttgttttgcagGCTATAGCTGCCATGGCCTGGGGGACAGATTCTTGTCCAAAGGTTGAGAAGATTTTTGGTCCTGGGAACCAGTATGTCACAGCTGCTAAGATGATTCTTC
ttttgtttt CT-rich tract
attgtattttttct 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgtgtctgtgttagttttttttcgcttatgttttcatgctggtgattgtattttttctctctaagattgtagacatttcgattttgttttgcagGCTATAGCTGCCATGGCCTGGGGGACAGATTCTTGTCCAAAGGTTGAGAAGATTTTTGGTCCTGGGAACCAGTATGTCACAGCTGCTAAGATGATTCTTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG