Sequence
atgc intronic sequence ATGC exonic sequencegtaagtccaaaactcataccctctctgttgctcccccaatatatttgttacatatatcttatcagctctaccatcaatttgaagaaagttgcaaaacactggttaaattatattgtatcttgttttccctgttattacttttcgttactgatactctcttcatgttcttgttggaagTCGGTGCTTATCCGAATGTGCAGAATTTATTTGGAGAACTTGGGATCAATGATCGGTTGCAGTGGAAGGAACACTCCATGATTTTTGCTATGCCAAGTAA
Basic information
species | Arabidopsis thaliana |
transcript | AT4G14210.2 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G14210.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os03g08570.1 (Oryza sativa), 3'ss of exon 5
gtaagtccaaaactcataccctctctgttgctcccccaatatatttgttacatatatcttatcagctctaccatcaatttgaagaaagttgcaaaacactggttaaattatattgtatcttgttttccctgttattacttttcgttactgatactctcttcatgttcttgttggaagTCGGTGCTTATCCGAATGTGCAGAATTTATTTGGAGAACTTGGGATCAATGATCGGTTGCAGTGGAAGGAACACTCCATGATTTTTGCTATGCCAAGTAA
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------------------------------------------------------------------ttttccttccatgctcacactgttttgt--cgtccacaacagtacat-atgtgacattgttcattttgtgcctgtatgtaacca--------tatacctttttggtttaagTTGGAGCTTATCCCAACATACAGAACTTGTTTGGCGAGCTTGGTATTAATGATCGGTTGCAATGGAAGGAACACTCCATGATATTTGCCATGCCAAACAA
upper sequence: AT4G14210.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA11G36810.1 (Glycine max), 3'ss of exon 4
gtaagtccaaaactcataccctctctgttgctcccccaatatatttgttacatatatcttatcagctctaccatcaatttgaagaaagttgcaaaacactggttaaattatattgtatcttgttttccctgttattacttttcgttactgatactctcttcatgttcttgttggaagTCGGTGCTTATCCGAATGTGCAGAATTTATTTGGAGAACTTGGGATCAATGATCGGTTGCAGTGGAAGGAACACTCCATGATTTTTGCTATGCCAAGTAA
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-----------------------------------------------------------tattggacatcatatta-tttaatcaa---tacagatct----tttaattat-tagaatccttattttgtagttat--ctttgctttaca---actttttccccctccccac----agTTGGGGCTTACCCTAATGTACAGAACTTATTTGGAGAACTTGGCATTAATGATCGGTTACAATGGAAGGAGCATTCTATGATTTTTGCTATGCCAAATAA
upper sequence: AT4G14210.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA18G00720.1 (Glycine max), 3'ss of exon 4
gtaagtccaaaactcataccctctctgttgctcccccaatatatttgttacatatatcttatcagctctaccatcaatttgaagaaagttgcaaaacactggttaaattatattgtatcttgttttccctgttattacttttcgttactgatactctcttcatgttcttgttggaagTCGGTGCTTATCCGAATGTGCAGAATTTATTTGGAGAACTTGGGATCAATGATCGGTTGCAGTGGAAGGAACACTCCATGATTTTTGCTATGCCAAGTAA
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-----------------------------------------------------------tattggaaatcatatta-tttaatcaa---tacagatct----ttcaattat-cggaatccttatgttgcagttat--ctttgctttaca---actttttccccctccccac----agTTGGGGCTTACCCTAATGTGCAGAACCTTTTTGGAGAACTTGGCATTAATGATCGGTTACAATGGAAAGAGCATTCTATGATTTTTGCTATGCCAAATAA
upper sequence: AT4G14210.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv09s0002g00100.t01 (Vitis vinifera), 3'ss of exon 5
gtaagtccaaaactcataccctctctgttgctcccccaatatatttgttacatatatcttatcagctctaccatcaatttgaagaaagttgcaaaacactggttaaattatattgtatcttgttttccctgttattacttttcgttactgatactctcttcatgttcttgttggaagTCGGTGCTTATCCGAATGTGCAGAATTTATTTGGAGAACTTGGGATCAATGATCGGTTGCAGTGGAAGGAACACTCCATGATTTTTGCTATGCCAAGTAA
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-----------------------------------------------------------------atccacc-ctatcctgataca----tcatcatgtctgtaaga--attttttacctaattcttaatctgattcttggtaa--aataataatttgtttgctctcctttt---agTTGGGGCTTACCCAAATGTGCAGAACCTGTTTGGAGAACTTGGTATTAATGATCGGTTGCAGTGGAAGGAACATTCTATGATATTTGCAAAGCCAAGCAA
upper sequence: AT4G14210.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: EFJ10018 (Selaginella moellendorffii), 3'ss of exon 4
gtaagtccaaaactcataccctctctgttgctcccccaatatatttgttacatatatcttatcagctctaccatcaatttgaagaaagttgcaaaacactggttaaattatattgtatcttgttttccctgttattacttttcgttactgatactctcttcatgttcttgttggaagTCGGTGCTTATCCGAATGTGCAGAATTTATTTGGAGAACTTGGGATCAATGATCGGTTGCAGTGGAAGGAACACTCCATGATTTTTGCTATGCCAAGTAA
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---------------------------------------------------------------------------------------------------------------------------gtgagtttctgatacttccgattttaagtttctaatccctgcttacgtttccagTCGGAGCATATCCCAACGTGCAAAACTTGTTTGGAGAACTTGGCATCAATGATAGGCTGCAGTGGAAGGAGCACAGCATGATCTTTGCAAGGCCCGATAA
upper sequence: AT4G14210.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: EFJ23885 (Selaginella moellendorffii), 3'ss of exon 5
gtaagtccaaaactcataccctctctgttgctcccccaatatatttgttacatatatcttatcagctctaccatcaatttgaagaaagttgcaaaacactggttaaattatattgtatcttgttttccctgttattacttttcgttactgatactctcttcatgttcttgttggaagTCGGTGCTTATCCGAATGTGCAGAATTTATTTGGAGAACTTGGGATCAATGATCGGTTGCAGTGGAAGGAACACTCCATGATTTTTGCTATGCCAAGTAA
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---------------------------------------------------------------------------------------------------------------------------gtgagtttctgatacttccgattctaagcttctaatccctgcttacgtttccagTCGGAGCATATCCCAACGTGCAAAACTTGTTTGGAGAGCTTGGTATCAATGACAGGCTGCAGTGGAAGGAGCACAGCATGATCTTTGCAAGGCCCGATAAMapped 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|116473796|gb|EG516388.1|EG516388EST: ATGGAAGGATGAAGATGGGGACTGGTATGAGACTGGTTTACATATTTTCT TCGGTGCTTATCCGAATGTGCAGAATTTATTTGGAGAACTTGGGATCAATG
genomic: ATGGAAGGATGAAGATGGGGACTGGTATGAGACTGGTTTACATATTTTCTgtaagtccaa ... ttgttggaagTCGGTGCTTATCCGAATGTGCAGAATTTATTTGGAGAACTTGGGATCAATG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttccctgttattacttttcgttactgatactctcttcatgttcttgttggaagTCGGTGCTTATCCGAATGTGCAGAATTTATTTGGAGAACTTGGGATCAATGATCGGTTGCAGTGGAAGGAACACTCCATGATTTTTGCTATGCCAAGTAA
tactgat putative branch site (score: 2)
ctctcttcatgttctt CT-rich tract
ttattactttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtccaaaactcataccctctctgttgctcccccaatatatttgttacatatatcttatcagctctaccatcaatttgaagaaagttgcaaaacactggttaaattatattgtatcttgttttccctgttattacttttcgttactgatactctcttcatgttcttgttggaagTCGGTGCTTATCCGAATGTGCAGAATTTATTTGGAGAACTTGGGATCAATGATCGGTTGCAGTGGAAGGAACACTCCATGATTTTTGCTATGCCAAGTAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
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