Sequence
atgc intronic sequence ATGC exonic sequence...aatcatatcacaaattttaattatgcttttcctgttgacttcatgtgctgagctgttctcgatttatgtaaaacttggcaaacatgtttggtgaatgcagAATTCAAGATTCCTTCAGTTTGTTTCCAAGATGAGCCGTGGTGAACTTATTATTGATGAGAATCAGGTCAAGCAAGCTTCAGCCCCCGGGGAATGGGCTA
Basic information
species | Arabidopsis thaliana |
transcript | AT5G56290.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G56290.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os08g39080.1 (Oryza sativa), 3'ss of exon 6
--------aatcatatcacaaattttaattatgcttttcctgttgacttcatgtgctgagctgttctcgatttatgtaaaacttggcaaacatgtttggtgaatgcagAATTCAAGATTCCTTCAGTTTGTTTCCAAGATGAGCCGTGGTGAACTTATTATTGATGAGAATCAGGTCAAGCAAGCTTCAGC-CCCCGGGGAATGGGCTA
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taccttttgtttcttttttggaagaactctaaattcttccagtttgtttcaaagattc-gccgtggtgaacttattct---tttgttttacttttttctggaa----gAACTCTAAGTTCTTCCAGTTTGTTTCAAAGATGAGCCGTGGTGAACTTATTATAGAAGATAATCAAGTAAAACAAGGTTCAGCATCCCAATCCAGTGGCT-
upper sequence: AT5G56290.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G115855_T01 (Zea mays), 3'ss of exon 6
aatcatatcaca-aattttaattatgcttttcctgttgacttcatgtg--ctgagctgttctcgatttatgtaaaact-tggcaaacatgtttggtgaatgcagAATTCAAGATTCCTTCAGTTTGTTTCCAAGATGAGCCGTGGTGAACTTATTATTGATGAGAATCAGGTCAAGCAAGCTTCAGC-CCCCGGGGAATGGGCTA
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-tttgtaagactcaatgccaaccagccttat---gttaaccataggtcatctggatcatcctctttaaggacctgacaataccattttttttctttttgaaaagAATTCTAAGTTCTTCCAGTTTGTTTCAAAGATGAGCCGGGGTGAACTTATTATAGAAGATAATCAGGTAAAAGAAGGTTTAGCATCCCAATCCAGTGGCT-
upper sequence: AT5G56290.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G080775_T01 (Zea mays), 3'ss of exon 6
aatcatatcacaaattttaattatgcttttcctgttgacttcatgt---gctgagctgttctcgat--ttatgtaaa-acttggcaa-acatgtttggtgaat-----gcagAATTCAAGATTCCTTCAGTTTGTTTCCAAGATGAGCCGTGGTGAACTTATTATTGATGAGAATCAGGTCAAGCAAGCTTCAGC-CCCCGGGGAATGGGCTA
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------------attttttaggactccatgtcagccagccttaggttaaccataggtaatctggatcatcctgtaaggacctgacaatatctctttttttctttttgggaagAATTCTAAGTTCTTCCAGTTTGTTTCAAAGATGAGCCGAGGTGAACTTATTATAGAAGATAATCAAGTAAAAGAAGGTTCAGCATCCCAATCCAGTGGCT-
upper sequence: AT5G56290.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv19s0015g01940.t01 (Vitis vinifera), 3'ss of exon 6
------aatcatatcacaaattttaattatgcttttcctgttgacttcatgtgctgagctgttctcgatttatgtaaaacttggcaaacatgtttggtgaatgcagAATTCAAGATTCCTTCAGTTTGTTTCCAAGATGAGCCGTGGTGAACTTATTATTGATGAGAATCAGGTCAAGCAAGCTTCAGCCCCCGGGGAATGGGCTA
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tttactagtc-tatcatataatcct-ttgtctttttatttattttttatttttttcagttgtctctagttta---aaaattcattttaaat-tttgggacttgcagAATTCAAAGTTTCTCCAATTTGTGTCAAAGATGAGTCGAGGTGAACTTATCATTGATGATAATCAAGTCAAGCCAGGTGCATCATCTTCATCTGGGGATTMapped 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|125190662|gb|EL205616.1|EL205616EST: CGTAAGCTTGCCCATACACTATCTCAAGATGGGAATCCGAAATTTCAG AATTCAAGATTCCTTCAGTTTGTTTCCAAGATGAGCCGGGGTGAACTTATT
genomic: CGTAAGCTTGCCCATACACTATCTCAAGATGGGAATCCGAAATTTCAGgtcagtataa ... gtgaatgcagAATTCAAGATTCCTTCAGTTTGTTTCCAAGATGAGCCGTGGTGAACTTATT
EST:
gi|125116945|gb|EL166284.1|EL166284EST: CTCGTAAGCTTGCCCATACACTATCTCAAGATGGGAATCCGAAATTTCAG AATTCAAGATTCCTTCAGTTTGTTTCCAAGATGAGCCGTGGTGAA
genomic: CTCGTAAGCTTGCCCATACACTATCTCAAGATGGGAATCCGAAATTTCAGgtcagtataa ... gtgaatgcagAATTCAAGATTCCTTCAGTTTGTTTCCAAGATGAGCCGTGGTGAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgctgagctgttctcgatttatgtaaaacttggcaaacatgtttggtgaatgcagAATTCAAGATTCCTTCAGTTTGTTTCCAAGATGAGCCGTGGTGAACTTATTATTGATGAGAATCAGGTCAAGCAAGCTTCAGCCCCCGGGGAATGGGCTA
atttatgtaaaactt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aatcatatcacaaattttaattatgcttttcctgttgacttcatgtgctgagctgttctcgatttatgtaaaacttggcaaacatgtttggtgaatgcagAATTCAAGATTCCTTCAGTTTGTTTCCAAGATGAGCCGTGGTGAACTTATTATTGATGAGAATCAGGTCAAGCAAGCTTCAGCCCCCGGGGAATGGGCTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
aatcata
- - - -tcacaaa
- - - - - - - - - - - - -cttttcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtaaaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caaacat