Sequence
atgc intronic sequence ATGC exonic sequenceACCTGGCACAGAATCGGTATTTTGAAGATGAAGCATTTATTGGATACTTGAAGTATCTTCAATACTGGCAGCGACCAGAGTACATCAAGTTCATTATgtaagttggaatatcttatggaattggtgtagtcttgtagagtcttgtgaaggtttggataatatatctttggtttcctatgttcttgttacag
Basic information
species | Arabidopsis thaliana |
transcript | AT5G19910.1 |
intron # | 3 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G19910.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: LOC_Os10g41450.1 (Oryza sativa), 5'ss of exon 3
ACCTGGCACAGAATCGGTATTTTGAAGATGAAGCATTTATTGGATACTTGAAGTATCTTCAATACTGGCAGCGACCAGAGTACATCAAGTTCATTATgtaagttggaatatcttatggaattggtgtagtcttgtagagtcttgtgaaggtttggataatatatctttggtttccta--tgttcttgttacag
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ATCTAGCACAGAATAGGTACTTTGAGGATGAGGCATTTATCGGGTATCTCAAGTATCTCAAATACTGGCAGCGTCCGGAGTACATCAAATACATAATgtgagtggccgtataatttagatctgtttg---ctagtaggtgcttgc------tgtgacaaaatagcttggtcacactggttgttgtttgtgtag
upper sequence: AT5G19910.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GRMZM2G139683_T03 (Zea mays), 5'ss of exon 3
ACCTGGCACAGAATCGGTATTTTGAAGATGAAGCATTTATTGGATACTTGAAGTATCTTCAATACTGGCAGCGACCAGAGTACATCAAGTTCATTATgtaagttggaatatcttatggaattggtgtagtcttgtagagtcttgtgaaggtttggataatatatctttggtttcctatgttcttgttacag
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ATCTAGCGCAGAATAGATATTTCGAGGATGAGGCATTTATCGGGTACCTCAAGTATCTAAAATACTGGCAGCGACCAGAGTATATCAAATACATAATgtgagt---gataccatattca------gtggtttt------ttctgcaacagaggaaatggcttgctcattgtttt---tgctgatgatgcag
upper sequence: AT5G19910.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA20G28990.1 (Glycine max), 5'ss of exon 3
ACCTGGCACAGAATCGGTATTTTGAAGATGAAGCATTTATTGGATACTTGAAGTATCTTCAATACTGGCAGCGACCAGAGTACATCAAGTTCATTATgtaagttggaatatcttatggaat-tggtgtagt-cttgtagagtcttgtgaaggtttggataatatatctt---tggtttcctatgttcttgttacag-
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ATTTGGCTCAGAATCGATACTTTGAGGATGAAGCATTCATTGGATACTTAAAGTATCTTCAATATTGGCAACGCCCTGAATATATTAAATTTATTATgtaagccttttcttcaaattaggtattatgtaatacaattatactccggcactgagttatttcaattaggttaaaaggattaaaaaatttagactaggga
upper sequence: AT5G19910.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA10G38750.2 (Glycine max), 5'ss of exon 4
ACCTGGCACAGAATCGGTATTTTGAAGATGAAGCATTTATTGGATACTTGAAGTATCTTCAATACTGGCAGCGACCAGAGTACATCAAGTTCATTATgtaagttggaatatcttatggaattggtgtagtcttgtagagtcttgtgaaggtttggataatatatctttggtt------tcctatgttcttgttacag----
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ATTTGGCCCAAAATCGATACTTTGAGGATGAAGCATTCATTGGATACTTAAAGTATCTTCAATATTGGCAACGCCCTGAATATATTAAATTTATTATgtaagcc----ttttcttcaaattaggtattatggaatactattctatctggcactgagtaatttcaattagggtaaaggattaaaaatttaggctagggatac
upper sequence: AT5G19910.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: Vv16s0039g02760.t01 (Vitis vinifera), 5'ss of exon 4
ACCTGGCACAGAATCGGTATTTTGAAGATGAAGCATTTATTGGATACTTGAAGTATCTTCAATACTGGCAGCGACCAGAGTACATCAAGTTCATTATgtaagttggaatatcttatggaattg---gtgtagtcttgtagagtct-tgtgaaggtttggataatata----tctttggtttcctatgttcttgttacag----------------------------------------------------------------------------------
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ATTTGGCTCAAAATCGCTATTTTGAAGATGAAGCTTTCATTGGCTACTTGAAATACCTTCAATATTGGCAACAACCAGAGTACATAAAATTCATAATgtaagc--aactctcttagagtcatgctcatctaataatgttatgcccatgttaaggtcatagcagcctaggaatcattgttctcctaccttctcttcttaccaaagcgtgtaacctttctgtgctttattttttatttttcattttcaagaatttgtattctcatggtgtggaatgattccagMapped 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|86059929|gb|DR355686.1|DR355686EST: TTGAAGTATCTTCAATACTGGCAGCGACCAGAGTACATCAATTTCATTAT GTACCCACACTGCCTATATTTCCTTGAACTTCTTCAAAACCCCAACTTCAG
genomic: TTGAAGTATCTTCAATACTGGCAGCGACCAGAGTACATCAAGTTCATTATgtaagttgga ... cttgttacagGTACCCACACTGCCTATATTTCCTTGAACTTCTTCAAAACCCCAACTTCAG
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ACCTGGCACAGAATCGGTATTTTGAAGATGAAGCATTTATTGGATACTTGAAGTATCTTCAATACTGGCAGCGACCAGAGTACATCAAGTTCATTATgtaagttggaatatcttatggaattggtgtagtcttgtagagtcttgtgaaggtttggataatatatctttggtttcctatgttcttgttacag
- - - - - - - - - - - - - - - - - - - - - - - TTGAAG