Sequence
atgc intronic sequence ATGC exonic sequenceCTATGCAGAGATTGATTGTCCAGTCTCAGCTCCAGAAAATTTTCCAAAAGATGATGAGCTTCATTTTGAGATTGAGTTGTTGGATTTTTCTAAAGCCAAGgcgagatctcatcactaaccaagataacagtgcattagttagccgaaagactctgaaattttgcatttcatctgttttgacttatgctttcctttcctttgtgttaatttccag
Basic information
species | Arabidopsis thaliana |
transcript | AT3G54010.1 |
intron # | 5 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G54010.2 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: LOC_Os03g25140.1 (Oryza sativa), 5'ss of exon 5
CTATGCAGAGATTGATTGTCCAGTCTCAGCTCCAGAAAATTTTCCAAAAGATGATGAGCTTCATTTTGAGATTGAGTTGTTGGATTTTTCTAAAGCCAAGgcgagatctcatcactaaccaagataacagtgcattagttagccgaaagactctgaaattttgcatttcatctgttttgacttatgctttcctttcctttgtgttaatttccag---
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CTATGCAGAGGAGGATTGTCCAGTTACAGCTCCTGACGGCTTTCCAAAAGATGATGAACTTCAATTTGAGATTGAGATGTTGGATTTCTTCAAAGCCAAAgttag-tcttgttg--------aataatgg--cttcagtgtgacttaaatccttaaattgctgtatat------ttgagagctattctgtgcaagctgttaggacaaattctcatga
upper sequence: AT3G54010.2 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: AC216247.3_FGT005 (Zea mays), 5'ss of exon 5
CTATGCAGAGATTGATTGTCCAGTCTCAGCTCCAGAAAATTTTCCAAAAGATGATGAGCTTCATTTTGAGATTGAGTTGTTGGATTTTTCTAAAGCCAAGgcgagatctcatcactaaccaagataacagtg-cattagttagccgaaagactctgaaattttgcatttcatctgttttgacttat-gctttcctttcctttgtgttaatttccag
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CTACGCTGAGGTTGATTGTCCAGTTGCAGCTCCAGATGGCTTCCCGAAAGATGATGAACTTCAATTTGAGATTGAAATGTTGGATTTCTTTAAAGCCAAGgtta-atctcatta-----------aatggtgacttgagtatgacttcaga-tatatatttcattactttcagagaactggcaaacagtttacatgtctattttaacaatttt---
upper sequence: AT3G54010.2 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GRMZM2G117746_T01 (Zea mays), 5'ss of exon 5
CTATGCAGAGATTGATTGTCCAGTCTCAGCTCCAGAAAATTTTCCAAAAGATGATGAGCTTCATTTTGAGATTGAGTTGTTGGATTTTTCTAAAGCCAAGgcgagatctcatcactaaccaagataacagtgcattagttagccgaaagactctgaaattttgcatttcatctgttttgacttatgctttcctttcctttgtgttaatttccag
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CTACGCTGAGGACGATTGTCCAGTTGCAACTCCAGATGGCTTTCCGAAGGATGATGAACTTCAATTTGAGATTGAAATGTTGGATTTCTTTAAAGCCAAGgtta-atctcatta--aatgatgactagagtatggct-tcaactgatgtatatttca--ttgatgtcagagaacttctggtccttg-tctgtttttttttaaaatat-------
upper sequence: AT3G54010.2 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: Vv08s0007g01460.t01 (Vitis vinifera), 5'ss of exon 6
CTATGCAGAGATTGATTGTCCAGTCTCAGCTCCAGAAAATTTTCCAAAAGATGATGAGCTTCATTTTGAGATTGAGTTGTTGGATTTTTCTAAAGCCAAGgcgagatctcatcactaaccaagataacagtgcattagttagccgaaagactctgaaattttgcatttcatctgttttgacttatgctt---tcctttcctttgtgttaatttccag
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CTATGGTGAGGCTAATTGTCCTCTTATGGTTCCTGATAATTTTCCGAAGGATGATGAGCTTCATTTTGAGATTGAGATGTTGGACTTCTTTAAAGTCAAGgcaagaaagagtttctatct---ttatctagacttt--------gatatgatatcaaattcctccccctacatgat--gacttatgttaaaattccttggcatattttaaatt----Mapped 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|124943486|gb|EL019664.1|EL019664EST: TGATGAGCTTTCATTTTGAGATTGAGTTGTTGGATTTTTCTAAAGCCAAG ATTGCAAGTGATGATCTGGGGGTCATCAAGAAG
genomic: TGATGAGC-TTCATTTTGAGATTGAGTTGTTGGATTTTTCTAAAGCCAAGgcgagatctc ... taatttccagATTGCAAGTGATGATCTGGGGGTCATCAAGAAG
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
CTATGCAGAGATTGATTGTCCAGTCTCAGCTCCAGAAAATTTTCCAAAAGATGATGAGCTTCATTTTGAGATTGAGTTGTTGGATTTTTCTAAAGCCAAGgcgagatctcatcactaaccaagataacagtgcattagttagccgaaagactctgaaattttgcatttcatctgttttgacttatgctttcctttcctttgtgttaatttccag
- - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT