Sequence
atgc intronic sequence ATGC exonic sequencegtaagatccatctttttcctttcagatatctatattcagtctcattatttcctttttttgtcgcaatgtgattattcccttgcttaatcttgtgtttcctgatatgtgggatattagGAAGCAAAATGTGGTATCTATGGTGCAAATTCTCCTGAGTGGATTATCAGCATGGAG
Basic information
species | Arabidopsis thaliana |
transcript | AT4G23850.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G23850.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os01g46750.2 (Oryza sativa), 3'ss of exon 3
----------------------------------------------------------------------gtaagatccatctttttcctttcagatatctatattcagtct-----cattatttcctttttttgtcgcaatgtgattattcccttgcttaatcttgtgttt-cctgatatgtgggatattagGAAGCAAAATGTGGTATCTATGGTGCAAATTCTCCTGAGTGGATTATCAGCATGGAG
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gtttggtcaataatttattatattttctatatatatgtcatgagatgggatgctaatttctttgaacattgtta-attgaattaaacattgtatgaactttttgttcagcttggaagcaacactttgatgtattcttatatcttgattaaagaatcataccatctcattttaatttgataattt---tgcagGGAAGCCGT-TGTGGTATCTATGGTGCTAATTGTCCTGAATGGATTATCACGATGGAG
upper sequence: AT4G23850.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G002614_T01 (Zea mays), 3'ss of exon 3
----------------------------------------------------------gtaagatccatcttt-ttcctttcagatatctatattcagtctcattatttcctttttttgtcgcaatgtgat-tattcccttgcttaatcttg--tgtttcctgatatgtgggatattagGAAGCAA--AATGTGGTATCTATGGTGCAAATTCTCCTGAGTGGATTATCAGCATGGAG
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gtttggtcactgttcttattgctctgctattttgtttgccacaaacttacttacctgagcaagttgtttttttacttctcacttggaagaacactgggaacttttggtcaccttatgcacattagtttgatgcactggtgcatctcttgctgactaaatttcaatatg-gcaattttgcagGGTAGTCGTTGTGGTATCTATGGTGCTAATTGTCCTGAATGGATTATCACAATGGAG
upper sequence: AT4G23850.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA11G02030.1 (Glycine max), 3'ss of exon 3
gtaagatccatctttttcctttcagatatct-atattca-gtctcattatttcctttttttgtcgcaatgtgattattcccttgcttaatcttgtgtttcctgatatgtgggatattagGAAGCAAAATGTGGTATCTATGGTGCAAATTCTCCTGAGTGGATTATCAGCATGGAG
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---------attttatatgattttgatatttcatatttgcatatgattatatttatagtttctagcaatttgttcatttca--gcttaattcatatattgctgatttgcagGGTGT--------AAAATGTGGTATTTATGGTGCCAATTCTGCAGAATGGATTATGAGCATGCAG
upper sequence: AT4G23850.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv02s0025g01410.t01 (Vitis vinifera), 3'ss of exon 3
gtaagatccatctttttcctt-tcagatatctatattcagtctcattatttcctttttttgtcgcaatgtgattattcccttgcttaatcttgtgtttcctgatatgtgggatattagGAAGCAAAATGTGGTATCTATGGTGCAAATTCTCCTGAGTGGATTATCAGCATGGAG
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-------ttttcttcttcttggttggagatct-tcctcattgagagtattttcttcgt--gtcaaattctatgtat---cttgcttatagatatattaactgct-----ggcttttagGGAGGACGATGTGGTATCTATGGTGCTAATTCTGCTGAGTGGATCATGAGCATGGAGMapped 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|164184807|gb|ES179082.1|ES179082EST: ACATTGTCATGAAACTTGGAAATTCTCTCAGAAGTGTTGGAGTTAAGGAC GAAGCAAAATGTGGTATCTATGGTGCAAATTTCCTCCTGAGTGGATTA
genomic: ACATTGTCATGAAACTTGGAAATTCTCTCAGAAGTGTTGGAGTTAAGGACgtaagatcca ... gggatattagGAAGCAAAATGTGGTATCTATGGTGCAAATT-C-TCCTGAGTGGATTA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gcaatgtgattattcccttgcttaatcttgtgtttcctgatatgtgggatattagGAAGCAAAATGTGGTATCTATGGTGCAAATTCTCCTGAGTGGATTATCAGCATGGAG
tcctgat putative branch site (score: 3)
tgattatt 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
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gtaagatccatctttttcctttcagatatctatattcagtctcattatttcctttttttgtcgcaatgtgattattcccttgcttaatcttgtgtttcctgatatgtgggatattagGAAGCAAAATGTGGTATCTATGGTGCAAATTCTCCTGAGTGGATTATCAGCATGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA