Sequence
atgc intronic sequence ATGC exonic sequencegtttgtcactcaccactctttaccatacacggtagcaaaaccgagaaaagatggcttatgagatatagtgaaacattgtagaatcaattttctgagacgtatctccaagtaagtaaaatggtgattggttttgcagGCTATGTAACATGGATATCATATCACAAGTGCAACAAATCATTTGCTTTGCGTTTCATGATAGTAAGCTTCTCATGGAGACATGTCAAGAAGCTAGAAAT
Basic information
species | Arabidopsis thaliana |
transcript | AT3G59870.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G59870.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA17G00330.1 (Glycine max), 3'ss of exon 5
gtttgtcactcaccactctttaccatacacggtagcaaaaccgagaaaagatggcttatgagatatagtgaaacattgtagaatcaattttctgagacgtatctccaagtaagtaaaatggtgattggttttgcagGCTATGTAACATGGATATCATATCACAAGTGCAACAAATCATTTGCTTTGCGTTTCATGATAGTAAGCTTCTCATGGAGACATGTCAAGAAGCTAGAAAT
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-------------------------tgcaggcta-tattgttattattattttttttttgagaaa-gttatgttattactgggtaaagattg-gggagttatttttcctt--------ccattgtttcacatgcagGCTATGTAATATGGATATCATTTCGCACGTGCAGCAAGTCATTTGCTTTGCTTTCCATGATAGTAGGTTGCTCATGGAAACTTGTCAAGAAGCAAAAAAT
upper sequence: AT3G59870.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA07G40350.2 (Glycine max), 3'ss of exon 5
gtttgtcactcaccactctttaccatacacggtagcaaaaccgagaaaagatggcttatgagatatagtgaaacattgtagaatcaattttctgagacgtatctccaagtaagtaaaatggtgattggttttgcagGCTATGTAACATGGATATCATATCACAAGTGCAACAAATCATTTGCTTTGCGTTTCATGATAGTAAGCTTCTCATGGAGACATGTCAAGAAGCTAGAAAT
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------------------------atgcaggcta-tattattattattttttgttttgagaaagctatgttgttattgcagtaaagatt----gggccattattttttctt-------ccattgtttcacatgcagGCTATGTAATATGGATATCATTTCGCACGTGCAGCAAGTCATTTGCTTTGCTTTCCATGATAGTCGGTTGCTCATGGAAACTTGTCAAGAAGCAAAAAAT
upper sequence: AT3G59870.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv05s0094g01380.t01 (Vitis vinifera), 3'ss of exon 6
---------------------------------------------gtttgtcactcaccactctttaccataca-cggtagcaaaaccgagaaaagatggcttatga---gatatagtgaaacattgtagaatcaatt------ttctgagacgtatctccaagtaa--gtaaaatggtg-attggttttgcagGCTATGTAACATGGATATCATATCACAAGTGCAACAAATCATTTGCTTTGCGTTTCATGATAGTAAGCTTCTCATGGAGACATGTCAAGAAGCTAGAAAT
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gtttgtaatagcttcctaaagcattggtctttgagcagatgaagccttttaggcatactcttttttctagtacaacgatcatctgcctttttcatgttatttagtgatttgatttattttttctttttcatttttgttgctaaatgctaaaaggggttttaatctgatagtgcctttctgtgacaaaactgcagGCTATGTAATATGGACATCATTTCACATGTACAGCAAGTCATTTGCTTTGCTTTTCATGATAGCAAGCTTCTCATGGAAACATGCCAAGAGGCCAAAAAT
upper sequence: AT3G59870.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: PP1S323_60V6.1 (Physcomitrella patens), 3'ss of exon 5
gtttgtcactcaccactctttaccatacacggtagcaaaaccgagaaaagatggcttatgagatatagtgaaacattgtagaatcaattttctgagacgtatctccaagtaagtaaaatggtgattggttttgcagGCTATGTAACATGGATATCATATCACAAGTGCAACAAATCATTTGCTTTGCGTTTCATGATAGTAAGCTTCTCATGGAGACATGTCAAGAAGCTAGAAAT
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------------gtagtgtttattttctattttttcagtctctgga--------cttttcaattactatgaaata------actcgat---ggaagatgcatctttgactctgtg---cttcgatttgtat-gcagACTATGCAACATGGACATTATATCACATGTGCAACAAGTTATATGCTTTGCCTTTCATGATAGTAATTTACTCATGGAGACTTGTAGTGAAGCTAAAAAC
upper sequence: AT3G59870.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: PP1S134_28V6.1 (Physcomitrella patens), 3'ss of exon 5
-----gtttgtc-actcaccactctttaccatacacggtagcaaaaccgagaaaagatggcttatgagatata-gtga--aacattgtagaatcaattttctgagacgtatctccaagtaagtaaaatggtgattggttttgcagGCTATGTAACATGGATATCATATCACAAGTGCAACAAATCATTTGCTTTGCGTTTCATGATAGTAAGCTTCTCATGGAGACATGTCAAGAAGCTAGAAAT
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gtaatgtttccagattcttggtgttttattttgtgtgtgactatgctccagtggcacatacgcgagggatatgcacgattgatattgtttacttgactttgcaatgtgaatttgtgattaactgtgtggtatgatatgtttgcagACTGTGCAATATGGACATTGTAACACATGTGCAACAAGTTATCTGCTTTGCCTTTCATGATAGTAAGTTGCTCATGGAGACTTGTAGTGAAGCAAAAAATMapped 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|116389074|gb|EG431666.1|EG431666EST: GTGATAGAAAAGCCTCACAACGACCATTTACCGTTATTAGAAGCCAGCAG GCTATGTAACATGGATATCATATCACAAGTGCAACAAATCATTTGCTTTGC
genomic: GTGATAGAAAAGCCTCACAACGACCATTTACCGTTATTAGAAGCCAGCAGgtttgtcact ... ggttttgcagGCTATGTAACATGGATATCATATCACAAGTGCAACAAATCATTTGCTTTGC
EST:
gi|86076243|gb|DR372000.1|DR372000EST: GTGATAGAAAAGCCTCACAACGACCATTTACCGTTATTAGAAGCCAGCAG GCTATGTAACATGGATATCATATCACAAGTGCAACAAATCATTTGCTTTGC
genomic: GTGATAGAAAAGCCTCACAACGACCATTTACCGTTATTAGAAGCCAGCAGgtttgtcact ... ggttttgcagGCTATGTAACATGGATATCATATCACAAGTGCAACAAATCATTTGCTTTGC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aatcaattttctgagacgtatctccaagtaagtaaaatggtgattggttttgcagGCTATGTAACATGGATATCATATCACAAGTGCAACAAATCATTTGCTTTGCGTTTCATGATAGTAAGCTTCTCATGGAGACATGTCAAGAAGCTAGAAAT
taagtaaaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttgtcactcaccactctttaccatacacggtagcaaaaccgagaaaagatggcttatgagatatagtgaaacattgtagaatcaattttctgagacgtatctccaagtaagtaaaatggtgattggttttgcagGCTATGTAACATGGATATCATATCACAAGTGCAACAAATCATTTGCTTTGCGTTTCATGATAGTAAGCTTCTCATGGAGACATGTCAAGAAGCTAGAAAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC