Sequence
atgc intronic sequence ATGC exonic sequencegtgagtattgagcctcttttaccttagtttcatcagtaaattgttaacatgcggttattgaattgtgtattattactttttgaagGTCACTTCAAGGAAACAGATTGACGGGTAGAATTCCAGAAGTTATTGGTCTAATGCAGGCTCTTGCTGTTTT
Basic information
species | Arabidopsis thaliana |
transcript | AT5G62230.2 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G62230.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: LOC_Os06g03970.1 (Oryza sativa), 3'ss of exon 9
--------------------------------gtgagtattgagcctcttttaccttagtttcatcagtaaattgttaacatgcggt-tattgaattgtgtattattactttttgaagGTCACTTCAAGGAAACAGATTGACGGGTAGAATTCCAGAAGTTATTGGTCTAATGCAGGCTCTTGCTGTTTT
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gtaagtgttcctgagttattgcaaatcctctaacatgtaatctgctgtttcactcttatgcatatagatgctttacttacagcctttatgttgaaccattt-ctattcatgttcatagGTCACTTCAAGGAAATAGACTGACTGGGAAAATTCCAGATGTGATTGGCCTGATGCAAGCTCTTGCTGTTCT
upper sequence: AT5G62230.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GRMZM2G082855_T03 (Zea mays), 3'ss of exon 9
----------gtga-gtattgagc-ctcttttaccttag-----tttcatcagtaaattgttaacatgcggttatt-gaattgtgtatt--attact-ttttgaagGTCACTTCAAGGAAACAGATTGACGGGTAGAATTCCAGAAGTTATTGGTCTAATGCAGGCTCTTGCTGTTTT
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gtaagtcttcctgatgtcttgaattcttctttaattcagcagacttgtgtactcatatatgtaccatgccgttctttgttttgatcattgcattgttgttttacagGTCACTTCAAGGAAATAGACTGATTGGCAAAATTCCTGAAGTGATTGGCCTCATGCAGGCTCTTGCTGTCCT
upper sequence: AT5G62230.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA20G29010.1 (Glycine max), 3'ss of exon 7
------------------------------------------------------------gtgagtattgagcctcttttaccttagtttcatcagtaaattgttaacatgcggttattgaattgtgtattattactttt-tgaagGTCACTTCAAGGAAACAGATTGACGGGTAGAATTCCAGAAGTTATTGGTCTAATGCAGGCTCTTGCTGTTTT
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gtacgtatactttgactgaagttattttaattatggcactactgtgaatcacttttgtttgacaatggtggactggtgggggggtcatgtcatattgaaaggataagtatatttatgatcaattat-cactgcaatttctgcctagGTCACTTCAAGGAAATAGATTAACTGGGGAGATTCCAGAAGTGATTGGTTTAATGCAAGCCCTTGCAATATT
upper sequence: AT5G62230.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: Vv16s0022g02030.t01 (Vitis vinifera), 3'ss of exon 9
-----------------------------------gtgagtattgagcctcttttaccttagtttcatcagtaa--attgttaacatgcggttattgaattgtgt---------attattactttttgaa---gGTCACTTCAAGGAAACAGATTGACGGGTAGAATTCCAGAAGTTATTGGTCTAATGCAGGCTCTTGCTGTTTT
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gtaagctttctagtttagatcattcttttggaaactggacaaatgaaagttatttacttggggaagagcattgatcaatgttgtgaaatgattggtgacatgatttaagataaaactcttggttctttaatcagGTCACTCCAAGGAAATAAGCTAACAGGAAAGATTCCAGAGGTGATTGGTCTAATGCAAGCCCTTGCTGTTTTMapped 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|86063079|gb|DR358836.1|DR358836EST: ATAACAGGAGAGATTCCTTACAATATCGGCTTCCTCCAAGTTGCTACTCT GTCACTTCAAGGAAACAGATTGACGGGTAGAATTCCAGAAGTTATTGGTCT
genomic: ATAACAGGAGAGATTCCTTACAATATCGGCTTCCTCCAAGTTGCTACTCTgtgagtattg ... ctttttgaagGTCACTTCAAGGAAACAGATTGACGGGTAGAATTCCAGAAGTTATTGGTCT
EST:
gi|86063083|gb|DR358840.1|DR358840EST: ATAACAGGAGAGATTCCTTACAATATCGGCTTCCTCCAAGTTGCTACTCT GTCACTTCAAGGAAACAGATTGACGGGTAGAAATTCCAGAAGTTATTGGTC
genomic: ATAACAGGAGAGATTCCTTACAATATCGGCTTCCTCCAAGTTGCTACTCTgtgagtattg ... ctttttgaagGTCACTTCAAGGAAACAGATTGACGGGTAGAA-TTCCAGAAGTTATTGGTC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.catcagtaaattgttaacatgcggttattgaattgtgtattattactttttgaagGTCACTTCAAGGAAACAGATTGACGGGTAGAATTCCAGAAGTTATTGGTCTAATGCAGGCTCTTGCTGTTTT
tgttaac putative branch site (score: 2)
ttacttttt putative PPT
ttattgaattgtgtat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagtattgagcctcttttaccttagtttcatcagtaaattgttaacatgcggttattgaattgtgtattattactttttgaagGTCACTTCAAGGAAACAGATTGACGGGTAGAATTCCAGAAGTTATTGGTCTAATGCAGGCTCTTGCTGTTTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT