Sequence
atgc intronic sequence ATGC exonic sequence...ttttggtgtggatcagttaaactgggttaggaccactgccttatctatcagcattcagcacctaaaaccaaaagttgtttacaattgtggattttggcagACTCGGTTCATTGACTTTCAAGAAACCAGACAATGTGAAATACCCATCCATGGATCTTGCTTATGCTGCTGGACGAGCTGGAGGCACAATGACTGGAGTT
Basic information
species | Arabidopsis thaliana |
transcript | AT5G62790.1 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G62790.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: LOC_Os01g01710.2 (Oryza sativa), 3'ss of exon 9
ttttggtgtggat-cagttaaactgggttaggac-cactgccttatctatcagcattcagcacctaaaaccaaaagttgtttacaattgtggattttggcagACTCGGTTCATTGACTTTCAAGAAACCAGACAATGTGAAATACCCATCCATGGATCTTGCTTATGCTGCTGGACGAGCTGGAGGCACAATGACTGGAGTT
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aaaagaactagatgcaacaaaaaattgttaagttatagtacttaaccgtgaagaccttttttcattgcacgaagggttaatttttaatttgataat--gcagGCTGGGTTCACTGACATTCAAAGCTCCTGACAATGTGAAATACCCGTCGATGGATCTCGCCTATGCAGCTGGAAGAGCTGGGGGCACCATGACAGGAGTT
upper sequence: AT5G62790.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA17G09740.1 (Glycine max), 3'ss of exon 10
-------------------------------------------------------------------------------------ttttggtgtggatcagttaaactgggttaggaccactgccttatctatcagc---attcag--cacctaaaaccaaaagttgtttacaatt---gtggattttggcagACTCGGTTCATTGACTTTCAAGAAACCAGACAATGTGAAATACCCATCCATGGATCTTGCTTATGCTGCTGGACGAGCTGGAGGCACAATGACTGGAGTT
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gtactatattctttccctgcagcttactaatttcaactctatcaaattctatcttcagtccataccaaagaaaatagacagatccagttgatatagagttttcaaatt---ttgaagcctttatgttgaatgaaaattttatctagtccaatttgaattatcgatggttcttatttgaggtgtgattatccagGATTGGTTCACTTACATTTAAAACTCCAGATAATGTAAAGTATCCATCCATGAATCTTGCCTATGCTGCTGGCCGTGCTGGAGGCACAATGACAGGAGTT
upper sequence: AT5G62790.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA05G02190.1 (Glycine max), 3'ss of exon 10
-------------------------------------------------------------------------------------ttttggtgtggatcagttaaactgggttaggaccactgccttatctat-cagcattcag--cacctaaaaccaaaagttgtttacaattg---tggattttggcagACTCGGTTCATTGACTTTCAAGAAACCAGACAATGTGAAATACCCATCCATGGATCTTGCTTATGCTGCTGGACGAGCTGGAGGCACAATGACTGGAGTT
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gtactgtaatctttccctgcagcttactaatttcaactctatcaaattctattttcagtccattctaaagaaaatagacagatccagttgatatagagttttcaaatttgga-agcatttatgttaaatgaaaattttattcaacccaatttgaattattgatggttcttatttgaaatgtggttatgcagGCTTGGTTCACTTACATTTAAAACTCCAGATAATGTAAAGTATCCATCCATGAATCTTGCATTTTCTGCTGGCCGTGCTGGAGGCACAATGACAGGAGTT
upper sequence: AT5G62790.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: Vv17s0000g08390.t01 (Vitis vinifera), 3'ss of exon 10
ttttggtgtggatcagttaaactgggttaggaccactgccttatctatcagcattcagcacctaaaaccaaaagttgtttacaattg---tggattttggcagACTCGGTTCATTGACTTTCAAGAAACCAGACAATGTGAAATACCCATCCATGGATCTTGCTTATGCTGCTGGACGAGCTGGAGGCACAATGACTGGAGTT
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tttccagattaaacaataaatatggtgtgaaaataatgaaa-acttgcaatcagtttattagtttgcttgaca--tgattgaaattggaatggaatggtgcagGCTTGGGTCACTGACATTTAAAACTCCTGACAATGTGAAATATCCATCCATGGATCTTGCCTATGCTGCTGGACGGGCTGGAGGCACCATGACAGGAGTTMapped 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|124898039|gb|EH974253.1|EH974253EST: TAGAGTTCCTTGTTCTGAAGTAACTTGGCCAAGACTTGAAACCTTTGCAA ACTCGGTTCATTGACTTTCAAGAAA
genomic: TAGAGTTCCTTGTTCTGAAGTAACTTGGCCAAGACTTGA--CCTTTGCAAgtaagctaac ... attttggcagACTCGGTTCATTGACTTTCAAGAAA
EST:
gi|86084256|gb|DR380015.1|DR380015EST: GATAGAGTTCCTTGTTCTGAAGTAACTTGGCCAAGACTTGACCTTTGCAA ACTCGGTTCATTGACTTTCAAGAAACCAGACAATGTGAAATACCCATCCAT
genomic: GATAGAGTTCCTTGTTCTGAAGTAACTTGGCCAAGACTTGACCTTTGCAAgtaagctaac ... attttggcagACTCGGTTCATTGACTTTCAAGAAACCAGACAATGTGAAATACCCATCCAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatcagcattcagcacctaaaaccaaaagttgtttacaattgtggattttggcagACTCGGTTCATTGACTTTCAAGAAACCAGACAATGTGAAATACCCATCCATGGATCTTGCTTATGCTGCTGGACGAGCTGGAGGCACAATGACTGGAGTT
acctaaa putative branch site (score: 3)
tttacaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttttggtgtggatcagttaaactgggttaggaccactgccttatctatcagcattcagcacctaaaaccaaaagttgtttacaattgtggattttggcagACTCGGTTCATTGACTTTCAAGAAACCAGACAATGTGAAATACCCATCCATGGATCTTGCTTATGCTGCTGGACGAGCTGGAGGCACAATGACTGGAGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG