Sequence
atgc intronic sequence ATGC exonic sequencegtaaataattatgctcaactctccagtgtattctttgaattgatttatgtttatctctcgctaacttcctgactctttcttctcatgttaccgtatataattgaagATACGAGTCTCTGGAGTTCTATCAAATGCTCCTTATCTTCTAAATGTCGATTGTGATCACTACATCAATAATAGCAAAGCTCTTAGAGAAGCAATGTGTT
Basic information
species | Arabidopsis thaliana |
transcript | AT5G09870.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G09870.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA05G32100.1 (Glycine max), 3'ss of exon 9
gtaaataattatgctcaactctccagtgtattctttgaattgatttatgtttatctctcgctaacttcc--tgactctttcttctcatgttaccgtatataattgaagATACGAGTCTCTGGAGTTCTATCAAATGCTCCTTATCTTCTAAATGTCGATTGTGATCACTACATCAATAATAGCAAAGCTCTTAGAGAAGCAATGTGTT
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----gtaagtat---caattcacttttat----tttggttcagcttcagatgatgttccattgaccttaaataacttgtttttgtaatgatattaaatatg--tgaagGTGCGGGCATCAGCAATTATCACAAATGCACCGTATCTTCTGAATGTTGATTGTGATCACTACATTAACAATAGCAAGGCACTTAGAGAAGCTATGTGTT
upper sequence: AT5G09870.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA08G15380.1 (Glycine max), 3'ss of exon 9
gtaaataattatgctcaactctccagtgtatt-ctttgaattgatttatgtttatctctcgctaacttc--ctgactctttcttctcatgttaccgtatataattgaagATACGAGTCTCTGGAGTTCTATCAAATGCTCCTTATCTTCTAAATGTCGATTGTGATCACTACATCAATAATAGCAAAGCTCTTAGAGAAGCAATGTGTT
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----------gtaagcatcaattcactttattattttggttcaggttcagctgattttccattgaccttaaataacttgtttttgtaatgatattaaatatg--tgaagGTACGGGCTTCAGCAATTATCACTAATGCACCCTATCTTCTGAATGTTGATTGTGATCACTACATTAACAATAGCAAGGCACTTAGAGAAGCTATGTGTT
upper sequence: AT5G09870.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: Vv07s0031g02060.t01 (Vitis vinifera), 3'ss of exon 9
-----------------------------------------------gtaaataattatgctcaactctc-----cagtgtattctttgaatt-gatttatgtttatctctcgctaacttcctgactctttcttctcatgttaccgtatataattgaagATACGAGTCTCTGGAGTTCTATCAAATGCTCCTTATCTTCTAAATGTCGATTGTGATCACTACATCAATAATAGCAAAGCTCTTAGAGAAGCAATGTGTT
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gtaaaccttaaatcaataacaccttcatagatcctttttctttggttgcctttccttgtcttctgtttttacttttagtataatacctggtttcgatgaataaacacttggcacagaatttattgagctttgttgctgtttttatgaat---atccaagGTGCGAGTTTCAGCAGTCATTTCAAATGCCCCGTATCTTCTGAACGTTGACTGTGACCATTATATCAACAATAGCAAGGCACTTAGAGAAGCTATGTGTTMapped 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|116455074|gb|EG497666.1|EG497666EST: AGAGACCCGGATTTGACCATCACAAGAAGGCTGGAGCCATGAACTCCCTG ATACGAGTCTCTGGAGTTCTATCAAATGCTCCTTATCTTCTAAATGTCGAT
genomic: AGAGACCCGGATTTGACCATCACAAGAAGGCTGGAGCCATGAACTCCCTGgtaaataatt ... ataattgaagATACGAGTCTCTGGAGTTCTATCAAATGCTCCTTATCTTCTAAATGTCGAT
EST:
gi|125229761|gb|EL243846.1|EL243846EST: TTGACCATCACAAGAAGGCTGGAGCCATGAACTCCCTG ATACGAGTCTCTGGAGTTCTATCAAATGCTCCTTATCTTCTAAATGTCGAT
genomic: TTGACCATCACAAGAAGGCTGGAGCCATGAACTCCCTGgtaaataatt ... ataattgaagATACGAGTCTCTGGAGTTCTATCAAATGCTCCTTATCTTCTAAATGTCGAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatctctcgctaacttcctgactctttcttctcatgttaccgtatataattgaagATACGAGTCTCTGGAGTTCTATCAAATGCTCCTTATCTTCTAAATGTCGATTGTGATCACTACATCAATAATAGCAAAGCTCTTAGAGAAGCAATGTGTT
tcctgac putative branch site (score: 2)
tatataattgaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaataattatgctcaactctccagtgtattctttgaattgatttatgtttatctctcgctaacttcctgactctttcttctcatgttaccgtatataattgaagATACGAGTCTCTGGAGTTCTATCAAATGCTCCTTATCTTCTAAATGTCGATTGTGATCACTACATCAATAATAGCAAAGCTCTTAGAGAAGCAATGTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA