Sequence
atgc intronic sequence ATGC exonic sequencegtatgttttccttgtacttcactgtggactggccagataatgtttttccgctttaaggttgatacccatttttcggctaaatatttcctttttcgtattttagGTACTAATCATGGACAAACTTACTGTCAAGATAATGTCGTACGCCTGCAAAATGGCTGATATCACACAAGAAGGAGTTTCAT
Basic information
species | Arabidopsis thaliana |
transcript | AT1G12360.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G12360.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G012942_T01 (Zea mays), 3'ss of exon 2
gtatgttttccttgtacttcactgtggactggccagataatgtttttccgctttaaggttgatacccatttttcggctaaatatttcctttttcgtattttagGTACTAATCATGGACAAACTTACTGTCAAGATAATGTCGTACGCCTGCAAAATGGCTGATATCACACAAGAAGGAGTTTCAT
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-------------gta-ttcttggcgaatgga--ggaagatgttcttctagtttcaaatgt---tccattttcatgcacataaaattgtgtcatgaatttcagGTTCTAATCATGGACAAACTTACTGTCAAGATAATGTCATTTTCATGCAAGATGGCAGATATCACAGAAGAAGGGGTTTCAT
upper sequence: AT1G12360.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA05G03970.1 (Glycine max), 3'ss of exon 3
gtatgttttccttgtacttcactgtggactgg---ccagataatgtttttccgctttaag-gttgatacccatttttcggctaaatatttcctttttcgtattttagGTACTAATCATGGACAAACTTACTGTCAAGATAATGTCGTACGCCTGCAAAATGGCTGATATCACACAAGAAGGAGTTTCAT
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--ttctttttcaagaaatctgctagagcttgaaatctagtaaaaacattgatacttcaattgtttatcatcttgtattggttcatgagctgcttgcctgca-----gGTACTAATAATGGACAAACTTACTGTAAAGATAATGTCTCATTCTTGCAAGATGGCTGATATCACTGATGAAGGCGTTTCAT
upper sequence: AT1G12360.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA17G14450.1 (Glycine max), 3'ss of exon 2
gtatgttttccttgtacttcactgtggactgg---ccagataatgtttttccgctttaag-gttgatacccatttttcggctaaatatttcctttttcgtattttagGTACTAATCATGGACAAACTTACTGTCAAGATAATGTCGTACGCCTGCAAAATGGCTGATATCACACAAGAAGGAGTTTCAT
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--ttctttttcaagaaatcagctagagcttgaaatctagtaaaattgttgatacttcaattgtttatcatcttgtattggttcatgagctgcttgcctgca-----gGTACTCATAATGGACAAACTTACTGTGAAGATAATGTCTCATTCTTGCAAGATGGCTGATATCACTGATGAAGGTGTTTCAT
upper sequence: AT1G12360.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA11G03230.1 (Glycine max), 3'ss of exon 2
gtatgttttccttgtacttcactgtggactgg----ccagataatgtttttccgctttaaggttgatacccatttttcggctaaatatttcctttttcgtattttagGTACTAATCATGGACAAACTTACTGTCAAGATAATGTCGTACGCCTGCAAAATGGCTGATATCACACAAGAAGGAGTTTCAT
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tgaagtattgaaggtgaattaaag-aaactaaagtaccaagtaaaagttgaaaattcaatgattaccatct-tatactggttcatgggttgcttgcctgca-----gGTATTAATAATGGATAAACTTACTGTGAAGATAATGTCTCACTCATGCAAGATGACTGATATCACTGATGAAGGTGTTTCATMapped 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|152034146|gb|BP868618.2|BP868618EST: ATGAGATGCTTAGATCTGCAAAGACAGGGAGCTCAAAATCCACCTGGAAG GTACTAATCATGGACAAACTTACTGTCAAGATAATGTCGTACGCCTGCAAA
genomic: ATGAGATGCTTAGATCTGCAAAGACAGGGAGCTCAAAATCCACCTGGAAGgtatgttttc ... cgtattttagGTACTAATCATGGACAAACTTACTGTCAAGATAATGTCGTACGCCTGCAAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cgctttaaggttgatacccatttttcggctaaatatttcctttttcgtattttagGTACTAATCATGGACAAACTTACTGTCAAGATAATGTCGTACGCCTGCAAAATGGCTGATATCACACAAGAAGGAGTTTCAT
ggctaaa putative branch site (score: 3)
tttcctttttcgtatt putative PPT
taaatatttccttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgttttccttgtacttcactgtggactggccagataatgtttttccgctttaaggttgatacccatttttcggctaaatatttcctttttcgtattttagGTACTAATCATGGACAAACTTACTGTCAAGATAATGTCGTACGCCTGCAAAATGGCTGATATCACACAAGAAGGAGTTTCAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG