Sequence
atgc intronic sequence ATGC exonic sequenceCTTATCGGAAGCTCGCTAGGAGTTATCATCCAGATGTGAACAAgtaagtgaagggtttagtttactttgtatccagtataaggtcttcgtctgtttatattatttaccttcctgcatcaagattggtgtgtttcttgttacaa...
Basic information
species | Arabidopsis thaliana |
transcript | AT4G39960.1 |
intron # | 5 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G39960.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: LOC_Os05g26914.1 (Oryza sativa), 5'ss of exon 5
CTTATCGGAAGCTCGCTAGGAGTTATCATCCAGATGTGAACAAgtaagtg--aagggtttagtttactttgtatccagtataaggtcttcgt-ctgtttatattatttaccttcctgcatca-agattggtgtgtttcttgttacaa-------------------------------------------------------------
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CCTATAGGAAGCTTGCTAGGAGCTACCATCCTGATGTGAACAAgtaagtactaaccattatatgggaattgtgtttcagctacactcgatatattgcttctttttctcctttcgatccattataaacctgagtactagttgttgcattacctttttcataactacataatcaaataagcaattgttatgcttgtgtatttttctttag
upper sequence: AT4G39960.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GRMZM2G091811_T01 (Zea mays), 5'ss of exon 5
CTTATCGGAAGCTCGCTAGGAGTTATCATCCAGATGTGAACAAgtaagtgaagggtt-tagt--ttactttgtatccagtataaggtcttcgtctgtttatattatttaccttcctgcatcaagattggtgtgtttcttgttacaa--
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CCTATCGGAAGCTTGCTAGGAGCTATCATCCAGATGTAAACAAgtaagttggctattgcaataatcacttttcagctactatca--tcaccattcttttgcttt--tcggatgcttagagaaactccagta-gtcgcctaaagaatcc
upper sequence: AT4G39960.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GRMZM5G856084_T01 (Zea mays), 5'ss of exon 5
CTTATCGGAAGCTCGCTAGGAGTTATCATCCAGATGTGAACAAgtaagtgaagggtt----tag---tttactttgtatccagtataaggtcttcgtctgtttat-attatttaccttcctgcatcaag----attg---gtgtgtttcttgttacaa---------------------------------------------------------------
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CCTATCGGAAGCTTGCTAGGAGCTATCATCCAGATGTAAACAAgtgagttggctattgcaatagagaatcacttttcagctactatca--ccatcatcattttgttgcttttcgggtgcttatagccagctgtactgcctgtatattcttctttgtacattagacatctctctcatttagtcagtcaaataatgaaagtatctatttatgatctattttag
upper sequence: AT4G39960.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GLYMA18G01960.1 (Glycine max), 5'ss of exon 5
CTTATCGGAAGCTCGCTAGGAGTTATCATCCAGATGTGAACAAgtaagtgaagggtttagtttactttgtatccagtataaggtcttcgtctgtttatattatttaccttcctgcatcaagattggtgtgtttcttgttacaa-----
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CTTATCGGAAGCTTGCCCGGAGTTATCATCCTGATGTGAACAAgtgagtttt---tctttcttctttcatattgaacatcgtctactt-tctgattctgttcccttgccttgttccccactctcttttttttgctt-ttaaaattttt
upper sequence: AT4G39960.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GLYMA11G38040.1 (Glycine max), 5'ss of exon 5
CTTATCGGAAGCTCGCTAGGAGTTATCATCCAGATGTGAACAAgtaagtgaagggtttagtttactttgtatccagtataaggtcttcgtctgtttatattatttaccttcctgcatcaagattggtgtgtttc---ttgttacaa-
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CTTATCGGAAGCTTGCCCGGAGTTGTCATCCTGATGTGAACAAgtatgttct---tttttcttccttcatattgaacattgtctactttctgattcccttcccttgccttgttcc-ccactgttgctgtggacaagatggtttggat
upper sequence: AT4G39960.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: Vv00s0324g00040.t01 (Vitis vinifera), 5'ss of exon 8
CTTATCGGAAGCTCGCTAGGAGTTATCATCCAGATGTGAACAAgtaagt-gaagggtttagtttactttgtatccagtataaggtcttc--gtctgtttatattatttaccttcctgcatcaagattggtgtgtttcttgttacaa
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CTTATCGAAAGCTTGCCAGGAGTTATCATCCAGATGTGAACAAgtgagttgaaaagccatttcttaatcatatataat-taatatcatcagggttgtccattccaattgcttgatgttat--agcttgttacttctgagaagtgaaMapped 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|124977810|gb|EL051088.1|EL051088EST: CTTATCGGAAGCTCGCTAGGAGTTATCATCCAGATGTGAACAA GGATGCTGGGGCAGAAGAT
genomic: CTTATCGGAAGCTCGCTAGGAGTTATCATCCAGATGTGAACAAgtaagtgaag ... ttgattacagGGATGCTGGGGCAGAAGAT
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
CTTATCGGAAGCTCGCTAGGAGTTATCATCCAGATGTGAACAAgtaagtgaagggtttagtttactttgtatccagtataaggtcttcgtctgtttatattatttaccttcctgcatcaagattggtgtgtttcttgttacaa
- - - - - - - - - - - - - - - CAGATG