Sequence
atgc intronic sequence ATGC exonic sequencegtatgtcctcatcaaaatcaaatgatttaaatgaagaaaaaacaatgtgacttaaaccggttgtaacttactggtttgtagGCGGAGGGTGTGACACATTCCGGTCCAACCAAGCTTGTGTTGTACTTTACCGGAGCCACCAACATCCTCTATACCTTCGGTGGACACGCTGTGACCGT
Basic information
species | Arabidopsis thaliana |
transcript | AT5G01240.2 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G01240.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os01g63770.1 (Oryza sativa), 3'ss of exon 5
------------------gtatgtcctcatcaaaatca-aatgattta----aatgaagaaaaaacaatgtgacttaaaccggttgtaacttac-------tggtttgtagGCGGAGGGTGTGACACATTCCGGTCCAACCAAGCTTGTGTTGTACTTTACCGGAGCCACCAACATCCTCTATACCTTCGGTGGACACGCTGTGACCGT
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gtgagataagaagagggaaactgtccttgtcactttctcgatcatccatcgcgtctactacatgtccatttagcttgggtttgcagtgactgatgatcgtttgcgtcgcagGCCGAAGGCATCACCCACACCGGTCCAACCAAGCTGGTGCTGTACTTCACCGGCGCCACCAACATCCTCTACACCTTCGGCGGCCACGCCGTCACAGT
upper sequence: AT5G01240.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G127949_T07 (Zea mays), 3'ss of exon 5
gtatgtcctcatcaaaatca-----aatgatttaaatgaagaaaaaacaatg-tgacttaa----accg--gttgtaacttactggtttgtagGCGGAGGGTGTGACACATTCCGGTCCAACCAAGCTTGTGTTGTACTTTACCGGAGCCACCAACATCCTCTATACCTTCGGTGGACACGCTGTGACCGT
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gtgagccccccccacagccaccgccaccggatccgatcgctattgtctaccactgattcaccgtccccgtcgtcctcgccgacgcacatgcagGCCGAAGGCGTGGCGCACTCCGGCCCCACCAAGCTCGTGCTCTACTTCACCGGCGCCACCAACATCCTCTACACCTTCGGCGGCCACGCCGTCACAGT
upper sequence: AT5G01240.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G067022_T02 (Zea mays), 3'ss of exon 4
gtatgtcctcatcaaaatca--aatgatttaaatgaagaaa-------aaacaatgtgactta--aaccggttgtaacttactggtttg--tagGCGGAGGGTGTGACACATTCCGGTCCAACCAAGCTTGTGTTGTACTTTACCGGAGCCACCAACATCCTCTATACCTTCGGTGGACACGCTGTGACCGT
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gtgagcccccccggcccccgtcgctcattcaattcatggcggcgtctcgaccagtgttactgactgtccctccgcgtgtcggcgcgccggacagGTCCCAGGCGTCACCCACTCTGGCCCCAGCAAGCTCGTGCCCTACTTCACCGGCGCCACCAACATCCTCTACACCTTCGGCGGCCACGCGATCACTGTMapped 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|124910813|gb|EH984893.1|EH984893EST: CCACCTACACCGCTTGGTACCTCACCATCGCCTCTTTTCTCCATGGTCGG GCGGAGGGTGTGACACATTCCGGTCCAACCAAGCTTGTGTTG
genomic: CCACCTACACCGCTTGGTACCTCACCATCGCCTCTTTTCTCCATGGTCAGgtatgtcctc ... tggtttgtagGCGGAGGGTGTGACACATTCCGGTCCAACCAAGCTTGTGTTG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttaaatgaagaaaaaacaatgtgacttaaaccggttgtaacttactggtttgtagGCGGAGGGTGTGACACATTCCGGTCCAACCAAGCTTGTGTTGTACTTTACCGGAGCCACCAACATCCTCTATACCTTCGGTGGACACGCTGTGACCGT
aacttac putative branch site (score: 2)
aaaaaacaat 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
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gtatgtcctcatcaaaatcaaatgatttaaatgaagaaaaaacaatgtgacttaaaccggttgtaacttactggtttgtagGCGGAGGGTGTGACACATTCCGGTCCAACCAAGCTTGTGTTGTACTTTACCGGAGCCACCAACATCCTCTATACCTTCGGTGGACACGCTGTGACCGT
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