Sequence
atgc intronic sequence ATGC exonic sequencegtttgctattgtcttatttattttcaatttttattataccaataatgatcctccttttgttgtgctgtcagacgcataaaatttgaaccacttttctatccacaatagacgtctatttgattaagctaataagcttcactcgttctcttagATACATTGTCAAAGATCTTCTTGGCCATGGGACTTTTGGTCAGGTTGCTAAATGCTGGGTTCCTGAGACAAACAGCTTTGTTGCTGTAAAAGTAATAAAA
Basic information
species | Arabidopsis thaliana |
transcript | AT5G35980.2 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G35980.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os02g47410.3 (Oryza sativa), 3'ss of exon 2
gtttgctattgtcttatttattttcaatttttattataccaataatgatcctccttttgttgtgctgtcagacgcataaaatttgaaccacttttctatccacaata-gacgtctatttgattaagct--aataagcttcac-tcgttctct-tagATACATTGTCAAAGATCTTCTTGGCCATGGGACTTTTGGTCAGGTTGCTAAATGCTGGGTTCCTGAGACAAACAGCTTTGTTGCTGTAAAAGTAATAAAA
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--------------------------------------------------------tggttctactaccagtagagagcattgtaaaacacctctaaagttaaactatgaacagcatcagattggactgcactcatctttttattgttctaagtagGTACGTTATTAAAGAAATGCTTGGCCAAGGTACGTTTGGACAGGTTGCTAAATGCTGGGATGGAGAAACTAACAGCTATGTTGCAGTAAAGGTTATAAAA
upper sequence: AT5G35980.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA16G18110.1 (Glycine max), 3'ss of exon 4
gtttgctattgtcttatttattttcaatttttattatac-caataatgatcctccttttgttgtgc-tgtcagacgcataaaatttgaaccacttttctatccacaatagacgtct----atttgattaag--ctaataagcttcactcgttctctt-----agATACATTGTCAAAGATCTTCTTGGCCATGGGACTTTTGGTCAGGTTGCTAAATGCTGGGTTCCTGAGACAAACAGCTTTGTTGCTGTAAAAGTAATAAAA
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------gtttgtcatccatatttccttcttttgtttcatatagtcatgatatatatttgtttatgaataccaaaagc-taaatgttgattttcagttgataccaccttacccatctgaccaccttattatcttcttataaactttgcattttgatgtggtgcagATATATTGTCAAAGATCTCCTTGGCCACGGGACATTTGGACAAGTGGCTAAATGCTGGGATTCAGATACCAACAGTTTTGTTGCTGTGAAGATCATTAAA
upper sequence: AT5G35980.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv16s0039g00610.t01 (Vitis vinifera), 3'ss of exon 1
gtttgctattgtcttatttattttcaatttttattataccaataatgatcctccttttgttgt-gctgtcagacgcataaaatttgaaccacttttctatccacaatagacgtctatttgattaagctaataagcttcactcgttctcttagATACATTGTCAAAGATCTTCTTGGCCATGGGACTTTTGGTCAGGTTGCTAAATGCTGGGTTCCTGAGACAAACAGCTTTGTTGCTGTAAAAGTAATAAAA
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----------------------------------------aattgcaattaatcatttaaaattaccgactgtggcatgttattt--------cttttattgaacatcttattttgaggaattgatctt-tatgcttca---acatttgcagATACATCATCAAAGATATTCTTGGCCATGGGACATTTGGGCAGGTTGCTAAATGCTGGGTTACAGAAACTAACAGTTTCACTGCTGTTAAAATTATTAAAMapped 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|124943241|gb|EL019438.1|EL019438EST: CTAATTCTGGCTGTAAATGATGATTTTTGCAGTTCAGATTCACGGCAGAG ATACATTGTCAA
genomic: CTAATTCTGGCTGTAAATGATGATTTTTGCAGTTCAGATTCACGGCAGAGgtttgctatt ... gttctcttagATACATTGTCAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatccacaatagacgtctatttgattaagctaataagcttcactcgttctcttagATACATTGTCAAAGATCTTCTTGGCCATGGGACTTTTGGTCAGGTTGCTAAATGCTGGGTTCCTGAGACAAACAGCTTTGTTGCTGTAAAAGTAATAAAA
agctaat putative branch site (score: 3)
cttcactcgttctctt putative PPT
tatttgattaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttgctattgtcttatttattttcaatttttattataccaataatgatcctccttttgttgtgctgtcagacgcataaaatttgaaccacttttctatccacaatagacgtctatttgattaagctaataagcttcactcgttctcttagATACATTGTCAAAGATCTTCTTGGCCATGGGACTTTTGGTCAGGTTGCTAAATGCTGGGTTCCTGAGACAAACAGCTTTGTTGCTGTAAAAGTAATAAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG