Sequence
atgc intronic sequence ATGC exonic sequencegtaagttttcgaatgtccactgttgcaaattgttctggtaccaaatgtgtattaactttatgatgtctcagGTATCGAATAACAGAGGGTGTAAATCTGCCTTTCCGTGTATTACCAACAATCAAAGAACTTGGTCGTACACGTATGGAAGTAAATGTCAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G46630.2 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G46630.2 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GRMZM2G331032_T01 (Zea mays), 3'ss of exon 8
-----------------------------------gtaagttttcgaatg---tccactgtt----gcaaattgttctggtaccaaatgtgtattaactttatgatgtctcagGTATCGAATAACAGAGGGTGTAAATCTGCCTTTCCGTGTATTACCAACAATCAAAGAACTTGGTCGTACACGTATGGAAGTAAATGTCAAG
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gtaaatcttctgattcctcttttatgtttgtaattttgtccctgctaatgacttgcactattaaatgcactttggctgggttttcagt-tgtgatagataaatt-tgttgtagGTATCGAATCACAGAGGGTGTAAACCTTCCATTCCGTGTTCTGCCGACAATCAAGGAATTGGGCCGAACACGCATGGAGATCAACGTGAAA
upper sequence: AT5G46630.2 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: Vv02s0012g00910.t01 (Vitis vinifera), 3'ss of exon 8
--------------------------------gtaagttttcgaatgtccactgttgca-aattgttctggtaccaaatgtgtattaactttatgatgtctcagGTATCGAATAACAGAGGGTGTAAATCTGCCTTTCCGTGTATTACCAACAATCAAAGAACTTGGTCGTACACGTATGGAAGTAAATGTCAAG
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aagagataccagatggggtgttgtagttggttaatggttccagaatgaagatccttgtttaatttttttacctccacctttacaattatatttt----ccatagGTATCGTATCACTGAGGGTGTAAATCTTCCATTCCGAGTATTGCCAACAATTAAGGAACTGGGTCGGACACGCATGGAAGTGAATGTCAAG
upper sequence: AT5G46630.2 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: EFJ22278 (Selaginella moellendorffii), 3'ss of exon 8
gtaagttttcga-atgtccactgttgca-aattgttctggtaccaaatgtgtattaactttatgatgtctcagGTATCGAATAACAGAGGGTGTAAATCTGCCTTTCCGTGTATTACCAACAATCAAAGAACTTGGTCGTACACGTATGGAAGTAAATGTCAAG
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----gtactggacaagtttgtgatggtatagctaacttggtactta-tatcttttcatatctt----ttccagGTATCGAATCACTGAAGGGATCAACCTTCCCTTTCGAGTTTTTCCCAGCATCAAAGAACTTGGTCGCACGCGTATGGAAGTGAATGTGAAG
upper sequence: AT5G46630.2 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: EFJ25669 (Selaginella moellendorffii), 3'ss of exon 8
gtaagttttcga-atgtccactgttgca-aattgttctggtaccaaatgtgtattaactttatgatgtctcagGTATCGAATAACAGAGGGTGTAAATCTGCCTTTCCGTGTATTACCAACAATCAAAGAACTTGGTCGTACACGTATGGAAGTAAATGTCAAG
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----gtactagacaagtttgtgatggtatagctaacttggtactta-tatcttttcatatctt----ttccagGTATCGAATCACTGAAGGGATCAACCTTCCCTTTCGAGTTTTTCCCAGCATCAAAGAACTTGGTCGCACGCGTATGGAAGTGAATGTGAAGMapped 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|164208363|gb|ES173192.1|ES173192EST: TAGAAGACTGTTAGTTTTGTACCACCGGATGGAGAGTTTGAACTGATGAA GTATCGAATAACAGAGGGTGTAAATC
genomic: -AGAAGACTGTTAGTTTTGTACCACCGGATGGAGAGTTTGAACTGATGAAgtaagttttc ... gatgtctcagGTATCGAATAACAGAGGGTGTAAATC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ccactgttgcaaattgttctggtaccaaatgtgtattaactttatgatgtctcagGTATCGAATAACAGAGGGTGTAAATCTGCCTTTCCGTGTATTACCAACAATCAAAGAACTTGGTCGTACACGTATGGAAGTAAATGTCAAG
tattaac putative branch site (score: 1)
tattaactttatgat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagttttcgaatgtccactgttgcaaattgttctggtaccaaatgtgtattaactttatgatgtctcagGTATCGAATAACAGAGGGTGTAAATCTGCCTTTCCGTGTATTACCAACAATCAAAGAACTTGGTCGTACACGTATGGAAGTAAATGTCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG