Sequence
atgc intronic sequence ATGC exonic sequencegttcgtttacttactcctgtcttcgtcatatatatgtgtatgctagttgctttgtctataacctttctttttaaacctgtgcagATTCGGCCAGACCGTCAAACTTTGTACTGGAGTGCCACTTGGCCTAAGGAGGTGGAACAACTATCGAAGAAGTTTCTTTATAACCCATACAAA
Basic information
species | Arabidopsis thaliana |
transcript | AT1G55150.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G55150.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA08G20670.1 (Glycine max), 3'ss of exon 5
---------gttcg-tttacttactc---ctgtcttcgtcatatatatgtgtatgctagttgctttgtctat---aacctttctttttaaacctgtgcagATTCGGCCAGACCGTCAAACTTTGTACTGGAGTGCCACTTGGCCTAAGGAGGTGGAACAACTATCGAAGAAGTTTCTTTATAACCCATACAAA
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attaatccaattcgatttagaaagacagattgctgaagttgcattttaaaatttctttattctgctggtcatctgatcactttttttttgttttacttagATTCGTCCAGATCGTCAAACTTTGTATTGGAGTGCTACCTGGCCAAAGGAGGTTGAACAATTGGCAAGGAAGTTCCTTTATAACCCATACAAA
upper sequence: AT1G55150.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA07G11880.1 (Glycine max), 3'ss of exon 5
-----------------gttcgtttacttactcctgtcttcgtcatatatatgtgtatgctagttgctttgtctataacctttctttttaaacctgtgcagATTCGGCCAGACCGTCAAACTTTGTACTGGAGTGCCACTTGGCCTAAGGAGGTGGAACAACTATCGAAGAAGTTTCTTTATAACCCATACAAA
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aattaatccaaatcaatctagaaatacagattgctgaagctg-cattttaaagtttctttattctgcttgtcatatgatcactgttttttgtttttcttagATTCGTCCAGATCGTCAAACTTTGTATTGGAGTGCTACCTGGCCAAAGGAGGTCGAACAATTGGCAAGGAAGTTCCTTTATAACCCATACAAA
upper sequence: AT1G55150.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA07G01260.1 (Glycine max), 3'ss of exon 5
-----------gttcgtttacttactc---ctgtcttcgtcatatatatgtgtatgctagt--tgctttgtctataacctttctttttaaacctgtgcagATTCGGCCAGACCGTCAAACTTTGTACTGGAGTGCCACTTGGCCTAAGGAGGTGGAACAACTATCGAAGAAGTTTCTTTATAACCCATACAAA
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aattaatccaaatcgatttagaaatacagattgctgaagctgcattttaaagtttctttattctgcttgtcatatgatcactgttttttgtttttcttagATTCGTCCAGATCGTCAAACTTTGTATTGGAGTGCTACCTGGCCAAAGGAGGTCGAACAATTGGCAAGGAAGTTCCTTTATAACCCATACAAA
upper sequence: AT1G55150.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv09s0002g02100.t01 (Vitis vinifera), 3'ss of exon 5
gttcg--tttacttactcctgtcttcgtcata--tatatgtgt---atgctagttgctttgtctataacc--tttcttttta-------aacctgtgcagATTCGGCCAGACCGTCAAACTTTGTACTGGAGTGCCACTTGGCCTAAGGAGGTGGAACAACTATCGAAGAAGTTTCTTTATAACCCATACAAA
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atccggcttacctttctcctctcttccttgtaattgtatctgttgaattctgcataatctggagatatcaggttcctatttattggtttgctttatgtagATTCGTCCTGATCGTCAAACCCTCTATTGGAGTGCTACATGGCCCAAGGAGGTGGAACAACTTGCTAGGAAGTTCCTTTACAACCCATGTAAAMapped 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|116454669|gb|EG497261.1|EG497261EST: GAATGCTTGATATGGGGTTTGACCCTCAGATCCGGAAAATTGTTTCACAT ATTCGGCCAGACCGTCAAACTTTGTACTGGAGTGCCACTTGGCCTAAGGAG
genomic: GAATGCTTGATATGGGGTTTGACCCTCAGATCCGGAAAATTGTTTCACATgttcgtttac ... acctgtgcagATTCGGCCAGACCGTCAAACTTTGTACTGGAGTGCCACTTGGCCTAAGGAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atatatgtgtatgctagttgctttgtctataacctttctttttaaacctgtgcagATTCGGCCAGACCGTCAAACTTTGTACTGGAGTGCCACTTGGCCTAAGGAGGTGGAACAACTATCGAAGAAGTTTCTTTATAACCCATACAAA
ctataac putative branch site (score: 3)
tttctttttaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttcgtttacttactcctgtcttcgtcatatatatgtgtatgctagttgctttgtctataacctttctttttaaacctgtgcagATTCGGCCAGACCGTCAAACTTTGTACTGGAGTGCCACTTGGCCTAAGGAGGTGGAACAACTATCGAAGAAGTTTCTTTATAACCCATACAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT