Sequence
atgc intronic sequence ATGC exonic sequencegtgatatttagattgcattgaatttattttttgacaattatagatgattggattgggttggattggatttatcttctaaaatgtgtatgtttgtttgtaattagGTATTGTCTGCTCAATTAGGAAGAAAGCCTGAGGATATTGTCAAGTTAGATGCTAATGAGAACCCATATGGTCCTCCTCCAGAG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G10330.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G10330.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA16G27220.1 (Glycine max), 3'ss of exon 2
gtgatatttagattgcattgaatttattttttgacaattatagatgattggattgggttggattgga---tttatcttctaaaatgtgtatgtttgtttgtaattagGTATTGTCTGCTCAATTAGGAAGAAAGCCTGAGGATATTGTCAAGTTAGATGCTAATGAGAACCCATATGGTCCTCCTCCAGAG
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----actctgggccacaac--acttgtctgtggttactttagtggggcaaaattgttccccgctacaatgctggttattaacaaaagaagaggctttctgttgc-agGTTTTATCAGCTCGCCTTGGACGTAAGCCTGAGGATATCGTGAAGTTAGATGCTAATGAAAATCCTTATGGTCCCCCTCCAGAG
upper sequence: AT5G10330.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv18s0072g00940.t01 (Vitis vinifera), 3'ss of exon 2
gtgatatttagattgcattgaatttattttttgacaattatagatgattggattgggttggattggatttatcttctaaaatgtg-tatgtttgtttgtaat-tagGTATTGTCTGCTCAATTAGGAAGAAAGCCTGAGGATATTGTCAAGTTAGATGCTAATGAGAACCCATATGGTCCTCCTCCAGAG
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ttagtaatta---tgcatgg---ttaatgaggcacttgaataaatagtcatgttaattaataattcagctttcaaattgaatgaaatgtgtttattattaatacagGTTTTGTCATCACGTCTTGGCAGGAAGCCTGAAGATATTGTCAAGCTAGATGCAAATGAAAACCCTTACGGTCCACCCCCAGAGMapped 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|86072939|gb|DR368696.1|DR368696EST: GTCCACATTTGAGACAATTGGGTGCTTATCAGCCAATTTTACCCTTTGAG GTATTGTCTGCTCAATTAGGAAAAAAGCCTGAGGATATTGTCAAGTTAGAT
genomic: GTCCACATTTGAGACAATTGGCTGCTTATCAGCCAATTTTACCCTTTGAGgtgatattta ... ttgtaattagGTATTGTCTGCTCAATTAGGAAGAAAGCCTGAGGATATTGTCAAGTTAGAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ggattgggttggattggatttatcttctaaaatgtgtatgtttgtttgtaattagGTATTGTCTGCTCAATTAGGAAGAAAGCCTGAGGATATTGTCAAGTTAGATGCTAATGAGAACCCATATGGTCCTCCTCCAGAG
ttctaaa putative branch site (score: 2)
tttgttt putative PPT
atttatcttctaaaat 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 |
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gtgatatttagattgcattgaatttattttttgacaattatagatgattggattgggttggattggatttatcttctaaaatgtgtatgtttgtttgtaattagGTATTGTCTGCTCAATTAGGAAGAAAGCCTGAGGATATTGTCAAGTTAGATGCTAATGAGAACCCATATGGTCCTCCTCCAGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC