Sequence
atgc intronic sequence ATGC exonic sequencegtatgtggaattggaattactcacatgaattggtggattatactctttgaatatattttgataggctcgactttgtgttttgcttgaagCTACCTTGTTTGGACAACTATGGAGGTTAGAACCACTGCCTACAGAGAAGAAAGAGATGTGGAGAAGAGAAATGGAATGGCTTCTCTGTGTCAGTGATCA
Basic information
species | Arabidopsis thaliana |
transcript | AT5G02010.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G02010.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA07G16790.1 (Glycine max), 3'ss of exon 2
----------------------------------------------------gtatgtggaattgg----aattactcaca-tgaattggtggattatactctttgaatatattttgataggctcgactttgtgttttgcttgaagCTACCTTGTTTGGACAACTATGGAGGTTAGAACCACTGCCTACAGAGAAGAAAGAGATGTGGAGAAGAGAAATGGAATGGCTTCTCTGTGTCAGTGATCA
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gtatgcaaaatgcacaattgaagcagttactgtgtttttatttggttttttctttttattaattggtgcaagttggttgtggtgaattttagagtgctattcttgcctgtgattgtgat-ggctctttcctttgctgaatatgtagCTACCCTCTTTGGGCAACTTTGGAGATTAGAGCCCCTACGTTCAGAGAAGAAAGCAATGTGGCGACGAGAAATAGAGTGGTTTCTTTCTGTCAGTGATCA
upper sequence: AT5G02010.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv08s0007g01380.t01 (Vitis vinifera), 3'ss of exon 2
---------gtatgtggaattggaattactcacatga-----attggtggattatactctttgaatatat---tttgataggctcgactttgtgttttgc----ttgaagCTACCTTGTTTGGACAACTATGGAGGTTAGAACCACTGCCTACAGAGAAGAAAGAGATGTGGAGAAGAGAAATGGAATGGCTTCTCTGTGTCAGTGATCA
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gtatgctatgtgtttattttttgaagtgtttggatgatgggaattataaatttacaacattggcttttttccttctaatagttactgctctttcttttcccgatttccagCTACCCTGTTTGGGCAACTTTGGCGATTGGAACCTTTACCTGCAGAGAAGAAGGCTATGTGGCGAAGAGAGATGGAATGGCTTCTTTGCGTTAGTGATCA
upper sequence: AT5G02010.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv08s0007g01390.t01 (Vitis vinifera), 3'ss of exon 2
-----------gtatgtggaattggaattactcacatgaattggtggattatactctttgaatatattttgataggctcgactttgtgttttgcttgaagCTACCTTGTTTGGACAACTATGGAGGTTAGAACCACTGCCTACAGAGAAGAAAGAGATGTGGAGAAGAGAAATGGAATGGCTTCTCTGTGTCAGTGATCA
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ttctaaactttttctcccgattttcttttttgtgcatttttcttcaattttttttttctaattaaacatagattatttttctttcttttcccatgtgtagCTACCCTGTTTGGGAAAATCTGGAAATTGGAACCTTTAGATCCAATGAAGAAGGCGATGTGGCGAAGAGACAAGGAATGGCTTCTTTCTGTCAGTGATCAMapped 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|124883254|gb|EH962156.1|EH962156EST: AAACGCAATCACTAATCTTTGTG CTACCTTAGTTTGGACAACTATGGAGGTTAGAACCACTGC
genomic: AAACGCAATCACTAATCTTTGTGgtatgtggaa ... ttgcttgaagCTACCTT-GTTTGGACAACTATGGAGGTTAGAACCACTGC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ggattatactctttgaatatattttgataggctcgactttgtgttttgcttgaagCTACCTTGTTTGGACAACTATGGAGGTTAGAACCACTGCCTACAGAGAAGAAAGAGATGTGGAGAAGAGAAATGGAATGGCTTCTCTGTGTCAGTGATCA
ttttgat putative branch site (score: 4)
ttttgctt putative PPT
tttgaatatattttga 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgtggaattggaattactcacatgaattggtggattatactctttgaatatattttgataggctcgactttgtgttttgcttgaagCTACCTTGTTTGGACAACTATGGAGGTTAGAACCACTGCCTACAGAGAAGAAAGAGATGTGGAGAAGAGAAATGGAATGGCTTCTCTGTGTCAGTGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA