Sequence
atgc intronic sequence ATGC exonic sequence...atccattagttgttgactgaaatgtaaaaaaggtttgattgcattgtgtgaattcatttaccgtgctatgtgtgtgttaatgtatattatatatgtgtagGTATAACGGAAATCGCCATGTGAGTATGGGAGCTGAGAAATGGCTGGACATTGAGTTTTGGGACACACCTAAAGAATGTTTCAAAGTTTTGAAGTCTCGC
Basic information
species | Arabidopsis thaliana |
transcript | AT5G15390.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G15390.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G026869_T01 (Zea mays), 3'ss of exon 1
---atccattagttgttgactgaaatgtaaaaaaggtttgattgcattgtgtgaattcatttaccgtgctatgtgtgtgttaatgtatattatatatgtgtagGTATAACGGAAATCGCCATGTGAGTATGGGAGCTGAGAAATGGCTGGACATTGAGTTTTGGGACACACCTAAAGAATGTTTCAAAGTTTTGAAGTCTCGC
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taagggtgaaaattcacaagtttgatattacatccttttgaaatgataggttccactcaagtaaactgttcttcattca--aatgcttctt-tgctttttcagGTATAGAGACAACAGGCATGTGAGCATGGGTGCTGAGAAATGGCTTGACATTGAGATATGGAACTCACCTGCAGAATGTTTCAGTGCATTAAAAAAACGC
upper sequence: AT5G15390.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA18G49880.1 (Glycine max), 3'ss of exon 1
atccattagttgttgac-tgaaatgtaaaaaaggtttgattgcattgtgtgaattcatttaccgtgctatgtgtgtgttaatgtatattatatatgtgtagGTATAACGGAAATCGCCATGTGAGTATGGGAGCTGAGAAATGGCTGGACATTGAGTTTTGGGACACACCTAAAGAATGTTTCAAAGTTTTGAAGTCTCGC
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--------gttattattacgagttatgaacagtgttatttgacattgt-tgaaaatgctgttattgaaatgttttgcctgacttcc-ttgt-----tgcagGTATAAAGATAATCGCCATGTGAGCATGGGTGCAGAGAAATGGTTGGACATTGAACTGTGGGACTCTACAAAGGAGTGCTTTAAAATGTTGAAATCACGC
upper sequence: AT5G15390.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA08G26320.1 (Glycine max), 3'ss of exon 1
-------atccattagttgttgactgaaatgtaaaaaaggtttgattgcattgtgtgaattcatttaccgtgctatgtgtgtgttaatgtatattatatatgtgtagGTATAACGGAAATCGCCATGTGAGTATGGGAGCTGAGAAATGGCTGGACATTGAGTTTTGGGACACACCTAAAGAATGTTTCAAAGTTTTGAAGTCTCGC
|| | ||| | | | | || | | |||| | | | ||| || |||| | || | || | || |||||||| | |||||||||||||| ||||| || ||||||||| |||||||||| | |||||| | | || || || || ||| | ||||| || |||
ataagaggggtgttgcgttctgattttgttattataatc-cataactgcagttaagagactgctttcaattgaaatgttt-tgcctggcttccttgt-----tgcagGTATAAAGATAATCGCCATGTGAGCATGGGTGCAGAGAAATGGTTGGACATTGAACTGTGGGACTCTACAAAGGAGTGCTTTAAAATGTTGAAATCACGC
upper sequence: AT5G15390.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv14s0108g01380.t01 (Vitis vinifera), 3'ss of exon 1
atccattagttgttgactgaaatgtaaaaaaggtttgattgcattgtgtgaattcatttaccgtgctatgtgtgtgttaatgt----atattatatatgtgtagGTATAACGGAAATCGCCATGTGAGTATGGGAGCTGAGAAATGGCTGGACATTGAGTTTTGGGACACACCTAAAGAATGTTTCAAAGTTTTGAAGTCTCGC
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---gatgttgccgtaccttttttctttctagacctctttttcagtgta-ggataccccgagtcaagaatatccttgctaaagtcaccatccattctttttccagGTACAAAGACAATCGCCATGTTAGCATGGGAGCTGAGAAATGGTTAGATATTGAACTTTGGAATTCCACACAAGAGTGCTTTGAAGTTCTGAAATCACGTMapped 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|125284146|gb|EL298231.1|EL298231EST: GCGTTGGGGATTCAATCTGTACATGTTGTTTCCTGTGACAGCTCCAAAAG GTATAACGGAAATCGCCATGTGAGTAT
genomic: GCGTTGGGGATTCAATCTGTACATGTTGTTTCCTGTGACAGCTCCAAAAGgtgccccttt ... atatgtgtagGTATAACGGAAATCGCCATGTGAGTAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtgtgaattcatttaccgtgctatgtgtgtgttaatgtatattatatatgtgtagGTATAACGGAAATCGCCATGTGAGTATGGGAGCTGAGAAATGGCTGGACATTGAGTTTTGGGACACACCTAAAGAATGTTTCAAAGTTTTGAAGTCTCGC
tgttaat putative branch site (score: 3)
ttaatgtatattatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atccattagttgttgactgaaatgtaaaaaaggtttgattgcattgtgtgaattcatttaccgtgctatgtgtgtgttaatgtatattatatatgtgtagGTATAACGGAAATCGCCATGTGAGTATGGGAGCTGAGAAATGGCTGGACATTGAGTTTTGGGACACACCTAAAGAATGTTTCAAAGTTTTGAAGTCTCGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - ctgaaat
- - - - - - - - - - - - taaaaaa
- - - - - - - - - - - - - - - -ggtttga