Sequence
atgc intronic sequence ATGC exonic sequencegtttttgcagtaaagtctcttatgtaaattatcctttttttttttttttaggttcgtgattttacgatgatgttttagGTTAACATGGAGTATGGTCTTGATCCAATGATTGGGGAAGCCATAATGGAAGCTGCACAAGAAGTAGCAGAAGGAAAGCTCAATGATCATTTCCCTCTTG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G50950.3 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G50950.3 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA10G02040.2 (Glycine max), 3'ss of exon 2
gtttttgcagtaaagtctcttatgtaaattatcctttttttttttttttaggttcgt-----gattttacgatgatgtttt-----agGTTAACATGGAGTATGGTCTTGATCCAATGATTGGGGAAGCCATAATGGAAGCTGCACAAGAAGTAGCAGAAGGAAAGCTCAATGATCATTTCCCTCTTG
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---------gtcaacattcatatatatcttcacttcttctacttgcactatcctctttcaaaaattatcaattgttgttttgatgcagGTGAACATGGAGTATGGTCTTGATCCCATCGTGGGAGAAGCAATAATGCAAGCGGCACAAGAAGTAGCCGAGGGAAAACTAAACGAACATTTTCCTCTCG
upper sequence: AT5G50950.3 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA02G01930.2 (Glycine max), 3'ss of exon 2
-----------gtttttgcagtaaagtct-cttatgtaaattatccttttt--ttttttttttaggttcgt--gattttacgatgatgtttt------agGTTAACATGGAGTATGGTCTTGATCCAATGATTGGGGAAGCCATAATGGAAGCTGCACAAGAAGTAGCAGAAGGAAAGCTCAATGATCATTTCCCTCTTG
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tttctgctaaaattatatcaaaagattatatttttttcaattggtctcttaaattattattccatcctccttcaattgatcaattatagttttaatgcagGTGAACATGGAGTATGGTCTTGATCCCAACGTCGGAGAAGCAATAATGCAAGCAGCACAAGAAGTAGCCGAGGGAAAACTAAACGACCATTTTCCTCTCG
upper sequence: AT5G50950.3 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv07s0005g00880.t01 (Vitis vinifera), 3'ss of exon 3
--------------------gtttttgcagtaaagtctctta----tgtaaattatcctttttttttttttttaggttcgtgattttacgatgatgttttagGTTAACATGGAGTATGGTCTTGATCCAATGATTGGGGAAGCCATAATGGAAGCTGCACAAGAAGTAGCAGAAGGAAAGCTCAATGATCATTTCCCTCTTG
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atgtatagttgatttttgtaacatcttcattacattttcatactggtctgagtaattggttgatgtaagattta--ctctcaattgcattattctattgtagGTCAACATGGAATATGGTCTTGATCCATCCATAGGCAAAGCAATAATGCAAGCAGCCCAAGAAGTGTCAGAGGGAAAACTAAATGATCATTTTCCGCTCGMapped 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|116443356|gb|EG485948.1|EG485948EST: CCGAACCAATCGTCCGAGCTTTTGGTGTCTTGAAGAAATGTGCTGCCAAG GTTAACATGGAGTATGGTCTTGATCCAATGATTGGGGAAGCCATAATGGAA
genomic: CCGAACCAATCGTCCGAGCTTTTGGTGTCTTGAAGAAATGTGCTGCCAAGgtttttgcag ... gatgttttagGTTAACATGGAGTATGGTCTTGATCCAATGATTGGGGAAGCCATAATGGAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtaaattatcctttttttttttttttaggttcgtgattttacgatgatgttttagGTTAACATGGAGTATGGTCTTGATCCAATGATTGGGGAAGCCATAATGGAAGCTGCACAAGAAGTAGCAGAAGGAAAGCTCAATGATCATTTCCCTCTTG
ttatcctttttttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttttgcagtaaagtctcttatgtaaattatcctttttttttttttttaggttcgtgattttacgatgatgttttagGTTAACATGGAGTATGGTCTTGATCCAATGATTGGGGAAGCCATAATGGAAGCTGCACAAGAAGTAGCAGAAGGAAAGCTCAATGATCATTTCCCTCTTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA