Sequence
atgc intronic sequence ATGC exonic sequencegtaagttacttactttttttcctcttcaccctatattttttctttgaaagtaatttcccgagttttgaatgtttcagACGTTTGAGGAAGCAGACACAAAACACGATGGAAAGATCGATAAGGAAGAGTGGAGAAGCCTTGTTCTTAGACATCCCAGCCTTCTGAAGAACATGACTC
Basic information
species | Arabidopsis thaliana |
transcript | AT5G55990.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G55990.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA08G44580.1 (Glycine max), 3'ss of exon 7
----------------------------------------gtaagttacttactttttttcctcttcaccctatattttt-----tctttgaaagtaatttc----ccgagttttgaatgt-ttcagACGTTTGAGGAAGCAGACACAAAACACGATGGAAAGATCGATAAGGAAGAGTGGAGAAGCCTTGTTCTTAGACATCCCAGCCTTCTGAAGAACATGACTC
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gttttaccccattttctataacttacatttctaagttctaatagtgcacatgagtcttaagagtctcattttctctttttgaaaactcacatggatagtttcaacattaaattttggatttctttagACCTTCGAGGAAGCAGATACAAAGCATGATGGCAAGATTGACAAGGAAGAGTGGAGAAACCTTGTTTTGCGCCATCCGTCACTTTTGAAGAACATGACCC
upper sequence: AT5G55990.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA18G08230.1 (Glycine max), 3'ss of exon 8
------------------------------------------------gtaagttacttactt-tttttcctcttcaccctatattttttctttgaaagtaatttc-ccgagttttgaatgtttcagACGTTTGAGGAAGCAGACACAAAACACGATGGAAAGATCGATAAGGAAGAGTGGAGAAGCCTTGTTCTTAGACATCCCAGCCTTCTGAAGAACATGACTC-
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ttttacccctattcttctatcacttacatttctaagttctaattgtgcacaagaatcttaagagtctctttttctctttttgaaaactcacatgaatagtttcgacattaaattttggatttcttagaCCTTCGAGGAAGCAGATACAAAGCATGATGGCAAAATTGACAAGGAAGAGTGGAGAAACCTTGTTTTGCGCCATCCGTCACTTTTGAAGAACATGACCCT
upper sequence: AT5G55990.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: Vv00s1569g00020.t01 (Vitis vinifera), 3'ss of exon 6
--------------------gtaagttacttactttttttcc-tcttcaccctatattttttctttgaaagtaatttcccgagttttgaat--gtttcagACGTTTGAGGAAGCAGACACAAAACACGATGGAAAGATCGATAAGGAAGAGTGGAGAAGCCTTGTTCTTAGACATCCCAGCCTTCTGAAGAACATGACTC
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gatattgattggattggaatgaatatttttagcattccaaacatatttatcttgcaataagcttcctattatatttttaatattcttatttttatttcagACCTTTGAGGAAGCTGATACTAAACATGATGGGAAGATAGACAAGGAAGAATGGCGAAGCCTTGTTTTGCGACATCCATCTCTTTTGAAGAATATGACCC
upper sequence: AT5G55990.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: Vv19s0015g01070.t01 (Vitis vinifera), 3'ss of exon 6
----------------------gtaagttacttactttttttcctcttcaccctatattttttctttgaaagtaatttcccgagttttgaat-gtttcagACGTTTGAGGAAGCAGACACAAAACACGATGGAAAGATCGATAAGGAAGAGTGGAGAAGCCTTGTTCTTAGACATCCCAGCCTTCTGAAGAACATGACTC
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ctccttggttaagcagcaagttgagggaaactcaatttggattttgtatttgttgcatccatctcttataacctttttttattttggtgcattgttccagACCTTTGAGGAAGCTGACACAAAACATGATGGAAAGATTGACAAAGAAGAGTGGAGAAGCCTTGTTCTACGACACCCATCCCTTTTGAAGAATATGACTCMapped 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|125005953|gb|EL078222.1|EL078222EST: TTGAAGGATACTGTCATTGAGGATATTAATCGACAAG ACGTTTGAGGAAGCAGACACAAAACACGATGGAAAGATCGATAAGGAAGAG
genomic: TTGAAGGATACTGTCATTGAGGATA-TAATCGACAAGgtaagttact ... aatgtttcagACGTTTGAGGAAGCAGACACAAAACACGATGGAAAGATCGATAAGGAAGAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcttcaccctatattttttctttgaaagtaatttcccgagttttgaatgtttcagACGTTTGAGGAAGCAGACACAAAACACGATGGAAAGATCGATAAGGAAGAGTGGAGAAGCCTTGTTCTTAGACATCCCAGCCTTCTGAAGAACATGACTC
tatattttttctttga 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagttacttactttttttcctcttcaccctatattttttctttgaaagtaatttcccgagttttgaatgtttcagACGTTTGAGGAAGCAGACACAAAACACGATGGAAAGATCGATAAGGAAGAGTGGAGAAGCCTTGTTCTTAGACATCCCAGCCTTCTGAAGAACATGACTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC