Sequence
atgc intronic sequence ATGC exonic sequencegtaagagttttctgtttctgtaatttgcgttttggttttgtggattgcgatgcctctcttactttgtacaatttctttggtactctgtggaacaccagGAATGATCTTTGGGCTCTCGGCTGCACTCTCTATCAGATGCTTTCGGGGACTTCCCCATTTAAAGATGCAAGTGAATGGCTGATTTTCCAAAGAATTATA
Basic information
species | Arabidopsis thaliana |
transcript | AT5G04510.2 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G04510.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os01g65230.1 (Oryza sativa), 3'ss of exon 6
gtaagagttttctgtttctgtaatttgcgttttggttttgtggattgcgatgcctctcttactttgtacaatttctttggta---ctctgtgga---acaccagGAATGATCTTTGGGCTCTCGGCTGCACTCTCTATCAGATGCTTTCGGGGACTTCCCCATTTAAAGATGCAAGTGAATGGCTGATTTTCCAAAGAATTATA
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-agcaagctttagagtgctgtgttttgtgttgatactgtatgagttattatgatatcttta---tacataatttctctgatgaacctttatctgttcttgacagAAATGACTTATGGGCATTGGGGTGTACTCTATATCAATTGCTTTCTGGCTCTTCACCATTTAAAGATGCCAGTGAGTGGTTAATTTTCCAGAGAATTATA
upper sequence: AT5G04510.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA10G34430.1 (Glycine max), 3'ss of exon 6
-----gtaagagttttctgtttctgtaatttgcgttttggttttgtggattgcgatgcctctcttactttgtacaatttctttggtactctgtggaacaccagGAATGATCTTTGGGCTCTCGGCTGCACTCTCTATCAGATGCTTTCGGGGACTTCCCCATTTAAAGATGCAAGTGAATGGCTGATTTTCCAAAGAATTATA
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catgcaccgagtttcttcatttcttttgttt-cataccaggtccctatataataacttttcttctgtgttttgt--ttccccccctcaaatatatcacaacagAAATGACCTTTGGGCACTTGGCTGCACATTATACCAAATGCTTTCTGGAACTTCCCCTTTTAAAGACGCAAGTGAATGGCTTATTTTTCAAAGAATTATA
upper sequence: AT5G04510.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA20G33140.1 (Glycine max), 3'ss of exon 6
--gtaagagttttctgtttctgtaatttgcgttttggttttgtggattgcgatgcctctcttactttgtacaatttc-tttggtactctgtggaacaccagGAATGATCTTTGGGCTCTCGGCTGCACTCTCTATCAGATGCTTTCGGGGACTTCCCCATTTAAAGATGCAAGTGAATGGCTGATTTTCCAAAGAATTATA
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gcactgagtttcttcatttcttttgttt-cataccaggtccctatataataacttttcttctgttttttgtttttttgccctcaaatatatatcacaacagAAATGACCTTTGGGCACTTGGCTGCACATTATACCAAATGCTTTCTGGAACTTCCCCTTTTAAAGACGCGAGTGAATGGCTTATTTTTCAAAGAATTATA
upper sequence: AT5G04510.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv13s0074g00100.t01 (Vitis vinifera), 3'ss of exon 7
-gtaagagttttctgtttctgtaatttgcgttttggttttgtggattgcgatgcctctcttactttgtacaatttctttggtactctgtggaacac---cagGAATGATCTTTGGGCTCTCGGCTGCACTCTCTATCAGATGCTTTCGGGGACTTCCCCATTTAAAGATGCAAGTGAATGGCTGATTTTCCAAAGAATTATA
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gaaaaaaaaagaagaaaagtgttggtttcaat--ggttctgtcagatcatgtactttctttggtggataacatatttactgttgttaacttcatacatacagAAACGATCTTTGGGCACTTGGCTGCACTTTGTACCAGATGCTTTCTGGAACTTCTCCTTTTAAAGATGCAAGTGAATGGCTTATTTTCCAAAGAATTATA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attgcgatgcctctcttactttgtacaatttctttggtactctgtggaacaccagGAATGATCTTTGGGCTCTCGGCTGCACTCTCTATCAGATGCTTTCGGGGACTTCCCCATTTAAAGATGCAAGTGAATGGCTGATTTTCCAAAGAATTATA
ctcttac putative branch site (score: 3)
aatttcttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagagttttctgtttctgtaatttgcgttttggttttgtggattgcgatgcctctcttactttgtacaatttctttggtactctgtggaacaccagGAATGATCTTTGGGCTCTCGGCTGCACTCTCTATCAGATGCTTTCGGGGACTTCCCCATTTAAAGATGCAAGTGAATGGCTGATTTTCCAAAGAATTATA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA