Sequence
atgc intronic sequence ATGC exonic sequence...cacactttcatttcttgaaatttagatcgaggtaaaccttaatacagaatggtaatgacaatctagcatccccttttggttgcttcctgaatttgagcagGTTAAAATTTGGGATCCAAGTCTGCGTGGTTCTGAACTTCGAGCAACTTTGAAAGGACATACTGG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G49040.1 |
intron # | 23 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G49040.1 (Arabidopsis thaliana), 3'ss of exon 23
lower sequence: LOC_Os01g39380.1 (Oryza sativa), 3'ss of exon 24
--cacactttcatttcttgaaatttagatcgaggtaaaccttaatacagaatggtaatgacaatctagcatccccttttggttgcttcctgaat-ttgagcagGTTAAAATTTGGGATCCAAGTCTGCGTGGTTCTGAACTTCGAGCAACTTTGAAAGGACATACTGG
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tatacagctt-gtagctaatgctgcattactaggaaatctgttgctcaggaaa--aattcttgtggatattttactgatactttgtttatgtacattttacagGTAAAAATATGGGATCCAAGTTTGCGTGGTTCTGAACTTCGGACAACACTTAAAGGGCACACTAG
upper sequence: AT1G49040.1 (Arabidopsis thaliana), 3'ss of exon 23
lower sequence: GRMZM2G074466_T01 (Zea mays), 3'ss of exon 4
cacactttcatttcttgaaatttagatcgaggtaaaccttaatacagaatggtaatgacaatctagcatcc---ccttttggttgcttcctgaatttgagcagGTTAAAATTTGGGATCCAAGTCTGCGTGGTTCTGAACTTCGAGCAACTTTGAAAGGACATACTGG
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--tcccctgatttgaattgagctatgctgaattattacatggtatctttatctgtctttgatttggacactgaacatttagtttgtttcgtacatctca-cagGTAAAAATTTGGGATCCAAGTTTGCGTGGTTCTGAACTTCGAGCAACACTTAAAGGGCATACTAG
upper sequence: AT1G49040.1 (Arabidopsis thaliana), 3'ss of exon 23
lower sequence: GLYMA08G04510.1 (Glycine max), 3'ss of exon 23
cacactttcatttcttgaaatttagatcgaggtaaaccttaatacagaatggt--aatgacaatctagcatccccttttggttgct------tcc---tgaatttgagcagGTTAAAATTTGGGATCCAAGTCTGCGTGGTTCTGAACTTCGAGCAACTTTGAAAGGACATACTGG
| | | | || || | || | | | | ||| || | || || | ||| | | || | | || | | | || | | ||||||||| || |||||||| ||||| |||||||||||||| | |||||||| ||||| |||||| |
-------gtaagtttcaatatctatcacatggaataacctggtactgagttgtttcattgccttctggtacccagaatgaggtgatatgctgttcatgtgcaaatatgcagGTTAAGATCTGGGATCCTAGTCTTCGTGGTTCTGAACTCAGGGCAACTTTAAAAGGCCATACTAG
upper sequence: AT1G49040.1 (Arabidopsis thaliana), 3'ss of exon 23
lower sequence: GLYMA05G35210.1 (Glycine max), 3'ss of exon 6
cacactttcatttcttgaaatttagatcgaggtaaaccttaatacagaatggt--aatgacaatctagcatccccttttggttgct------tcc---tgaatttgagcagGTTAAAATTTGGGATCCAAGTCTGCGTGGTTCTGAACTTCGAGCAACTTTGAAAGGACATACTGG
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-------gtaagtttcaatatctatcatatggaattacctggtactgagttgtttcattgccttctggtacccagaatgaggtgatatgctgttcatgtgcaaatatgcagGTTAAGATCTGGGATCCTAGTCTTCGTGGTTCTGAACTCAGGGCAACTTTAAAAGGGCATACTAG
upper sequence: AT1G49040.1 (Arabidopsis thaliana), 3'ss of exon 23
lower sequence: Vv17s0000g03950.t01 (Vitis vinifera), 3'ss of exon 23
cacactttcatttcttgaaatttagatcgaggtaaaccttaa--tacagaatggtaatgacaatctagcatccccttttggttgcttcctgaatttgagcagGTTAAAATTTGGGATCCAAGTCTGCGTGGTTCTGAACTTCGAGCAACTTTGAAAGGACATACTGG
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--aacttccaatgatcaatacataaattctataaagcattaaactgcagcactggaatagaaaagcatggtggttatcatttttttttccataactgtgcagGTGAAGATCTGGGATCCTACTCTTCGTGGTTCTGAACTTAGGGCAACTTTGAAAGGACATACAAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agaatggtaatgacaatctagcatccccttttggttgcttcctgaatttgagcagGTTAAAATTTGGGATCCAAGTCTGCGTGGTTCTGAACTTCGAGCAACTTTGAAAGGACATACTGG
tgaattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cacactttcatttcttgaaatttagatcgaggtaaaccttaatacagaatggtaatgacaatctagcatccccttttggttgcttcctgaatttgagcagGTTAAAATTTGGGATCCAAGTCTGCGTGGTTCTGAACTTCGAGCAACTTTGAAAGGACATACTGG
cacactt
- - - - - - - - - - - - - - - - - -accttaa
- - - - - - - - - - - - - - - - - - - - - tacagaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - atgacaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttgcttc