Sequence
atgc intronic sequence ATGC exonic sequencegtatggttcatatacataaaaattacgatttaacttttgtgtcttcgatttatttgacaaaacaaagggttttgtttccttctaattgttgttacatatatatgcagGTGGATTTGACACTGCACATGCTGCTGCTCG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G67180.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G67180.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA01G39520.1 (Glycine max), 3'ss of exon 2
----------------------------------------gtatggttcatatacataaaaattac---gatttaac--ttttgtgtcttcgatttatttgacaaaacaaagggtttt------gtttccttctaattgttgttac------atatatatgcagGTGGATTTGACACTGCACATGCTGCTGCTCG
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gtgagtattacgatgtggatgattgcatatgtggtagttgttgttgttgttgtacacttgtgctgttttattttaataatgttttgttttggatacaaattgggaggcagactaatttttagggatgactgacgagatggttttgtctgggtaaatttgtgcagGTGGATTTGACACAGCACATGCAGCTGCTCG
upper sequence: AT5G67180.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA17G18640.1 (Glycine max), 3'ss of exon 2
-gtatggttcatatacataaaaattacgatttaacttttgtgtcttcgatttatttgacaaaacaaagggttttgtttccttctaattgttgttacatatatatgcagGTGGATTTGACACTGCACATGCTGCTGCTCG
| || | | | | | | ||| | | || ||| |||| || | | |||| ||| | | || | | ||||||||||||||| |||||||| ||||||||
aagagtgtgagtgtgtgtgttgtgtgtgggtggggatttttttttttttttt-tttgtggtgactgacttgatggtttttgtctgggta-------aaatttgtctagGTGGATTTGACACAGCACATGCGGCTGCTCG
upper sequence: AT5G67180.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA11G05720.1 (Glycine max), 3'ss of exon 1
--gtatggttcatatacataaaaattacgatttaacttttgtgtcttcgatttatttgacaaaacaaagggttttgtttccttctaattgttgttacatatatatgcagGTGGATTTGACACTGCACATGCTGCTGCTCG
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ttttgttgtggatactaattgggaggcagacaagagagtattgtgcgaaattttttagtgatgactgacgagatggttttgtctgggt---------aaatttgtgtagGTGGATTTGACACAGCACATGCAGCTGCTCG
upper sequence: AT5G67180.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA05G18170.1 (Glycine max), 3'ss of exon 2
----gtatggttcatatacataaaaattacgatttaacttttgtgtcttcgatttatttgacaaaacaaagggttttgtttccttctaattgttgttacatatatatgcagGTGGATTTGACACTGCACATGCTGCTGCTCG
| |||| || | | ||| | | | | |||| | | || ||| |||| || | | |||| ||| | | || | | ||||||||||||||| |||||||| ||||||||
tgtgatgtggtg-gtagagacaaagagtgtgggtgggattttttttttt---tttttttgtggtgactgacttgatggtttttgtctgggta-------aaatttgtctagGTGGATTTGACACAGCACATGCGGCTGCTCG
upper sequence: AT5G67180.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv07s0031g00220.t01 (Vitis vinifera), 3'ss of exon 2
-------------------------------------gtatggttcatatacataaaaattacgatttaacttttgtgtcttcgatttatttgacaaaacaaa-gggttttgtttccttctaattgttgttacatatatatgcagGTGGATTTGACACTGCACATGCTGCTGCTCG
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gtatgttttctctaaaaagaaaaataaaattactttgttttggttgatagg-gcaacattgtagataacataatcttttttccgattgtgatgactgatgagatgggttttccatttttcctttttctctttggtgtctgaatagGTGGATTTGACACCGCACATGCAGCTGCTCG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttgacaaaacaaagggttttgtttccttctaattgttgttacatatatatgcagGTGGATTTGACACTGCACATGCTGCTGCTCG
ttctaat putative branch site (score: 2)
taattgttgttacata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatggttcatatacataaaaattacgatttaacttttgtgtcttcgatttatttgacaaaacaaagggttttgtttccttctaattgttgttacatatatatgcagGTGGATTTGACACTGCACATGCTGCTGCTCG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT