Sequence
atgc intronic sequence ATGC exonic sequencegtgaatccaacttttgggaactactattatctgaattatcgtgttttactgtacagaacacatgtattaagctcaatttcagcaatgaagttttggtctttggagttatttttcattcatctgaacatctttgtctacaacctgtgtgcagATGGCTGAAGTAACACGCGTGGATGCAGTTTGGCCTGGTTGGGGTCATGCATCTGAAAACCCCGAATTACCTGATGCCCTAGATGCAAAAGGAATCATAT
Basic information
species | Arabidopsis thaliana |
transcript | AT1G36160.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G36160.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os05g22940.1 (Oryza sativa), 3'ss of exon 5
gtgaatccaacttttgggaactactattatctgaattatcgtgttttactgtacagaacacatgtattaagctcaatttcagcaatgaagttttggtctttggagttatttttcattcatctgaacatctttgtctacaacctgtgtgcagATGGCTGAAGTAACACGCGTGGATGCAGTTTGGCCTGGTTGGGGTCATGCATCTGAAAACCCCGAATTACCTGATGCCCTAGATGCAAAAGGAATCATAT
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-----------------------------gttagttcagctcatccctcaacacaacattttcgtttcta-tttaagttagggaaaaatctctacgaccctccaatttctgaacatccaatttt-caccatcaactgcaatc-----acagATAGCAGAGAGAACAGGTGTTTCTGCTGTTTGGCCTGGTTGGGGTCATGCATCTGAGAATCCTGAACTTCCAGATGCGCTGACTGCAAAAGGAATTGTTT
upper sequence: AT1G36160.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os10g21910.1 (Oryza sativa), 3'ss of exon 1
gtgaatccaacttttgggaactactattatctgaattatcgtgttttactgtacagaacacatgtattaagctcaatttcagcaatgaagt--tttggtctttggagttatttttcattcatctgaacatctttgtctacaacctgtgtgcagATGGCTGAAGTAACACGCGTGGATGCAGTTTGGCCTGGTTGGGGTCATGCATCTGAAAACCCCGAATTACCTGATGCCCTAGATGCAAAAGGAATCATAT
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----------------------------------gttagcacaattgatcat------cat-cgtagcctttttcatcttaccagtggattgatttgccgtaggtaattggttgttaatattgtgta-atctt--------acctgt-cacagATAGCAGAGAGAACACATGTTTCTGCAGTTTGGCCTGGCTGGGGTCATGCATCTGAGAATCCTGAACTTCCGGACGCACTGAAGGAGAAAGGAATAATTT
upper sequence: AT1G36160.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G377341_T02 (Zea mays), 3'ss of exon 1
gtgaatccaacttttgggaactactattatctgaattatcgtgttttactgtacagaacacatgtattaagctcaatttcagcaatgaagttttggtctttggagttatttttcattcatctgaacatctttgtctacaacctgtgtgcagATGGCTGAAGTAACACGCGTGGATGCAGTTTGGCCTGGTTGGGGTCATGCATCTGAAAACCCCGAATTACCTGATGCCCTAGATGCAAAAGGAATCATAT
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-------------------gttagcacaattc--atcatctggaattatggaaatcttcacata-attgtgtttaggtttac--atgtattttt---cactg----tgtactttggtaatt--aacat-ttcgagttcaactt---cacagATTGCAGAGAGAACTCGCGTATCTGCAGTTTGGCCTGGCTGGGGTCATGCGTCTGAGAACCCAGAACTTCCAGATGCTCTAGATGAGAAAGGAATCATTT
upper sequence: AT1G36160.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM5G858094_T01 (Zea mays), 3'ss of exon 3
gtgaatccaact--tttgggaact-actatta-tctga-attatcgtgttttactgtacagaacacatgtattaagctcaatttcagcaatgaagttttggtctttggagttatttttcattcatctgaacatctttgtctacaacctgtgtgcagATGGCTGAAGTAACACGCGTGGATGCAGTTTGGCCTGGTTGGGGTCATGCATCTGAAAACCCCGAATTACCTGATGCCCTAGATGCAAAAGGAATCATAT
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gttagccttgctaatctgttagtttactactggtctgctgtttcctttatttgttgtata----atgattgacatatttaagtagagaaatttatatttctcctctgctgttgtggaa-gtccaattgt-caccattaactgtgaaatat-tgcagATGGCACAAAAACTAGGTGTTTCTGCTGTTTGGCCTGGTTGGGGTCATGCTTCTGAGAATCCTGAACTGCCAGATGTATTGACCGCAAAAGGGATCGTTT
upper sequence: AT1G36160.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: AC197672.3_FGT002 (Zea mays), 3'ss of exon 3
gtgaatccaacttttgggaactactattatctgaattatcgtgttttactgtacagaacacatgtattaagctcaatttcagcaatgaagttttggtctttggagttatttttcattcatctgaacatctttgtctacaacctgtgtgcagATGGCTGAAGTAACACGCGTGGATGCAGTTTGGCCTGGTTGGGGTCATGCATCTGAAAACCCCGAATTACCTGATGCCCTAGATGCAAAAGGAATCATAT
||| | | || | || || | || | | |||| ||||| || | | || || | | || |||| | | | ||||||| || ||| | | | || ||| ||||||||||||||||||||||| ||||| || || || | || ||||| | |||||||||||| | |
-----------------------------------------------gctgaagcagtcccaaacag-ggccttaagtagagaagcttatatttgtcctttgctattgtggaa-gtccaattgt-taccattaactacgaaatat-tgcagATAGCAGAAAGAGTAGGTGTTTCTGCTGTTTGGCCTGGTTGGGGTCATGCTTCTGAGAATCCTGAGCTGCCGGATGCATTGACCGCAAAAGGAATCGTTT
upper sequence: AT1G36160.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA04G11550.1 (Glycine max), 3'ss of exon 1
gtgaatccaacttttgggaactactattatctgaattatcgtgttttactgtacagaacacatgtattaagctcaatttcagcaatgaagttttggtctttggagttatttttcattcatctgaacatctttgtctacaacctg-tgtgcagATGGCTGAAGTAACACGCGTGGATGCAGTTTGGCCTGGTTGGGGTCATGCATCTGAAAACCCCGAATTACCTGATGCCCTAGATGCAAAAGGAATCATAT
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---------------------------------------------ttattcttgtcattatagattttagtgcttat----gtaataatgattc--tttttacctatataacttatatattctg-cttactggcatgcaatgtacttcccagATGGCTGAGATAACTCATGTTGATGCGGTGTGGCCTGGTTGGGGTCATGCATCAGAAAATCCTGAGCTCCCAGATGCATTAAAAGCAAAAGGAATTGTAT
upper sequence: AT1G36160.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA06G11120.1 (Glycine max), 3'ss of exon 1
gtgaatccaacttttgggaactactattatctgaattatcgtgttttactgtacagaacacatgtattaagctcaatttcagcaatgaagttttggtctttggagttatttttcattcatctgaacatctttgtctacaacctg-tgtgcagATGGCTGAAGTAACACGCGTGGATGCAGTTTGGCCTGGTTGGGGTCATGCATCTGAAAACCCCGAATTACCTGATGCCCTAGATGCAAAAGGAATCATAT
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---------------------------------------------ttgttcttgtcattgtagattttagtgcttatgt-agtaatgattcttttgacct---atataacttatata-atctg--cttactggcatgcaatgtactgcccagATGGCTGAGATAACTCATGTTGATGCGGTGTGGCCTGGTTGGGGTCATGCATCAGAAAATCCTGAGCTTCCAGATGCATTAAAAGCAAAAGGAATTGTAT
upper sequence: AT1G36160.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv18s0001g04980.t01 (Vitis vinifera), 3'ss of exon 2
gtgaatccaacttttgggaactactattatctgaattatcgtgttttactgtacagaacacatgtattaagctcaatttcagcaa--tgaagttttggtctttggagttatttttcatt-catctgaacatctttgtctacaacctgtgtgcagATGGCTGAAGTAACACGCGTGGATGCAGTTTGGCCTGGTTGGGGTCATGCATCTGAAAACCCCGAATTACCTGATGCCCTAGATGCAAAAGGAATCATAT
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----------------------------------------------------aagtaaatccggaatgaaatttcattcttgctagctgttgtttttgcctgttg-gctatgtttgattatacctaaatctggttggtttgacaatgc-tacagATGGCAGAGATAACACATGTTGATGCAGTTTGGCCTGGTTGGGGCCATGCATCTGAGAACCCTGAGCTGCCAGATGCTCTGAATGCTAAGGGGATTGTAT
upper sequence: AT1G36160.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: PP1S158_40V6.1 (Physcomitrella patens), 3'ss of exon 1
gtgaatccaacttttgggaactactattatctgaattatcgtgttttactgtacagaacacatgtattaagctcaatttcagcaatgaagttttggtctttggagttatttttcattcatctgaacatctttgtctacaacctgtgtgcagATGGCTGAAGTAACACGCGTGGATGCAGTTTGGCCTGGTTGGGGTCATGCATCTGAAAACCCCGAATTACCTGATGCCCTAGATGCAAAAGGAATCATAT
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------------------gtttgtgctccttctccttgctattcttcactgca-agtacccaccagaattgttca--ctggatggtaatgtacggttgttt----ttattctctatt-gtctcca-atttacgcgtattggct---tgcagATTGCAGAGAGAACCGGGGTGCAAGCCGTATGGCCTGGATGGGGTCACGCATCTGAAAACCCCGAGCTCCCAGACTCCCTCTTGGCGCGAGGCATTCTGT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctttggagttatttttcattcatctgaacatctttgtctacaacctgtgtgcagATGGCTGAAGTAACACGCGTGGATGCAGTTTGGCCTGGTTGGGGTCATGCATCTGAAAACCCCGAATTACCTGATGCCCTAGATGCAAAAGGAATCATAT
ttatttttcattcat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgaatccaacttttgggaactactattatctgaattatcgtgttttactgtacagaacacatgtattaagctcaatttcagcaatgaagttttggtctttggagttatttttcattcatctgaacatctttgtctacaacctgtgtgcagATGGCTGAAGTAACACGCGTGGATGCAGTTTGGCCTGGTTGGGGTCATGCATCTGAAAACCCCGAATTACCTGATGCCCTAGATGCAAAAGGAATCATAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA