Sequence
atgc intronic sequence ATGC exonic sequence...tctttgataatttatctactttattcaaaagacaatgaatccagatcctggttacctaccaaaatactaaagcttcatcttgtcattatatgatatacagGCCTGTATGAGCGGATTACATTGGAGAAATAGTCCCTTGATCATGTCACAATGTGGTTCCAAAGGATCTCCTATCAATATCAGTCAGATGGTCGCATGTG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G60040.1 |
intron # | 16 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G60040.1 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: LOC_Os04g41490.1 (Oryza sativa), 3'ss of exon 15
-------tctttgata-atttatctactttattcaaaagacaatgaatccagatcctggttacctaccaaaatactaaagcttcatcttgtcattatatgatatacagGCCTGTATGAGCGGATTACATTGGAGAAATAGTCCCTTGATCATGTCACAATGTGGTTCCAAAGGATCTCCTATCAATATCAGTCAGATGGTCGCATGTG
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tactggagacccgatgcaattattttgttgactcaaaacaaaatta-ttcaaatttgattttgcactttttttattgaa--tgcacttaaac-ttatttat----cagGTCTGTATGAATACACTTCACTGGAGGAACAGCCCATTGATCATGTCTCAGTGTGGATCTAAAGGTTCTCCAATCAACATTAGTCAGATGGTTGCATGTG
upper sequence: AT5G60040.1 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: GRMZM2G080176_T01 (Zea mays), 3'ss of exon 15
tctttgataatttatctactttattcaaaagacaatgaatccagatcctggt-tacctaccaaaatactaaagcttcatcttgtcattatatgatatacagGCCTGTATGAGCGGATTACATTGGAGAAATAGTCCCTTGATCATGTCACAATGTGGTTCCAAAGGATCTCCTATCAATATCAGTCAGATGGTCGCATGTG
| | | |||| | | | | | | | | | || |||| | | | | | | | |||||| || | | | | |||| || ||| | || ||||| || || || ||||| ||||| || |||||||||||||| ||||| |||||||||||||||||||| |||||||
gatgtagtgattttgccaggtgactagtgactgtgtccactctgaatttggtatgctttttagcggatcgttgaatt-tcttgtgatgaaacttttttcagGTGTGCATGGATACGCTTCACTGGAGGAACAGCCCATTGATTATGTCTCAGTGTGGTTCCAAAGGTTCTCCAATCAATATCAGTCAGATGGTTGCATGTG
upper sequence: AT5G60040.1 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: GLYMA11G15530.1 (Glycine max), 3'ss of exon 13
tctttgataatttatctactttattcaaaagacaatgaatccagatcctggttacctaccaaaatactaaagcttcatcttgtcattatatgatatacagGCCTGTATGAGCGGATTACATTGGAGAAATAGTCCCTTGATCATGTCACAATGTGGTTCCAAAGGATCTCCTATCAATATCAGTCAGATGGTCGCATGTG
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-------gtatccattt-ctttttcctaaag-taatctgtctgtgtgt--gtttcagacaaatgtct----gcctatcaatgattttgtatttttctcagGTCTGCATGCAAACCCTACACTGGAGAAATAGTCCATTGATCATGTCACAATGTGGCTCCAAAGGATCTTCTATTAATATCAGTCAAATGGTTGCCTGTG
upper sequence: AT5G60040.1 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: Vv06s0004g03740.t01 (Vitis vinifera), 3'ss of exon 15
--tctttgataatttatctactttattcaaaagacaatgaatccagatcctggttacctaccaaaatactaaagcttcatcttgtcattatatgatata-cagGCCTGTATGAGCGGATTACATTGGAGAAATAGTCCCTTGATCATGTCACAATGTGGTTCCAAAGGATCTCCTATCAATATCAGTCAGATGGTCGCATGTG
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tttcttttgtactgatttttaattgtt--atatacttttaactaaggtatagaaagtatttttaaggaa-gcaacttaatttgttctttaatttttgcaatagGTTTGCATGGAAGAACTACATTGGAGGAATAGCCCTTTGATTATGTCCCAATGTGGTTCCAAAGGATCTCCTATCAATATTAGCCAAATGATTGCATGTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcctggttacctaccaaaatactaaagcttcatcttgtcattatatgatatacagGCCTGTATGAGCGGATTACATTGGAGAAATAGTCCCTTGATCATGTCACAATGTGGTTCCAAAGGATCTCCTATCAATATCAGTCAGATGGTCGCATGTG
tactaaa putative branch site (score: 1)
tcattatatgatata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tctttgataatttatctactttattcaaaagacaatgaatccagatcctggttacctaccaaaatactaaagcttcatcttgtcattatatgatatacagGCCTGTATGAGCGGATTACATTGGAGAAATAGTCCCTTGATCATGTCACAATGTGGTTCCAAAGGATCTCCTATCAATATCAGTCAGATGGTCGCATGTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - -aaagaca
- - - - - - - - - - - - - - - - - - - - ccagatc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - taccaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -actaaag