Sequence
atgc intronic sequence ATGC exonic sequencegtaaagttttgtcttaactgtctattgggttacactttagccctcttcgagcaacattgttttcaattattattacttgcatcatctatttccttctcccagGATATCGAGGCTACAATTCATTGTGCAGAGTGGCTTTCTATCGTTGGTGGTTCCAGCACTGGAGAGCAAAGAATTAG
Basic information
species | Arabidopsis thaliana |
transcript | AT2G45540.2 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G45540.2 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: LOC_Os04g46894.1 (Oryza sativa), 3'ss of exon 6
------------------gtaaag--ttttgtcttaactgtctattgggtta----cactttagccctcttcgagcaacattgttttcaat-----tattattacttgcatca-tctatttccttct----------------------cccagGATATCGAGGCTACAATTCATTGTGCAGAGTGGCTTTCTATCGTTGGTGGTTCCAGCACTGGAGAGCAAAGAATTAG
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gcaagctatttttcttttgtagagcatcctatgcagaaaatcttttccgctgttgccatcccaaccttcctctcttatttgtgtttgtgatgcttgtatcattgctgattttggcctatttcctcataattttgttgttgctgtgacaatttagGATGTGGAAGCAACAATTCATTGTGCAGAGTGGCTTTCAATGGTTGGAGGATCTAGCACAGGAGACCAAAGAATCAG
upper sequence: AT2G45540.2 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: LOC_Os02g44380.2 (Oryza sativa), 3'ss of exon 1
----gtaaagttt-tgtcttaactgtctattgggttacactttagccctcttcgagcaacattgttttcaattattattacttgcatcatctatttccttctcccagGATATCGAGGCTACAATTCATTGTGCAGAGTGGCTTTCTATCGTTGGTGGTTCCAGCACTGGAGAGCAAAGAATTAG
|| | || | || || || |||||| | | | ||| | | | | | ||| |||| | || || || | | || | ||||||| | ||||| || || ||||||||||| |||||||| || ||||| || || |||||||| || |||||||||||
gcaagtgactttgatatcatatctttctatttgatattaactta--ctttataggattgtaacctttctttttatggtaac----attatat-ctgggtttttccagGATGTAGAGGCAACGATACATTGTGCAGAATGGCTTTCAATGGTTGGAGGATCTAGCACTGGGGACCAAAGAATTAG
upper sequence: AT2G45540.2 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GRMZM2G044143_T01 (Zea mays), 3'ss of exon 6
------------------------------------------------------------gtaaagttttgtcttaactgtctattgggttacact--ttagccctcttcgagcaacattgttttcaattattattacttgcatcatctatttccttct-cccagGATATCGAGGCTACAATTCATTGTGCAGAGTGGCTTTCTATCGTTGGTGGTTCCAGCACTGGAGAGCAAAGAATTAG
| | |||| ||| || || || | || | | | | | ||||| ||| || ||| | || | | | | || ||||| | ||||| |||||||||||||| |||||||| || || ||||| || || ||||||||||| ||||| || ||
gcaagatattttttaagcagaacatccttagtaacatacatgtttcatagtgtcatggccatctgcccctctcttctttgtggataggtttctgatggttgtatcacagccaactacattttttgttcataatatcttgtttgtcctttccctgcaactatttagGATGTGGAGGCAACAATTCATTGTGCGGAGTGGCTCTCAATAGTTGGAGGATCTAGCACTGGAGACCAAAGGATCAG
upper sequence: AT2G45540.2 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: Vv15s0048g01650.t01 (Vitis vinifera), 3'ss of exon 6
-gtaaagttttgtcttaactgtctattgggttacactttagccctc---ttcgagcaacattgttttcaattattattacttgcatcatctatttccttctcccagGATATCGAGGCTACAATTCATTGTGCAGAGTGGCTTTCTATCGTTGGTGGTTCCAGCACTGGAGAGCAAAGAATTAG
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tatatccttctactttga-tgt-tgcttggacatgctatcatcttcaatttatagtttgatgagtttcatttat-attgtttg-gttat-tacttccttctac-agGATATTGAAGCTACAATTCATTGTGCAGAATGGCTGTCCATGGTGGGGGGCTCTAGCACAGGAGACCAACGCATCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cgagcaacattgttttcaattattattacttgcatcatctatttccttctcccagGATATCGAGGCTACAATTCATTGTGCAGAGTGGCTTTCTATCGTTGGTGGTTCCAGCACTGGAGAGCAAAGAATTAG
catcatctatttcctt CT-rich tract
aacattgttttcaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaagttttgtcttaactgtctattgggttacactttagccctcttcgagcaacattgttttcaattattattacttgcatcatctatttccttctcccagGATATCGAGGCTACAATTCATTGTGCAGAGTGGCTTTCTATCGTTGGTGGTTCCAGCACTGGAGAGCAAAGAATTAG
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